title: ERCC3WT/WT irofulven_biological replicate 6

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 6
Proj_08988_htseq_all_samples.csv

tag: cell type

tag: genotype

tag: treatment


title: TAMIGA_05200036C0007R

status: Public on Jun 01 2020

type: RNA

city: South San Francisco

first: Radia

last: Johnson

state: CA

address: 1 DNA Way

country: United Kingdom

institute: Genentech

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing:
Background correction was implemented using blank samples along with the global negative control probes. Sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) and UHR control samples (used for cross-normalisation) using the NanoStringQCPro package on Bioconductor.

label: Nucleotide/fluorophore barcode

molecule: total RNA

organism: Homo sapiens

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

tag: age

tag: Sex

value: Female

tag: corticosteroids

value: Off

tag: surgical status

value: Partial resection

value: Placebo

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: TAMIGA


title: Glarius_GLARIUS_8_07

scan_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

data_processing:
Raw data were preprocessed using functions from NanoStringQCPro R package in particular positive control normalisation, background correction (using both water samples and negative control probes) and RNA content normalisation (median normalisation). Prior to clustering analysis, sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) using the NanoStringQCPro package on Bioconductor.

value: Male

value: BEVACIZUMAB+IRINOTECAN

value: Proliferative

value: Classical

value: Non-methylated


title: Sample 33_Single Dermal Fibroblast

type: SRA

city: Stanford

first: Alina

last: Isakova

address: 318 Campus drive

department: Bioengineering

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
Sequences from the NovaSeq were de-multiplexed using bcl2fastq version 2.19.0.316. Reads were trimmed from polyA tails using cutadapt v 1.18 with the following parameters: -m 18 -j 4 -a AAAAAAAAAA -a TTTTTTTTTT. Reads were then aligned to the human (GRCh38) or mouse genome (GRCm38) using STAR v2.7.0d 37 with the following parameters --outFilterMismatchNoverLmax 0.05 --outFilterMatchNmin 18 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0  --outMultimapperOrder Random. Reads mapping to multiple locations were assigned either to a location with the best mapping score or, in the case of equal multimapping score – to the genomic location randomly chosen as “primary”.
Genome_build: GRCm38, GRCh38
Supplementary_files_format_and_content: tab-delimited text files of count tables

source_name: Single Dermal Fibroblast

growth_protocol: HEK293T cells were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 5% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063). They were collected 2h after passaging and sorted in either 96-well plates with 3uL lysis buffer or 384-well paltes with 0.3 uL of lysis buffer in each well.    Human primary dermal fibroblasts were obtained from ATCC (ATCC® PCS-201-012™). Cells were cultured and passaged four times in Fibroblast Basal Medium (ATCC® PCS-201-030™) supplemented with 5ng/mL rh FGF β, 7.5mM L-glutamine, 50 ug/mL Ascorbic acid, 5ug/mL rh Insulin, and 1% Fetal Bovine Serum (Fibroblast Growth kit- low serum, ATCC® PCS-201-041™).  MCF7 cells (ATCC® HTB¬22™) were cultured in complete DMEM high glucose medium (Gibco, ThermoFisher 11965092) supplemented with 10% Fetal Bovine Serum (ThermoFisher 16000044), 1mM Sodium Pyruvate (ThermoFisher 11360070) and 100 μg/mL Pencillin/Streptomycin (ThermoFisher 15070063).  mESCs were maintained and differentiated as described previously35,36. Briefly, mESCs were grown in serum-free 2i+LIF medium (complete medium: DMEM/F12 glutaMAX (Gibco, ThermoFisher  10565018) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V (ThermoFisher, 15260037), 1% MEM-non-essential amino acids (c  11140050), and 110 μM 2-mercaptoethanol (Pierce); supplemeted with MEK inhibitor PD0325901 (0.8 μM), GSK3β inhibitor CHIR99021 (3.3 μM) and 10ng/mL mouse LIF (Gibco, PMC9484) in tissue culture (TC) dishes pretreated with 7.5 μg/ml polyL-ornithine (Sigma) and 5 μg/ml laminine (BD). To induce spontaneous embryoid body formation cells were washed with PBS, dissociated with StemPro Accutase (Gibco, ThermoFisher cat# A1110501), transferred to serum-rich medium (complete medium: DMEM/F12 glutaMAX (Gibco) , 1% N2 supplement (Gemini Bio), 2% B27 supplement (Gemini Bio), 0.05% BSA fraction V, 1% MEM-non-essential amino acids, and 110 μM 2-mercaptoethanol; supplemented with 10% FBS (ThermoFisher 10439001) and diluted to 10^6 cells/mL. Each 10 uL of cell suspension were plated as a hanging drop in 10 cm2 TC dishes (15-20 drops per dish). 10uL of fresh serum-rich media was added to each drop on day 4 of the culture. Primed mESCs were collected 6h after hanging drop culture. Embryoid bodies were collected and dissociated at days 4, 8 and 12 of culture.

extract_protocol:
Lysis plates were prepared by dispensing 0.3μL lysis buffer (4 U Recombinant RNase Inhibitor (RRI) (Takara Bio, 2313B), 0.12% TritonTM X-100 (Sigma, 93443-100ML), 1μM Smart-seq4 oligo-dT primer (5’-Biotin- /5BiosG/CATAGTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGT30VN-3’;IDT) (see Supplementary Table 3 for a full list of oligos used in the present study) into 384-well hard-shell PCR plates (Bio-Rad HSP3901) using Mantis liquid handler (Formulatrix). 96-well lysis plates were prepared with 3 μl lysis buffer. All plates were sealed with AlumaSeal CS Films (Sigma-Aldrich Z722634), spun down and snap-frozen on dry ice.   Cells were stained with calcein-AM and ethidium homodimer-1 (LIVE/DEAD® Viability/Cytotoxicity Kit, ThermoFisher L3224) and individual live cells were sorted in 384 well lysis plates using SONY sorter (SH800S) with 100um nozzle chip. Plates were spun down and stored at -80 degrees immediately after sorting.
Smart-seq-total

tag: cell line

value: primary cell

tag: day of differentiation


title: Sample 38_Single Dermal Fibroblast


title: ERCC3WT/WT irofulven_biological replicate 5

city: New York

first: Sabine

last: Topka

state: NY

address: 417 E. 68Th St.Zuckerman Research Bldg.

department: Medicine

institute: MSKCC

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 5
Proj_08988_htseq_all_samples.csv

data_processing:
On average, 86 million paired reads were generated per sample and 36% of the data mapped to the transcriptome.
The output data (FASTQ files) were mapped to the human genome, converted to BAM format and expression count matrix generated from the mapped reads using HTSeq (https://htseq.readthedocs.io/en/release_0.11.1/).
Read counts were normalized for individual transcript lengths, log transformed, and differential gene expression analysis was performed using the R package DeSeq2
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing gene counts and differnetial gene expression results

source_name: HMLE

growth_protocol: Isogenic cell line xenografts were generated by injecting 10 million hRAS-V12 driven ERCC3 wildtype or heterozygous R109X mutant HMLE cells together with matrigel (50:50) subcutaneously in 6-week-old athymic female mice.

