title: RMB4664

city: SINGAPORE

first: JIA CHI

last: TAN

address: 8a Biomedical Grove

institute: SIgN

data_processing:
Raw reads were aligned to the mouse reference genome GRCm38 from GENCODE using RSEM program version 1.2.19 with default parameters. Gene expression values in transcripts per million (TPM) were calculated using the same RSEM program and the mouse GENCODE annotation version 4.
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM

source_name: Bone marrow

extract_protocol:
RNA was extracted with picopure extraction buffer according to manufacturer's protocol.
Single cell cDNA libraries were using the SMARTSeq v2 protocol (Picelli et al., 2014) with the following modifications: 1. 1mg/ml BSA Lysis buffer (Ambion® Thermo Fisher Scientific, Waltham, MA, USA); 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina, San Diego, CA, USA). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Perkin Elmer Labchip (Perkin Elmer, Waltham, MA, USA). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (Illumina, San Diego, CA, USA) (250 samples/lane).

tag: strain

value: tpMo

tag: markers


title: RMB4673

status: Public on Jun 29 2020

type: SRA

country: Singapore

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type


title: RMB4665


title: RMB4679


title: RMB4671


title: RMB4672


title: RMB4680


title: RMB4663


title: RMB4656


title: 1772158108_C11_B8

city: Stanford

first: Wanxin

last: Wang

state: CA

address: James H Clark Center, 318 Campus Drive, room E300

country: USA

institute: Stanford Univeristy

data_processing:
bcl2fastq v2.17.1.14 was used for demultiplexing and generating *.fastq.
Raw reads in the *.fastq files were trimmed to 75bp using fastqx,
duplicate-removed using picard MarkDuplicates, and
aligned to reference using STAR with default parameters.
Aligned reads were converted to counts using HTSeq.
Genome_build: Ensembl human reference genome GRCh38.87 (dna.primary_assembly)
Supplementary_files_format_and_content: comma separated file including HTSeq count for each cell

molecule: polyA RNA

organism: Homo sapiens

source_name: endometrium biopsy

extract_protocol:
Single cells were lysed using the reagents (Takara/Clontech) and default protocol for Fluidigm C1 mRNA Seq
RNA libraries were prepared for sequencing using Illumina Nextera-XT protocols for single cells

tag: time in menstrual cycle

tag: tissue

value: endometrium biopsy

tag: donor condition

value: fertile healthy

tag: gender

value: female


title: RMB4657


title: 1772158108_C13_C3


title: 1772158108_C10_B9


title: 1772158108_C12_B7


title: RMB4655


title: 1772158108_C09_B1


title: RMB4649


title: 1772158108_C05_A8


title: 1772158108_C34_F7


title: 1772158108_C04_A9


title: RMB4650


title: RMB4643


title: 1772158108_C03_A1


title: 1772158107_C96_H10


title: 1772158108_C02_A2


title: 1772158107_C95_H11


title: RMB4634


title: RMB4642


title: RMB4635


title: RMB4627


title: 1772158107_C93_H4


title: RMB4619


title: RMB4618


title: RMB4610


title: 1772158107_C87_G4


title: RMB4620


title: RMB4612


title: 1772158107_C92_H5


title: RMB4626


title: 1772158107_C94_H12


title: 1772158107_C80_F5


title: 1772158107_C85_G6


title: RMB4611


title: 1772158107_C82_F12


title: 1772158107_C83_F11


title: 1772158107_C77_E11


title: 1772158107_C74_E5


title: RMB4602


title: RMB4603


title: RMB4604


title: 1772158107_C73_E6


title: 1772158107_C79_F6


title: RMB4595


title: 1772158107_C67_D4


title: RMB4596


title: RMB4594


title: RMB4682

value: preNeu


title: 1772158107_C60_B12


title: RMB4683


title: 1772158107_C57_B6


title: RMB4675


title: 1772158107_C48_H9


title: RMB4681


title: 1772158107_C47_H8


title: RMB4676


title: RMB4668


title: 1772158107_C43_H1


title: 1772158107_C42_G9


title: RMB4667


title: 1772158107_C38_G2


title: 1772158107_C55_B4


title: RMB4674


title: RMB4660


title: 1772158107_C34_F7


title: RMB4659


title: 1772158107_C33_F3


title: 1772158107_C32_F2


title: RMB4653


title: 1772158107_C29_E8


title: 1772158107_C61_C4


title: 1772158107_C59_B11


title: RMB4652


title: 1772158107_C27_E3


title: RMB4651


title: RMB4645


title: 1772158107_C17_C8


title: 1772158107_C16_C9


title: RMB4644


title: RMB4638


title: 1772158107_C09_B1


title: 1772158107_C12_B7


title: RMB4637


title: 1772158105_C95_H11


title: RMB4666


title: RMB4636


title: RMB4629


title: 1772158107_C02_A2


title: 1772158107_C01_A3


title: RMB4630


title: RMB4658


title: RMB4622


title: 1772158105_C75_E4


title: 1772158105_C73_E6


title: RMB4628


title: 1772158105_C93_H4


title: RMB4614


title: RMB4621


title: 1772158105_C72_D12


title: 1772158105_C77_E11


title: 1772158105_C70_D10


title: RMB4605


title: RMB4613


title: 1772158105_C71_D11


title: 1772158105_C69_D6


title: RMB4598


title: 1772158105_C68_D5


title: RMB4597


title: RMB4678

value: proneu


title: 1772158105_C66_C12


title: RMB4677


title: RMB4670


title: 1772158105_C63_C6


title: 1772158105_C62_C5


title: RMB4662


title: 1772158105_C58_B10


title: 1772158105_C57_B6


title: 1772158105_C54_A12


title: 1772158105_C61_C4


title: 1772158105_C59_B11


title: RMB4669


title: 1772158105_C52_A10


title: RMB4661


title: RMB4654


title: RMB4648


title: RMB4606


title: RMB4646


title: 1772158105_C53_A11


title: 1772158105_C51_A6


title: RMB4647


title: RMB4641


title: 1772158105_C64_C10


title: RMB4633


title: RMB4639


title: 1772158105_C44_H2


title: 1772158105_C47_H8


title: RMB4624


title: RMB4632


title: 1772158105_C48_H9


title: 1772158105_C50_A5


title: RMB4631


title: RMB4617


title: RMB4640


title: 1772158105_C45_H3


title: 1772158105_C38_G2


title: 1772158105_C40_G7


title: 1772158105_C39_G3


title: RMB4623


title: RMB4625


title: RMB4616


title: 1772158105_C37_G1


title: RMB4615


title: 1772158105_C36_F9


title: RMB4609


title: RMB4607


title: 1772158105_C35_F8


title: RMB4608


title: 1772158105_C34_F7


title: 1772158105_C41_G8


title: 1772158105_C33_F3


title: RMB4601


title: 1772158105_C32_F2


title: 1772158105_C31_F1


title: RMB4599


title: RMB4600


title: 1772158105_C30_E9


title: 1772158105_C29_E8


title: RMB4591


title: RMB4592


title: 1772158105_C28_E7


title: RMB4593


title: RMB4589


title: 1772158105_C26_E2


title: 1772158105_C23_D8


title: RMB4590


title: 1772158105_C22_D9


title: RMB4587


title: 1772158105_C20_D2


title: 1772158105_C24_D7


title: RMB4588


title: 1772158105_C25_E1


title: RMB4586

value: CMP


title: RMB4585


title: 1772158105_C17_C8


title: 1772158105_C15_C1


title: RMB4582


title: 1772158105_C14_C2


title: 1772158105_C13_C3


title: RMB4581


title: RMB4584


title: RMB4580


title: RMB4579


title: 1772158105_C09_B1


title: 1772158105_C11_B8


title: RMB4578


title: 1772158105_C08_B2


title: 1772158105_C07_B3


title: RMB4576


title: RMB4574


title: RMB4573


title: 1772158105_C06_A7


title: RMB4575


title: 1772158105_C02_A2


title: 1772158105_C19_D3


title: 1772158103_C96_H10


title: RMB4583


title: RMB4572


title: RMB4570


title: 1772158103_C93_H4


title: 1772158103_C90_G10


title: RMB4569


title: 1772158103_C86_G5


title: 1772158103_C88_G12


title: 1772158103_C84_F10


title: RMB4567


title: RMB4566


title: 1772158103_C83_F11


title: 1772158103_C82_F12


title: 1772158103_C81_F4


title: RMB4568


title: RMB4563


title: RMB4577


title: 1772158105_C04_A9


title: 1772158103_C78_E10


title: RMB4562


title: RMB4571


title: RMB4560


title: 1772158103_C76_E12


title: 1772158103_C95_H11


title: 1772158103_C75_E4


title: 1772158103_C71_D11


title: 1772158103_C73_E6


title: RMB4557


title: RMB4559


title: 1772158103_C66_C12


title: RMB4556


title: RMB4555


title: 1772158103_C62_C5


title: RMB4564


title: RMB4554


title: RMB4565


title: 1772158103_C60_B12


title: RMB4553


title: 1772158103_C59_B11


title: RMB4551


title: 1772158103_C53_A11


title: 1772158103_C51_A6


title: RMB4550


title: RMB4561


title: RMB4558


title: 1772158103_C70_D10


title: RMB4549


title: RMB4548


title: RMB4547


title: 1772158103_C47_H8


title: 1772158103_C43_H1


title: RMB4546


title: 1772158103_C41_G8


title: RMB4545


title: RMB4544


title: 1772158103_C61_C4


title: RMB4543


title: 1772158103_C39_G3


title: 1772158103_C32_F2


title: RMB4542


title: RMB4552


title: 1772158103_C36_F9


title: RMB4540


title: RMB4541


title: 1772158103_C31_F1


title: 1772158103_C49_A4


title: RMB4539


title: RMB4538


title: 1772158103_C30_E9


title: 1772158103_C28_E7


title: 1772158103_C45_H3


title: 1772158103_C44_H2


title: RMB4536


title: RMB4537


title: 1772158103_C20_D2


title: 1772158103_C18_C7


title: RMB4534


title: 1772158103_C17_C8


title: 1772158103_C40_G7


title: RMB4533


title: 1772158103_C13_C3


title: 1772158103_C16_C9


title: 1772158103_C12_B7


title: RMB4531


title: RMB4530


title: 1772158103_C09_B1


title: RMB4532


title: 1772158103_C07_B3


title: 1772158103_C03_A1


title: RMB4529


title: 1772158103_C01_A3


title: RMB4527


title: RMB4525


title: RMB4535


title: 1772158101_C95_H11


title: RMB4526


title: 1772158101_C92_H5


title: 1772158101_C91_H6


title: RMB4522


title: RMB4521


title: RMB4520


title: 1772158101_C90_G10


title: RMB4524


title: RMB4523


title: 1772158101_C89_G11


title: 1772158101_C88_G12


title: RMB4519


title: RMB4517


title: RMB4518


title: 1772158101_C87_G4


title: 1772158103_C08_B2


title: 1772158103_C05_A8


title: RMB4516


title: RMB4528


title: RMB4515


title: 1772158101_C86_G5


title: 1772158101_C84_F10


title: 1772158101_C96_H10


title: 1772158101_C83_F11


title: RMB4514


title: RMB4513


title: 1772158101_C80_F5


title: RMB4512


title: 1772158101_C82_F12


title: 1772158101_C79_F6


title: RMB4511


title: RMB4510


title: RMB4509


title: RMB4508


title: 1772158101_C77_E11


title: 1772158101_C76_E12


title: RMB4507


title: 1772158101_C78_E10


title: 1772158101_C74_E5


title: 1772158101_C73_E6


title: RMB4506


title: 1772158101_C72_D12


title: 1772158101_C85_G6


title: RMB4504


title: RMB4502


title: RMB4505


title: RMB4503


title: 1772158101_C71_D11


title: 1772158101_C70_D10


title: RMB4500


title: RMB4499


title: RMB4501


title: 1772158101_C64_C10


title: 1772158101_C65_C11


title: 1772158101_C68_D5


title: 1772158101_C62_C5


title: RMB4498


title: 1772158101_C60_B12


title: RMB4497


title: 1772158101_C59_B11


title: RMB4496


title: 1772158101_C57_B6


title: RMB4495


title: 1772158101_C56_B5


title: RMB4494


title: RMB4493


title: 1772158101_C55_B4


title: 1772158101_C54_A12


title: RMB4492


title: 1772158101_C53_A11


title: RMB4491


title: RMB4490


title: 1772158101_C50_A5


title: 1772158101_C49_A4


title: 1772158101_C46_H7


title: 1772158101_C51_A6


title: RMB4488


title: RMB4487


title: RMB4489


title: RMB4486


title: 1772158101_C41_G8


title: RMB4484


title: 1772158101_C44_H2


title: 1772158101_C38_G2


title: RMB4483


title: 1772158101_C37_G1


title: RMB4482


title: 1772158101_C36_F9


title: RMB4481


title: 1772158101_C34_F7


title: 1772158101_C33_F3


title: RMB4480


title: RMB4479


title: 1772158101_C31_F1


title: RMB4478


title: RMB4477


title: 1772158101_C30_E9


title: 1772158101_C39_G3


title: 1772158101_C26_E2


title: RMB4485


title: RMB4476


title: 1772158101_C24_D7


title: 1772158101_C23_D8


title: RMB4475


title: RMB4474


title: 1772158101_C21_D1


title: 8min_Systemic HL&HS_3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: Systemic HL&HS

