title: 4T1.2, Day4, single cell 37


title: 4T1.2, Day4, single cell 40

status: Public on Jul 01 2024

type: SRA

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

country: China

institute: Tsinghua university

library_source: transcriptomic single cell

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

tag: host

value: Female BALB/c mice

tag: cell line

tag: cell type

value: metastatic tumor cells


title: 4T1.2, Day4, single cell 36


title: 4T1.2, Day4, single cell 41


title: 4T1.2, Day4, single cell 38


title: 4T1.2, Day4, single cell 50


title: 4T1.2, Day4, single cell 35


title: 4T1.2, Day4, single cell 33


title: 4T1.2, Day4, single cell 34


title: 4T1.2, Day4, single cell 31


title: 4T1.2, Day4, single cell 30


title: 4T1.2, Day4, single cell 28


title: 4T1.2, Day4, single cell 29


title: 4T1.2, Day4, single cell 27


title: 4T1.2, Day4, single cell 26


title: 4T1.2, Day4, single cell 23


title: 4T1.2, Day4, single cell 24


title: 4T1.2, Day4, single cell 25


title: 4T1.2, Day4, single cell 20


title: 4T1.2, Day4, single cell 21


title: 4T1.2, Day4, single cell 22


title: 4T1.2, Day4, single cell 19


title: 4T1.2, Day4, single cell 18


title: 4T1.2, Day4, single cell 16


title: 4T1.2, Day4, single cell 13


title: 4T1.2, Day4, single cell 15


title: 4T1.2, Day4, single cell 14


title: 4T1.2, Day4, single cell 11


title: 4T1.2, Day4, single cell 12


title: 4T1.2, Day4, single cell 32


title: 4T1.2, Day4, single cell 9


title: 4T1.2, Day4, single cell 8


title: 4T1.2, Day4, single cell 10


title: 4T1.2, Day4, single cell 7


title: 4T1.2, Day4, single cell 5


title: 4T1.2, Day4, single cell 4


title: 4T1.2, Day4, single cell 2


title: 4T1.2, Day4, single cell 1


title: 4T1.2, Day4, single cell 3


title: 4T1, Day22, Fat, Pad, single cell 96


title: 4T1, Day22, Fat, Pad, single cell 93


title: 4T1, Day22, Fat, Pad, single cell 90


title: 4T1, Day22, Fat, Pad, single cell 91


title: 4T1, Day22, Fat, Pad, single cell 92


title: 4T1.2, Day4, single cell 17


title: 4T1, Day22, Fat, Pad, single cell 88


title: 4T1, Day22, Fat, Pad, single cell 94


title: 4T1, Day22, Fat, Pad, single cell 89


title: 4T1, Day22, Fat, Pad, single cell 87


title: 4T1, Day22, Fat, Pad, single cell 86


title: 4T1.2, Day4, single cell 161


title: 4T1, Day22, Fat, Pad, single cell 85


title: 4T1.2, Day4, single cell 6


title: 4T1.2, Day4, single cell 162


title: 4T1, Day22, Fat, Pad, single cell 83


title: 4T1, Day22, Fat, Pad, single cell 81


title: 4T1, Day22, Fat, Pad, single cell 82


title: 4T1, Day22, Fat, Pad, single cell 80


title: 4T1, Day22, Fat, Pad, single cell 78


title: 4T1, Day22, Fat, Pad, single cell 79


title: 4T1, Day22, Fat, Pad, single cell 77


title: 4T1, Day22, Fat, Pad, single cell 76


title: 4T1, Day22, Fat, Pad, single cell 95


title: 4T1, Day22, Fat, Pad, single cell 73


title: 4T1, Day22, Fat, Pad, single cell 75


title: 4T1, Day22, Fat, Pad, single cell 72


title: 4T1, Day22, Fat, Pad, single cell 71


title: 4T1, Day22, Fat, Pad, single cell 74


title: 4T1, Day22, Fat, Pad, single cell 69


title: 4T1, Day22, Fat, Pad, single cell 67


title: 4T1, Day22, Fat, Pad, single cell 70


title: 4T1, Day22, Fat, Pad, single cell 65


title: 4T1, Day22, Fat, Pad, single cell 66


title: 4T1, Day22, Fat, Pad, single cell 68


title: 4T1, Day22, Fat, Pad, single cell 64


title: 4T1, Day22, Fat, Pad, single cell 63


title: 4T1, Day22, Fat, Pad, single cell 84


title: 4T1, Day22, Fat, Pad, single cell 62


title: 4T1, Day22, Fat, Pad, single cell 60


title: 4T1, Day22, Fat, Pad, single cell 61


title: 4T1, Day22, Fat, Pad, single cell 57


title: 4T1, Day22, Fat, Pad, single cell 59


title: 4T1, Day22, Fat, Pad, single cell 55


title: 4T1, Day22, Fat, Pad, single cell 58


title: 4T1, Day22, Fat, Pad, single cell 53


title: 4T1, Day22, Fat, Pad, single cell 51


title: 4T1, Day22, Fat, Pad, single cell 52


title: 4T1, Day22, Fat, Pad, single cell 49


title: 4T1, Day22, Fat, Pad, single cell 56


title: 4T1, Day22, Fat, Pad, single cell 54


title: 4T1, Day22, Fat, Pad, single cell 48


title: 4T1, Day22, Fat, Pad, single cell 50


title: 4T1, Day22, Fat, Pad, single cell 47


title: 4T1, Day22, Fat, Pad, single cell 46


title: 4T1, Day22, Fat, Pad, single cell 45


title: CM-ADGRF5-KO 4

city: 3601 Spruce Street

first: Yan

last: Zhou

state: PA

address: 333 Cottman Ave

department: Bioinformatics

country: USA

institute: Fox Chase Cancer Center

library_source: transcriptomic

data_processing:
Raw sequence reads were aligned to the mouse genome (GRCm38) using the STAR algorithm
The number of raw counts in each known gene  was enumerated using htseq-count from the HTSeq package.
Differential expression between samples and across different conditions was assessed for statistical significance using the R/ Bioconductor package DESeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimiited text file include raw count values for each sample

molecule: total RNA

source_name: Heart, Left Ventricle

extract_protocol:
RNA was isolated using the Pure Link RNA Mini Kit (Invitrogen) and processed as per manufacturer’s instructions.
Truseq stranded mRNA library kit, Hiseq rapid SR cluster kit and HiSeq rapid SBS kit were used to make the mRNA library from 1000ng of total RNA from each sample according to the product guide

tag: strain

tag: tissue

value: Heart, Left Ventricle

tag: Sex

value: Female

tag: genotype

value: GPR116-/- (myocyte-specific)


title: CM-ADGRF5-KO 3


title: 4T1, Day22, Fat, Pad, single cell 43


title: CM-ADGRF5-KO 2

value: Male


title: CM-ADGRF5-KO 1


title: 4T1, Day22, Fat, Pad, single cell 40


title: 4T1, Day22, Fat, Pad, single cell 42


title: NLC 4

value: wild-type


title: 4T1, Day22, Fat, Pad, single cell 39


title: NLC 3


title: 4T1, Day22, Fat, Pad, single cell 38


title: NLC 1


title: 4T1, Day22, Fat, Pad, single cell 44


title: NLC 2


title: PLC, CMV, rep6

city: Vancouver

first: Ali

last: Farrokhi

state: BC

address: BC Childrens Hospital Research Institute, 950 west 28th Ave- Ro0m 3062

country: Canada

institute: University of British Columbia

description: 0108-R680-N2 CMV

data_processing:
Torrent Suite 5.14.1
Sequencing reads were trimmed for quality/adaptors using the BaseCaller module of the Torrent Suite analysis pipeline (Arguments: –trim-qual-cutoff 15 –barcode-filter-minreads 10 –phasing-residual-filter=2.0 –max-phasing-levels 2 –num-unfiltered 1000 –barcode-filter-postpone 1 –wells-normalization on)
Trimmed sequence reads were mapped to GRCm38/mm10 using the TMAP Alignment module of the Torrent Suite analysis pipeline (Arguments: mapall -q 50000 ... stage1 map4)
Read count extraction and normalization were performed using the AmpliSeq RNA Plug-in for the Ion Torrent S5.
Software: Torrent Suite 5.14.1, ion-analysis 5.14.16-1, ion-dbreports 5.14.24-1, ion-gpu 5.14.2-1, ion-pipeline 5.14.28-1, ion-torrentpy 5.14.15-1, ion-torrentr 5.14.15-1. S5 Script 0.1.31, LiveView 2762, DataCollect 3972, OIA 51231, OS 0, Graphics 134, Ion Chef IC.5.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file including RPM-normalized counts for each sample.

source_name: Spleen

growth_protocol: PLC were FACS sorted 7 days post-treatment from MCMV-infected and non-infected mice into RNA-later.

extract_protocol:
Total RNA was isolated from sorted PLC using AllPrep DNA/RNA Mini kit (Qiagen). RNA concentration was determined using a Qubit 3.0 Flourometer (Invitrogen) and quality was assessed using a bioanalyzer (Agilent).
Library preparation from RNA samples and sequencing was performed on Ion Chef and Ion Torrent S5 platforms (Thermo Fisher Scientific) using the Ion Ampliseq Transcriptome Mouse Gene Expression Panel Chef-Ready Kit (Thermo Fisher Scientific) following Ion AmpliSeq Library Preparation on the Ion Chef System Quick Reference. The resulting barcoded cDNA library was quantified using an Ion Library TagMan Quantification Kit. The AmpliSeq RNA Plug-in was used to perform differential expression analysis.

treatment_protocol: Mice received 3×10^3 plaque-forming unit (pfu) of K181-luc MCMV or an equivalent volume of PBS via intraperitoneal (i.p.) injection.

value: Spleen

value: B-cell precursor (BCP)

tag: disease state

value: Preleukemia

value: Emu-Ret hemizygote

value: BALB/c background

tag: treatment

value: MCMV-infected


title: 4T1, Day22, Fat, Pad, single cell 31


title: 4T1, Day22, Fat, Pad, single cell 33


title: 4T1, Day22, Fat, Pad, single cell 37


title: 4T1, Day22, Fat, Pad, single cell 35


title: 4T1, Day22, Fat, Pad, single cell 34


title: PLC, CMV, rep3


title: 4T1, Day22, Fat, Pad, single cell 41


title: 4T1, Day22, Fat, Pad, single cell 32


title: 4T1, Day22, Fat, Pad, single cell 36


title: PLC, CMV, rep5


title: PLC, CMV, rep2


title: 4T1, Day22, Fat, Pad, single cell 29


title: PLC, CMV, rep4


title: HAP1, wild-type, treated with NS8593

type: RNA

city: Munich

first: Vladimir

last: Chubanov

state: Non-US/Canada

address: Goethestraße 33

department: Walther-Straub-Institut

country: Germany

institute: Ludwig-Maximilians-Universität München

description:
SAMPLE 4
Derived from a 39-year-old man with chronic myeloid leukemia in blast crisis

hyb_protocol: 2.5 µg of fragmented and labeled ssDNA were hybridized for 16-18h hr at 45°C on GeneChip Human Gene 1.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix  GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix Expression Console (version 1.4.0) using Affymetrix default analysis settings and RMA as processing algorithm.