extract_protocol:
Fresh frozen tumor tissues were subsequently preserved in RNAlater (Invitrogen) and RNA was extracted using the RNeasy Midi Kit (Qiagen). After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.99-1ug of total RNA with an RNA integrity number varying from 3.8-10 underwent ribosomal depletion.
Library preparation was performed using the TruSeq Stranded Total RNA LT Kit (Illumina catalog # RS-122-1202) according to instructions provided by the manufacturer with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 100bp/100bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina).

treatment_protocol: Once tumors reached an average volume of 100 mm3, mice (8-10 mice/group) were randomized to receive either vehicle or irofulven 3.5 mg/kg i.p. for 5 consecutive days. The treatment cycle was repeated every 21 days for a total of three cycles.

tag: cell type

value: mammary epithelial cells

tag: genotype

value: ERCC3 WT/WT

tag: treatment

value: Irofulven 3.5 mg/kg i.p


title: Sample 32_Single Dermal Fibroblast


title: TAMIGA_05200033B0016R

label_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples.

tag: age

tag: Sex

tag: corticosteroids

value: Total resection


title: Glarius_GLARIUS_8_05

hyb_protocol: Per NanoString Total RNA Standard Protocol for formalin-fixed, paraffin-embedded (FFPE) samples

tag: surgical status

tag: phillips subtype

tag: tcga subtype


title: Sample 37_Single Dermal Fibroblast


title: TAMIGA_05200041C0007R

value: Bevacizumab

tag: kps

tag: mmse

tag: rpa

value: Grade III


title: Glarius_GLARIUS_8_04

value: Female

value: Partial resection

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: TAMIGA_05200032B0016R

value: Off

value: Proneural

value: Grade NA

tag: who category

tag: dataset


title: ERCC3WT/WT irofulven_biological replicate 4

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 4
Proj_08988_htseq_all_samples.csv

tag: cell type


title: Sample 31_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: ERCC3WT/WT irofulven_biological replicate 2

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 2
Proj_08988_htseq_all_samples.csv

tag: genotype

tag: treatment


title: ERCC3WT/WT irofulven_biological replicate 3

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 3
Proj_08988_htseq_all_samples.csv


title: Glarius_GLARIUS_8_03

tag: age

tag: Sex

value: Male


title: ERCC3WT/WT irofulven_biological replicate 1

description:
HMLE cell line-derived ERCC3WT/WT tumor from irofulven treated mouse, biological replicate 1
Proj_08988_htseq_all_samples.csv


title: Glarius_GLARIUS_8_06

tag: surgical status

value: TEMOZOLOMIDE

tag: phillips subtype

value: Mesenchymal


title: Sample 29_Single Dermal Fibroblast


title: TAMIGA_05200031B0016R

tag: corticosteroids

value: Unclassified

tag: tcga subtype

value: Classical

tag: kps

value: Grade IV

value: TAMIGA


title: ERCC3WT/WT vehicle_biological replicate 8

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 8
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells

value: ERCC3 WT/WT

value: vehicle:1% EtOH in D5W


title: Sample 30_Single Dermal Fibroblast

value: primary cell


title: Glarius_GLARIUS_7_11

value: Total resection

value: Proliferative

tag: os (diagnosis)

value: Non-methylated


title: TAMIGA_05200030B0016R

value: Female

value: Off

tag: mmse

tag: rpa

tag: os cnsr (event = 1, censor = 0)


title: Glarius_GLARIUS_8_01

tag: mgmt status


title: TAMIGA_05200029B0016R

value: On

value: Placebo

value: Proneural

tag: who category

tag: dataset


title: ERCC3WT/WT vehicle_biological replicate 7

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 7
Proj_08988_htseq_all_samples.csv

tag: cell type


title: Sample 27_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: Glarius_GLARIUS_8_02

tag: age

value: Partial resection

tag: treatment

value: BEVACIZUMAB+IRINOTECAN

value: Mesenchymal


title: Sample 26_Single Dermal Fibroblast


title: TAMIGA_05200028B0016R

tag: Sex

value: Male

tag: surgical status

value: Classical

value: Grade IV


title: TAMIGA_05200027C0017R

tag: corticosteroids

tag: phillips subtype

value: TAMIGA


title: Glarius_GLARIUS_7_10

tag: tcga subtype


title: Sample 28_Single Dermal Fibroblast


title: ERCC3WT/WT vehicle_biological replicate 6

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 6
Proj_08988_htseq_all_samples.csv

value: mammary epithelial cells

tag: genotype

value: ERCC3 WT/WT

value: vehicle:1% EtOH in D5W


title: Glarius_GLARIUS_7_09

tag: os (diagnosis)


title: TAMIGA_05200023B0016R

value: Total resection

tag: kps

tag: mmse

tag: rpa

value: Grade III


title: ERCC3WT/WT vehicle_biological replicate 5

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 5
Proj_08988_htseq_all_samples.csv


title: Sample 25_Single Dermal Fibroblast

value: primary cell


title: Sample 24_Single Dermal Fibroblast


title: TAMIGA_05200022B0016R

value: Off

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category


title: TAMIGA_05200021C0017R

value: Proliferative

tag: dataset


title: Glarius_GLARIUS_7_08

value: TEMOZOLOMIDE

value: Non-methylated


title: ERCC3WT/WT vehicle_biological replicate 4

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 4
Proj_08988_htseq_all_samples.csv

tag: cell type


title: Sample 23_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: ERCC3WT/WT vehicle_biological replicate 3

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 3
Proj_08988_htseq_all_samples.csv

tag: treatment


title: ERCC3WT/WT vehicle_biological replicate 2

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 2
Proj_08988_htseq_all_samples.csv


title: Glarius_GLARIUS_7_06

tag: age

tag: Sex

tag: surgical status

value: Partial resection

value: Unclassified


title: Sample 22_Single Dermal Fibroblast


title: Sample 21_Single Dermal Fibroblast


title: Glarius_GLARIUS_7_02

tag: phillips subtype

tag: tcga subtype

value: Mesenchymal


title: Sample 20_Single Dermal Fibroblast


title: T1D subject ID:b857

city: Paris

first: Felipe

middle: Leal

last: Valentim

state: Île-de-France

address: Bâtiment Cervi, 4ème étage, pièce 052

country: France

institute: INSERM/UPMC

description: Whole blood RNA-seq, sample from T1D subject

data_processing:
Nextera adaptor removal:Trimmomatic (Bolger et al., 2014)
Reads alignment:  hisat2 (Kim et al., 2015)
Read counts: featureCounts (Liao et al., 2014)
Read counts normalization: DESeq2 (Anders and Huber, 2010)
SAM to BAM conversion: samtools (Li et al., 2009)
Genome_build: The GRCh37 assembly in Ensembl (Yates et al., 2016)
Supplementary_files_format_and_content: reads_count.gene_level.txt: Raw read counts as outputed by featureCounts for all samples.