data_processing:
Illumina's two-channel SBS sequencing
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Arabidopsis stems

growth_protocol: Arabidopsis thaliana Col plants were grown in peat pellets at 23°C under long day growth conditions (14-hour light/10-hour dark, 50 µmol m−2 s−1)

extract_protocol:
Total RNA was isolated using Qiagen kit (Rneasy Plant Mini Kit) according to the manufacturer’s instructions.
TruSeqHT

treatment_protocol: Local leaves of bolting Col plants were exposed to a light intensity of 1700 µmol m-2 sec-1 using a gooseneck light source (ACE I; Schott), or heat stress by placing a heat block 2 cm underneath the treated leaf, or to the combination of both stresses in the same leaf or in two different leaves for periods of 0, 2 and 8 min.

tag: repeat

tag: time

tag: treatment

value: No treatment

tag: genotype

value: wild type

value: Stems


title: 8min_Systemic HL&HS_1

description: Systemic HL&HS


title: 8min_Systemic HL&HS_2

description: Systemic HL&HS


title: RMB4473


title: 1772158101_C20_D2


title: 8min_Local HL (HL&HS)_3

description: Local HL (HL&HS)

source_name: Arabidopsis leaves

value: High light stress

value: Leaves


title: 8min_Local HS (HL&HS)_2

description: Local HS (HL&HS)

value: Heat stress


title: 8min_Local HS (HL&HS)_3

description: Local HS (HL&HS)


title: 8min_Local HL (HL&HS)_2

description: Local HL (HL&HS)


title: 8min_Systemic HL+HS_3

description: Systemic HL+HS


title: 8min_Local HS (HL&HS)_1

description: Local HS (HL&HS)


title: 1772158101_C19_D3


title: RMB4471


title: 8min_Systemic HL+HS_2

description: Systemic HL+HS


title: 8min_Local HL (HL&HS)_1

description: Local HL (HL&HS)


title: RMB4472


title: 8min_Systemic HL+HS_1

description: Systemic HL+HS


title: 1772158101_C16_C9


title: 8min_Local HL+HS_3

description: Local HL+HS

value: High light+Heat stress


title: RMB4470


title: 1772158101_C15_C1


title: 1772158101_C11_B8


title: 8min_Local HL+HS_1

description: Local HL+HS


title: 8min_Local HL+HS_2

description: Local HL+HS


title: 8min_Systemic HL_2

description: Systemic HL


title: 8min_Systemic HL_1

description: Systemic HL


title: 1772158101_C10_B9


title: RMB4468


title: RMB4469


title: 8min_Local HL_3

description: Local HL


title: RMB4467


title: 8min_Local HL_1

description: Local HL


title: 8min_Local HL_2

description: Local HL


title: 1772158101_C09_B1


title: 8min_Systemic HS_3

description: Systemic HS


title: 1772158101_C08_B2


title: 8min_Systemic HS_2

description: Systemic HS


title: 8min_Systemic HS_1

description: Systemic HS


title: 1772158101_C07_B3


title: 8min_Local HS_3

description: Local HS


title: RMB4464


title: 8min_Systemic HL_3

description: Systemic HL


title: 8min_Local HS_2

description: Local HS


title: RMB4465


title: 1772158101_C05_A8


title: 8min_Local HS_1

description: Local HS


title: RMB4463


title: 2min_Systemic HL&HS_2

description: Systemic HL&HS


title: RMB4466


title: 1772158101_C04_A9


title: 2min_Systemic HL&HS_3

description: Systemic HL&HS


title: 1772158101_C03_A1


title: 2min_Systemic HL&HS_1

description: Systemic HL&HS


title: 2min_Local HS (HL&HS)_3

description: Local HS (HL&HS)


title: RMB4462


title: RMB4461


title: 2min_Local HS (HL&HS)_2

description: Local HS (HL&HS)


title: 1772158101_C01_A3


title: 2min_Local HS (HL&HS)_1

description: Local HS (HL&HS)


title: 2min_Systemic HL+HS_2

description: Systemic HL+HS


title: 2min_Systemic HL+HS_1

description: Systemic HL+HS


title: 2min_Local HL (HL&HS)_1

description: Local HL (HL&HS)


title: 2min_Local HL+HS_1

description: Local HL+HS


title: 2min_Local HL (HL&HS)_2

description: Local HL (HL&HS)


title: 2min_Local HL (HL&HS)_3

description: Local HL (HL&HS)


title: 2min_Local HL+HS_2

description: Local HL+HS


title: 2min_Local HL+HS_3

description: Local HL+HS


title: 2min_Systemic HL+HS_3

description: Systemic HL+HS


title: RMB4457


title: RMB4456


title: RMB4459


title: RMB4458


title: RMB4460


title: breast tumour 138B

type: RNA

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

label: biotin

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from baseline (A) and surgery (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: Sex

tag: timepoint

value: surgery(B)

value: breast tumour


title: 2min_Systemic HS_2

description: Systemic HS


title: RMB4455


title: 2min_Local HS_1

description: Local HS


title: breast tumour 47A

value: baseline(A)


title: RMB4454


title: 2min_Local HS_2

description: Local HS


title: 2min_Local HS_3

description: Local HS


title: 2min_Systemic HS_1

description: Systemic HS


title: RMB4453


title: breast tumour 206B


title: breast tumour 138A


title: breast tumour 202B


title: 2min_Systemic HL_3

description: Systemic HL


title: 2min_Systemic HL_2

description: Systemic HL


title: 2min_Systemic HL_1

description: Systemic HL


title: 2min_Local HL_2

description: Local HL


title: 2min_Local HL_1

description: Local HL


title: RMB4450


title: RMB4449


title: RMB4448


title: breast tumour 133A


title: 2min_Local HL_3

description: Local HL


title: Pa16C 3Day DMSO 2

type: genomic

city: Chapel Hill

first: Joel

last: Durand

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

institute: The University of North Carolina at Chapel Hill

description:
201904660186_R02C01
Pa16C treated with DMSO, assayed after 3 days

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

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

data_processing: R (minfi package)

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

growth_protocol: Pa16C cells grown in DMEM with 10%FBS

extract_protocol: genomic DNA was extracted and purified from cell lines using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Cells were treated every other day with 0.25uM of SCH772984 or DMSO

tag: cell line

value: pancreatic cancer

value: DMSO

value: Day 3

tag: replicate


title: Pa16C 3Day SCH 2

description:
201904660186_R04C01
Pa16C treated with SCH assayed after 3 days


title: RMB4452


title: breast tumour 125A

value: female


title: 0min_Systemic CT_2

description: Systemic CT


title: Pa16C 7Day SCH 2

description:
201904660186_R08C01
Pa16C treated with SCH assayed after 7 days

value: Day 7


title: 0min_Systemic CT_3

description: Systemic CT


title: Pa16C 7Day DMSO 1

description:
201904660186_R05C01
Pa16C treated with DMSO, assayed after 7 days


title: breast tumour 74B


title: 2min_Systemic HS_3

description: Systemic HS


title: 0min_Systemic CT_1

description: Systemic CT


title: Pa16C 7Day SCH 1

description:
201904660186_R07C01
Pa16C treated with SCH assayed after 7 days


title: RMB4451


title: breast tumour 133B


title: RMB4447


title: 0min_Local CT_3

description: Local CT


title: Mutant Di19, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of mutant  10-days-old seedlings

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Arabidopsis Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: The data were analyzed with Bioconductor packages-affy and gcrma in R version 3.4.0.

label: Biotin

source_name: 10 days old mutant seedlings

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: The Arabidopsis seeds were grown in 1/2MS medium  under white light (50-60µmol m-2 s -1) at 22ºC and 16h-light : 8h-dark cycle after 72 hrs of stratification. 10 days old seedlings (equivalent to 100mg fresh weight) were harvested and snap frozen in liquid nitrogen.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. The quality check of total RNA was done using RNA 6000 Nano Lab Chip on the 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: No special treatment was given to plants before harvesting.

tag: ecotype

value: mutant

value: seedlings


title: RMB4445


title: 0min_Local CT_2

description: Local CT

value: No treatment


title: Mutant Di19, Biological replicate 2


title: PSMD14 exon 11 Output 9d

city: Barcelona

first: Pablo

last: Baeza

address: Dr. Aiguader, 88

department: Systems Biology

country: Spain

institute: Centre for Genomic Regulation

description:
PCR amplicon
Mature mRNA containing PSMD14 exon 11.

library_source: genomic

data_processing:
Library strategy: (DNA-seq of PCR amplicon)
Demultiplex sample replicates (DiMSum - https://github.com/lehner-lab/DiMSum)
Paired-end merging (DiMSum - https://github.com/lehner-lab/DiMSum)
Base-calling (DiMSum - https://github.com/lehner-lab/DiMSum)
Supplementary_files_format_and_content: DiMSum output file (tab-delimited plain text file)

source_name: Cell culture

growth_protocol: For each experimental replicate, 10 ng of the library were transfected into 250 000 HEK293 cells in one well of a 6-well plate using Lipofectamine 2000 (11668027, Thermo scientific) and OPTIMEM I Reduced Serum Medium (31985-047, Thermo scientific). Six hours post-transfection, the cell culture medium was replaced with DMEM Glutamax (61965059, Life Technologies) containing 10% FBS and Pen/Strep antibiotics. 48 hours post-transfection, total RNA was isolated using the automated Maxwell LEV 16 simplyRNA tissue kit (AS1280, Promega).

extract_protocol:
For each of the experimental replicates, 10 ng of the library were transfected into 250 000 HEK293 cells in one well of a 6-well plate using Lipofectamine 2000 (11668027, Thermo scientific) and OPTIMEM I Reduced Serum Medium (31985-047, Thermo scientific). Six hours post-transfection, the cell culture medium was replaced with DMEM Glutamax (61965059, Life Technologies) containing 10% FBS and Pen/Strep antibiotics. 48 hours post-transfection (72 in the case of the siRNA experiments), total RNA was isolated using the automated Maxwell LEV 16 simplyRNA tissue kit (AS1280, Promega).
Accuprime Pfx (12344024, ThermoFisher Scientific) was used following the manufacturer's instructions to amplify 20 ng of single-stranded library DNA for 25 cycles with the following flanking intronic primers: FAS_i5_GC_F and FAS_i6_GC_R (Baeza-Centurion et al. 2019). The amplified library was then recombined with pCMV FAS wt minigene exon 5-6-7 (Förch et al. 2000) using the In-Fusion HD Cloning kit (639649, Clontech) in a 1:8 vector:insert optimized ratio and transformed into Stellar competent cells (636766, Clontech) to maximise the number of individual transformants (800,000 individual clones). The library was then amplified by growing for 18 hours in LB medium containing ampicillin. The final plasmid library were purified using the Quiagen plasmid maxi kit (50912163, Quiagen) and quantified with a NanoDrop spectrophotometer.