label: Biotin

organism: Homo sapiens

source_name: HAP1 cells

label_protocol: Biotinylated single-stranded DNA were prepared according to the standard Affymetrix protocol (Whole Transcript Expression arrays) from 100 ng total RNA  using the WT terminal labeling kit

growth_protocol: HAP1 cells were maintained in 25 cm flasks with IMDM containing 10% fetal bovine serum, 100 U/ml penicillin and 100 µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the GenElute mammalian total RNA purification kit (Sigma-Aldrich).

treatment_protocol: Samples 1-3: Wild-type, TRPM7 KO-01 and TRPM7 KO-04 HAP1 cells were cultured in IMDM medium supplemented with 10 mM MgCl2 (IMDM-Mg medium). At 50% confluence, the IMDM-Mg was exchanged to the regular IMDM medium and the cells were cultured for additional 24h. Sample 4: At 50% confluence, wild-type HAP1 cells were exposed to the fresh medium containing 30 µM NS8593 and cultured for an additional 24 h.

tag: cell line source

value: Near-haploid cell line derived from the KBM-7 cell line

tag: tumor stage

value: Chronic myelogenous leukemia

value: Wild-type

tag: trpm7 status

value: pharmacological inactivation

tag: gender


title: PLC, CMV, rep1

description: 0103-R680-N1 CMV


title: 4T1, Day22, Fat, Pad, single cell 27

value: Female BALB/c mice


title: HAP1, TRPM7 KO, clone KO-04

description:
SAMPLE 3
Derived from a 39-year-old man with chronic myeloid leukemia in blast crisis

value: TRPM7 KO-04

value: untreated

value: genetic inactivation


title: PLC, CNT, rep4

value: PBS-infected


title: HAP1, TRPM7 KO, clone KO-01

description:
SAMPLE 2
Derived from a 39-year-old man with chronic myeloid leukemia in blast crisis

value: TRPM7 KO-01

value: Male


title: PLC, CNT, rep3

value: Spleen


title: 4T1, Day22, Fat, Pad, single cell 26

value: metastatic tumor cells


title: HAP1, wild-type

description:
SAMPLE 1
Derived from a 39-year-old man with chronic myeloid leukemia in blast crisis

value: control


title: 4T1, Day22, Fat, Pad, single cell 24


title: 4T1, Day22, Fat, Pad, single cell 30


title: PLC, CNT, rep1

description: 0125- R676-5-CNT

value: B-cell precursor (BCP)

value: Preleukemia

value: Emu-Ret hemizygote


title: 4T1, Day22, Fat, Pad, single cell 23


title: 4T1, Day22, Fat, Pad, single cell 21


title: 4T1, Day22, Fat, Pad, single cell 28


title: 4T1, Day22, Fat, Pad, single cell 19


title: 4T1, Day22, Fat, Pad, single cell 22


title: 4T1, Day22, Fat, Pad, single cell 20


title: 4T1, Day22, Fat, Pad, single cell 16


title: 4T1, Day22, Fat, Pad, single cell 18


title: 4T1, Day22, Fat, Pad, single cell 17


title: 4T1, Day22, Fat, Pad, single cell 15


title: 4T1, Day22, Fat, Pad, single cell 25


title: 4T1, Day22, Fat, Pad, single cell 13


title: PLC, CNT, rep2

value: BALB/c background


title: 4T1, Day22, Fat, Pad, single cell 11


title: 4T1, Day22, Fat, Pad, single cell 12


title: 4T1, Day22, Fat, Pad, single cell 14


title: 4T1, Day22, Fat, Pad, single cell 8


title: HS360-Day0-rep2 [344-D0-CTRL-B]

type: genomic

city: Oslo

first: Mari

last: Spildrejorde

state: OSLO

address: Sognsvannsveien 9

department: Research and Innovation, Neuroscience research unit

country: Norway

institute: Oslo University Hospital

description:
Day 0", "male", "hESCs", "control
344-D0-CTRL-B

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip v-1-0_B3 using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner settings

data_processing:
R software, Minfi package v 1.36.0m Background correction was performed using NOOB method and β values were normalized using functional normalization. Probes with detection p values >0.01 (n = 11740) and cross-reactive probes (n = 43256) were removed, resulting in a final data set consisting of 811233
betas_detP.txt: Normalized Average Beta (functional normalization) and detection P values
"rgSet,Rdata". Minfi object with all data except SNP probes, removed due to data sensitivity.
meth_unmeth_detP.txt: Unmethylated, methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

source_name: HS360, day 0, hESCs undifferentiated

label_protocol: Standard Illumina Protocol

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol: Total RNA was extracted from cultured cells using Norgen RNA/DNA purification kit or Qiagen RNeasy kit and treated with DNase according to manufacturer´s instructions.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13.  For cells that were exposed to either 50-400 nM citalopram, fresh media with citalopram was added every day from Day 1 until collection day (Day 6, 10 and 13)

value: hESCs

value: Day 0 control


title: 4T1, Day22, Fat, Pad, single cell 7


title: 4T1, Day22, Fat, Pad, single cell 6


title: 4T1, Day22, Fat, Pad, single cell 5


title: HS360-Day6-CIT400-rep5 [341-D6-CIT400-E]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
341-D6-CIT400-E

source_name: HS360, day 6, neural induction, exposed to 400 nM citalopram

value: neural rosettes

value: Day 6 400 nM citalopram


title: HS360-Day6-CIT200-rep6 [339-D6-CIT200-F]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
339-D6-CIT200-F

source_name: HS360, day 6, neural induction, exposed to 200 nM citalopram

value: Day 6 200 nM citalopram


title: 4T1, Day22, Fat, Pad, single cell 10

value: Female BALB/c mice


title: 4T1, Day22, Fat, Pad, single cell 3


title: HS360-Day6-CIT200-rep4 [337-D6-CIT200-D]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
337-D6-CIT200-D


title: 4T1, Cell, Line, single cell 54


title: HS360-Day6-CIT100-rep6 [336-D6-CIT100-F]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
336-D6-CIT100-F

source_name: HS360, day 6, neural induction, exposed to 100 nM citalopram

value: Day 6 100 nM citalopram


title: HS360-Day0-rep1 [343-D0-CTRL-A]

description:
Day 0", "male", "hESCs", "control
343-D0-CTRL-A


title: HS360-Day0-rep3 [345-D0-CTRL-C]

description:
Day 0", "male", "hESCs", "control
345-D0-CTRL-C


title: 4T1, Day22, Fat, Pad, single cell 9


title: HS360-Day6-CIT400-rep6 [342-D6-CIT400-F]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
342-D6-CIT400-F


title: 4T1, Cell, Line, single cell 52


title: HS360-Day6-CIT100-rep4 [334-D6-CIT100-D]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
334-D6-CIT100-D


title: HS360-Day6-CIT200-rep5 [338-D6-CIT200-E]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
338-D6-CIT200-E


title: 4T1, Day22, Fat, Pad, single cell 4


title: 4T1, Day22, Fat, Pad, single cell 2


title: 4T1, Day22, Fat, Pad, single cell 1


title: HS360-Day6-CIT100-rep5 [335-D6-CIT100-E]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
335-D6-CIT100-E


title: UOK262_Fhdef_rep2

city: New Haven

first: Ranjit

last: Bindra

state: CT

address: 15 York Street

department: Therapeutic Radiology

institute: Yale University

description: hereditary and metastatic renal cell carcinoma with tubulo-papillary and clear cell histology, HLRCC

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Human EPIC Bead Array (850k) using the standard Illumina protocol.

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

data_processing: IDAT files processed via methylprep to produce intensity signals, beta values, mvalues, detection pvalues. Background signal distribution calculated via pOOBAH (P-value Out Of Band probes for Array Hybridization)

source_name: Clear cell renal cell carcinoma metastasis

label_protocol: Standard Illumina Protocol.

growth_protocol: Standard adherent cell passaging conditions, grown to 80% confluence.

extract_protocol: Genomic DNA was extracted from cell pellets using the Qiagen DNeasy blood and tissue kit according to manufacturer protocol.


title: 4T1, Cell, Line, single cell 53


title: 4T1, Cell, Line, single cell 49


title: Yunk_shFH_rep1

source_name: Normal kidney nephrectomy

value: Normal kidney nephrectomy

value: normal kidney with FH shRNA knockdown


title: HS360-Day6-CIT50-rep4 [331-D6-CIT50-D]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
331-D6-CIT50-D

source_name: HS360, day 6, neural induction, exposed to 50 nM citalopram

value: Day 6 50 nM citalopram


title: HS360-Day6-CIT50-rep6 [333-D6-CIT50-F]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
333-D6-CIT50-F


title: 4T1, Cell, Line, single cell 51


title: UOK268_Fhdef_rep1

description: localized type 2 papillary kidney cancer

source_name: Papillary kidney cancer

value: Papillary kidney cancer


title: HS360-Day6-rep5 [329-D6-CTRL-E]

description:
Day 6", "male", "neural rosettes", "neural induction
329-D6-CTRL-E

source_name: HS360, day 6, neural induction

value: Day 6 control


title: HS360-Day6-CIT50-rep5 [332-D6-CIT50-E]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
332-D6-CIT50-E


title: U87_IDH1R132H_rep1

description: CRISPR Cas9 c.395G>A knock-in mutation encoding IDH1R132H

source_name: Human glioma cell line

value: Human glioma cell line

value: IDH1 +/R132H U-87MG cell line


title: 4T1, Cell, Line, single cell 50

value: metastatic tumor cells


title: HS360-Day6-CIT400-rep4 [340-D6-CIT400-D]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
340-D6-CIT400-D


title: HS360-Day6-CIT400-rep3 [327-D6-CIT400-C]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
327-D6-CIT400-C


title: HS360-Day6-CIT400-rep2 [326-D6-CIT400-B]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
326-D6-CIT400-B


title: Yunk_shNT_rep2

value: normal kidney with non-targeting shRNA


title: 4T1, Cell, Line, single cell 47


title: 4T1, Cell, Line, single cell 43


title: HS360-Day6-rep6 [330-D6-CTRL-F]

description:
Day 6", "male", "neural rosettes", "neural induction
330-D6-CTRL-F


title: 4T1, Cell, Line, single cell 48


title: HS360-Day6-rep4 [328-D6-CTRL-D]

description:
Day 6", "male", "neural rosettes", "neural induction
328-D6-CTRL-D


title: Yunk_shFH_rep2


title: U87_wildtype_rep1

value: Parental U-87MG cell line


title: 4T1, Cell, Line, single cell 45


title: 4T1, Cell, Line, single cell 44


title: Yunk_wildtype_rep1

value: normal kidney


title: HS360-Day6-CIT200-rep2 [323-D6-CIT200-B]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
323-D6-CIT200-B