source_name: Whole blood

extract_protocol:
Total RNA from whole blood has been extracted following a two-step procedure. First, RNA from blood collected on PAX-Gene tubes has been extracted using Maxwell 16 LEV simplyRNA blood kit (Promega) following manufacturer recommendations and second b-globin, dominant RNA from red blood cells, has been removed using the GLOBINclear kit (Ambion) on extracted RNA.
RNA sequencing has been performed from using the TruSeq Stranded mRNA preparation kit (Illumina) on 500 ng b-globin depleted RNA with a RNA Integrity Number > 8 (measured on Bioanalyzer following manufacturer recommendations). Libraries were sequenced following a pair-end 2x75 bp protocol on NextSeq 500 or HiSeq 4000 (Illumina) at LIGAN Equipex (Lille, France).

tag: patient diagnosis

value: type 1 diabetes

tag: tissue

value: Whole blood

value: M

tag: batch


title: TAMIGA_05200018C0007R

value: Female

tag: corticosteroids

value: On

value: Classical

tag: kps

tag: mmse

tag: rpa

value: Grade IV

tag: os (diagnosis)

value: TAMIGA


title: Glarius_GLARIUS_7_04

value: Total resection

value: BEVACIZUMAB+IRINOTECAN

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: ERCC3WT/WT vehicle_biological replicate 1

description:
HMLE cell line-derived ERCC3WT/WT tumor from vehicle treated mouse, biological replicate 1
Proj_08988_htseq_all_samples.csv

tag: cell type

value: mammary epithelial cells

tag: genotype

value: ERCC3 WT/WT

value: vehicle:1% EtOH in D5W


title: Glarius_GLARIUS_6_12

tag: age

value: Male

tag: treatment

value: Proneural

value: Non-methylated


title: TAMIGA_05200006C0007R

tag: Sex

value: Off

tag: surgical status

value: Partial resection

value: Bevacizumab

tag: who category

tag: dataset


title: Sample 19_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: T1D subject ID:cf1e

tag: patient diagnosis

value: type 1 diabetes

tag: tissue

value: Whole blood

value: F

tag: batch


title: TAMIGA_05200012B0015R

value: Female

tag: corticosteroids

value: Placebo

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

value: Grade IV


title: TAMIGA_05200015C0007R

tag: age

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: TAMIGA


title: Glarius_GLARIUS_6_11

tag: Sex

tag: surgical status

value: Total resection

tag: treatment

value: BEVACIZUMAB+IRINOTECAN


title: Glarius_GLARIUS_6_10

value: Male

value: TEMOZOLOMIDE

value: Classical


title: Sample 18_Single Dermal Fibroblast

tag: cell line

tag: day of differentiation


title: TAMIGA_005200323C007R

value: On

value: Proneural

tag: who category

tag: dataset


title: T1D subject ID:5cd9

tag: patient diagnosis

tag: tissue

value: M

tag: batch


title: Sample 17_Single Dermal Fibroblast

value: primary cell


title: Sample 16_Single Dermal Fibroblast


title: T1D subject ID:3f22

value: type 1 diabetes


title: TAMIGA_05200003C0007R

tag: corticosteroids

value: Off

value: Partial resection

tag: phillips subtype

value: Proliferative

tag: tcga subtype

tag: kps


title: T1D subject ID:1d36

value: Whole blood

tag: age


title: Sample 15_Single Dermal Fibroblast


title: Glarius_GLARIUS_7_01

value: Mesenchymal

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: Glarius_GLARIUS_6_08

tag: Sex

value: Unclassified

tag: mgmt status


title: ARTE_FFPET_Control_56

value: Female

tag: surgical status

tag: treatment

value: RT+BEV

tag: mmse

tag: rpa

value: ARTE


title: ARTE_FFPET_Control_55

value: Male

value: Biopsy

tag: who category

tag: dataset


title: Glarius_GLARIUS_6_07

value: Total resection

value: BEVACIZUMAB+IRINOTECAN

value: Classical


title: T1D subject ID:082a

tag: patient diagnosis

tag: tissue

value: M


title: Sample 12_Single Dermal Fibroblast

tag: cell line

value: primary cell

tag: day of differentiation


title: healthy subject ID:fbfa

description: Whole blood RNA-seq, sample from healthy subject

value: healthy

tag: batch


title: ARTE_FFPET_Control_53

tag: corticosteroids

value: Off

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps


title: healthy subject ID:fbbe

value: Whole blood

tag: Sex

tag: age


title: ARTE_FFPET_Control_52

value: On

tag: surgical status

value: Partial resection

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: ARTE_FFPET_Control_54

tag: treatment

value: RT

tag: mmse

tag: rpa

value: Non-methylated

tag: who category


title: Glarius_GLARIUS_6_06


title: Sample 13_Single Dermal Fibroblast

tag: cell line


title: Glarius_GLARIUS_6_05

value: Proliferative


title: ARTE_FFPET_Control_50

value: RT+BEV

value: Methylated

tag: dataset

value: ARTE


title: Glarius_GLARIUS_6_09

value: Male


title: healthy subject ID:fb03

tag: patient diagnosis

tag: tissue

value: F

tag: batch


title: Glarius_GLARIUS_6_04

value: Total resection

value: BEVACIZUMAB+IRINOTECAN

tag: phillips subtype

tag: tcga subtype

value: Mesenchymal


title: Sample 10_Single Dermal Fibroblast

value: primary cell

tag: day of differentiation


title: healthy subject ID:eba3

value: healthy

tag: Sex

tag: age


title: Sample 14_Single Dermal Fibroblast


title: ARTE_FFPET_Control_49

tag: corticosteroids

tag: surgical status

value: Proneural

tag: kps

tag: os (diagnosis)


title: healthy subject ID:e6b4

value: Whole blood


title: healthy subject ID:e42f


title: ARTE_FFPET_Control_48

value: Female

value: Off

value: Biopsy

tag: treatment

value: Unclassified

value: Classical

tag: mmse

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: Sample 8_Single Dermal Fibroblast

tag: cell line


title: Glarius_GLARIUS_5_10

value: TEMOZOLOMIDE

value: Non-methylated


title: healthy subject ID:e2c4

tag: patient diagnosis

value: M


title: Glarius_GLARIUS_5_09

value: Male

value: Partial resection


title: Sample 11_Single Dermal Fibroblast


title: Sample 6_Single Dermal Fibroblast


title: Sample 9_Single Dermal Fibroblast


title: healthy subject ID:d23c

tag: tissue

value: F


title: Glarius_GLARIUS_5_12

value: Total resection

value: BEVACIZUMAB+IRINOTECAN


title: healthy subject ID:cc82

tag: batch


title: Glarius_GLARIUS_5_08

tag: phillips subtype


title: Sample 7_Single Dermal Fibroblast

value: primary cell


title: Sample 5_Single Dermal Fibroblast


title: Glarius_GLARIUS_6_03

tag: tcga subtype


title: healthy subject ID:c44c

value: healthy


title: ARTE_FFPET_Control_45

value: On

value: RT+BEV

value: Proliferative

tag: rpa

tag: who category

tag: dataset

value: ARTE


title: Sample 4_Single Dermal Fibroblast

tag: day of differentiation


title: ARTE_FFPET_Control_46

tag: age

tag: Sex

tag: corticosteroids

value: Off

tag: surgical status

value: Mesenchymal

value: Proneural


title: ARTE_FFPET_Control_44

value: Female

tag: treatment

tag: kps

tag: mmse

tag: os (diagnosis)