title: Wild-type, Biological replicate 2

description: Gene expression data of control 10-days-old seedlings

source_name: 10 days old wild type seedlings

value: wild type


title: Pa16C 3Day SCH 1

description:
201904660186_R03C01
Pa16C treated with SCH assayed after 3 days


title: 0min_Local CT_1

description: Local CT


title: RMB4444


title: Pa16C 7Day DMSO 2

description:
201904660186_R06C01
Pa16C treated with DMSO, assayed after 7 days


title: Wild-type, Biological replicate 1


title: RMB4446


title: RMB4443


title: PSMD14 exon 11 Output 9b


title: breast tumour 57A


title: breast tumour 74A


title: breast tumour 53B


title: breast tumour 57B


title: PSMD14 exon 11 Output 9a


title: breast tumour 120A


title: 22_DG

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
QC check, data processing, and peak calling of ATAC-seq were performed by using AIAP
peaks across all samples were merged using bedtools merge
counts for each peak were measured bedtools coverageand merged across samples
counts were corrected for batch effect using RUVr from the RUVSeq R package (v 1.16.1) according to the protocol described in the vignette using option k=3.
Adjusted bedgraph files were generated by supplying raw bedgraphs for each sample, raw counts, and RUVSeq adjusted counts to BeCorrect (v 1.0.0)
Genome_build: rn6
Supplementary_files_format_and_content: bedgraph

organism: Rattus norvegicus

source_name: Dentate Gyrus

extract_protocol:
The brains were removed, dissected out into discrete brain areas (striatum, dentate gyrus, Ammon’s horn, prefrontal cortex, and cerebellum) and stored at − 80 °C until assayed.  The dentate gyrus was dissected out according to a previously described protocol76 modified for the rat brain. Briefly, the brain was cut sagittally to divide the hemispheres, which were then placed medial side up after removal of the regions posterior to lambda. The dentate gyrus and Ammon’s horn (CA1 and CA3) (which were visible upon removal of thalamus and hypothalamus) were dissected out using fine tip surgical instruments. Liver and muscle tissues were also collected and stored at –80°C until analysis.
The Omni-ATAC protocol on Nuclei Isolated from frozen tissue was slightly modified. A frozen tissue fragment approximately 5-10 mg was placed into a pre-chilled 2 ml Dounce homogenizer containing 0.5 ml of cold 1x homogenization buffer (320 mM sucrose, 0.1mM EDTA, 0.1% NP40, 5mM CaCl2, 3mM Mg(Ac)2, 10 mM Tris pH 7.8, 1x protease inhibitors(Roche, cOmplete), 167 uM β-mercaptoethanol, in water). Tissue was homogenized with approximately 10 strokes with the loose “A” pestle, followed by 20 strokes with the tight “B” pestle. Residual debris were removed by centrifugation for 1 min at 100 RCF. Avoiding pelleted debris, 400 ul was transferred to a pre-chilled 2 ml round bottom Lo-Bind Eppendorf tube. An equal volume (400 ul) of a 50% iodixanol solution (50% iodixanol in 1x homogenization buffer) was added and mixed by pipetting to make a final concentration of 25% iodixanol. 600 ul of a 29% iodixanol solution (29% iodixanol in 1x homogenization buffer containing 480 mM sucrose) was layered underneath the 25% iodixanol mixture. A clearly defined interface should be visible. In a similar fashion, 600ul of a 35% iodixanol solution (35% iodixanol in 1x homogenization containing 480 mM surcose) was layered underneath the 29% iodixanol solution. Again, a clearly defined interface should be visible between all three layers. In a swinging bucket centrifuge, nuclei were centrifuged for 20minute at 4800 RCF. After centrifugation, nuclei are present at the interface of the 29% and 35% iodixanol solutions. This nuclei band was collected in a 300 ul volume and transferred to a prechilled tube containing 1 ml of ATAC-seq RSB (10mM Tris pH 7.4, 10mM NaCl, 3mM MaCl2) with 0.1% Tween-20. Nuclei were pelleted by centrifugation at 500 RCF for 10 minutes in a pre-chilled 4°C fixed-angle centrifuge. Supernatant was removed using two pipetting steps, in which the supernatant was aspirated with p1000 pipette first, the remaining 100ul was carefully aspirated with a p200 pipette. 20 ul 2x TD buffer (20mM Tris pH 7.6, 10mM MgCl2, 20% Dimethyl Formamide) was added to the nuclear pellet and mixed by pipetting up and down 6 times. Nuclei were counted after addition of trypan blue which stains all nuclei. 50,000 counted nuclei were then transferred to a tube with 2x TD buffer being filled in up to 25ul. 25ul of transposition mix (2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) was then added to the nuclei in the 25ul 2x TD buffer. Transposition reactions were mixed and incubated at 37°C for 30 minutes with simply tapping every 10 minutes. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns.

treatment_protocol: Adult male Sprague-Dawley rats (Harlan, Indianapolis, IN, USA) (weighing 250–300 g on arrival) were pair-housed under a 12 h light/dark cycle in a temperature-controlled (20–22 °C) and humidity-controlled room. Food and water were available ad libitum. The animals were allowed to acclimatize for one week before the start of the study. All animal procedures were conducted between 7:00 A.M. and 7:00 P.M. in strict accordance with the National Institutes of Health (NIH) Guide for the Care and Use of Laboratory Animals and were approved by the Institutional Animal Care and Use Committee (IACUC) at Wayne State University (animal protocol #A 16-03-067). The description of animal procedures meets the ARRIVE recommended guidelines described by The National Centre for the Replacement, Refinement and Reduction of Animals in Research.

value: Sprague-Dawley

value: Brain

tag: age

value: 8 weeks


title: Pa16C 3Day DMSO 1

description:
201904660186_R01C01
Pa16C treated with DMSO, assayed after 3 days


title: PSMD14 exon 11 Output 9c


title: RMB4442

tag: strain


title: PSMD14 exon 11 Output 8d


title: RMB4441

tag: markers


title: 21_DG

tag: cell type


title: PSMD14 exon 11 Output 8c


title: RMB4440


title: breast tumour 116A


title: breast tumour 116B


title: breast tumour 50A


title: PSMD14 exon 11 Output 8b


title: breast tumour 50B


title: RMB4439


title: PSMD14 exon 11 Output 8a


title: RMB4438


title: RMB4437


title: 22_AH

source_name: Ammon’s Horn


title: 21_AH


title: 15_AH


title: breast tumour 48B


title: RMB4436


title: 14_AH


title: 15_DG


title: PSMD14 exon 11 Output 7b


title: RMB4435


title: D3 Native and watermarked single locus glycolysis

city: Delft

first: Jean-Marc

last: Daran

address: Julianalaan 67

department: Department of Biotechnology

country: Netherlands

institute: Delft University of Technology

description: S. cerevisiae IMX2028 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

data_processing:
For each transcript, sequence markers of 21 bp were identified that are unique in the transcript relative to the entire transcriptome and genome.
With an exact matching algorithm, these markers can uniquely identify the transcript of origin of a read in RNA-seq data.
Aho-Corasick exact string matching algorithm was used to quantify transcripts.
Differential expression was performed using DE-Seq2.
Genome_build: CEN.PK113-7D, Salazar et al.
Supplementary_files_format_and_content: *.tsv: Tab-delimited files, raw transcript counts.

organism: Saccharomyces cerevisiae

source_name: Shake flask mid exponential phase

growth_protocol: Liquid cultures were grown in 500 ml shake flasks filled with 100 ml of medium at 30o C with 200 rpm agitation. Complex media (further referred to as YPD) contained 10 g l-1 yeast extract, 20 g l-1 peptone and 20 g l-1 glucose. Synthetic minimal medium (further referred as SMG) consisted of 3 g l−1KH2PO4, 0.5 g l−1MgSO4·7H2O, 5 g l−1(NH4)2SO4, 1 ml l−1of a trace element solution, and 1 ml l−1of a vitamin solution as previously described 13 and supplemented with 20 g l−1 glucose. For solid medium, 20 g l−1 agar was added prior autoclaving.

extract_protocol:
The resulting ice pellet was gently thawed on ice and spun down at 4700 x g for 5 min at 0 o C. Pellets were then resuspended in 1.2 mL of ice-cold AE buffer (50 mM sodium acetate and 10 mM EDTA, pH 5.0), followed by addition of 1.2 mL of acid phenol/chloroform/isoamyl alcohol mix and 0.12 mL 10 % sodium dodecyl sulfate. The resulting mix was vortexed for 30 s and incubated for 5 min at 65 °C. After homogenizing for 30 sec by vortexing, 800 µL aliquots were distributed in RNase-free screw-cap tubes (Tai et al. 2005). After centrifugation (15 min at 10,000 x g), the aqueous phase was transferred to a new tube containing 0.4 mL of acid phenol/chloroform. The mix was vortexed for 30 seconds, centrifuged (15 min at 10,000 x g) and the aqueous phase was again transferred to a new tube. RNA was then ethanol precipitated and re-suspended in RNase-free water. Prior to cDNA synthesis, purity, concentration and integrity of the RNA in the samples was assessed with the Nanodrop (Thermo Fisher Scientific), Qubit (Thermo Fisher Scientific) and Tapestation 220 with RNA Screen Tape (Agilent Technologies), respectively, according the manufacturers’ recommendations.
cDNA libraries were prepared using the TruSeq RNA V2 kit (Illumina) and sequenced on HISeq 2500 (Illumina) at Novogene (HK) Company Ltd (Hong Kong, China).

tag: carbon source

value: Glucose

value: MATa ura3-52 his3-1 leu2-3,112 MAL2-8c SUC2 hxk1::KlLEU2 tdh1 tdh2 gpm2 gpm3 eno1 pyk2 pdc5 pdc6 adh2 adh5 adh4 glk1::Sphis5<delta>::(pGAL1-I SceI-tCYC1) can1::( ARS418 CAN1 AH FBA1 AH H TPI1 HP PGK1 PQ ADH1 QN PYK1 NO TDH3 OA ENO2 AB HXK2 BC PGI1 CD PFK1 DJ PFK2 J BP HIS3 BP L GPM1 LM PDC1 M AR ARS1211 AR CAN1) sga1::( ARS418sga1 AH FBA1_*AH H TPI1_*HP PGK1_*PQ ADH1_*QN PYK1_*NO TDH3_*OA ENO2_*AB HXK2_*BC PGI1_*CD PFK1_*DJ PFK2_*J BP HIS3BP L GPM1_*LM PDC1_*M AR ARS1211AR sga1)


title: breast tumour 48A

tag: tissue


title: 14_DG


title: breast tumour 125B

value: surgery(B)


title: breast tumour 34A

value: breast tumour


title: RMB4434


title: D2 Native and watermarked single locus glycolysis

treatment_protocol: Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.


title: PSMD14 exon 11 Output 7d


title: breast tumour 31B


title: breast tumour 31A

value: baseline(A)


title: PSMD14 exon 11 Output 7c


title: breast tumour 173B


title: PSMD14 exon 11 Output 6c


title: W3 Watermarked single locus glycolysis

description: S. cerevisiae IMX1770 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: MATa ura3-52 his3-1 leu2-3,112 MAL2-8c SUC2 hxk1::KlLEU2 tdh1 tdh2 gpm2 gpm3 eno1 pyk2 pdc5 pdc6 adh2 adh5 adh4 pyk1 pgi1 tpi1 tdh3 pfk2::(pTEF-cas9-tCYC1 natNT1) pgk1 gpm1 fba1 hxk2 pfk1 adh1 pdc1 eno2 glk1::Sphis5<delta>::(pGAL1-I-SceI-tCYC1) can1::(ARS418CAN1 AH FBA1_*AH H TPI1_*HP PGK1_*PQ ADH1_*QN PYK1_*NO TDH3_*OA ENO2_*AB HXK2_*BC PGI1_*CD PFK1_*DJ PFK2_*J BP HIS3BP L GPM1_*LM PDC1_*M AR ARS1211AR CAN1) sga1::KlURA3


title: RHP7220


title: RHP7221


title: D1 Native and watermarked single locus glycolysis


title: PSMD14 exon 11 Output 6b


title: RHP7219


title: breast tumour 34B


title: PSMD14 exon 11 Output 6a


title: RHP7218

value: CMP


title: W2 Watermarked single locus glycolysis


title: PSMD14 exon 11 Output 7a


title: W1 Watermarked single locus glycolysis


title: PSMD14 exon 11 Output 5d


title: RHP7217


title: breast tumour 99B


title: breast tumour 97B


title: PSMD14 exon 11 Output 5c


title: RHP7216


title: PSMD14 exon 11 Output 6d


title: N2 Native single locus glycolysis

description: S. cerevisiae IMX1771 was grown in SMG until mid-exponential phase (OD660nm of 12.5). Culture samples corresponding to ca. 240 mg of biomass wet weight were directly quenched in liquid nitrogen.