title: 4T1, Cell, Line, single cell 41


title: HS360-Day6-CIT400-rep1 [325-D6-CIT400-A]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
325-D6-CIT400-A


title: UOK262_Fhdef_rep1

value: Clear cell renal cell carcinoma metastasis


title: 4T1, Cell, Line, single cell 39


title: HS360-Day6-CIT100-rep3 [321-D6-CIT100-C]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
321-D6-CIT100-C

value: neural rosettes


title: HS360-Day6-CIT200-rep3 [324-D6-CIT200-C]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
324-D6-CIT200-C


title: 4T1, Cell, Line, single cell 38


title: NCCFH1_Fhdef_rep2

description: hereditary metastatic papillary renal cell carcinoma type 2

source_name: Papillary renal cell carcinoma

value: Papillary renal cell carcinoma


title: 4T1, Cell, Line, single cell 46


title: NCCFH1_Fhdef_rep1


title: HS360-Day6-CIT200-rep1 [322-D6-CIT200-A]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
322-D6-CIT200-A

value: Day 6 200 nM citalopram


title: 4T1, Cell, Line, single cell 40

value: Female BALB/c mice


title: HS360-Day6-CIT100-rep2 [320-D6-CIT100-B]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
320-D6-CIT100-B

value: Day 6 100 nM citalopram


title: Yunk_wildtype_rep2

value: Normal kidney nephrectomy


title: HS360-Day6-CIT100-rep1 [319-D6-CIT100-A]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
319-D6-CIT100-A


title: 4T1, Cell, Line, single cell 37


title: HS360-Day6-CIT50-rep2 [317-D6-CIT50-B]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
317-D6-CIT50-B


title: 4T1, Cell, Line, single cell 36


title: Yunk_shNT_rep1


title: HS360-Day6-CIT50-rep3 [318-D6-CIT50-C]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
318-D6-CIT50-C


title: UOK268_Fhdef_rep2

description: localized type 2 papillary kidney cancer


title: 4T1, Cell, Line, single cell 34


title: 4T1, Cell, Line, single cell 35


title: HS360-Day6-CIT50-rep1 [316-D6-CIT50-A]

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
316-D6-CIT50-A


title: HS360-Day6-rep2 [314-D6-CTRL-B]

description:
Day 6", "male", "neural rosettes", "neural induction
314-D6-CTRL-B


title: 4T1, Cell, Line, single cell 32


title: HS360-Day6-rep3 [315-D6-CTRL-C]

description:
Day 6", "male", "neural rosettes", "neural induction
315-D6-CTRL-C


title: HS360-Day6-rep1 [313-D6-CTRL-A]

description:
Day 6", "male", "neural rosettes", "neural induction
313-D6-CTRL-A


title: 4T1, Cell, Line, single cell 33


title: 4T1, Cell, Line, single cell 31


title: HS360-Day13-CIT400-rep6 [312-D13-CIT400-F]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
312-D13-CIT400-F

source_name: HS360, day 13, end of self-pattering stage, exposed to 400 nM citalopram

value: self-patterning

value: Day 13 400 nM citalopram


title: 4T1, Cell, Line, single cell 29


title: 4T1, Cell, Line, single cell 30


title: HS360-Day13-CIT200-rep5 [311-D13-CIT200-E]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
311-D13-CIT200-E

source_name: HS360, day 13, end of self-pattering stage, exposed to 200 nM citalopram

value: Day 13 200 nM citalopram


title: HS360-Day13-CIT100-rep5 [310-D13-CIT100-E]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
310-D13-CIT100-E

source_name: HS360, day 13, end of self-pattering stage, exposed to 100 nM citalopram

value: Day 13 100 nM citalopram


title: HS360-Day13-CIT400-rep3 [307-D13-CIT400-C]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
307-D13-CIT400-C


title: 4T1, Cell, Line, single cell 28


title: 4T1, Cell, Line, single cell 27


title: 4T1, Cell, Line, single cell 26


title: HS360-Day13-CIT400-rep4 [308-D13-CIT400-D]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
308-D13-CIT400-D


title: 4T1, Cell, Line, single cell 23


title: HS360-Day13-CIT400-rep5 [309-D13-CIT400-E]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
309-D13-CIT400-E


title: 4T1, Cell, Line, single cell 25


title: HS360-Day13-CIT400-rep1 [305-D13-CIT400-A]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
305-D13-CIT400-A


title: HS360-Day13-CIT400-rep2 [306-D13-CIT400-B]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
306-D13-CIT400-B


title: HS360-Day13-CIT200-rep3 [303-D13-CIT200-C]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
303-D13-CIT200-C


title: 4T1, Cell, Line, single cell 24


title: HS360-Day13-CIT200-rep4 [304-D13-CIT200-D]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
304-D13-CIT200-D


title: 4T1, Cell, Line, single cell 22


title: 4T1, Cell, Line, single cell 21


title: HS360-Day13-CIT200-rep2 [302-D13-CIT200-B]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
302-D13-CIT200-B


title: HS360-Day13-CIT100-rep4 [300-D13-CIT100-D]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
300-D13-CIT100-D


title: 4T1, Cell, Line, single cell 18


title: 4T1, Cell, Line, single cell 19


title: HS360-Day13-CIT100-rep3 [299-D13-CIT100-C]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
299-D13-CIT100-C


title: 4T1, Cell, Line, single cell 17


title: HS360-Day13-CIT100-rep2 [298-D13-CIT100-B]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
298-D13-CIT100-B


title: HS360-Day13-CIT100-rep1 [297-D13-CIT100-A]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
297-D13-CIT100-A


title: HS360-Day13-CIT50-rep6 [296-D13-CIT50-F]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
296-D13-CIT50-F

source_name: HS360, day 13, end of self-pattering stage, exposed to 50 nM citalopram

value: Day 13 50 nM citalopram


title: HS360-Day13-rep6 [294-D13-CTRL-F]

description:
Day 13", "male", "self-patterning", "NPCs", "control
294-D13-CTRL-F

source_name: HS360, day 13, end of self-pattering stage

value: Day 13 control


title: 4T1, Cell, Line, single cell 13

value: metastatic tumor cells


title: 4T1, Cell, Line, single cell 14


title: HS360-Day13-rep4 [292-D13-CTRL-D]

description:
Day 13", "male", "self-patterning", "NPCs", "control
292-D13-CTRL-D


title: HS360-Day13-rep5 [293-D13-CTRL-E]

description:
Day 13", "male", "self-patterning", "NPCs", "control
293-D13-CTRL-E


title: 4T1, Cell, Line, single cell 11


title: HS360-Day13-CIT50-rep4 [291-D13-CIT50-D]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
291-D13-CIT50-D


title: 4T1, Cell, Line, single cell 12


title: 4T1, Cell, Line, single cell 9


title: 4T1, Cell, Line, single cell 10


title: 4T1, Cell, Line, single cell 8


title: 4T1, Cell, Line, single cell 7


title: HS360-Day13-CIT50-rep3 [290-D13-CIT50-C]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
290-D13-CIT50-C


title: HS360-Day13-CIT200-rep1 [301-D13-CIT200-A]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
301-D13-CIT200-A


title: HS360-Day13-CIT50-rep1 [288-D13-CIT50-A]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
288-D13-CIT50-A


title: HS360-Day13-CIT50-rep2 [289-D13-CIT50-B]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
289-D13-CIT50-B


title: 4T1, Cell, Line, single cell 16


title: 4T1, Cell, Line, single cell 6


title: 4T1, Cell, Line, single cell 4


title: HS360-Day13-rep2 [286-D13-CTRL-B]

description:
Day 13", "male", "self-patterning", "NPCs", "control
286-D13-CTRL-B


title: 4T1, Cell, Line, single cell 5


title: 4T1, Cell, Line, single cell 15


title: HS360-Day13-rep1 [285-D13-CTRL-A]

description:
Day 13", "male", "self-patterning", "NPCs", "control
285-D13-CTRL-A


title: HS360-Day13-CIT50-rep5 [295-D13-CIT50-E]

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
295-D13-CIT50-E


title: HS360-Day10-CIT400-rep5 [283-D10-CIT400-E]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
283-D10-CIT400-E

source_name: HS360, day 10, middle of self-pattering stage, exposed to 400 nM citalopram

value: Day 10 400 nM citalopram


title: 4T1, Cell, Line, single cell 2


title: HS360-Day10-CIT400-rep6 [284-D10-CIT400-F]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
284-D10-CIT400-F


title: 4T1, Cell, Line, single cell 1


title: HS360-Day10-CIT200-rep5 [282-D10-CIT200-E]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
282-D10-CIT200-E

source_name: HS360, day 10, middle of self-pattering stage, exposed to 200 nM citalopram

value: Day 10 200 nM citalopram


title: HS360-Day10-CIT100-rep5 [280-D10-CIT100-E]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
280-D10-CIT100-E

source_name: HS360, day 10, middle of self-pattering stage, exposed to 100 nM citalopram

value: Day 10 100 nM citalopram


title: 4T1, Day16, single cell 191


title: 4T1, Day16, single cell 190


title: HS360-Day10-CIT200-rep4 [281-D10-CIT200-D]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
281-D10-CIT200-D


title: HS360-Day10-CIT100-rep4 [279-D10-CIT100-D]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
279-D10-CIT100-D


title: HS360-Day10-CIT50-rep6 [278-D10-CIT50-F]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
278-D10-CIT50-F

source_name: HS360, day 10, middle of self-pattering stage, exposed to 50 nM citalopram

value: Day 10 50 nM citalopram


title: 4T1, Day16, single cell 188


title: 4T1, Day16, single cell 189


title: HS360-Day10-rep6 [276-D10-CTRL-F]

description:
Day 10", "male", "self-patterning", "NPCs", "control
276-D10-CTRL-F

source_name: HS360, day 10, middle of self-pattering stage

value: Day 10 control


title: 4T1, Day16, single cell 186


title: HS360-Day10-rep5 [275-D10-CTRL-E]

description:
Day 10", "male", "self-patterning", "NPCs", "control
275-D10-CTRL-E


title: 4T1, Day16, single cell 187


title: HS360-Day13-rep3 [287-D13-CTRL-C]

description:
Day 13", "male", "self-patterning", "NPCs", "control
287-D13-CTRL-C


title: HS360-Day10-rep4 [274-D10-CTRL-D]

description:
Day 10", "male", "self-patterning", "NPCs", "control
274-D10-CTRL-D


title: 4T1, Day16, single cell 185


title: 4T1, Day16, single cell 183


title: 4T1, Day16, single cell 184


title: 4T1, Cell, Line, single cell 42


title: HS360-Day10-CIT50-rep5 [277-D10-CIT50-E]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
277-D10-CIT50-E