title: ARTE_FFPET_Control_42

value: Biopsy

value: Classical

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: Glarius_GLARIUS_5_06


title: ARTE_FFPET_Control_43

value: Male

value: Partial resection

value: RT


title: ARTE_FFPET_Control_47

value: Total resection


title: healthy subject ID:b462

tag: patient diagnosis

tag: tissue

value: Whole blood

value: M

tag: batch


title: Sample 3_Single Dermal Fibroblast

tag: cell line

value: primary cell


title: Glarius_GLARIUS_5_05

value: BEVACIZUMAB+IRINOTECAN

tag: phillips subtype

tag: tcga subtype


title: Sample 2_Single Dermal Fibroblast

tag: day of differentiation


title: ARTE_FFPET_Control_41

tag: age

tag: rpa

tag: who category

tag: dataset


title: Sample 1_Single Dermal Fibroblast


title: healthy subject ID:74ca

value: healthy

tag: Sex


title: healthy subject ID:ac48


title: 22PcEP_CSS_DHT1_3

city: New York City

first: Zeda

last: Zhang

address: 1275 York Aveune

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were aligned to the standard human genome (hg38) using Hisat
Aligned reads were counted at each gene locus using the annotation
Differential gene expression analysis was performed using DESeq2 v1.26.0
Genome_build: hg38
Supplementary_files_format_and_content: csv file containing differential gene expression analysis results and gene counts

source_name: Prostate cancer cell line

growth_protocol: 0.5 million per well of CWR22Pc-EP was seeded in collagen I coated  6-well plate a day before treatment. Culture condition: RPMI-1640, FBS(10%), PenStrep (1%), L-glutamine (1%), Sodium Pyruvate (1%), HEPES pH=7.6 (1%).

extract_protocol:
RNA extraction was performed according to manufacture's instuction in PureLinkTM RNA Mini Kit (Thermo Fisher Scientific #12183025)
RNA-Seq libraries were prepared using the Illumina TruSeq stranded mRNA kit, with 10 cycles of PCR amplification, starting from 500 ng of total RNA, at the Genome Technology Center (GTC) at NYU.

treatment_protocol: 24 hr post seeding, enzalutamide (500nM), NRG1 recombinant protein (10ng/ml), or 10%CSS (charcoal stripped FBS) media was added into different conditions, treatment was performed in three biological replicates

tag: pten status

value: wild type

tag: tumor stage

value: primary tumor

tag: androgen sensitivity

value: sensitive

tag: treatment

value: CSS + DHT(1nM)


title: ARTE_FFPET_Control_38

tag: corticosteroids

value: On

tag: surgical status

value: Proneural

tag: kps

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: ARTE


title: Glarius_GLARIUS_5_03

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

value: Non-methylated


title: ARTE_FFPET_Control_39

tag: age

value: Male

value: RT+BEV

tag: rpa

value: Methylated


title: Glarius_GLARIUS_5_02

value: Partial resection

value: TEMOZOLOMIDE

value: Unclassified


title: 22PcEP_CSS_DHT1_2

tag: cell line


title: healthy subject ID:737b

tag: patient diagnosis

tag: tissue

value: Whole blood

tag: Sex

value: F

tag: batch


title: ARTE_FFPET_Control_37

tag: treatment

value: Proliferative

value: Classical

tag: who category

tag: dataset


title: Glarius_GLARIUS_5_01

tag: surgical status

value: Total resection

value: BEVACIZUMAB+IRINOTECAN


title: Glarius_GLARIUS_4_12


title: 22PcEP_CSS_DHT1_1

tag: pten status

value: wild type

tag: tumor stage

value: primary tumor

tag: androgen sensitivity

value: sensitive

value: CSS + DHT(1nM)


title: ARTE_FFPET_Control_36

tag: corticosteroids

value: On

value: Mesenchymal

tag: kps

tag: mmse

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated

value: ARTE


title: 22PcEP_CSS_NRG1_3

tag: cell line

value: CSS + NRG1(10ng/ml)


title: healthy subject ID:5dbf

tag: patient diagnosis

value: healthy

tag: tissue

value: M

tag: age


title: healthy subject ID:45d4

value: Whole blood

tag: Sex

tag: batch


title: ARTE_FFPET_Control_35

value: Male

value: Off

value: Partial resection

tag: treatment

value: RT+BEV

tag: phillips subtype

tag: tcga subtype

tag: rpa

tag: who category

tag: dataset


title: ARTE_FFPET_Control_34

tag: corticosteroids

tag: surgical status

value: RT

value: Proneural

tag: kps

value: Methylated


title: Glarius_GLARIUS_4_09

value: TEMOZOLOMIDE

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Glarius_GLARIUS_4_10

value: BEVACIZUMAB+IRINOTECAN

tag: mgmt status


title: healthy subject ID:3a5c

tag: patient diagnosis

value: F


title: Glarius_GLARIUS_5_04

value: Classical


title: ARTE_FFPET_Control_33

value: Female

value: On

tag: mmse

value: Non-methylated


title: Glarius_GLARIUS_4_08

tag: age

value: Total resection


title: 22PcEP_CSS_NRG1_1

tag: cell line

tag: pten status

value: wild type

tag: tumor stage

value: primary tumor

tag: androgen sensitivity

value: sensitive

value: CSS + NRG1(10ng/ml)


title: healthy subject ID:74b4

value: healthy

tag: tissue

value: Whole blood

tag: Sex

tag: batch


title: 22PcEP_CSS_DMSO_3

tag: treatment

value: CSS + DMSO


title: 22PcEP_CSS_DMSO_2


title: ARTE_FFPET_Control_32

value: Male

tag: corticosteroids

value: Partial resection

value: RT+BEV

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: rpa

tag: who category

tag: dataset

value: ARTE


title: Glarius_GLARIUS_5_07

tag: surgical status

value: TEMOZOLOMIDE

value: Proliferative

value: Classical

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: healthy subject ID:20fe

tag: patient diagnosis

value: M

tag: age


title: 22PcEP_CSS_DMSO_1

tag: cell line

tag: pten status

tag: tumor stage

tag: androgen sensitivity


title: Glarius_GLARIUS_4_06

tag: Sex

value: Total resection

tag: treatment

value: BEVACIZUMAB+IRINOTECAN

value: Unclassified

value: Non-methylated


title: Glarius_GLARIUS_4_05

value: Female

tag: phillips subtype


title: 22PcEP_CSS_NRG1_2

value: wild type

value: primary tumor

value: sensitive

value: CSS + NRG1(10ng/ml)