value: MATa ura3-52 his3-1 leu2-3,112 MAL2-8c SUC2 hxk1::KlLEU2 tdh1 tdh2 gpm2 gpm3 eno1 pyk2 pdc5 pdc6 adh2 adh5 adh4 pyk1 pgi1 tpi1 tdh3 pfk2::(pTEF-cas9-tCYC1 natNT1) pgk1 gpm1 fba1 hxk2 pfk1 adh1 pdc1 eno2 glk1::Sphis5<delta>::(pGAL1-I-SceI-tCYC1) can1::(ARS418 CAN1 AH FBA1 AH H TPI1 HP PGK1 PQ ADH1 QN PYK1 NO TDH3 OA ENO2 AB HXK2 BC PGI1 CD PFK1 DJ PFK2 J BP HIS3 BP L GPM1 LM PDC1 M AR ARS1211 AR CAN1) sga1::KlURA3


title: PSMD14 exon 11 Output 5b


title: RHP7215


title: breast tumour 19B

value: female


title: N1 Native single locus glycolysis


title: breast tumour 142B


title: breast tumour 38A


title: RHP7213


title: PSMD14 exon 11 Output 5a


title: RHP7214


title: PDX of bone metastasis, patient 176

city: Paris

first: Elisabetta

last: Marangoni

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: Copy number data HBCx-176

hyb_protocol: According to the manufacturer's protocol.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner

data_processing: Chromosome Analysis Suite processed using the GAP methodology

source_name: human breast cancer xenograft 176

growth_protocol: Engrafted into the interscapular fat pad of female Swiss nude mice

extract_protocol: DNA were isolated using the QIAamp DNA Mini Kit (Qiagen, Hamburg, GmbH)

treatment_protocol: Endocrine treatments

tag: disease state

value: Oestrogen receptor positive breast cancer

value: PDX of bone metastasis


title: PDX of bone metastasis, patient 139

description: Copy number data HBCx-139

source_name: human breast cancer xenograft 139

label_protocol: According to the manufacturer's protocol.


title: PDX of bone metastasis, patient 180

description: Copy number data HBCx-180

source_name: human breast cancer xenograft 180


title: breast tumour 142A


title: PSMD14 exon 11 Output 4c


title: breast tumour 137B


title: +CPI colitis C1 sample CD3 gd TCR sequencing

city: Boston

first: Shengbao

last: Suo

state: MA

address: 360 Longwood Ave

institute: Dana-Farber Cancer Institute

description:
T cell receptor
C1-gdTCR

data_processing:
Library strategy: TCR-seq
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v3.0.2)
“cellranger count” function is used to align sequencing reads to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and count the unique molecular identifier (UMI
All patient samples from each dataset were then aggregated by using the “cellranger aggr” function without depth normalization
After getting the digital cell by gene expression matrix, the cells with poor quality (cells with high percentage of mitochondrial gene reads, cells express less than 200 genes and cells which show high doublet scores determined by DoubletFinder (v2.0.2)) were filted
Raw TCR sequencing data were processed by using 10X Genomics Cell Ranger (abTCR: v3.1.0, gdTCR: v3.0.0). Briefly, FASTQ reads were aligned to human GRCh38 V(D)J reference genome (V3.1.0) by using the “cellranger vdj” function
Genome_build: GRCh38
Supplementary_files_format_and_content: Each RNA sequenting sample contains a compressed tab-delimited text files including matrix.mtx (UMI count matrix in a sparse matrix format), genes.tsv (Gene names) and barcodes.tsv (Cell barcodes). TCR sequencing data for each gdTCR sample are saved in a csv file, which is generated by 'cellranger vdj' function and shows the detailed clonotype information.

source_name: Colon pinch biopsy

growth_protocol: single cell suspensions were prepared from colon biopsies.

extract_protocol:
Manufacturer's protocols for 5' barcoded GEX and V(D)J TCR
Manufacturer's protocols for 5' barcoded GEX and V(D)J TCR

treatment_protocol: Biopsies were transferred to 6 cm tissue culture dishes placed on ice, and cut into <1 mm pieces with a razor blade while immersed in a small volume in DMEM to preserve tissue hydration. Tissue pieces were centrifuged (400 g for 5 min at 4°C for all centrifuge steps) and resuspended in 2 mL of collagenase-containing enzymatic digestion solution prepared according to manufacturer’s instructions (Miltenyi Human Tumor Dissociation Kit #30-095-929). Biopsies were incubated at 37°C for 25-30 min with mixing using a P1000 pipet tip (10 minute intervals) and intervening gentle vortexing (2-5 minute intervals). Digestion produced a nearly uniform single cell suspension, after which cells were filtered through a 70 m nylon mesh filter. Filtered cell suspensions were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco) for 1 minute at RT, then immediately diluted with 10 mL of PBS buffer containing 0.5% FBS and 1 mM EDTA to halt osmotic stress. Cells were centrifuged and subsequently resuspended in Zombie NIR (Biolegend #423106) viability dye solution (1:500 in PBS), followed by 15 min incubation at RT in the dark. Cells were counted with a hemocytometer, generally yielding >100,000 live cells per biopsy. Following viability dye staining, cells were allocated for sorting/single-cell RNA-seq. For patients with biopsies spanning multiple regions, descending colon and sigmoid-rectum cell suspensions were combined in equal numbers to provide an aggregate analysis of the lower colon. Cells stained with viability dye (0.4-0.6 x 106) were resuspended in 100 L FACS wash buffer (FWB; PBS, 2%FBS, 1 mM EDTA) with the addition of the following antibodies: TruStain FcX (Biolegend 422302), CD3-PE/Dazzle (Biolegend 300450), CD45-Pacific Blue (Biolegend 304022), CD66b-PE/Cy7 (Biolegend 305116) and CD15-APC (Biolegend 301908). Cells were incubated on ice for 20 minutes, washed with 1 mL FWB, and then resuspended in 500 L FWB for sorting on a FACS Aria II or III (BD Biosciences). For the majority of samples, 12-15 x 103 live CD45+CD66b- mononuclear cells (MNC) cells and CD3+ cells (pre-gated on live MNC) were separately sorted into T cell media (RMPI + 10% FBS) and immediately transferred to ice.

tag: tissue region

value: Sigmoidal colon, rectum

tag: checkpoint inhibitor (cpi)-treated

value: yes

tag: colon status

value: +CPI colitis

tag: cell marker

tag: 10x chemistry

value: scRNA-seq (10X Genomics 5' V1 VDJ)


title: breast tumour 132B

tag: Sex


title: RHP7212


title: PSMD14 exon 11 Output 4b


title: N3 Native single locus glycolysis

tag: genotype


title: RHP7211


title: RHP7210


title: +CPI no colitis NC1 sample CD3 TCR sequencing

description:
NC1-TCR
T cell receptor
TCR_filtered_contig_annotations_all.csv

data_processing:
Library strategy: TCR-seq
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v3.0.2)
“cellranger count” function is used to align sequencing reads to the human reference genome (GRCh38, v3.0.0, from 10X Genomics), and count the unique molecular identifier (UMI)
All patient samples from each dataset were then aggregated by using the “cellranger aggr” function without depth normalization
After getting the digital cell by gene expression matrix, the cells with poor quality (cells with high percentage of mitochondrial gene reads, cells express less than 200 genes and cells which show high doublet scores determined by DoubletFinder (v2.0.2)) were filtered)
Raw TCR sequencing data were processed by using 10X Genomics Cell Ranger (v3.1.0). Briefly, FASTQ reads were aligned to human GRCh38 V(D)J reference genome (v3.1.0, from 10X Genomics) by using the “cellranger vdj” function
Genome_build: GRCh38
Supplementary_files_format_and_content: *genes-barcodes-matrix.tar.gz (Each RNA sequencing sample contains a tar archive including matrix.mtx (UMI count matrix in a sparse matrix format), genes.tsv (Gene names) and barcodes.tsv (Cell barcodes). )
TCR_filtered_contig_annotations_all.csv (TCR sequencing data for all CD3 samples are saved in a csv file, which is generated by 'cellranger vdj' function and shows the detailed clonotype information.)

extract_protocol: Manufacturer's protocols for 5' barcoded GEX and V(D)J TCR

treatment_protocol: Biopsies were transferred to 6 cm tissue culture dishes placed on ice, and cut into <1 mm pieces with a razor blade while immersed in a small volume in DMEM to preserve tissue hydration. Tissue pieces were centrifuged (400 g for 5 min at 4°C for all centrifuge steps) and resuspended in 2 mL of collagenase-containing enzymatic digestion solution prepared according to manufacturer’s instructions (Miltenyi Human Tumor Dissociation Kit #30-095-929). Biopsies were incubated at 37°C for 25-30 min with mixing using a P1000 pipet tip (10 minute intervals) and intervening gentle vortexing (2-5 minute intervals). Digestion produced a nearly uniform single cell suspension, after which cells were filtered through a 70 um nylon mesh filter. Filtered cell suspensions were centrifuged and resuspended in 3 mL ACK red blood cell lysis buffer (Gibco) for 1 minute at RT, then immediately diluted with 10 mL of PBS buffer containing 0.5% FBS and 1 mM EDTA to halt osmotic stress. Cells were centrifuged and subsequently resuspended in Zombie NIR (Biolegend #423106) viability dye solution (1:500 in PBS), followed by 15 min incubation at RT in the dark. Cells were counted with a hemocytometer, generally yielding >100,000 live cells per biopsy. Following viability dye staining, cells were allocated for sorting/single-cell RNA-seq. For patients with biopsies spanning multiple regions, descending colon and sigmoid-rectum cell suspensions were combined in equal numbers to provide an aggregate analysis of the lower colon. Cells stained with viability dye (0.4-0.6 x 106) were resuspended in 100 uL FACS wash buffer (FWB; PBS, 2%FBS, 1 mM EDTA) with the addition of the following antibodies: TruStain FcX (Biolegend 422302), CD3-PE/Dazzle (Biolegend 300450), CD45-Pacific Blue (Biolegend 304022), CD66b-PE/Cy7 (Biolegend 305116) and CD15-APC (Biolegend 301908). Cells were incubated on ice for 20 minutes, washed with 1 mL FWB, and then resuspended in 500 uL FWB for sorting on a FACS Aria II or III (BD Biosciences). For the majority of samples, 12-15 x 10e3 live CD45+CD66b- mononuclear cells (MNC) cells and CD3+ cells (pre-gated on live MNC) were separately sorted into T cell media (RMPI + 10% FBS) and immediately transferred to ice.