title: HS360-Day10-CIT400-rep3 [272-D10-CIT400-C]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
272-D10-CIT400-C


title: 4T1, Cell, Line, single cell 3


title: HS360-Day10-CIT400-rep4 [273-D10-CIT400-D]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
273-D10-CIT400-D


title: 4T1, Day16, single cell 192


title: 4T1, Day16, single cell 181


title: 4T1, Day16, single cell 180


title: 4T1, Day16, single cell 178


title: 4T1, Day16, single cell 179


title: 4T1, Day16, single cell 177


title: HS360-Day10-CIT100-rep3 [266-D10-CIT100-C]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
266-D10-CIT100-C


title: 4T1, Day16, single cell 176


title: 4T1, Day16, single cell 175


title: HS360-Day10-CIT50-rep4 [263-D10-CIT50-D]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
263-D10-CIT50-D


title: HS360-Day10-CIT100-rep1 [264-D10-CIT100-A]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
264-D10-CIT100-A


title: 4T1, Day16, single cell 173


title: 4T1, Day16, single cell 174


title: HS360-Day10-CIT100-rep2 [265-D10-CIT100-B]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
265-D10-CIT100-B


title: HS360-Day10-CIT50-rep3 [262-D10-CIT50-C]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
262-D10-CIT50-C


title: HS360-Day10-CIT50-rep2 [261-D10-CIT50-B]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
261-D10-CIT50-B


title: 4T1, Day16, single cell 170


title: HS360-Day10-rep3 [259-D10-CTRL-C]

description:
Day 10", "male", "self-patterning", "NPCs", "control
259-D10-CTRL-C


title: 4T1, Day16, single cell 182


title: HS360-Day10-CIT50-rep1 [260-D10-CIT50-A]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
260-D10-CIT50-A


title: 4T1, Day16, single cell 172


title: HS360-Day10-CIT400-rep2 [271-D10-CIT400-B]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
271-D10-CIT400-B


title: 4T1, Day16, single cell 168


title: HS360-Day10-rep2 [258-D10-CTRL-B]

description:
Day 10", "male", "self-patterning", "NPCs", "control
258-D10-CTRL-B


title: HS360-Day10-CIT400-rep1 [270-D10-CIT400-A]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
270-D10-CIT400-A


title: 4T1, Day16, single cell 167


title: HS360-Day10-CIT200-rep3 [269-D10-CIT200-C]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
269-D10-CIT200-C


title: 4T1, Day16, single cell 169


title: HS360-Day10-CIT200-rep2 [268-D10-CIT200-B]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
268-D10-CIT200-B


title: HS360-Day10-CIT200-rep1 [267-D10-CIT200-A]

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
267-D10-CIT200-A


title: HS360-Day10-rep1 [257-D10-CTRL-A]

description:
Day 10", "male", "self-patterning", "NPCs", "control
257-D10-CTRL-A


title: 4T1, Day16, single cell 166


title: 4T1, Day16, single cell 165


title: 4T1, Day16, single cell 164


title: 4T1, Day16, single cell 162


title: 4T1, Day16, single cell 163


title: 4T1, Day16, single cell 171


title: 4T1, Day16, single cell 161


title: 4T1, Day16, single cell 160


title: 4T1, Day16, single cell 158


title: 4T1, Day16, single cell 157


title: 4T1, Day16, single cell 159


title: 4T1, Day16, single cell 154


title: 4T1, Day16, single cell 156


title: 4T1, Day16, single cell 155


title: 4T1, Day16, single cell 153


title: 4T1, Day16, single cell 152


title: 4T1, Day16, single cell 151


title: 4T1, Day16, single cell 150


title: 4T1, Day16, single cell 149


title: 4T1, Day16, single cell 148


title: 4T1, Day16, single cell 147


title: 4T1, Day16, single cell 146


title: 4T1, Day16, single cell 145


title: 4T1, Day16, single cell 144


title: 4T1, Day16, single cell 142


title: 4T1, Cell, Line, single cell 20


title: 4T1, Day16, single cell 143


title: 4T1, Day16, single cell 139


title: 4T1, Day16, single cell 140


title: 4T1, Day16, single cell 141


title: 4T1, Day16, single cell 138


title: Genomic DNA from normal proximal tubules_T22_PT

city: Narita-shi

first: Takeshi

last: Marumo

state: Chiba

address: Kouzunomori 4-3

department: School of Medicine

country: Japan

institute: International University of Health and Welfare

description: Non-cancerous kidney tissue from a patient with renal cell carcinoma

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: GenomeStudio methylation software

label: Cy5 and Cy3

extract_protocol: NucleoSpin Tissue XS (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany)

value: normal proximal tubules

tag: sample type

value: Proxymal tubules microdissected from kidney slice fixed with 4% paraformaldehyde


title: Genomic DNA from normal proximal tubules_T17_PT


title: 4T1, Day16, single cell 137

value: Female BALB/c mice


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD37_PT

description: Biopsy sample of histologically diagnosed diabetic nephropathy


title: Genomic DNA from normal proximal tubules_T18_PT


title: Genomic DNA from normal proximal tubules_T19_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD36_PT


title: Genomic DNA from normal proximal tubules_T21_PT


title: 4T1, Day16, single cell 136


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD32_PT


title: Sample12

city: Calgary

first: Ana

middle: Isabel

last: Hernandez Cordero

state: Alberta

address: 303 13th Avenue SW, unit 1004

institute: Heart Lung Innovation Centre

description: Blood sample

hyb_protocol: bisulphite converted DNA and DNA methylation by  Illumina MethylationEPIC BeadChipv1 microarray

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

data_processing: detection p cutoff 1xe-10, Sample cutoff 0.05, Probe cutoff 0.05, background correction, BMIQ normalization and batch correction

source_name: Peripheral blood buffy coat

extract_protocol: genomic DNA was extracted from uffy coat and purify using Qiagen DNeasy Kit according to standard instructions

value: Male

tag: age


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD34_PT


title: 4T1, Day16, single cell 134


title: 4T1, Day16, single cell 135


title: 4T1, Day16, single cell 133


title: Sample39

description: Blood sample

value: Female


title: Genomic DNA from normal proximal tubules_T20_PT


title: Sample33

description: Blood sample


title: Sample19

description: Blood sample


title: 4T1, Day16, single cell 131


title: Genomic DNA from normal proximal tubules_T25_PT


title: Sample4

description: Blood sample


title: Genomic DNA from normal proximal tubules_T16_PT


title: Sample18

description: Blood sample


title: 4T1, Day16, single cell 130


title: Sample13

description: Blood sample


title: Sample11

description: Blood sample


title: Sample17

description: Blood sample


title: 4T1, Day16, single cell 129


title: 4T1, Day16, single cell 128


title: Sample16

description: Blood sample


title: Sample34

description: Blood sample


title: Sample7

description: Blood sample


title: 4T1, Day16, single cell 127


title: Sample38

description: Blood sample


title: 4T1, Day16, single cell 132


title: 4T1, Day16, single cell 126


title: 4T1, Day16, single cell 124


title: Sample36

description: Blood sample


title: 4T1, Day16, single cell 123


title: 4T1, Day16, single cell 122


title: Sample35

description: Blood sample


title: 4T1, Day16, single cell 121


title: 4T1, Day16, single cell 120


title: 4T1, Day16, single cell 118


title: 4T1, Day16, single cell 117


title: 4T1, Day16, single cell 119


title: 4T1, Day16, single cell 116


title: 4T1, Day16, single cell 115


title: 4T1, Day16, single cell 114


title: Sample44

description: Blood sample


title: 4T1, Day16, single cell 113


title: 4T1, Day16, single cell 125


title: Sample41

description: Blood sample


title: 4T1, Day16, single cell 112


title: 4T1, Day16, single cell 111


title: Sample31

description: Blood sample


title: Sample43

description: Blood sample


title: 4T1, Day16, single cell 110


title: 4T1, Day16, single cell 109


title: Sample42

description: Blood sample


title: Sample46

description: Blood sample


title: 4T1, Day16, single cell 108


title: Sample57

description: Blood sample


title: 4T1, Day16, single cell 107


title: 4T1, Day16, single cell 105


title: Sample59

description: Blood sample


title: Sample65

description: Blood sample


title: Sample50

description: Blood sample


title: 4T1, Day16, single cell 106


title: 4T1, Day16, single cell 103


title: 4T1, Day16, single cell 104


title: Sample76

description: Blood sample


title: 4T1, Day16, single cell 102


title: Sample29

description: Blood sample


title: 4T1, Day16, single cell 101


title: Sample9

description: Blood sample


title: Sample27

description: Blood sample


title: Sample69

description: Blood sample


title: Sample73

description: Blood sample


title: 4T1, Day16, single cell 100


title: Sample21

description: Blood sample


title: Sample88

description: Blood sample


title: Sample83

description: Blood sample


title: Sample85

description: Blood sample


title: Sample15

description: Blood sample


title: 4T1, Day16, single cell 98


title: Sample26

description: Blood sample


title: 4T1, Day16, single cell 99


title: Sample78

description: Blood sample


title: Sample75

description: Blood sample


title: Sample86

description: Blood sample


title: Sample28

description: Blood sample


title: Sample62

description: Blood sample


title: 4T1, Day16, single cell 95


title: Sample93

description: Blood sample


title: Sample25

description: Blood sample


title: 4T1, Day16, single cell 96


title: 4T1, Day16, single cell 90


title: Sample20

description: Blood sample


title: 4T1, Day16, single cell 93


title: Sample24

description: Blood sample


title: Sample22

description: Blood sample


title: Sample23

description: Blood sample


title: 4T1, Day16, single cell 97


title: 4T1, Day16, single cell 92


title: 4T1, Day16, single cell 91


title: Sample30

description: Blood sample


title: Sample74

description: Blood sample


title: 4T1, Day16, single cell 88


title: 4T1, Day16, single cell 86


title: 4T1, Day16, single cell 94


title: 4T1, Day16, single cell 87


title: Sample5

description: Blood sample


title: 4T1, Day16, single cell 84


title: 4T1, Day16, single cell 89


title: 4T1, Day16, single cell 85


title: Sample92

description: Blood sample


title: 4T1, Day16, single cell 83


title: 4T1, Day16, single cell 82


title: 4T1, Day16, single cell 81


title: Sample90

description: Blood sample


title: Sample91

description: Blood sample


title: 4T1, Day16, single cell 79


title: 4T1, Day16, single cell 78


title: 4T1, Day16, single cell 77


title: Sample71

description: Blood sample


title: Sample72

description: Blood sample


title: 4T1, Day16, single cell 76


title: Sample70

description: Blood sample


title: 4T1, Day16, single cell 74


title: 4T1, Day16, single cell 73


title: Sample14

description: Blood sample


title: 4T1, Day16, single cell 72


title: 4T1, Day16, single cell 80


title: Sample3

description: Blood sample


title: 4T1, Day16, single cell 71


title: 4T1, Day16, single cell 75


title: 4T1, Day16, single cell 70


title: Sample8

description: Blood sample


title: Sample52

description: Blood sample


title: Sample1

description: Blood sample


title: 4T1, Day16, single cell 67


title: Sample2

description: Blood sample


title: Sample55

description: Blood sample


title: 4T1, Day16, single cell 68


title: Sample81

description: Blood sample


title: Sample54

description: Blood sample


title: Sample6

description: Blood sample


title: 4T1, Day16, single cell 69


title: Sample32

description: Blood sample


title: Sample66

description: Blood sample


title: Sample45

description: Blood sample


title: Sample79

description: Blood sample


title: 4T1, Day16, single cell 66


title: 4T1, Day16, single cell 64


title: Sample68

description: Blood sample


title: Sample64

description: Blood sample


title: Sample56

description: Blood sample


title: 4T1, Day16, single cell 65


title: Sample80

description: Blood sample


title: Sample49

description: Blood sample


title: Sample47

description: Blood sample


title: Sample10

description: Blood sample


title: Sample77

description: Blood sample


title: 4T1, Day16, single cell 62


title: 4T1, Day16, single cell 60


title: genomic DNA from N19 METTL7B overexpression 4

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

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

data_processing:
RStudio v4.1.3
GEO_MatrixProcessed .txt files represent Average Beta.
GEO_SignalIntensities .txt represent unmethylated and methylated signal intensities.