title: healthy subject ID:107f

value: healthy

tag: tissue

value: Whole blood

tag: batch


title: 22PcEP_FBS_Enz+NRG_3

value: NRG1:10ng/ml, Enz:500nM


title: Glarius_GLARIUS_4_04

value: Male

value: Partial resection

value: Proneural

tag: tcga subtype


title: healthy subject ID:0990

value: F


title: 22PcEP_FBS_Enz+NRG_2


title: ARTE_FFPET_Control_29

tag: corticosteroids

value: Off

value: RT+BEV

value: Mesenchymal

tag: kps

tag: mmse

tag: rpa

value: Methylated

tag: who category

tag: dataset

value: ARTE


title: ARTE_FFPET_Control_30

tag: age

value: Female

tag: surgical status

value: Biopsy

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Non-methylated


title: healthy subject ID:08d3

tag: patient diagnosis

tag: Sex

value: M


title: ARTE_FFPET_Control_28

tag: treatment

value: RT

tag: phillips subtype

value: Classical


title: ARTE_FFPET_Control_26

value: On


title: Glarius_GLARIUS_4_03

value: Total resection

value: BEVACIZUMAB+IRINOTECAN

value: Unclassified


title: Glarius_GLARIUS_4_02

value: Male

value: TEMOZOLOMIDE

value: Proneural


title: 22PcEP_FBS_Enz+NRG_1

tag: cell line

tag: pten status

value: wild type

tag: tumor stage

value: primary tumor

tag: androgen sensitivity

value: sensitive

value: NRG1:10ng/ml, Enz:500nM


title: healthy subject ID:32d0

value: healthy

tag: tissue

value: Whole blood

value: F

tag: batch


title: healthy subject ID:0865


title: Glarius_GLARIUS_4_07

tag: tcga subtype

value: Non-methylated


title: healthy subject ID:2ac7

value: M


title: ARTE_FFPET_Control_25

tag: corticosteroids

value: Off

value: Partial resection

value: RT+BEV

value: Mesenchymal

tag: kps

tag: mmse

tag: rpa

tag: who category

tag: dataset

value: ARTE


title: Glarius_GLARIUS_4_01

tag: age

value: Male

tag: surgical status

value: Total resection

value: BEVACIZUMAB+IRINOTECAN

value: Classical

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status


title: ARTE_FFPET_Control_31

tag: Sex

tag: treatment

tag: phillips subtype


title: healthy subject ID:04b3

tag: patient diagnosis

tag: tissue


title: healthy subject ID:0341

tag: batch


title: ARTE_FFPET_Control_24

tag: corticosteroids

value: Biopsy

value: Proneural

tag: tcga subtype

value: Methylated


title: ARTE_FFPET_Control_23

value: RT

tag: kps

tag: mmse


title: 22PcEP_FBS_NRG1_3

tag: cell line

tag: pten status

value: wild type

tag: tumor stage

value: primary tumor

tag: androgen sensitivity

value: sensitive


title: Glarius_GLARIUS_3_11

tag: age

tag: surgical status

value: TEMOZOLOMIDE

tag: os (diagnosis)

value: Non-methylated


title: healthy subject ID:0131

value: healthy

value: Whole blood

tag: Sex

value: M


title: 22PcEP_FBS_Enz_1

tag: treatment


title: healthy subject ID:b3ea

value: F


title: ARTE_FFPET_Control_22

value: Male

value: On

value: Partial resection

tag: phillips subtype

value: Unclassified

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

tag: dataset

value: ARTE


title: 22PcEP_FBS_Enz_2


title: Patient_1_Tumor_rep3

first: Miguel

last: Brown

state: New York

address: 1230 York Ave Box 186

institute: The Rockefeller University

data_processing:
Reads were adapter and 3'end quality trimmed using cutadapt v1.15 with parameter --quality-base=20
Resultant fastq file was aligned using STAR aligner v2.5.2a, params --runMode alignReads --twopassMode Basic --readFilesCommand zcat --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 8 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --quantTranscriptomeBan "Singleend"
PDX sample were pre-aligned to the mouse mm10 genome before aliging to human to filter out perfect hits from possible stromal cell contamination
Bam files were merged when appropriate using novosort 1.03.09 then quantified using eXpress 1.5.1, counts were then collapsed by gene and summed using effective counts and tpm from output using gencode v 24 backmapped to grch37 for annotation
Genome_build: hg19
Supplementary_files_format_and_content: tsv files with efective read counts and tpms as determined by eXpress quantification.  Counts were filtered by protein_coding and lincRNA only, then collpased and summed on gene name suing the gencode24 backmapped to grch37 reference

source_name: Tumor

extract_protocol:
A GI pathologist circled areas of high tumor cellularity on H&E sections of the tumor and PDX. RNA was extracted from the same area of an adjacent section using RNeasy FFPE kit (Qiagen, cat # 73504) after treating with Deparaffinization Solution (Qiagen, cat # 19093)
RNA library preparation and sequencing: Exome capture was carried out using the RNA access kit (Illumina, cat # RS-301-2001) for the majority of samples

tag: cell/tissue type

value: pancreatic adenocarcinoma tumor


title: 22PcEP_FBS_NRG1_1


title: Glarius_GLARIUS_3_09

value: BEVACIZUMAB+IRINOTECAN

value: Proneural

tag: tcga subtype


title: Patient_7_Tumor


title: 22PcEP_FBS_NRG1_2

tag: cell line

value: wild type


title: 22PcEP_FBS_Enz_3

tag: pten status

value: primary tumor


title: ARTE_FFPET_Control_20

value: Female

tag: corticosteroids

value: Off

value: Total resection

value: RT+BEV

value: Proliferative

value: Classical

tag: kps

tag: mmse


title: Patient_1_Tumor_rep2


title: Glarius_GLARIUS_3_08

tag: age

tag: surgical status

value: Non-methylated


title: 22PcEP_FBS_DMSO_3

tag: tumor stage

tag: androgen sensitivity

value: sensitive

value: DMSO


title: ARTE_FFPET_Control_17

tag: Sex

value: Male

value: On

value: Partial resection

tag: treatment

tag: phillips subtype

value: Mesenchymal

tag: os (diagnosis)


title: ARTE_FFPET_Control_19

value: Unclassified

tag: rpa

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

tag: who category

value: ARTE


title: ARTE_FFPET_Control_18

value: RT

value: Proneural

tag: tcga subtype

tag: dataset


title: Glarius_GLARIUS_3_06

value: TEMOZOLOMIDE


title: Glarius_GLARIUS_3_07

value: BEVACIZUMAB+IRINOTECAN


title: Patient_4_Tumor

tag: cell/tissue type

value: pancreatic adenocarcinoma tumor


title: 22PcEP_FBS_DMSO_2

tag: cell line

tag: pten status

value: wild type

value: primary tumor


title: Glarius_GLARIUS_3_12

tag: age


title: Patient_2_Tumor


title: Glarius_GLARIUS_3_10

value: Female

tag: surgical status

value: open biopsy


title: Glarius_GLARIUS_3_04

value: Classical

value: Non-methylated


title: ARTE_FFPET_Control_15

value: Male

tag: corticosteroids

value: RT+BEV

tag: kps

tag: mmse


title: Patient_3_Tumor


title: D14

city: Chicago

first: Larisa

last: Nonn

state: IL

address: 840 S. Wood St, MC847

department: Pathology

institute: University of Illinois at Chicago

description: single-cell RNA

data_processing:
CellRanger 3.2.1  demultiplexing raw base call (BCL) files into FASTQ file
CellRanger 3.2.1  demultiplexing raw base call (BCL) files into FASTQ file
Genome_build: Ensembl_GRCh38
Supplementary_files_format_and_content: CellRanger 3.2.1 Generated Gene Expression Matrix for import into R

source_name: Primary Prostate Epithelial Cells

growth_protocol: Human prostate PrE cells were grown from collagenase digested patient tissue onto a cell culture dish until ~70 confluent. Cells were collected and frozen into aliquots. A aliquot was thawed into PrEGM media (lonza) and grown to 70% confluent, cells were seeded singly in 33% matrigel grown in KSFM media supplemente with DHT and charcoal stripped FBS to form organoids. Throughout growth, media was supplemented with vehicle (<0.01% EtOH), or 10nM 1,25D (vitamin D). Organoids were collected at day 8 and day 14.