value: Descending, sigmoidal colon; rectum

tag: checkpoint inhibitor-treated

value: +CPI no colitis


title: PSMD14 exon 11 Output 4a

tag: cell line


title: RHP7209


title: PSMD14 exon 11 Output 3d


title: PSMD14 exon 11 Output 3c


title: PSMD14 exon 11 Output 4d


title: +CPI colitis C1 sample CD3 TCR sequencing

description:
C1-TCR
T cell receptor
TCR_filtered_contig_annotations_all.csv


title: RHP7208


title: hsa_6F_L6.LB18

city: Basel

first: Klas

last: Hatje

state: Basel

address: Grenzacherstrasse 124

country: Switzerland

institute: Roche Pharma Research and Early Development

description:
hsa_readCounts.txt
hsa_totalRPM.txt

data_processing:
The sequences received in fastq format were processed using sRNAbench version 10/14 (http://bioinfo2.ugr.es:8080/ceUGR/srnabench/) with the following parameters: microRNA=hsa; recursiveAdapterTrimming=true; adapter=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC; predict=true; isoMiR=true; noMM=0; alignType=n; adapterMinLength=10; maintainOrig=true; removeBarcode=0; minRC=2; adapterMM=1; seed=20; minReadLength=15. The processing included mapping to the human genome version hg19 with Bowtie (http://bowtie-bio.sourceforge.net), quantification of known microRNAs as annotated in miRBase (http://www.mirbase.org), and prediction of novel microRNAs. Sequence reads per microRNA were normalized by reads per million mapped reads (RPM) with the total number of genome mapped reads per sample. Quality control was applied including read statistics and unbiased clustering of counts and RPMs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts and RPM values

growth_protocol: Naïve cells were grown on irradiated (30 gy) CF1 mouse embryonic fibroblasts (MEFs) (Millipore; PMEF-CFL) with daily media changes of t2iLGoY, prepared as previously described (Guo et al., 2016). The naïve hESC lines HNES1 and HNES2 cells were previously derived (Guo et al., 2016). Cells were grown in a humidified incubator at 37°C, 7% CO2, 5% O2. Primed hPSC were grown on geltrex precoated plates (A1413302) in E8 medium (A15169-01). Cells were fed daily by aspirating all medium and replacing it with fresh, room temperature medium.

extract_protocol:
RNA extractions from cell pellets (1 x 10^6 cells) were performed using the miRNeasy mini kit (217004; Qiagen), following the manufacturer’s protocol.
For miRNAseq, purified total RNA was sent to EA | Q² Solutions (5927 S. Miami Blvd., Suite 100, Morrisville, NC 27560, US) who performed library preparation and miRNA sequencing.

treatment_protocol: To prime naïve cells, 1 – 5 x 10^4 cells/cm2 were plated onto a well of a six well plate (precoated with geltrex for >1 h). Medium was switched to E8 after 48 hours.

tag: developmental stage

value: embryo

tag: day


title: RHP7207

tag: strain


title: PSMD14 exon 11 Output 3b


title: hsa_6E_L6.LB15

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Output 3a


title: RHP7206

tag: markers


title: hsa_6D_L6.LB12

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Output 2d


title: hsa_6C_L6.LB9

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7205

tag: cell type


title: breast tumour 137A

tag: timepoint


title: breast tumour 123B

tag: tissue


title: breast tumour 126A


title: breast tumour 126B


title: breast tumour 203A


title: breast tumour 132A


title: PSMD14 exon 11 Output 2c


title: breast tumour 185B


title: breast tumour 4A


title: RHP7204


title: RHP7203


title: PSMD14 exon 11 Output 2b


title: hsa_3F_L6.LB17

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: hsa_6A_L6.LB3

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7200


title: breast tumour 160A


title: breast tumour 185A


title: hsa_3E_L6.LB14

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Output 1d


title: hsa_6B_L6.LB6

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Output 1c


title: breast tumour 160B


title: RHP7199


title: RHP7198


title: RHP7202


title: PSMD14 exon 11 Output 1a


title: hsa_3D_L6.LB11

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Input 12

description:
PCR amplicon
Plasmid library.


title: hsa_3B_L6.LB5

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7197


title: hsa_3A_L6.LB2

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7196


title: hsa_3C_L6.LB8

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Input 11

description:
PCR amplicon
Plasmid library.


title: hsa_1F_L6.LB16

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7195


title: PSMD14 exon 11 Output 2a


title: PSMD14 exon 11 Output 1b


title: RHP7194


title: PSMD14 exon 11 Input 10

description:
PCR amplicon
Plasmid library.


title: PSMD14 exon 11 Input 9

description:
PCR amplicon
Plasmid library.


title: hsa_1D_L6.LB10

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Input 8

description:
PCR amplicon
Plasmid library.


title: hsa_1C_L6.LB7

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: RHP7193


title: RHP7201


title: PSMD14 exon 11 Input 7

description:
PCR amplicon
Plasmid library.


title: hsa_1E_L6.LB13

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: breast tumour 100B


title: RHP7191


title: breast tumour 112A


title: RHP7192


title: PSMD14 exon 11 Input 6

description:
PCR amplicon
Plasmid library.


title: breast tumour 109A


title: breast tumour 114A


title: breast tumour 109B


title: hsa_1A_L6.LB1

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: PSMD14 exon 11 Input 5

description:
PCR amplicon
Plasmid library.


title: breast tumour 53A


title: hsa_1B_L6.LB4

description:
hsa_readCounts.txt
hsa_totalRPM.txt


title: Fibach_Capture

city: Headington

first: Damien

last: Downes

state: Oxfordshire

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Medicine

institute: The University of Oxford

data_processing:
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
genome build: hg19
processed data files format and content: custom tsv (chr start stop interactions viewpoint)

source_name: Erythroid culture

growth_protocol: Erythroid cells were differentiated in a two-phase liquid culture as described (Pope et al 2000 PMID 10863975; Fibach & Prus 2005 PMID 18432954). Briefly, peripheral blood mononuclear cells were isolated using Ficoll-Histopaque and cultured in phase I medium (Complete MEM, 10% (v/v) preselected FBS, 1µg/ml cyclosporin A, 10% (v/v) conditioned medium from 5637 human bladder carcinoma cell line) which lacks erythropoietin (EPO). After 7 days non-adherent cells were washed with MEM and transferred to Phase II media (Complete MEM, 30% (v/v) preselected FBS, 1% (w/v) demonised BSA, 0.1 mM 2-mercaptoethanol, 10µM dexamethasone, 0.3 mg/ml human holo-transferrin, 10 ng/ml human recombinant stem cell factor, 1 U/ml human EPO) for a further 6 days. Cells were fixed with formaldehyde for ChIP-seq (1% v/v) and NG CaptureC (2% v/v).

extract_protocol: 3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies). 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Nextseq 500 (150 bp paired-end reads)

value: Erythroid culture

tag: gender

value: Male

tag: antibody


title: PSMD14 exon 11 Input 4

description:
PCR amplicon
Plasmid library.


title: breast tumour 33B

value: surgery(B)

value: breast tumour


title: LCMV

city: San Francisco

first: Brian

middle: J

last: Laidlaw

address: 513 Parnassus Avenue, HSE 1001

institute: University of California, San Francisco

data_processing:
Sequences reported as fastq and matrix.mtx, barcodes.tsv, and features.tsv files
Matrix.mtx, barcodes.tsv, and features.tsv files were imported into R studio
Seurat used to analyze differential expression
Cells were filtered based on number of genes expressed, number of unique molecular identifiers, and the percentage of mitochondrial genes present to exclude outlier cells as described in the Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet with DEGS for all clusters and for Mem subclusters

source_name: Spleen

extract_protocol:
Immediately post-sorting, the indicated B cell populations were run on the 10X Chromium (10X Genomics) and then through library preparation by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v3 Chemistry). Libraries were run on the HiSeq4000 for Illumina sequencing. Post-processing and quality control were performed by the Genomics Core Facility at the Institute for Human Genetics at UCSF using the 10X Cell Ranger package (v3.0.2, 10X Genomics). Reads were aligned to mm10 reference assembly and analyzed using the Seurat and Monocle software packages. Cells were filtered based on number of genes expressed, number of unique molecular identifiers, and the percentage of mitochondrial genes present to exclude outlier cells as described in the Seurat package.
Library preparation was performed by the Institute for Human Genetics at UCSF following the recommended protocol for the Chromium Single Cell 3’ Reagent Kit (v3 Chemistry).

treatment_protocol: LCMV Armstrong day 11

tag: infection

value: LCMV Armstrong day 11

value: 90% GC B cells (B220+IgDloGL7+CD95+), 5% FO B cells (B220+IgDhiGL7-CD95-CD38+), 5% MBCs (B220+IgDloGL7-CD38+S1pr2-Tomato+)


title: breast tumour 47B


title: PSMD14 exon 11 Input 3

description:
PCR amplicon
Plasmid library.


title: breast tumour 191B


title: breast tumour 97A

value: baseline(A)


title: breast tumour 114B

value: female


title: breast tumour 120B


title: LB_3

city: Shenyang

first: Chenghao

last: Zhao

address: No.120 Dongling Road

country: China

institute: Shenyang Agricultural University

data_processing:
Base calling  was performed following the standard Illumina protocol.
Raw paired-end reads of  RNA-Seq were filtered and adapter sequences were trimmed out by Trimmomatic (v0.35)
Cleaned reads from each sample was aligned to maize B73 reference genome (AGPv3.30) and using HISAT v 0.1.6-beta
HTSeq (v0.6.1) was used to count the number of mapped reads to each gene
The transcript abundances were estimated by RPKM (Reads Per Kilobases per Million reads) to quantify the gene expression levels
Genome_build: Zea mays B73 AGPv3.30
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each sample

organism: Zea mays

source_name: leaves

growth_protocol: Plants were grown under normal condition under different plant densities

extract_protocol:
Total RNA was extracted using Trozol reagent (Invitrogen) according to manufacturer’s protocol.
RNA sequencing libraries were prepared according to the manufacturer’s protocol of the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (E7530L,NEB).

tag: cultivar

value: Xianyu 335

tag: treatment

value: low plant density

value: leaves

tag: leaf position

value: 3rd leaf below ear

value: grain-filling stage


title: LB_2


title: PSMD14 exon 11 Input 1

description:
PCR amplicon
Plasmid library.


title: breast tumour 18A

tag: Sex


title: LE_3

value: ear leaf


title: PSMD14 exon 11 Input 2

description:
PCR amplicon
Plasmid library.


title: KO_2

data_processing:
Sequences reported as fastq files
Fastq files alligned to mm10 genome with STAR
Mappable reads counted with HTseq and imported into RStudio
DESeq2 used  to analyze differential expression
Genome_build: mm10
Supplementary_files_format_and_content: Excel sheet with normalized counts for all samples

extract_protocol:
Cells were isolated by sorting using an Aria sorter and total RNA purified using the RNeasy Micro kit (Qiagen). RNA quality was assessed with an Agilent 2100 Bioanalyzer (RNA integrity number>9 for all samples)
Barcoded sequencing libraries were generated with 100ng of RNA with an Ovation RNAseq System V2 (Nugen), KAPA Hyper Prep Kit for Illumina (KAPA Biosystems), and NEXTflex DNA barcodes (Bioo Scientific). Single-end sequencing was performed on an Illumina HiSeq 4000 (UCSF Center for Advanced Technology)

tag: genotype/variation

value: KO


title: KO_1


title: LB_1


title: Ancestral FAS exon 6 Library Output 9d

description:
PCR amplicon
Mature mRNA containing the ancestral FAS exon 6.


title: Het_2

value: het


title: KO_3


title: Het_1


title: LE_2


title: breast tumour 18B


title: Ancestral FAS exon 6 Library Output 9c


title: YUMMER1.7 H2B-eGFP treated with IL-18 [YRWT18]

city: New Haven

first: Meaghan

last: McGeary

state: CT

address: 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine

data_processing:
Quality Control, Barcod processing, alignment, feature counting and sample aggratation by CellRanger Single Cell Software Suite (v.2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Raw gene-by-cell matrix of gene expression, including barcodes, and expressed genes.

source_name: subcutaneous tumor

extract_protocol:
Tumors were removed from mice on day 13, dissociated by sterile mincing and treated with 1mg/mL collagenase (Sigma) and DNase (1:1000) and 2% FBS in RPMI and incubated for 30 minutes at 37'C, then filtered through a 100 uM cell strainer. Cells were washed, treated with ACK buffer to remove red blood cells and washed again. To sort, cells were stained wtih anti-CD45 (BioLegend; 1:100), anti-CD3 (BioLegend; 1:100) and viability dye, in RPMI + 1% FBS for 30 minutes at 4'C and GFP+, GFP-CD45+CD3e+, GFP-CD45+CD3e- cells were sorted using BD FACSAria. Cells were then re-pooled at a combination of 50% CD45+CD3e+, 25% CD45+CD3e-, 25% GFP+CD45-CD3e-.
Droplet-based 3' end single cell RNA sequencing was performed using the Chromium Controller and Illumina HiSeq 4000. Libraries were prepared using Chromium Single Cell 3' Reagent Kits v2 according to manufacturer's protocol (10X genomics). Generated libraries were sequenced on Illumina HiSeq 4000.