growth_protocol: GIC were maintained in NeuroCult NS-A Proliferation kit medium, 1% Pen/Strep, 2µg/ml Heparin, 20ng/ml murine EGF and 10ng/ml human FGF. iNSC were cultured in 0.5X Advanced DMEM/F-12 , 0.5X Neurobasal medium, 1X Neurobasal Induction supplement and 1X pen/strep

extract_protocol: DNA extraction with NORGEN Biotek DNA/RNA/Protein Purification Plus kit. 500ng of genomic DNA used

value: METTL7B overexpression

value: induced neural stem cells


title: genomic DNA from N19 METTL7B overexpression 3


title: Sample87

description: Blood sample


title: genomic DNA from N19 METTL7B overexpression 2


title: Sample48

description: Blood sample


title: 4T1, Day16, single cell 59


title: 4T1, Day16, single cell 58


title: 4T1, Day16, single cell 57


title: genomic DNA from N19 PK 4

value: WT


title: Sample84

description: Blood sample


title: genomic DNA from N19 METTL7B overexpression 1


title: genomic DNA from N19 PK 2


title: 4T1, Day16, single cell 54


title: genomic DNA from N19 PK 3


title: Sample89

description: Blood sample


title: 4T1, Day16, single cell 55


title: genomic DNA from N19 PK 1


title: 4T1, Day16, single cell 61


title: 4T1, Day16, single cell 63


title: 4T1, Day16, single cell 56


title: 4T1, Day16, single cell 51


title: genomic DNA from G19 METTL7B knockdown 2

value: METTL7B knockdown

value: Glioblastoma initiating cells


title: 4T1, Day16, single cell 50


title: genomic DNA from G19 METTL7B knockdown 1


title: Sample60

description: Blood sample


title: genomic DNA from G19 METTL7B knockdown 3


title: Sample67

description: Blood sample


title: genomic DNA from G19 Scramble 4


title: 4T1, Day16, single cell 48


title: genomic DNA from G19 Scramble 3


title: genomic DNA from G19 Scramble 2


title: 4T1, Day16, single cell 47


title: 4T1, Day16, single cell 46


title: 4T1, Day16, single cell 43


title: 4T1, Day16, single cell 41


title: 4T1, Day16, single cell 40


title: 4T1, Day16, single cell 53


title: genomic DNA from G19 METTL7B knockdown 4


title: 4T1, Day16, single cell 39


title: Sample82

description: Blood sample


title: 4T1, Day16, single cell 45


title: 4T1, Day16, single cell 38


title: 4T1, Day16, single cell 37


title: 4T1, Day16, single cell 42


title: Sample51

description: Blood sample


title: Sample40

description: Blood sample


title: 4T1, Day16, single cell 36


title: 4T1, Day16, single cell 35


title: genomic DNA from G19 Scramble 1


title: 4T1, Day16, single cell 34


title: 4T1, Day16, single cell 52


title: Sample37

description: Blood sample


title: Sample63

description: Blood sample


title: 4T1, Day16, single cell 33


title: 4T1, Day16, single cell 32


title: Sample53

description: Blood sample


title: 4T1, Day16, single cell 31


title: 4T1, Day16, single cell 30


title: 4T1, Day16, single cell 49


title: Sample58

description: Blood sample


title: Sample61

description: Blood sample


title: 4T1, Day16, single cell 29


title: 4T1, Day16, single cell 44


title: 4T1, Day16, single cell 28


title: 4T1, Day16, single cell 27


title: 4T1, Day16, single cell 26


title: 4T1, Day16, single cell 23


title: 4T1, Day16, single cell 25


title: 4T1, Day16, single cell 24


title: 4T1, Day16, single cell 22


title: 4T1, Day16, single cell 20


title: 4T1, Day16, single cell 19


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD22_PT

description: Biopsy sample of histologically-diagnosed diabetic nephropathy


title: 4T1, Day16, single cell 18


title: sma-9(ok1628)-3, L2

city: Piscataway

first: Christopher

last: Rongo

state: NJ

address: 190 Frelinghuysen Road, #163

department: Waksman Institute

institute: Rutgers University

data_processing:
Reads were mapped to the C. elegans genome (WS245) and gene counts generated with STAR 2.5.1a. Normalization and statistical analysis on gene counts were performed with EdgeR using generalized linear model functionality and tagwise dispersion estimates
Assembly: Wormbase Ce11 WS245
Supplementary files format and content: Normalized Counts for all samples from EdgeR

organism: Caenorhabditis elegans

source_name: worm

growth_protocol: C. elegans strains were grown at 20°C using standard methods unless otherwise indicated

extract_protocol:
Developmentally synchronized animals were obtained by hypochlorite treatment of gravid adults to isolate embryos. Animals were grown on NGM plates at 20°C until the late L2 stage. Total RNA was isolated from animals using Trizol (Invitrogen) combined with Bead Beater lysis in three biological replicates for each genotype
PolyA selected

value: mutant

tag: development stage

value: worm


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD27_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD24_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD19_PT


title: 4T1, Day16, single cell 16

value: metastatic tumor cells


title: 4T1, Day16, single cell 21


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD14_PT


title: 4T1, Day16, single cell 17


title: sma-9(ok1628)-2, L2


title: 4T1, Day16, single cell 15


title: sma-3(wk30)-3, L2


title: sma-9(ok1628)-1, L2


title: 4T1, Day16, single cell 14


title: sma-3(wk30)-2, L2


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD15_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD5_PT


title: 4T1, Day16, single cell 13


title: sma-3(wk30)-1, L2


title: 4T1, Day16, single cell 12


title: N2-3, L2

value: wild type


title: 4T1, Day16, single cell 11


title: Genomic DNA from normal proximal tubules_T7_PT


title: N2-2, L2


title: Genomic DNA from normal proximal tubules_T14_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD20_PT


title: 4T1, Day16, single cell 10


title: N2-1, L2


title: Genomic DNA from normal proximal tubules_T9_PT


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD4_PT


title: 4T1, Day16, single cell 8


title: T2C DACT2-SMOC2 locus Interzone

city: Rotterdam

first: Karol

last: Nowosad

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

library_source: genomic

data_processing:
library strategy: low-input Targeted Chromatin Capture (low-T2C)
In the T2C primary analysis, the quality of reads was checked by FASTQC followed by removal of adapters using AdapterTrimmer tool.
Reads were mapped to the Gallus Gallus 5 reference genome with the BWA aligner and the BWA-backtrack method.
Alignments were subsequently annotated with the restriction fragments in which they were located.
The proximity matrix was then constructed from the mapped primary alignments with their mapped primary mates.
Further analyses and filtering based on the proximity matrix were performed in the R environment for statistical computing.
Assembly: GalGal5
Supplementary files format and content: T2C proximity matrix

organism: Gallus gallus

source_name: T2C DACT2-SMOC2 locus interzone from hindlimb digit

growth_protocol: Chick White Leghorn embryonated eggs were incubated at 38.5ºC in fixed humidity for 7.5 days, followed by evaluation of developmental stage based on the Hamilton Hamburger classification (HH). The joint interzones and adjacent phalange samples were microdissected from hindlimb digit-3

extract_protocol:
For each sample, 100 specimens were collected from the 3rd hindlimb digit of developing chicken ebmryo (HH32) and pooled togethe to obtain 10^6 cells per tissue. Further, samples were dissociated using Collagenase-II and passed through a 40-m cell strainer. The 1mln of cells were cross-linked and after a series of washes, the cell nuclei were further extracted. Subsequently, the chromatin was digested with the ApoI restriction enzyme. Digested chromatin was ligated with T4-DNA Ligase followed by further incubation with Proteinase K and RNAse-A (10 mg/ml). Next, the DNA was purified using Phenol:Chloroform according to the manufacturer’s instructions. The re-ligated DNA was digested with DpnII, and purified by Phenol:Chloroform prior to T2C library preparation
The obtained chromatin was sheared to 250-400 bp-sized fragments and concentration was determined by Quant-it. For each sample, 100 ng of sheared chromatin was end-repaired and A-tailed using the Kapa hyper prep kit. SeqCap library adaptors were ligated followed by AMPure bead clean-up. The pre-capture library was amplified by PCR using KAPA HiFi hotstart readymix for 9 cycles, and pre-capture library was purified. Next, a pooled hybridization mixture was prepared for each pre-capture library and subsequently DNA was hybridized for 16 hours at 47°C with custom baits. The captured library was amplified by PCR using Kapa HiFi mix and purified by AMPure XP beads. Finally, the captured T2C libraries were denatured and sequenced on an Illumina HiSeq 2500 sequencer with a custom recipe of 6 dark cycles, followed by paired end 101 sequencing with single index using the rapid v2 chemistry according to manufacturer’s instructions (Illumina).