extract_protocol:
Organoids were collected from Matrigel by dispase and digested to single cells using TryPLE. Single cells were collected using 10x genomics technology.
Chromium Genome Reagent Kit (v3 Chemistry)
single cell RNA-seq

tag: cell type

value: Primary Epithelial Cells

tag: tissue

value: Prostate

tag: culture condition

value: Matrigel - day 14, 10nM 1,25D


title: 22PcEP_FBS_DMSO_1

tag: tumor stage

tag: androgen sensitivity

value: sensitive

tag: treatment

value: DMSO


title: Patient_3_PDX

source_name: patient-derived xenograft (PDX)

value: human tumor tissue grafted into an immuno-compromised mouse


title: V14

description: single-cell RNA

value: Matrigel - day 14, vehicle


title: ARTE_FFPET_Control_13

tag: Sex

value: On

value: Partial resection

tag: phillips subtype

value: Proliferative

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

tag: mgmt status

value: Methylated

tag: who category

value: ARTE


title: Glarius_GLARIUS_3_02

tag: age

tag: surgical status

value: BEVACIZUMAB+IRINOTECAN

value: Mesenchymal

tag: tcga subtype


title: Glarius_GLARIUS_3_03

value: Total resection

value: TEMOZOLOMIDE

value: Proneural

value: Classical

value: Non-methylated


title: ARTE_FFPET_Control_14

value: Male

tag: corticosteroids

value: Biopsy

value: RT

tag: kps

tag: mmse

tag: dataset


title: Patient_2_PDX

tag: cell/tissue type

value: human tumor tissue grafted into an immuno-compromised mouse


title: D8

description: single-cell RNA

tag: cell type

value: Primary Epithelial Cells

tag: tissue

value: Prostate

tag: culture condition

value: Matrigel - day 8, 10nM 1,25D


title: Patient_4_PDX


title: Glarius_GLARIUS_2_12

tag: Sex

value: Partial resection

tag: treatment

tag: phillips subtype


title: ARTE_FFPET_Control_11

value: Female

value: On

value: RT+BEV

tag: rpa

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Methylated


title: 1534-ADC-6: 7860_wt_D300-2

city: NASHVILLE

first: Aguirre

middle: A

last: de Cubas

state: TN

address: 2220 Pierce Ave

department: Hematology and Oncology

institute: Vanderbilt University Medical Center

data_processing:
Sequencing reads were aligned against the human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87) using the Spliced Transcripts Alignment to a Reference (STAR) software
Reads were preprocessed and index using SAMtools
Mapped reads were annotated and quantified using featureCounts
Normalization and differential expression was performed using DESeq2
Expression matrix produced using variance stabilized transformation function
Genome_build: human GENCODE genome (V28), Version Hg19 (January 2017 freeze, GRCh37, Ensembl 87)
Supplementary_files_format_and_content: tab-delimited text files include Raw Counts values for each Sample

source_name: 786-0 RCC cells

growth_protocol: Cells cultured

extract_protocol:
Total RNA was extracted using the miRNeasy Kit (Qiagen)
Illumina libraries prepared using poly-A enrichment.

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.

tag: cell line

value: 300nM Decitabine

tag: replicate

value: rep 2


title: V8

description: single-cell RNA

value: Matrigel - day 8, vehicle


title: ARTE_FFPET_Control_10

tag: age

value: Off

tag: surgical status

value: Total resection

value: Unclassified

tag: tcga subtype

value: Classical

tag: mgmt status

tag: who category

value: ARTE


title: Patient_1_PDX

tag: cell/tissue type

value: human tumor tissue grafted into an immuno-compromised mouse


title: Patient_1_Normal_rep2

source_name: Pancreas

value: adjacent normal pancreas


title: Glarius_GLARIUS_2_10

value: BEVACIZUMAB+IRINOTECAN

value: Mesenchymal

value: Non-methylated


title: Glarius_GLARIUS_2_11

value: Male

value: Proneural


title: ARTE_FFPET_Control_12

tag: corticosteroids

value: Partial resection

value: RT+BEV

tag: kps

tag: mmse

tag: dataset


title: Patient_4_Normal


title: ARTE_FFPET_Control_08

tag: Sex

value: Female

tag: treatment

value: RT


title: Glarius_GLARIUS_2_09

tag: phillips subtype


title: 1534-ADC-5: 7860_wt_D300-1

value: 300nM Decitabine

value: rep 1


title: ARTE_FFPET_Control_07

value: Off

tag: rpa

tag: os (diagnosis)

value: Methylated


title: 1534-ADC-4: 7860_wt_D100-2

tag: cell line

value: 100nM Decitabine

value: rep 2


title: Patient_2_Normal


title: Patient_3_Normal


title: ARTE_FFPET_Control_05

value: On

value: Total resection

value: Proliferative

value: Classical

tag: os cnsr (event = 1, censor = 0)

value: ARTE


title: Glarius_GLARIUS_2_08

tag: age

value: BEVACIZUMAB+IRINOTECAN

value: Mesenchymal

value: Non-methylated


title: 1534-ADC-2: 7860_wt_D0-2

value: DMSO

tag: replicate


title: Glarius_GLARIUS_3_01

value: Female

tag: surgical status

value: Partial resection

value: Proneural

tag: tcga subtype


title: Glarius_GLARIUS_2_07

value: Male

tag: mgmt status


title: Glarius_GLARIUS_2_05


title: 1534-ADC-3: 7860_wt_D100-1

value: rep 1


title: ARTE_FFPET_Control_06

value: Biopsy

value: RT+BEV

tag: who category


title: Patient_1_Organoid_rep3

source_name: Organoid

extract_protocol:
The RNeasy Mini kit (Qiagen, cat # 74104) was used for extracting RNA from both 2D cell lines and organoids. Approximately 3 million cells and 1 million cells were used as starting material for 2D and organoids, respectively.
A GI pathologist circled areas of high tumor cellularity on H&E sections of the tumor and PDX. RNA was extracted from the same area of an adjacent section using RNeasy FFPE kit (Qiagen, cat # 73504) after treating with Deparaffinization Solution (Qiagen, cat # 19093)
RNA library preparation and sequencing: Exome capture was carried out using the RNA access kit (Illumina, cat # RS-301-2001) for the majority of samples