treatment_protocol: Mice bearing YUMMER1.7 tumors were treated twice weekly, beginning at day 7 with either sterile PBS (controL), 0.32 mg/kg IL18, or 0.32 mg/kg DR-18.

tag: strain background

value: wt IL-18

value: subcutaneous tumor

tag: cell line genotype


title: LE_1

tag: developmental stage


title: YUMMER1.7 H2B-eGFP B2M-/- treated with DR18 [B2M-DR18]

value: H2B-eGFP B2M-/-


title: breast tumour 14B

value: surgery(B)


title: LA_3

value: high plant density

value: 3rd leaf above ear


title: YUMMER1.7 H2B-eGFP B2M-/- [B2M]


title: breast tumour 20A

value: breast tumour


title: YUMMER1.7 H2B-eGFP treated with DR18 [YR-DR18]


title: breast tumour 20B


title: LA_2


title: Ancestral FAS exon 6 Library Output 8d

tag: cell line


title: breast tumour 100A

value: baseline(A)


title: Ancestral FAS exon 6 Library Output 8c


title: HB_1


title: LA_1


title: Ancestral FAS exon 6 Library Output 8b


title: HB_2


title: YUMMER1.7-H2B-eGFP [YR]

description: YR


title: HB_3


title: breast tumour 1A

value: female


title: breast tumour 201B


title: breast tumour 1B


title: Ancestral FAS exon 6 Library Output 7d


title: breast tumour 84B


title: Ancestral FAS exon 6 Library Output 8a


title: Cdx2 ES input DNA

first: Andrew

middle: Zhuo

last: Xiao

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

description: Peak files include ChIP and input island read counts.

data_processing:
Library strategy: ssDNA-seq
Basecalling and adapter sequence trimming was performed using the standard Illumina workflow.
Reads were aligned to the mm9 genome using Bowtie2 v2.3.1 with default parameters.
Non-uniquely mapped reads were filtered out using MapQ > 10 for the "unique-mapping" peak file.
PCR and optical duplicates were removed with Picard v2.9.0.
Peaks were called using SICER v1.1 using an FDR cutoff of 0.01 and input DNA as control with window 200 bp (w200) and gap 600 bp (g600), or alternatively w100 g200.
Genome_build: mm9
Supplementary_files_format_and_content: bed files with 8 tab delimited columns: chrom, start, end, ChIP island read count, CONTROL (input) island read count, p value, fold change, FDR threshold

source_name: ES cell

growth_protocol: ES cells were maintained on feeder cells in DMEM supplemented with 15% fetal bovine serum, 1% non-essential amino acids, 2 mM l-glutamine, 1,000 units of mLIF, 0.1 mM β-mercaptoethanol, and antibiotics. In addition, Cdx2 ES cell media was supplemented with 2 µg/ml doxycycline.

extract_protocol:
Briefly, live cells were treated with 100 mM KMnO4 then lysed. Each subsequent treatment was followed by phenol:chloroform extraction. Lysates were first treated with proteinase and Rnase, then free 3' ends blocked by cordycepin-5’-triphosphate addition wtih TdT. ssDNA was digested with S1 nuclease then free 3' ends biotinylated. Samples were sonicated with Covaris S220 to generate DNA fragments between 200 and 700 bp and biotinylated fragments pulled down using streptavidin-coated beads. Fragments were released by incubating with S1 nuclease and purified with MinElute PCR Purification Kit (Qiagen)
Libraries were prepared using the NEBNext Ultra II DNA Library Prep kit according to the manufacturer’s instructions without size selection.

tag: genotype


title: Ancestral FAS exon 6 Library Output 9a


title: Ancestral FAS exon 6 Library Output 7c


title: HE_3

value: Xianyu 335


title: HE_1


title: HE_2


title: Ancestral FAS exon 6 Library Output 7b


title: during regeneration

city: Dona Paula

first: Aabha

last: Deshpande

state: Goa

address: Dona Paula circle

department: Chemical Oceanography Department

institute: CSIR- National Institute of Oceanography

data_processing:
Quality Control with FastQC
Trimming with Trimmomatic
De-novo transcriptom assembly using Trinity
Unigene prediction and validation using RSEM, CD-HIT
CDS prediction and validation using Transdecoder and RSEM
Differential epression using DE

organism: Cinachyrella cavernosa

source_name: tissue

growth_protocol: Sponges were maintained in aquaria (~100L volume) for acclimatization. The sponges were acclimatized for two weeks in natural sea water at room temperature and were fed twice a week.

extract_protocol:
Tissue samples were flash frozen with liquid nitrogen. Total RNA was isolated using the traditional TRIzol method
The RNA-Seq paired-end sequencing libraries were prepared using IlluminaTruSeq stranded mRNA sample prep kit using manufacturer’s instructions.

treatment_protocol: Acclimatized sponges in triplets were transferred to smaller aquaria (~25L volume) for the experiment. Sponges were inflicted with wounds (approximately 10% of total volume of sponge) modeled on fish bites.

tag: time period

value: sample taken during regeneration


title: breast tumour 6A

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

source_name: breast tumour

extract_protocol: mRNA from baseline (A) and surgery (B) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).


title: before wound infliction

value: sample taken before wound infliction


title: Ancestral FAS exon 6 Library Output 6c


title: Ancestral FAS exon 6 Library Output 7a


title: HA_3

value: leaves


title: Ancestral FAS exon 6 Library Output 6d


title: HA_2

value: grain-filling stage


title: HA_1


title: TT2 ES input DNA

value: Wild-type


title: breast tumour 212A


title: Ancestral FAS exon 6 Library Output 6b


title: breast tumour 212B


title: embryos, Control, batch I32, rep6

city: Saint Paul lez Durance

first: olivier

last: ARMANT

address: Cadarache BP3

department: SERIS

institute: IRSN

description:
Control
Sample_I32_Schield_C6

data_processing:
Quality (selection of Q>30) and adapter trimming with Trimgalor v0.4.2
Mapping with 2PASS STAR v020201 against  GRCz11 zebrafish reference genome and Ensembl v95 exon-exon junctions
Quantification and normalization with Desq2 v1.22.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Read count files from RNAstar

organism: Danio rerio

source_name: entire embryos

growth_protocol: Zebrafish eggs were collected just after fertlization and grown in 9mm Petri dishes with embryo medium (60mg/L Instant Ocean, 0.01 % (w/v) of methylene blue). Eggs were grown in Panasonic incubator (MIRE) at 28°C.

extract_protocol:
Total RNA extraction with trizol, no DNaseI treatment, followed by two rounds of mRNA extraction with polydT magnetic Beads (Illumina)
Stranded mRNAseq Illumina with dual UDT indexes

treatment_protocol: External continuous irradiation to gamma radiation (137Cs) at  0.005mGy/h, 0.05mGy/h, 0.5mGy/h, 5mGy/h 50mGy/h or non-exposed controls

tag: genetic background

value: AB

tag: developemental stage

value: Shield

tag: stress

value: control

tag: irradiation batch

tag: dose rate

value: entire embryos


title: breast tumour 93A

tag: timepoint

tag: tissue


title: breast tumour 90B


title: after regeneration

value: sample taken after regeneration


title: breast tumour 6B

value: surgery(B)


title: Ancestral FAS exon 6 Library Output 6a

source_name: Cell culture


title: Ancestral FAS exon 6 Library Output 9b


title: embryos, Control, batch I32, rep4

description:
Control
Sample_I32_Schield_C4


title: breast tumour 83A


title: embryos, Control, batch I32, rep3

description:
Control
Sample_I32_Schield_C3


title: Ancestral FAS exon 6 Library Output 5d


title: embryos, Control, batch I32, rep2

description:
Control
Sample_I32_Schield_C2


title: Ancestral FAS exon 6 Library Output 5c


title: embryos, Control, batch I32, rep5

description:
Control
Sample_I32_Schield_C5


title: Ancestral FAS exon 6 Library Output 5b


title: NR-28913_10_min_DSN

city: Jerusalem

first: Iddo

middle: Z.

last: Ben-Dov

address: Ein Kerem

department: Nephrology and Hypertension

country: Israel

institute: Hadassah Medical Center

description:
sma_mapped_reads.txt.gz
Jat

data_processing:
HiSeq 2500 standard base-calling
Mapping to Schistosoma sp. genomes using miRDeep2's mapper.pl
Genome_build: SchistoDB-38_SmansoniPuertoRico_Genome.fasta; SchistoDB-38_SjaponicumAnhui_Genome.fasta; SchistoDB-38_ShaematobiumEgypt_Genome.fasta
Supplementary_files_format_and_content: Compressed text files which are derived from miRDeep2's mapper.pl script output, using default parameters. Reads were mapped against the respective species genome.

organism: Schistosoma mansoni

extract_protocol:
TRIzol extraction followed by glycogen-fascilitated isopropanol precipitation
ligation & gel-based small RNA cDNA library (see PMID: 24489795)

tag: strain

value: pooled male and female

tag: Stage

value: adult

tag: [rna], ng/µl

tag: host

value: mouse

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: 10 min

tag: 3' adapter sequence

value: TTGGTTCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, Control, batch I32, rep1

description:
Control
Sample_I32_Schield_C1


title: Ancestral FAS exon 6 Library Output 5a

data_processing:
Library strategy: (DNA-seq of PCR amplicon)
Demultiplex sample replicates (DiMSum - https://github.com/lehner-lab/DiMSum)
Paired-end merging (DiMSum - https://github.com/lehner-lab/DiMSum)
Base-calling (DiMSum - https://github.com/lehner-lab/DiMSum)
Supplementary_files_format_and_content: DiMSum output file (tab-delimited plain text file)

extract_protocol:
For each of the experimental replicates, 10 ng of the library were transfected into 250 000 HEK293 cells in one well of a 6-well plate using Lipofectamine 2000 (11668027, Thermo scientific) and OPTIMEM I Reduced Serum Medium (31985-047, Thermo scientific). Six hours post-transfection, the cell culture medium was replaced with DMEM Glutamax (61965059, Life Technologies) containing 10% FBS and Pen/Strep antibiotics. 48 hours post-transfection (72 in the case of the siRNA experiments), total RNA was isolated using the automated Maxwell LEV 16 simplyRNA tissue kit (AS1280, Promega).
Accuprime Pfx (12344024, ThermoFisher Scientific) was used following the manufacturer's instructions to amplify 20 ng of single-stranded library DNA for 25 cycles with the following flanking intronic primers: FAS_i5_GC_F and FAS_i6_GC_R (Baeza-Centurion et al. 2019). The amplified library was then recombined with pCMV FAS wt minigene exon 5-6-7 (Förch et al. 2000) using the In-Fusion HD Cloning kit (639649, Clontech) in a 1:8 vector:insert optimized ratio and transformed into Stellar competent cells (636766, Clontech) to maximise the number of individual transformants (800,000 individual clones). The library was then amplified by growing for 18 hours in LB medium containing ampicillin. The final plasmid library were purified using the Quiagen plasmid maxi kit (50912163, Quiagen) and quantified with a NanoDrop spectrophotometer.