tag: developmental stage

value: interzone


title: T2C DACT2-SMOC2 locus Phalange

source_name: T2C DACT2-SMOC2 locus phalange from hindlimb digit

value: phalange


title: 4T1, Day16, single cell 7

tag: host


title: kin-3_piRNA_2

city: Shrewsbury

first: Chunwei

state: MA

address: 70 Shrewsbury Green Dr, Unit L, Unit L

institute: UMass medical school

library_source: other

data_processing:
Adaptors were trimmed from fastq files using cutadapt v1.18.
Reads were trimmed to retain only 18-30 nts using cutadapt v1.18.
The reads were mapped to piRNAs with an arbitrary length of overhanging sequence either side of the 21U sequence using the exact matches using bowtie v1.2.1.1.
Reads were normalized to the total reads using excel.
Assembly: piRNAdb.cel.v1_7_6.fa
Supplementary files format and content: txt

molecule: other

source_name: whole worm

extract_protocol:
The small RNA cloning was conducted. Total RNAs were extracted by Trizol (Sigma Alrich) and small RNAs were enriched by an mir-Vana miRNA isolation kit (Thermo Scientific).
Samples were pretreated with homemade PIR-1 . The small RNAs were then ligated to a 3’ adaptor (5’ rAppAGATCGGAAGAGCACACGTCTGAACTCCAGTCA/3ddC/3’; IDT) by T4 RNA ligase 2(NEB). The 5’ adaptor containing 6 nt barcode was ligated using T4 RNA ligase 1. The ligated products were reverse transcribed using SuperScript III (Thermo Fisher Scientific). The cDNAs were amplified by PCR and the libraries were sequenced using the HiSeq systems (Illumina) platform at the UMass Medical School Deep Sequencing Core Facility.

value: whole worm

value: cultured with 500uM IAA


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD13_PT

value: Proxymal tubules microdissected from kidney slice fixed with 4% paraformaldehyde


title: Genomic DNA from normal proximal tubules_T5_PT


title: 4T1, Day16, single cell 6

value: Female BALB/c mice

tag: cell line


title: 4T1, Day16, single cell 9

tag: cell type


title: kin-3_piRNA_1


title: Genomic DNA from decitabine treated (300nM) SETD2 KO 786-0 cells 1

city: Charleston

first: Aguirre

last: de Cubas

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: Medical University of South Carolina

description:
SETD2 KO 786-0 300nM decitabine 1
7860.ko_D300_rep1

scan_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC (EPIC) BeadChip using standard Illumina protocol

data_processing: Raw IDAT files were processed with Illumina’s GenomeStudio software V2011.1 and Data was normalized using functional normalization preprocessing (preprocessFunnorm function from minfi package), which extends the idea of quantile normalization by adjusting for known covariates measuring unwanted variation, to generate methylation β and M values, which were used for all downstream analyses.

source_name: SETD2 KO 786-0 300nM decitabine 1

label_protocol: genomic DNA was extracted and purified from  samples using Qiagen DNeasy Kit according to standard instructions, and treated with Rnase

growth_protocol: Cells cultured

extract_protocol: DNA was extracted using the DNeasy (Qiagen) and treated with Rnase

treatment_protocol: Cells were treated daily with DMSO of Decitabine (100nM or 300nM) for three days. Fresh media added on day 4 and cells were harvested on day 5.

value: 786-0 cells

value: 300nM decitabine


title: Genomic DNA from DMSO treated SETD2 KO 786-0 cells 2

description:
SETD2 KO 786-0 DMSO 2
7860.ko_D0_rep2

source_name: SETD2 KO 786-0 DMSO 2

value: DMSO


title: prg-1_piRNA_2

value: untreated


title: Genomic DNA from normal proximal tubules_T4_PT


title: Genomic DNA from decitabine treated (100nM) SETD2 KO 786-0 cells 2

description:
SETD2 KO 786-0 100nM decitabine 2
7860.ko_D100_rep2

source_name: SETD2 KO 786-0 100nM decitabine 2

value: 100nM decitabine


title: prg-1_piRNA_1


title: Genomic DNA from decitabine treated (100nM) SETD2 KO 786-0 cells 1

description:
SETD2 KO 786-0 100nM decitabine 1
7860.ko_D100_rep1

source_name: SETD2 KO 786-0 100nM decitabine 1


title: 4T1, Day16, single cell 4


title: Genomic DNA from normal proximal tubules_T8_PT


title: 4T1, Day16, single cell 3


title: 4T1, Day10, single cell 96


title: prde-1_piRNA_2


title: Genomic DNA from decitabine treated (300nM) SETD2 KO 786-0 cells 2

description:
SETD2 KO 786-0 300nM decitabine 2
7860.ko_D300_rep2

source_name: SETD2 KO 786-0 300nM decitabine 2


title: WT_piRNA_1

value: WT


title: prde-1_piRNA_1


title: 4T1, Day16, single cell 1


title: Genomic DNA from proximal tubules of diabetic nephropathy_TD8_PT


title: WT_piRNA_2


title: Genomic DNA from normal proximal tubules_T1_PT


title: 4T1, Day10, single cell 94


title: Genomic DNA from normal proximal tubules_T3_PT


title: 4T1, Day10, single cell 95


title: Genomic DNA from normal proximal tubules_T6_PT


title: Genomic DNA from normal proximal tubules_T2_PT


title: Genomic DNA from DMSO treated SETD2 KO 786-0 cells 1

description:
SETD2 KO 786-0 DMSO 1
7860.ko_D0_rep1

source_name: SETD2 KO 786-0 DMSO 1


title: 4T1, Day16, single cell 2


title: 4T1, Day10, single cell 91


title: 4T1, Day10, single cell 92


title: 4T1, Day10, single cell 93


title: 4T1, Day10, single cell 90


title: 4T1, Day10, single cell 89


title: 4T1, Day16, single cell 5


title: 4T1, Day10, single cell 87


title: SAM24403197_BRM_dox_ML210_rep2

city: South San Francisco

first: Marc

last: Hafner

state: CA

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
cutadapt v3.4
30nt cell barcodes were extracted after 5' Adaptors were trimed from raw reads
MAGeCK  package v0.5.9
cell barcodes were counted with "mageck count" function from the MAGeCK  package using cell barcode reference
Log2 fold change of lineage barcodes were first calculated by adding a pseudocount of 1 to all barcode counts, averaging the counts per lineage barcode across replicates for each sample, then calculating the log2 fold change from baseline. Baseline was defined as the average barcode count from both replicates of the naïve cell populations. Enriched barcodes were defined as having a log2 fold change of > 2.5 and depleted barcodes were defined as having a log2 fold change of < -7.5 after treatment with dox and ML210.
Supplementary files format and content: KP4_BC30_count.csv contains the lineage barcode counts per sample
Supplementary files format and content: NGS3855_barcodes_log2fc_avg.tsv contains the log2 fold change calculated as described above. NGS3855_enriched_depleted_clones.csv contains the enriched and depleted clonal assignments.
Library strategy: deep sequencing of TraCe-seq barcodes

source_name: pancreatic

extract_protocol:
Genomic DNA was extracted from 1-2X106 cells using the Gentra Puregene genomic DNA isolation kit (Qiagen, Cat. No. 158745). Concentrations were measured using Qubit dsDNA BR assay.
The barcodes were amplified using Q5 2X Hot start PCR master mix (NEB, Cat. No. M0494L) with the following primers Forward: 5’-TCCACCGAACGCAACGCACGC-3’ and Reverse 5’-ACGACCGACCCGAACCACGAC-3’. PCR products were cleaned up using QIAquick PCR CleanUp Kit (Qiagen, Cat. No. 28104) and submitted for library preparation and sequencing (Thermofisher, Cat No. Q32850).

value: pancreatic

value: pancreatic cells

value: stable cell line expressing dox-inducible BRM

value: 2ug/ml Doxycycline + 2 μM ML210


title: 4T1, Day10, single cell 88

value: metastatic tumor cells


title: SAM24403194_BRM_nodox_ML210_rep2

value: 2 μM ML210


title: SAM24403195_BRM_nodox_ML210_rep3


title: 253949445557-7

city: Nice

first: Robert

last: Ballotti

state: Alpes maritimes

address: Hopital Archet2, Bat Archimed, 151, Rt de St Antoine de Ginestiere

country: France

institute: INSERM U1065, Team1  Bat Archimed, Hopîtal Archet2

hyb_protocol: Agilent : 600.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: We performed a quantile normalization (same distribution per array). Quality analysis was performed using graphical tools called diagnostics plots and an R package named ArrayQualityMetrics. No differential gene expression analysis was performed

label_protocol: Agilent - Low RNA input QuickAmp

growth_protocol: cells were grown in DMEN, 7% FCS

extract_protocol: Qiagen

treatment_protocol: No treatment

value: melanoma


title: 4T1, Day10, single cell 86


title: 4T1, Day10, single cell 84


title: SAM24403192_BRM_dox_rep2

value: 2ug/ml Doxycycline


title: 253949445557-5


title: 4T1, Day10, single cell 85


title: 253949445557-3


title: 253949445558-3


title: 4T1, Day10, single cell 83


title: 253949445557-1


title: 253949445558-1


title: SAM24403190_BRM_nodox_rep2


title: 4T1, Day10, single cell 81


title: 4T1, Day10, single cell 80


title: SAM24403189_BRM_nodox_rep1


title: WU_2

city: Suzhou

first: Yiqiang

last: Wang

state: Jiangsu

address: 111 Renai Road

institute: Xi'an Jiaotong-Liverpool University

data_processing:
V2-Dr.TOM Ⅱ
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) (or DEGseq or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: hg38
Supplementary files format and content: table files include  each Sample

source_name: blood vessel

growth_protocol: HUVEC cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using TRIzol lysis reagent (Life-iLab BiotEC38).
RNA libraries were prepared by BGI Genomics Co.,Ltd.

treatment_protocol: Exposed HUVEC to E peptide or M peptide at 5 μM overnight.

value: blood vessel

value: HUVEC

value: Human Umbilical Vein Endothelium


title: 4T1, Day10, single cell 79

value: Female BALB/c mice


title: WU_1


title: SAM24403196_BRM_dox_ML210_rep1


title: SAM24403193_BRM_nodox_ML210_rep1


title: 4T1, Day10, single cell 77


title: Pro_M3

value: M polypeptide treated overnight


title: 4T1, Day10, single cell 76


title: Pro_M2


title: Pro_M1


title: 4T1, Day10, single cell 75


title: Pro_E3

value: E polypeptide treated overnight


title: SAM24403191_BRM_dox_rep1


title: 4T1, Day10, single cell 82


title: Pro_E2


title: 4T1, Day10, single cell 74


title: 4T1, Day10, single cell 72


title: 4T1, Day10, single cell 71


title: 4T1, Day10, single cell 70


title: 4T1, Day10, single cell 69


title: Pro_E1


title: WU_3

description: The read2 fastq file was truncated. Submitters did not have a complete file.