tag: cell/tissue type

value: Organoid derived from PDX


title: ARTE_FFPET_Control_04

tag: corticosteroids

value: Off

value: RT

tag: kps


title: 1533-ADC-10: HKC_wt_D100-2

source_name: HKC proximal tubule cells

value: HKC

value: 100nM Decitabine

value: rep 2


title: ARTE_FFPET_Control_03

value: On

value: Total resection

tag: mmse

value: Methylated

tag: dataset

value: ARTE


title: Glarius_GLARIUS_2_04

tag: Sex

tag: treatment

value: BEVACIZUMAB+IRINOTECAN

value: Classical

value: Non-methylated


title: ARTE_FFPET_Control_02

value: Male

value: Partial resection

tag: phillips subtype

value: Mesenchymal

tag: rpa


title: 1533-ADC-9: HKC_wt_D100-1

tag: cell line

value: rep 1


title: Patient_1_Organoid_rep2

value: Organoid derived from PDX


title: 1534-ADC-1: 7860_wt_D0-1

value: DMSO


title: 1533-ADC-4: HKC_wt_D300-2

value: 300nM Decitabine


title: Glarius_GLARIUS_2_03

value: Female

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: ARTE_FFPET_Control_01

tag: age

value: Off

value: RT+BEV

value: Proneural


title: Glarius_GLARIUS_2_02

tag: surgical status

value: TEMOZOLOMIDE

value: Proliferative


title: Patient_1_Cell_line_rep2

source_name: Cell Line

value: Cell line derived from PDX


title: 1533-ADC-3: HKC_wt_D300-1

value: HKC

tag: replicate


title: QMf-25 mJ

city: Cleveland

first: Nikki

last: Harter

state: Ohio

address: 10900 Euclid Avenue

department: Biochemistry

institute: Case Western Reserve University

description:
irradiated
human miRNA Card B

data_processing:
Raw Ct values were obtained by using Applied Biosystems TaqMan SDS v2.4 software. These values were then imported into Applied Biosystems RQ manager or Expression Suite software to quantify the relative expression of miRNAs in each of the un-irradiated and irradiated samples. Both software packages use the comparative CT method (Delta Delta CT), which translates into an RQ value.
MammU6 was used as an endogenous control, and miRNAs with a Ct value >36 or failing to amplify with an efficiency coefficient less than 1.0 were omitted from the analysis by ABI's Expression suite software.

label: Fluorescence from FAM/SYBR green

source_name: primary melanocytes

growth_protocol: Cultured melanocytes were made quiescent prior to irradiation (solar UVA+UVB)

extract_protocol: By 64 hr post-irradiation, exosomes from the irradiated or un-irradiated melanocytes were subjected to RNA extraction using the Total Exosome RNA and Protein Kit (Invitrogen).

treatment_protocol: A dose of irradiation was applied to quiescent melanocytes on day 1 and then again 24 hrs later.

tag: cell type

value: melanocytes

tag: rna fraction

value: exosome

value: irradiated


title: QMe-25 mJ

description:
irradiated
human miRNA Card B


title: Patient_1_Organoid_rep4

tag: cell/tissue type


title: Patient_7_Cell_line

extract_protocol:
Illumina total RNAseq with ribo-zero depletion
A GI pathologist circled areas of high tumor cellularity on H&E sections of the tumor and PDX. RNA was extracted from the same area of an adjacent section using RNeasy FFPE kit (Qiagen, cat # 73504) after treating with Deparaffinization Solution (Qiagen, cat # 19093)
RNA library preparation and sequencing: Exome capture was carried out using the RNA access kit (Illumina, cat # RS-301-2001) for the majority of samples

value: Cell line derived from tumor


title: QMd-25 mJ

description:
irradiated
human miRNA Card B


title: Glarius_GLARIUS_13_02

value: Total resection

tag: tcga subtype

tag: mgmt status

value: Non-methylated


title: Patient_2_Cell_line

extract_protocol:
Illumina total RNAseq with ribo-zero depletion
The RNeasy Mini kit (Qiagen, cat # 74104) was used for extracting RNA from both 2D cell lines and organoids. Approximately 3 million cells and 1 million cells were used as starting material for 2D and organoids, respectively.
A GI pathologist circled areas of high tumor cellularity on H&E sections of the tumor and PDX. RNA was extracted from the same area of an adjacent section using RNeasy FFPE kit (Qiagen, cat # 73504) after treating with Deparaffinization Solution (Qiagen, cat # 19093)
RNA library preparation and sequencing: Exome capture was carried out using the RNA access kit (Illumina, cat # RS-301-2001) for the majority of samples


title: 1533-ADC-1: HKC_wt_D0-1

value: rep 1


title: QM-0 mJ-combo-B

description:
unirradiated
human miRNA Card B

value: unirradiated


title: QMc-25 mJ

description:
irradiated
human miRNA Card A

source_name: Primary melanocytes


title: Glarius_GLARIUS_12_10

value: Partial resection


title: Patient_3_Cell_line


title: Patient_1_Cell_line_rep1


title: QMb-25 mJ

description:
irradiated
human miRNA Card A

label: Fluourescence from FAM/SYBR green


title: UL74-Low Replicate1

city: Urbana

first: Erik

last: Procko

address: 601 S Goodwin Ave

institute: University of Illinois

description: PDGFRA library sorted for receptor surface expression and low binding to CMV trimer in presence of 100 nM PDGF (Independent Replicate 1)