tag: cell line


title: embryos, 0.5mGy/h, batch I32, rep6

description:
Exposed
Sample_I32_Schield_0.5mG_E6

value: gamma ionizing radiation


title: NR-28914_10_min_DSN

description:
sma_mapped_reads.txt.gz
Hat

value: NMRI

tag: Sex

value: female

value: TGTGTTCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, 0.5mGy/h, batch I32, rep5

description:
Exposed
Sample_I32_Schield_0.5mG_E5


title: embryos, 0.5mGy/h, batch I32, rep4

description:
Exposed
Sample_I32_Schield_0.5mG_E4


title: Ancestral FAS exon 6 Library Output 4d


title: NR-42582_10_min_DSN

description:
sma_mapped_reads.txt.gz
Gat

value: not applicable

value: adult worm

value: TGATGTCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Output 4c


title: Ancestral FAS exon 6 Library Output 4b


title: embryos, 0.5mGy/h, batch I32, rep3

description:
Exposed
Sample_I32_Schield_0.5mG_E3

value: AB

value: Shield


title: breast tumour 83B

first: Alice

last: Gao

address: 237 Fulham Road

institute: The Institute of Cancer Research

value: breast tumour


title: NR-45104_10_min_DSN

description:
sma_mapped_reads.txt.gz
Iat

value: male

value: TTACATCGTATGCTGTCCTCTGTGGAATTCT


title: NR-45105_10_min_DSN

description:
sma_mapped_reads.txt.gz
Fat

value: TATCATCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, 0.5mGy/h, batch I32, rep2

description:
Exposed
Sample_I32_Schield_0.5mG_E2

value: entire embryos


title: Ancestral FAS exon 6 Library Output 4a


title: breast tumour 84A

value: baseline(A)


title: Ancestral FAS exon 6 Library Output 3d


title: breast tumour 90A


title: embryos, 0.5mGy/h, batch I32, rep1

description:
Exposed
Sample_I32_Schield_0.5mG_E1


title: breast tumour 32A


title: breast tumour 4B

value: surgery(B)


title: NR-41318_10_min_DSN

description:
sma_mapped_reads.txt.gz
het

value: eggs

value: mouse

value: 10 min

value: TCTAGTCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Output 3c


title: embryos, Control, batch I30, rep6

description:
Control
Sample_I30_Schield_C6

value: control


title: NR-44217_10_min_DSN

description:
sma_mapped_reads.txt.gz
gct

value: not applicable

value: cercariae

value: Biomphalaria glabrata snails

value: TCGCGTCGTATGCTGTCCTCTGTGGAATTCT


title: 3_aP2-SREBP-1c

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

country: Germany

institute: German Diabetes Center

description: RMA expression value derived from TAC software; RMA gene analysis

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 1.0 arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console  using default analysis settings for RMA analyses  for  gene default and exon default .CHP files.

source_name: C57Bl6-TgN aP2-HA-hSREBP-1c-NT

label_protocol: 150 ng total RNAwas amplified using the Ambion WT Expression Kit and the WT Terminal Labeling Kit (Affymetrix, Freiburg, Germany).

extract_protocol: Total RNA extraction was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: C57Bl6 (C57Bl6) and B6-TgN(aP2-HA-SREBP-1cNT) (aP2-SREBP-1c) mice were bred and maintained under standard conditions (12h light/dark cycle; 22°C ± 1°C, 50% ± 5% humidity). At 6 weeks of age, male littermates of each genotype were kept under standardized conditions with free access to water and regular laboratory chow (13.7 mJ/kg: 53% carbohydrate, 36% protein, 11% fat (Ssniff, Soest, Germany)). Mice were sacrificed by CO2 asphyxiation (7:00 am) at 24 weeks of age. Blood samples were collected by left ventricular puncture, and liver were removed. The Animal Care Committee of the University Duesseldorf approved animal care and procedure (Approval#84-02.04.2015.A424; 02. April 2015).

tag: gender

tag: age

value: 24 weeks


title: 1_aP2-SREBP-1c


title: breast tumour 29A

city: London

value: female

value: breast tumour


title: breast tumour 15B


title: 2_aP2-SREBP-1c

value: male


title: breast tumour 14A


title: NR-41320_10_min_DSN

description:
sma_mapped_reads.txt.gz
jmt

value: NMRI

value: miracidia

value: mouse?

value: TCTGATCGTATGCTGTCCTCTGTGGAATTCT


title: breast tumour 29B

value: surgery(B)


title: NR-43231_10_min_DSN

description:
sma_mapped_reads.txt.gz
est

value: sporocysts

value: TCCTATCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, Control, batch I30, rep5

description:
Control
Sample_I30_Schield_C5

tag: genetic background

value: AB

tag: developemental stage

value: Shield

value: entire embryos


title: embryos, Control, batch I30, rep4

description:
Control
Sample_I30_Schield_C4

tag: stress

value: control

tag: irradiation batch


title: breast tumour 15A

tag: timepoint

value: baseline(A)


title: NR-44218_10_min_DSN

description:
sma_mapped_reads.txt.gz
cet

value: not applicable

value: eggs

value: mouse

value: 10 min

value: TCCACTCGTATGCTGTCCTCTGTGGAATTCT


title: 4_aP2-SREBP-1c

value: male

value: 24 weeks


title: Ancestral FAS exon 6 Library Output 3b


title: breast tumour 106B

value: female

tag: tissue

value: breast tumour


title: Ancestral FAS exon 6 Library Output 2d


title: embryos, Control, batch I30, rep3

description:
Control
Sample_I30_Schield_C3

tag: dose rate


title: breast tumour 10B

value: surgery(B)


title: NR-44214_10_min_DSN

description:
sma_mapped_reads.txt.gz
aSt

tag: strain

value: NMRI

tag: Stage

value: schistosomulae

value: human?

value: TCACTTCGTATGCTGTCCTCTGTGGAATTCT


title: NR-28913_5_min_DSN

description:
sma_mapped_reads.txt.gz
Jaf

value: pooled male and female

value: adult

tag: [rna], ng/µl

tag: host

value: 5 min

value: TTGGTTCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Output 2c


title: breast tumour 106A

value: baseline(A)


title: Ancestral FAS exon 6 Library Output 3a


title: breast tumour 10A


title: Ancestral FAS exon 6 Library Output 2b


title: embryos, Control, batch I30, rep1

description:
Control
Sample_I30_Schield_C1

value: AB

value: Shield

value: control

value: entire embryos


title: breast tumour 208B


title: Ancestral FAS exon 6 Library Output 2a


title: breast tumour 204B


title: embryos, 5mGy/h, batch I30, rep6

description:
Exposed
Sample_I30_Schield_5mG_E6

value: gamma ionizing radiation


title: breast tumour 208A

value: female


title: embryos, 5mGy/h, batch I30, rep5

description:
Exposed
Sample_I30_Schield_5mG_E5


title: Ancestral FAS exon 6 Library Output 1d


title: NR-42582_5_min_DSN

description:
sma_mapped_reads.txt.gz
Gaf

value: not applicable

value: adult worm

value: mouse

tag: barcode

tag: cdna cleavage by duplex specific nuclease?

value: TGATGTCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Output 1c

tag: cell line


title: NR-45105_5_min_DSN

description:
sma_mapped_reads.txt.gz
Faf

tag: Sex

tag: 3' adapter sequence

value: TATCATCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Output 1b


title: embryos, Control, batch I30, rep2

description:
Control
Sample_I30_Schield_C2


title: embryos, 5mGy/h, batch I30, rep3

description:
Exposed
Sample_I30_Schield_5mG_E3


title: NR-41320_5_min_DSN

description:
sma_mapped_reads.txt.gz
jmf

value: NMRI

value: miracidia

value: mouse?

value: TCTGATCGTATGCTGTCCTCTGTGGAATTCT


title: NR-45104_5_min_DSN

description:
sma_mapped_reads.txt.gz
Iaf

value: male

value: adult

value: 5 min

value: TTACATCGTATGCTGTCCTCTGTGGAATTCT


title: NR-28914_5_min_DSN

description:
sma_mapped_reads.txt.gz
Haf

value: TGTGTTCGTATGCTGTCCTCTGTGGAATTCT


title: NR-41318_5_min_DSN

description:
sma_mapped_reads.txt.gz
hef

value: eggs

value: TCTAGTCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, 5mGy/h, batch I30, rep2

description:
Exposed
Sample_I30_Schield_5mG_E2

value: AB

value: Shield

value: gamma ionizing radiation

value: entire embryos


title: NR-43231_5_min_DSN

description:
sma_mapped_reads.txt.gz
esf

value: not applicable

value: sporocysts

value: TCCTATCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, 5mGy/h, batch I30, rep4

description:
Exposed
Sample_I30_Schield_5mG_E4


title: NR-44217_5_min_DSN

description:
sma_mapped_reads.txt.gz
gcf

value: cercariae

value: Biomphalaria glabrata snails

value: TCGCGTCGTATGCTGTCCTCTGTGGAATTCT


title: embryos, 5mGy/h, batch I30, rep1

description:
Exposed
Sample_I30_Schield_5mG_E1


title: breast tumour 165A

value: female

value: baseline(A)

value: breast tumour


title: embryos, 50mGy/h, batch I30, rep6

description:
Exposed
Sample_I30_Schield_50mG_E6


title: Ancestral FAS exon 6 Library Input 11

description:
PCR amplicon
Plasmid library.


title: breast tumour 170A


title: breast tumour 170B

value: surgery(B)


title: breast tumour 165B


title: breast tumour 204A


title: breast tumour 154B


title: breast tumour 154A


title: embryos, 50mGy/h, batch I30, rep5

description:
Exposed
Sample_I30_Schield_50mG_E5


title: NR-44218_5_min_DSN

description:
sma_mapped_reads.txt.gz
cef

value: mouse

value: 5 min

value: TCCACTCGTATGCTGTCCTCTGTGGAATTCT


title: breast tumour 19A


title: breast tumour 103B


title: Ancestral FAS exon 6 Library Input 10

description:
PCR amplicon
Plasmid library.


title: embryos, 50mGy/h, batch I30, rep4

description:
Exposed
Sample_I30_Schield_50mG_E4

value: AB


title: Ancestral FAS exon 6 Library Input 9

description:
PCR amplicon
Plasmid library.


title: NR-44214_5_min_DSN

description:
sma_mapped_reads.txt.gz
aSf

value: NMRI

value: schistosomulae

value: human?

value: TCACTTCGTATGCTGTCCTCTGTGGAATTCT


title: Ancestral FAS exon 6 Library Input 8

description:
PCR amplicon
Plasmid library.


title: Ancestral FAS exon 6 Library Input 12

description:
PCR amplicon
Plasmid library.


title: embryos, 50mGy/h, batch I30, rep3

description:
Exposed
Sample_I30_Schield_50mG_E3

value: Shield

value: gamma ionizing radiation

value: entire embryos


title: NR-28913

description:
sma_mapped_reads.txt.gz
Jan

value: pooled male and female

value: adult

value: no

value: TTGGTTCGTATGCCGTCTTCTGCTTG


title: Ancestral FAS exon 6 Library Output 1a


title: breast tumour 103A

value: female

value: baseline(A)

value: breast tumour


title: embryos, 50mGy/h, batch I30, rep2

description:
Exposed
Sample_I30_Schield_50mG_E2


title: Ancestral FAS exon 6 Library Input 6

description:
PCR amplicon
Plasmid library.


title: Ancestral FAS exon 6 Library Input 7

description:
PCR amplicon
Plasmid library.


title: embryos, 50mGy/h, batch I30, rep1

description:
Exposed
Sample_I30_Schield_50mG_E1


title: NR-28914

description:
sma_mapped_reads.txt.gz
Han

value: mouse

value: TGTGTTCGTATGCCGTCTTCTGCTTG


title: Ancestral FAS exon 6 Library Input 5

description:
PCR amplicon
Plasmid library.


title: breast tumour 99A


title: embryos, Control, batch I14, rep4

description:
Control
Sample_I14_Schield_C4

value: AB

value: control


title: NR-45105

description:
sma_mapped_reads.txt.gz
Fan

value: TATCATCGTATGCCGTCTTCTGCTTG


title: breast tumour 194B

value: surgery(B)


title: NR-42582

description:
sma_mapped_reads.txt.gz
Gan

value: not applicable

value: adult worm

value: TGATGTCGTATGCCGTCTTCTGCTTG


title: embryos, Control, batch I14, rep3

description:
Control
Sample_I14_Schield_C3

value: Shield

value: entire embryos


title: breast tumour 38B


title: embryos, Control, batch I14, rep2

description:
Control
Sample_I14_Schield_C2


title: NR-41320

description:
sma_mapped_reads.txt.gz
jmn

value: NMRI

value: miracidia

value: mouse?