value: untreated


title: daf-2lf;skn-1gf rep3

city: Los Angeles

first: Chris

last: Turner

address: 3715 McClintock Ave

institute: University of Southern California

data_processing:
Third party data processing service Novogene was used
Assembly: ce10
Supplementary files format and content: Tab delimited text files with unprocessed gene counts for each condition

source_name: Whole Animal

growth_protocol: C. elegans strains were cultured on standard NGM plates with OP50 food source

extract_protocol:
Worms were lysed in TRIzol then RNA waas extracted using Direct-zol kit (Zymo)
Third party library construction service Novogene was used

value: Whole Animal


title: 4T1, Day10, single cell 78

city: Beijing

first: Hanqiu

address: Haidian District

institute: Tsinghua university

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)


title: daf-2lf;skn-1gf rep2


title: daf-2lf;skn-1gf rep1


title: 4T1, Day10, single cell 68


title: daf-2lf rep3


title: 4T1, Day10, single cell 66


title: 4T1, Day10, single cell 67


title: daf-2lf rep1


title: daf-2lf rep2


title: 4T1, Day10, single cell 65


title: skn-1gf rep 1


title: 4T1, Day10, single cell 64


title: skn-1gf rep 3


title: 4T1, Day10, single cell 63


title: skn-1gf rep 2


title: 4T1, Day10, single cell 73


title: 4T1, Day10, single cell 62


title: Wildtype control rep 3

value: WT


title: Wildtype control rep 2


title: Wildtype control rep 1


title: 4T1, Day10, single cell 59


title: 4T1, Day10, single cell 61


title: 4T1, Day10, single cell 60


title: 4T1, Day10, single cell 58


title: 4T1, Day10, single cell 57


title: VCD_Post6_OF

city: Stirling

last: Timmons

address: Bridge of Allan

institute: Augur Precision Medicine LTD

hyb_protocol: Standard

scan_protocol: Standard

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs. The full length transcript probe-set based data and the 3'UTR only probe-set based data are provided along with the custom CDF. A 3SD filter was utilised to distinguish gene expression above background
GC_Murine_ClariomD_cv_0.25_i_14_GRCm39_gencode_m32_transcript,binary.cdf; GC_Murine_ClariomD_cv_0.25_i_14_GRCm39_gencode_m32_3utr,binary.cdf
CDF probes were aligned to genome reference GRCm39 and transcriptome reference gencode_m32
Log 2 values generated using IRON from GC corrected CEL files

label: biotin

source_name: Mouse Hippocampus

label_protocol: Affymetrix WT kit

extract_protocol: Trizol

treatment_protocol: Female triple-transgenic AD (3xTg-AD)(26) mice were purchased through The Jackson Laboratory and the NIH supported Mutant Mouse Resource and Research Center (MMRRC). Mice were housed four animals per cage in an AAALAC-accredited animal facility at the University of Miami Miller School of Medicine. Ovotoxin vinylcyclohexene dioxide (VCD; Sigma, cat. #94956) was diluted in sesame oil (Fisher Scientific, cat #18-606-186). Animals were administered 160 mg/kg VCD (n = 19) to induce OF or sesame oil vehicle (n = 20) at a final volume of 100µL intraperitoneal (i.p.) starting at 4 months of age. Mice were injected 5 days a week for 3 weeks, for a total of 15 days. Mice representing peri-OF (Ctrl n = 9; VCD n = 8) were euthanized 90-100 d.p.i., when mice were 30-32 weeks old. Mice representing post-OF (Ctrl n = 10; VCD n = 10) were euthanized 217-224 d.p.i., approximately 48 weeks old. 28 RNA samples were successfully processed to completed CEL files passing QC.

tag: group

value: VCD

tag: time point

value: Post

value: Female


title: 4T1, Day10, single cell 56

last: Zheng


title: VCD_Post9_OF

tag: Sex


title: VCD_Post5_OF


title: VCD_Post8_OF


title: 4T1, Day10, single cell 55


title: VCD_Post7_OF


title: 4T1, Day10, single cell 54


title: VCD_Post4_OF


title: VCD_Post1_OF


title: VCD_Post2_OF


title: 4T1, Day10, single cell 53


title: 4T1, Day10, single cell 52


title: VCD_Peri6_OF

value: Peri


title: VCD_Peri4_OF


title: 4T1, Day10, single cell 50

value: metastatic tumor cells


title: VCD_Peri5_OF


title: 4T1, Day10, single cell 49


title: VCD_Peri3_OF


title: VCD_Peri2_OF


title: Control7_Peri

value: Control


title: 4T1, Day10, single cell 46


title: VCD_Peri1_OF


title: 4T1, Day10, single cell 47


title: 4T1, Day10, single cell 45


title: 4T1, Day10, single cell 44


title: Control4_Peri


title: 4T1, Day10, single cell 40


title: 4T1, Day10, single cell 42


title: 4T1, Day10, single cell 43


title: 4T1, Day10, single cell 39


title: Control3_Peri


title: 4T1, Day10, single cell 41


title: Control19_Post


title: Control17_Post


title: 4T1, Day10, single cell 51


title: Control16_Post


title: 4T1, Day10, single cell 38


title: 4T1, Day10, single cell 48


title: 4T1, Day10, single cell 37


title: Control14_Peri


title: 4T1, Day10, single cell 36


title: Control11_Post


title: 4T1, Day10, single cell 33


title: 4T1, Day10, single cell 34


title: Control6_Peri


title: 4T1, Day10, single cell 32


title: 4T1, Day10, single cell 30


title: Control20_Post


title: Control2_Peri


title: S44

city: Davis

first: Barbara

last: Blanco-Ulate

address: 1 Shields Ave.

department: Plant Sciences

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic v0.39 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 v2.3.4.1 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py  v0.913
Assembly: Pistacia vera c.v. Kerman (BioProject PRJNA1049825)
Supplementary files format and content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Pistacia vera

source_name: pistachio shell (endocarp)

extract_protocol:
At each time point pistachio fruit hull (exocarp) and shell (endocarp), and kernel (seed) tissue were separated, and flash frozen with liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as paired-end 150-bp reads on an Illumina Hiseq X Ten platform by IDseq

tag: tissue

value: pistachio shell (endocarp)

tag: sampling (growing_degree_days,_c)

tag: cultivar

value: Kerman


title: 4T1, Day10, single cell 29


title: S42


title: S43


title: 4T1, Day10, single cell 27


title: 4T1, Day10, single cell 28


title: S39


title: S37


title: 4T1, Day10, single cell 26


title: Control12_Post


title: S38


title: 4T1, Day10, single cell 24


title: 4T1, Day10, single cell 23


title: 4T1, Day10, single cell 35


title: 4T1, Day10, single cell 22


title: 4T1, Day10, single cell 25


title: S36


title: S34


title: Control10_Peri


title: Control1_Peri


title: 4T1, Day10, single cell 31


title: 4T1, Day10, single cell 20


title: S30


title: S31


title: 4T1, Day10, single cell 19


title: S29


title: S41


title: 4T1, Day10, single cell 18


title: 4T1, Day10, single cell 21


title: S27


title: 4T1, Day10, single cell 17


title: 4T1, Day10, single cell 16


title: S26


title: S25


title: 4T1, Day10, single cell 13


title: S35


title: S22


title: S19


title: S21


title: S18


title: 4T1, Day10, single cell 14


title: 4T1, Day10, single cell 11


title: 4T1, Day10, single cell 12


title: 4T1, Day10, single cell 9


title: S17


title: S16


title: 4T1, Day10, single cell 10


title: 4T1, Day10, single cell 8


title: S15


title: S14


title: 4T1, Day10, single cell 6


title: 4T1, Day10, single cell 7


title: 4T1, Day10, single cell 5


title: S13


title: S12


title: 4T1, Day10, single cell 4


title: S11


title: 4T1, Day10, single cell 3


title: 4T1, Day10, single cell 15


title: S23


title: 4T1, Day10, single cell 2


title: S10


title: S8


title: 4T1, Day10, single cell 1


title: S4


title: S6


title: 4T1, Day4, single cell 513


title: S2


title: 4T1, Day4, single cell 510


title: 4T1, Day4, single cell 512


title: 4T1, Day4, single cell 511


title: K48

source_name: pistachio kernel (seed)

value: pistachio kernel (seed)


title: 4T1, Day4, single cell 508


title: S1


title: U-2932, IKAROS

city: Summit

first: Matthew

middle: E

last: Stokes

address: 556 Morris Ave

institute: Bristol Myers Squibb

data_processing:
We used MACS version 2.2.7.1 to call peaks: macs2 callpeak --keep-dup all --nomodel --qvalue 0.05 --gsize 2749859687 --format BAM --name 03_ikaros_u2932_dmso_rep1.mLb.clN --treatment 03_ikaros_u2932_dmso_rep1.mLb.clN.sorted.bam --control 14_input_u2932_dmso_rep1.mLb.clN.sorted.bam
Assembly: GRCh38
Supplementary files format and content: narrowpeak
Supplementary files format and content: bigWig

source_name: cell line

extract_protocol:
DNA was extracted and purified using the standard phenol chloroform method, followed by ethanol precipitation.
Library was prepared using an automated system (Apollo 342, Wafergen Biosystems/Takara).

value: cell line

value: B-cell

tag: antibody

value: IKAROS


title: S5


title: 4T1, Day4, single cell 509

value: Female BALB/c mice


title: K47


title: K45


title: U-2932, INPUT


title: 4T1, Day4, single cell 506


title: 4T1, Day4, single cell 507


title: Mutagenesis_screen_bin3_r2_RNA

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

data_processing:
Adaptor Removal: Used cutadapt to trim adapter sequences specific to vector-based primers.
Reference Preparation: Created and indexed a reference sequence database of oligonucleotides. Generated a GTF annotation from oligonucleotide sequences.
Mapping: Aligned reads to the reference using bwa mem, ensuring at least 80% of reads aligned exactly once. Sorted and indexed aligned reads using samtools.
Read Counting, Normalization and Analysis: Counted reads aligning to genes with featureCounts, followed by replication correlation assessment. Normalized read counts using median of ratios method to correct for library size variations. Calculated correlations between read counts across sorting bins to rank candidate RNA switches.
Assembly: The analysis does not involve a standard genome build but utilizes a custom reference composed of synthesized oligonucleotide sequences tailored to the experimental design.
Supplementary files format and content: Tab-separated files with raw read counts for each oligonucleotide.
Library strategy: MPRA

source_name: Replicate 2, Bin 3, Mutagenesis screen

growth_protocol: The HEK293 cells (ATCC CRL-3216) were cultured in DMEM high-glucose medium supplemented with 10% FBS, L-glutamine (4 mM), sodium pyruvate (1 mM), penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco).

extract_protocol:
Following FACS sorting of cells based on eGFP/mCherry expression, genomic DNA was extracted from pelleted cells using the NucleoSpin Blood kit from Macherey Nagel, chosen based on cell quantity.
Libraries were constructed using Illumina-compatible primers designed for Addgene #213963 plasmid, incorporating staggered regions to ensure cluster diversity. PCR amplification was performed using NEBNext Ultra II Q5 Master Mix, followed by product purification with the Select-a-Size DNA Clean & Concentrator MagBead Kit (Zymo Research). Quality was verified using Agilent TapeStation or BioAnalyzer.
The libraries were sequenced to achieve a depth of >20 million reads per sample, with each sample uniquely barcoded using a combination of i5 and i7 indexes. This setup ensures sufficient coverage and identification of each library component in the pooled sample.

treatment_protocol: Cells were infected with lentivirus containing a plasmid library. Post-infection, cells underwent puromycin selection until recovery with >90% viability. The infection rate was kept below 30% as estimated by the fraction of mCherry-positive cells.


title: Mutagenesis_screen_bin5_r2_RNA

source_name: Replicate 2, Bin 5, Mutagenesis screen


title: Mutagenesis_screen_bin4_r2_RNA

source_name: Replicate 2, Bin 4, Mutagenesis screen


title: Mutagenesis_screen_bin6_r2_RNA

source_name: Replicate 2, Bin 6, Mutagenesis screen


title: Mutagenesis_screen_bin7_r2_RNA

source_name: Replicate 2, Bin 7, Mutagenesis screen


title: Mutagenesis_screen_bin8_r2_RNA

source_name: Replicate 2, Bin 8, Mutagenesis screen


title: Mutagenesis_screen_bin1_r2_RNA

source_name: Replicate 2, Bin 1, Mutagenesis screen


title: K44


title: Mutagenesis_screen_bin2_r2_RNA

source_name: Replicate 2, Bin 2, Mutagenesis screen


title: K43


title: Mutagenesis_screen_bin8_r1_RNA

source_name: Replicate 1, Bin 8, Mutagenesis screen


title: 4T1, Day4, single cell 504


title: Mutagenesis_screen_bin7_r1_RNA

source_name: Replicate 1, Bin 7, Mutagenesis screen


title: 4T1, Day4, single cell 503


title: Mutagenesis_screen_bin6_r1_RNA

source_name: Replicate 1, Bin 6, Mutagenesis screen


title: Mutagenesis_screen_bin5_r1_RNA

source_name: Replicate 1, Bin 5, Mutagenesis screen


title: K40


title: K41


title: Mutagenesis_screen_bin4_r1_RNA

source_name: Replicate 1, Bin 4, Mutagenesis screen


title: K39


title: Mutagenesis_screen_bin3_r1_RNA

source_name: Replicate 1, Bin 3, Mutagenesis screen


title: 4T1, Day4, single cell 501


title: Mutagenesis_screen_bin1_r1_RNA

source_name: Replicate 1, Bin 1, Mutagenesis screen


title: Functional_screen_bin8_r2_RNA

source_name: Replicate 2, Bin 8, Functional screen


title: 4T1, Day4, single cell 505


title: Functional_screen_bin7_r2_RNA

source_name: Replicate 2, Bin 7, Functional screen


title: Functional_screen_bin6_r2_RNA

source_name: Replicate 2, Bin 6, Functional screen


title: K38.2

source_name: pistachio kernel (seed)


title: 4T1, Day4, single cell 500


title: Functional_screen_bin4_r2_RNA

source_name: Replicate 2, Bin 4, Functional screen


title: K37


title: 4T1, Day4, single cell 499


title: 4T1, Day4, single cell 498


title: Functional_screen_bin5_r2_RNA

source_name: Replicate 2, Bin 5, Functional screen


title: K35


title: Functional_screen_bin2_r2_RNA

source_name: Replicate 2, Bin 2, Functional screen


title: Functional_screen_bin3_r2_RNA

source_name: Replicate 2, Bin 3, Functional screen


title: K34


title: 4T1, Day4, single cell 496


title: K33


title: Functional_screen_bin8_r1_RNA

source_name: Replicate 1, Bin 8, Functional screen


title: K32


title: 4T1, Day4, single cell 497


title: Functional_screen_bin6_r1_RNA

source_name: Replicate 1, Bin 6, Functional screen


title: Functional_screen_bin7_r1_RNA

source_name: Replicate 1, Bin 7, Functional screen


title: 4T1, Day4, single cell 495


title: Mutagenesis_screen_bin2_r1_RNA

source_name: Replicate 1, Bin 2, Mutagenesis screen


title: Functional_screen_bin5_r1_RNA

source_name: Replicate 1, Bin 5, Functional screen


title: 4T1, Day4, single cell 502


title: Functional_screen_bin2_r1_RNA

source_name: Replicate 1, Bin 2, Functional screen


title: Functional_screen_bin3_r1_RNA

source_name: Replicate 1, Bin 3, Functional screen


title: Functional_screen_bin4_r1_RNA

source_name: Replicate 1, Bin 4, Functional screen


title: 4T1, Day4, single cell 494


title: K30


title: 4T1, Day4, single cell 493


title: K28


title: Functional_screen_bin1_r2_RNA

source_name: Replicate 2, Bin 1, Functional screen


title: Mutagenesis_screen_bin7_r2_DNA

source_name: Replicate 2, Bin 7, Mutagenesis screen


title: Functional_screen_bin1_r1_RNA

source_name: Replicate 1, Bin 1, Functional screen


title: K29


title: 4T1, Day4, single cell 492


title: K27


title: Mutagenesis_screen_bin5_r2_DNA

source_name: Replicate 2, Bin 5, Mutagenesis screen


title: Mutagenesis_screen_bin6_r2_DNA

source_name: Replicate 2, Bin 6, Mutagenesis screen


title: Mutagenesis_screen_bin8_r2_DNA

source_name: Replicate 2, Bin 8, Mutagenesis screen


title: 4T1, Day4, single cell 490


title: Mutagenesis_screen_bin3_r2_DNA

source_name: Replicate 2, Bin 3, Mutagenesis screen


title: 4T1, Day4, single cell 491


title: Mutagenesis_screen_bin4_r2_DNA

source_name: Replicate 2, Bin 4, Mutagenesis screen


title: K26

source_name: pistachio kernel (seed)


title: K24


title: 4T1, Day4, single cell 488


title: 4T1, Day4, single cell 489


title: Mutagenesis_screen_bin8_r1_DNA

source_name: Replicate 1, Bin 8, Mutagenesis screen


title: Mutagenesis_screen_bin1_r2_DNA

source_name: Replicate 2, Bin 1, Mutagenesis screen


title: Mutagenesis_screen_bin7_r1_DNA

source_name: Replicate 1, Bin 7, Mutagenesis screen


title: K23


title: Mutagenesis_screen_bin6_r1_DNA

source_name: Replicate 1, Bin 6, Mutagenesis screen


title: 4T1, Day4, single cell 487


title: Mutagenesis_screen_bin5_r1_DNA

source_name: Replicate 1, Bin 5, Mutagenesis screen


title: K22


title: Mutagenesis_screen_bin2_r2_DNA

source_name: Replicate 2, Bin 2, Mutagenesis screen


title: Mutagenesis_screen_bin4_r1_DNA

source_name: Replicate 1, Bin 4, Mutagenesis screen


title: 4T1, Day4, single cell 486


title: Mutagenesis_screen_bin2_r1_DNA

source_name: Replicate 1, Bin 2, Mutagenesis screen


title: Mutagenesis_screen_bin3_r1_DNA

source_name: Replicate 1, Bin 3, Mutagenesis screen


title: 4T1, Day4, single cell 485


title: K18


title: Functional_screen_bin8_r2_DNA

source_name: Replicate 2, Bin 8, Functional screen


title: Functional_screen_bin7_r2_DNA

source_name: Replicate 2, Bin 7, Functional screen


title: K21


title: 4T1, Day4, single cell 484


title: K17


title: Functional_screen_bin5_r2_DNA

source_name: Replicate 2, Bin 5, Functional screen


title: EC_UP_13428_0_GC

description: Human Enterohinal Cortex

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs. The full length transcript probe-set based data are provided along with the custom CDF. A 2SD filter was utilised to distinguish protein coding gene expression above background
GC_Miami_CD_Brain_CDF_cv_0.3_i_8_Grch38_gencode43_transcript,binary.cdf
CDF probes were aligned to genome reference Grch38 and transcriptome reference gencode43
Log 2 values generated using IRON from GC corrected CEL files. No filter has been applied for detected above background. Critically, a filter of 2SD should be applied to remove non expressed protein coding genes, if this data is to be used for any global analysis

source_name: Human Enterohinal Cortex

treatment_protocol: Confirmation of lack of histopathology evidence for dementia at the source NIH funded brain banks (Harvard, Los Angeles, University of Miami, Mount Sinai, University of Pittsburgh and Minnesota University)

tag: treatment group and time

value: Free of Dementia Histopathology

value: M

tag: biobank

value: UP


title: K16


title: Functional_screen_bin4_r2_DNA

source_name: Replicate 2, Bin 4, Functional screen


title: 4T1, Day4, single cell 483


title: EC_UP_13407_0_GC

description: Human Enterohinal Cortex

value: F


title: 4T1, Day4, single cell 481


title: K15


title: EC_UP_13405_0_GC

description: Human Enterohinal Cortex


title: EC_UP_13400_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 479


title: 4T1, Day4, single cell 480


title: K13


title: Mutagenesis_screen_bin1_r1_DNA

source_name: Replicate 1, Bin 1, Mutagenesis screen


title: Functional_screen_bin2_r2_DNA

source_name: Replicate 2, Bin 2, Functional screen


title: EC_UP_13353_0_GC

description: Human Enterohinal Cortex


title: Functional_screen_bin3_r2_DNA

source_name: Replicate 2, Bin 3, Functional screen


title: Functional_screen_bin1_r2_DNA

source_name: Replicate 2, Bin 1, Functional screen


title: K19

source_name: pistachio kernel (seed)


title: K10


title: 4T1, Day4, single cell 482


title: K9


title: 4T1, Day4, single cell 477


title: 4T1, Day4, single cell 478


title: 4T1, Day4, single cell 476


title: K8


title: Functional_screen_bin6_r2_DNA

source_name: Replicate 2, Bin 6, Functional screen


title: EC_UP_13312_0_GC

description: Human Enterohinal Cortex


title: EC_UP_13344_0_GC

description: Human Enterohinal Cortex


title: K11


title: 4T1, Day4, single cell 475


title: Functional_screen_bin6_r1_DNA

source_name: Replicate 1, Bin 6, Functional screen


title: Functional_screen_bin7_r1_DNA

source_name: Replicate 1, Bin 7, Functional screen


title: EC_UP_13333_0_GC

description: Human Enterohinal Cortex


title: K7


title: Functional_screen_bin5_r1_DNA

source_name: Replicate 1, Bin 5, Functional screen


title: Functional_screen_bin8_r1_DNA

source_name: Replicate 1, Bin 8, Functional screen


title: EC_UP_13301_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 474


title: K6


title: 4T1, Day4, single cell 473


title: Functional_screen_bin3_r1_DNA

source_name: Replicate 1, Bin 3, Functional screen


title: EC_UP_13293_0_GC

description: Human Enterohinal Cortex


title: K2


title: EC_UP_13323_0_GC

description: Human Enterohinal Cortex


title: EC_UP_13291_0_GC

description: Human Enterohinal Cortex


title: Functional_screen_bin2_r1_DNA

source_name: Replicate 1, Bin 2, Functional screen


title: 4T1, Day4, single cell 471


title: K1


title: 4T1, Day4, single cell 470


title: EC_UP_13260_0_GC

description: Human Enterohinal Cortex