value: TCTGATCGTATGCCGTCTTCTGCTTG


title: NR-45104

description:
sma_mapped_reads.txt.gz
Ian

value: male

value: adult

value: no

value: TTACATCGTATGCCGTCTTCTGCTTG


title: Ancestral FAS exon 6 Library Input 4

description:
PCR amplicon
Plasmid library.


title: NR-41318

description:
sma_mapped_reads.txt.gz
hen

value: eggs

value: mouse

value: TCTAGTCGTATGCCGTCTTCTGCTTG


title: embryos, Control, batch I14, rep1

description:
Control
Sample_I14_Schield_C1

value: AB

value: control


title: embryos, 5microGy/h, batch I14, rep4

description:
Exposed
Sample_I14_Schield_5microG_E4

value: gamma ionizing radiation


title: Ancestral FAS exon 6 Library Input 3

description:
PCR amplicon
Plasmid library.


title: NR-44217

description:
sma_mapped_reads.txt.gz
gcn

value: not applicable

value: cercariae

value: Biomphalaria glabrata snails

value: TCGCGTCGTATGCCGTCTTCTGCTTG


title: NR-43231

description:
sma_mapped_reads.txt.gz
esn

value: NMRI

value: sporocysts

value: TCCTATCGTATGCCGTCTTCTGCTTG


title: Ancestral FAS exon 6 Library Input 1

description:
PCR amplicon
Plasmid library.


title: embryos, 5microGy/h, batch I14, rep3

description:
Exposed
Sample_I14_Schield_5microG_E3

value: Shield

value: entire embryos


title: breast tumour 191A

value: female

value: baseline(A)

value: breast tumour


title: embryos, 5microGy/h, batch I14, rep2

description:
Exposed
Sample_I14_Schield_5microG_E2


title: NR-44218

description:
sma_mapped_reads.txt.gz
cen

value: eggs

value: mouse

value: no

value: TCCACTCGTATGCCGTCTTCTGCTTG


title: breast tumour 177A


title: breast tumour 85B

value: surgery(B)


title: breast tumour 177B


title: embryos, Control, batch I13, rep4

description:
Control
Sample_I13_Schield_C4

value: AB

value: control


title: breast tumour 85A


title: NR-44214

description:
sma_mapped_reads.txt.gz
aSn

value: not applicable

value: schistosomulae

value: human?

value: TCACTTCGTATGCCGTCTTCTGCTTG


title: breast tumour 194A


title: Ancestral FAS exon 6 Library Input 2

description:
PCR amplicon
Plasmid library.


title: embryos, Control, batch I13, rep3

description:
Control
Sample_I13_Schield_C3


title: breast tumour 79A


title: embryos, Control, batch I13, rep2

description:
Control
Sample_I13_Schield_C2


title: breast tumour 79B


title: ECCITE-seq GDO: THP-1

city: New York

first: Efthymia

last: Papalexi

state: NY

address: 101 avenue of americas

institute: New York Genome Center

data_processing:
library strategy:  ECCITE-seq (Expanded CRISPR-compatible CITE-seq)
CITE-seq and ECCITE-seq RNA reads were mapped to the human genome (hg19). Transcripts were quanitfied using CellRanger v2.1.0
ADT, HTO and GDO counts were quantified using CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed into their experimental conditions after normalization (centered log ratio transformation, margin = 2) using the HTOdemux or MULTISeqDemux function in Seurat.
gRNA identitied were assigned using HTODemux unless otherwise specified in the methods section of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data provided as a TSV expression matrix where the rows correspond to genes (protein or guide names accordingly) and the columns to single cells.

source_name: Acute Myeloid Leukemia cell line THP-1

growth_protocol: For all scRNA-seq experiments: THP-1 cells were grown in RPMI +10% FBS media. Cells were spun down and resuspended in PBS 1X. Cell  viability was quantified using trypan blue.

extract_protocol: For the scRNA/CITE/ECCITE-seq experiment: a panel of antibodies (ADTs) was used to stain the cells according to the CITE/ECCITE-seq protocol. To identify cell doublets. and keep track of experimental conditions, we split cells into aliquots and stained each aliquot with a unique hashing (HTOs) antibody.  Samples were washed and recombined and loaded on a 10X genomics chip. 5prime 10X genomics was ran and the manufacturers protocols was followed for cDNA library generation. To recover HTOs, ADTs and GDOs we followed the CITE/ECCITE-seq protocol found here: https://cite-seq.com/protocol/.

treatment_protocol: To induce the expression of various immune checkpoint proteins cells were treated with Decitabine (Sigma-Aldrich A3656, 0.25μM) for three days, TGFβ1 for two days (Thermo Fisher Scientific PHG9204, 2.5ng/ml) and IFNγ for one day (R&D systems 284-IF-100, 10ng/ml).

tag: cell type

value: Acute Myeloid Leukemia cell line

tag: experiment type

value: ECCITE-seq GDO


title: ECCITE-seq HTO5-8: THP-1

value: ECCITE-seq HTO


title: embryos, 50microGy/h, batch I13, rep4

description:
Exposed
Sample_I13_Schield_50microG_E4

tag: genetic background

tag: developemental stage

value: Shield

value: gamma ionizing radiation

value: entire embryos


title: SF3B3si2 BT549 Rep2

city: Cleveland

first: Daniel

last: McGrail

state: Ohio

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

data_processing:
De-multiplex with bcl2fastq-1.8.4
Aligned/quantified with Tophat 2.1.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited counts tables
Supplementary_files_format_and_content: Raw counts

source_name: Cancer cells

extract_protocol:
Qiagen RNeasy Kit
Lexogen QuantSeq 3′ mRNA-Seq Library Prep Kit

tag: sirna


title: ECCITE-seq HTO1-4: THP-1


title: AQRsi1 BT549 Rep2


title: embryos, 50microGy/h, batch I13, rep3

description:
Exposed
Sample_I13_Schield_50microG_E3

tag: stress

tag: irradiation batch


title: embryos, 50microGy/h, batch I13, rep2

description:
Exposed
Sample_I13_Schield_50microG_E2

tag: dose rate

tag: tissue


title: ECCITE-seq ADT: THP-1

value: ECCITE-seq ADT


title: embryos, 50microGy/h, batch I13, rep1

description:
Exposed
Sample_I13_Schield_50microG_E1

value: 50 microGy/h


title: ECCITE-seq cDNA: THP-1

value: ECCITE-seq cDNA


title: embryos, Control, batch I13, rep1

description:
Control
Sample_I13_Schield_C1


title: Dexfenfluramine 5

city: Liege

first: Alexia

last: Hulin

address: Avenue de l'hopital 1

department: Cardiovascular Science

country: Belgium

institute: GIGA

data_processing:
Raw reads were demultiplexed and adapted-trimmed using Illumina software v2.17
the first three nucleotides of each read were removed using FATSX Toolkit,
Reads aligned to oryCun2 reference genome using Tophat v2.1.1
Quality of sequencing data was controlled using Picard tools
Raw gene counts were generating using Htseq count
Independent filtering was done to remove uninformative genes using HTSFilter. Unwanted variations were identified using svaseq() and RUVr() in R Bioconductor package RUVSeq
Genome_build: oryCun2
Supplementary_files_format_and_content: tab-delimited text files include Raw gene counts for each Sample with column header corresponding to treatment (Control w1 to w5, Serotonin s1 to s5, Pergolide p1 to p5 and dexfenfluramine d1 to d5)

organism: Oryctolagus cuniculus

source_name: Tricuspid valve

extract_protocol:
Tricuspid valves were flash frozen and total RNA was extracted using the miRNease mini Kit (quiagen)
Library were prepared using the SMARTer Stranded RNA-Seq Kit  (Clontech)

treatment_protocol: 16 weeks oral administration of serotonin (80 mg/Kg/day), pergolide (0.5 mg/Kg/day), dexfenfluramine (20mg/Kg/day) or water

tag: strain

value: New Zealand white rabbit

value: Tricuspid valve

tag: treatment

value: 16 weeks dexfenfluramine (20mg/Kg/day) oral administration


title: Dexfenfluramine 3


title: Dexfenfluramine 4


title: CITE-seq HTO: THP-1

data_processing:
library strategy: CITE-seq  (Cellular Indexing of Transcriptomes and Epitopes by Sequencing)
CITE-seq and ECCITE-seq RNA reads were mapped to the human genome (hg19). Transcripts were quanitfied using CellRanger v2.1.0
ADT, HTO and GDO counts were quantified using CITE-seq-count (https://github.com/Hoohm/CITE-seq-Count)
Cells were demultiplexed into their experimental conditions after normalization (centered log ratio transformation, margin = 2) using the HTOdemux or MULTISeqDemux function in Seurat.
gRNA identitied were assigned using HTODemux unless otherwise specified in the methods section of the manuscript.
Genome_build: hg19
Supplementary_files_format_and_content: Processed data provided as a TSV expression matrix where the rows correspond to genes (protein or guide names accordingly) and the columns to single cells.

value: CITE-seq HTO


title: CITE-seq ADT: THP-1

value: CITE-seq ADT


title: breast tumour 33A

value: female

tag: timepoint

value: baseline(A)

value: breast tumour


title: breast tumour 203B

value: surgery(B)


title: breast tumour 202A


title: breast tumour 32B


title: breast tumour 58A


title: CITE-seq cDNA: THP-1

value: Acute Myeloid Leukemia cell line

value: CITE-seq cDNA


title: Dexfenfluramine 2


title: breast tumour 206A


title: Pergolide 5

value: 16 weeks pergolide (0.5 mg/Kg/day) oral adminstration


title: Dexfenfluramine 1


title: breast tumour 123A


title: breast tumour 93B


title: endometrium_biopsy, day20, early-secretory, 10x

city: Stanford

first: Wanxin

last: Wang

address: James H Clark Center, 318 Campus Drive, room E300

institute: Stanford Univeristy

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_58

data_processing:
Raw reads in the *.fastq files were aligned to reference (GRCh38-3.0.0) and quantified using cellranger (3.1.0).
Downstream data analysis was performed in R using customized scripts and the Seurat package.
Raw counts were normalized to log transformed transcripts per million (log(TPM+1)) using NormalizeData() function in Seurat.
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: Raw counts and descriptive details for cells
ct_endo_10x.rds - raw counts for all 10x platform captured post-quality-filtered cells analyzed in this study
meta_celltypes_samplename.csv - cell type identity and sample (biopsy) of origin for each cell analyzed
umap_endo_10x.csv - umap coordinates for each cell analyzed

extract_protocol:
GEM generation & barcoding, reverse-transcription, cDNA generation were done following the manufacture’s protocol (Single cell 3’ reagent kits v3.1, Chromium Next GEM Chip G, 10x Genomics).
Library construction were done following the manufacture’s protocol (Single cell 3’ reagent kits v3.1, Chromium Next GEM Chip G, 10x Genomics).

tag: disease state

value: healthy

tag: fecundity

value: fertile

tag: time in menstrual cycle

tag: phase

value: early-secretory

value: endometrium biopsy


title: breast tumour 95B

tag: Sex


title: endometrium_biopsy, day16, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_63

value: proliferative


title: breast tumour 58B


title: Pergolide 4

value: New Zealand white rabbit


title: endometrium_biopsy, day26, early-secretory, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_60


title: breast tumour 95A


title: endometrium_biopsy, day26, late-secretory, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_57

value: late-secretory


title: breast tumour 101B


title: endometrium_biopsy, day19, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_41

value: early-mid-secretory


title: Pergolide 3

value: Tricuspid valve


title: endometrium_biopsy, day23, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_39


title: Pergolide 1


title: Pergolide 2


title: endometrium_biopsy, day22, mid-secretory, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_20

value: mid-secretory


title: breast tumour 149A

value: female


title: breast tumour 101A

value: baseline(A)


title: breast tumour 149B

value: breast tumour


title: endometrium_biopsy, day22, proliferative, 10x

description:
ct_endo_10x.rds
meta_celltypes_samplename.csv
umap_endo_10x.csv
endo_19


title: breast tumour 115B

value: surgery(B)


title: Control 4

value: control