data_processing:
Data was analyzed using Enrich: http://depts.washington.edu/sfields/software/enrich/
Fuser script (Fragment A): python Paired_read_fuser.py --path directory/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.bz2 --read2 sample_R2.fastq.bz2 --wtseq GACCCAGATGTAGCCTTTGTACCTCTAGGAATGACGGATTATTTAGTCATCGTGGAGGATGATGATTCTGCCATTATACCTTGTCGCACAACTGATCCCGAGACTCCTGTAACCTTACACAACAGTGAGGGGGTGGTACCTGCCTCCTATGACAGCAGACAGGGCTTTAATGGGACCTTC --read1_overlap_start 42 --read1_overlap_end 222 --read2_overlap_start 49 --read2_overlap_end 229 --mode B
Fuser script (Fragment B): python Paired_read_fuser.py --path directory/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.bz2 --read2 sample_R2.fastq.bz2 --wtseq ACTGTAGGGCCCTATATCTGTGAGGCCACCGTCAAAGGAAAGAAGTTCCAGACCATCCCATTTAATGTTTATGCTTTAAAAGCAACATCAGAGCTGGATCTAGAAATGGAAGCTCTTAAAACCGTGTATAAGTCAGGGGAAACGATTGTGGTCACCTGTGCTGTTTTTAACAATGAGGTGGTTGACCTTCAATGGACTTACCCT --read1_overlap_start 20 --read1_overlap_end 224 --read2_overlap_start 26 --read2_overlap_end 230 --mode B
Fuser script (Fragment C): python Paired_read_fuser.py --path directory/ --paired_mismatch_threshold 250 --read1 sample_R1.fastq.bz2 --read2 sample_R2.fastq.bz2 --wtseq GGAGAAGTGAAAGGCAAAGGCATCACAATGCTGGAAGAAATCAAAGTCCCATCCATCAAATTGGTGTACACTTTGACGGTCCCCGAGGCCACGGTGAAAGACAGTGGAGATTACGAATGTGCTGCCCGCCAGGCTACCAGGGAGGTCAAAGAAATGAAGAAAGTCACTATTTCTGTCCATGAG --read1_overlap_start 27 --read1_overlap_end 210 --read2_overlap_start 18 --read2_overlap_end 201 --mode B
Aligner script (Fragment A): python2.7 Fused_read_aligner.py --path directory/ --infile sample_R1.fast_B_qc1 --referenceDNA GACCCAGATGTAGCCTTTGTACCTCTAGGAATGACGGATTATTTAGTCATCGTGGAGGATGATGATTCTGCCATTATACCTTGTCGCACAACTGATCCCGAGACTCCTGTAACCTTACACAACAGTGAGGGGGTGGTACCTGCCTCCTATGACAGCAGACAGGGCTTTAATGGGACCTTC --referenceAA DPDVAFVPLGMTDYLVIVEDDDSAIIPCRTTDPETPVTLHNSEGVVPASYDSRQGFNGTF --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 30 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
Aligner script (Fragment B): python2.7 Fused_read_aligner.py --path directory/ --infile sample_R1.fast_B_qc1 --referenceDNA ACTGTAGGGCCCTATATCTGTGAGGCCACCGTCAAAGGAAAGAAGTTCCAGACCATCCCATTTAATGTTTATGCTTTAAAAGCAACATCAGAGCTGGATCTAGAAATGGAAGCTCTTAAAACCGTGTATAAGTCAGGGGAAACGATTGTGGTCACCTGTGCTGTTTTTAACAATGAGGTGGTTGACCTTCAATGGACTTACCCT --referenceAA TVGPYICEATVKGKKFQTIPFNVYALKATSELDLEMEALKTVYKSGETIVVTCAVFNNEVVDLQWTYP --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 30 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
Aligner script (Fragment C): python2.7 Fused_read_aligner.py --path directory/ --infile sample_R1.fast_B_qc1 --referenceDNA GGAGAAGTGAAAGGCAAAGGCATCACAATGCTGGAAGAAATCAAAGTCCCATCCATCAAATTGGTGTACACTTTGACGGTCCCCGAGGCCACGGTGAAAGACAGTGGAGATTACGAATGTGCTGCCCGCCAGGCTACCAGGGAGGTCAAAGAAATGAAGAAAGTCACTATTTCTGTCCATGAG --referenceAA GEVKGKGITMLEEIKVPSIKLVYTLTVPEATVKDSGDYECAARQATREVKEMKKVTISVHE --gap_max 8 --unresolvable_max 2 --maxmutrun 3 --avg_quality 30 --chaste 1 --Ncount_max 3 --use_N 0 --mode B
MapCounts script: python mapCounts.py --path directory/ --infile sample_R1.fast_B_qc1_PRO_qc2
MapRatios script: Example: python mapRatios.py --path directory/ --templatepath /deepseq_scripts/r_deepseq_scripts/ --infile2 mapcounts_library --infile1 mapcounts_sorted
MapParts script: python mapParts.py --path directory/ --infile mapratios_sorted_library --mode mutations:1
Unlink script: python mapUnlink.py --path directory/ --infile mapratios_sorted_library.m1 --type protein --mode ratios --size number_of_residues
In Excel, the log(base2) enrichment ratio of the wild type sequence was subtracted from the log(2) enrichment ratios for all single mutations.  The minimum log(2) enrichment ratio for severely depleted mutants was set at -4.
Genome_build: Not applicable
Supplementary_files_format_and_content: Excel spreadsheet of log(base2) enrichment ratios for each single amino acid substitution.  Also includes the frequency of each mutation in the naïve plasmid library.

source_name: Synthetic coding sequences

growth_protocol: Expi293F cells cultured in Expi293 Expression Medium (Life Technologies)

extract_protocol:
Total RNA was harvested from sorted cells using GeneJet RNA Purification Kit (Thermo Scientific) and cDNA prepared using Accuscript Hi-Fi (Agilent Genomics) primed with a gene-specific primer (RevTrans_PDGFRA_992R: TCATGCAGGTTGACAGCTTC). The D2-D3 encoding region was amplified for deep sequencing in two PCR steps; in the first, primer overhangs added sequences for annealing to the Illumina sequencing primers, and in the second, primer overhangs added unique barcodes and Illumina adaptors.
Primer pair for 1st round of PCR (Fragment A): Illumina_PDGFRA_325_for (TCTTTCCCTACACGACGCTCTTCCGATCTGAGAATGAGCTTGAAGGCAG) and Illumina_PDGFRA_567_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTACAGATATAGGGCCCTACAG).
Primer pair for 1st round of PCR (Fragment B): Illumina_PDGFRA_527_for (TCTTTCCCTACACGACGCTCTTCCGATCTAGGGCTTTAATGGGACCTTC) and Illumina_PDGFRA_770_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTCCTTTGCCTTTCACTTCTCC).
Primer pair for 1st round of PCR (Fragment C): Illumina_PDGFRA_724_for (TCTTTCCCTACACGACGCTCTTCCGATCTGTGGTTGACCTTCAATGGAC) and Illumina_PDGFRA_983_rev (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTTGACAGCTTCCAACTGGCT).
Primer pair for 2nd round of PCR (added I5 and I7 Illumina adaptors): MiSeq_Start_Adaptamer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) and MiSeq_Index_Adaptamer (CAAGCAGAAGACGGCATACGAGAT-6nt-barcode-GTGACTGGAGTTCAGACGTGTGCTCTTC)
Amplicons were deep sequenced on a NovaSeq 6000 using a 2x250 nt paired end protocol.

treatment_protocol: PDGFRα mutants were cloned into the episomal vector pCEP4 (Invitrogen) and were co-transfected with a large excess of carrier DNA such that a typical cell expressed no more than one sequence variant per cell.  After staining cells for surface PDGFRα expression (anti-myc Alexa 647 conjugate, Cell Signaling Technology) and binding to CMV trimer (gH/gL/gO-sfGFP) in the presence of competing PDGFs, cells were FACS sorted for receptor expression and either high (UL74-High gate) or low (UL74-Low gate) levels of bound trimer.

tag: protein

value: PDGFRA

tag: sort gate

value: Bottom 15% of PDGFRα-expressing cells that bind trimer


title: UL74-Low Replicate2

description: PDGFRA library sorted for receptor surface expression and low binding to CMV trimer in presence of 100 nM PDGF (Independent Replicate 2)


title: Patient_1_Organoid_rep1

value: Organoid derived from PDX


title: ZmMYB94 DAP-seq

city: Piscataway

first: Andrea

last: Gallavotti

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute

institute: Rutgers University

library_source: genomic

data_processing:
Library strategy: DAP-seq
Illumina software used for base calling
Sequenced reads were trimmed for adaptor sequence, then mapped to ZmB73v3 whole genome using bowtie2 v2.2.8 with default parameters. Reads were filtered using samtools with the following parameters -b -q 30 to give MAPQ > 30.
Peaks were called using GEM v2.5 with the following parameters: --d Read_Distribution_default.txt --k_min 6 --k_max 20 --outNP --q 5. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Genome_build: ZmB73v3.31
Supplementary_files_format_and_content: bigwig files were generated using deeptools with a bin size of 10bp and RPKM normalization. NarrowPeak files were generated by GEM v2.5.

molecule: genomic DNA

organism: Zea mays

source_name: 1-3cm maize ear

growth_protocol: genomic DNA was extracted from 1-3cm field grown ears

extract_protocol:
genomic DNA was purified using a standard phenol:chloroform extraction protocol. HALO-MYB94 fusion protein was expressed using Promega's TNT rabbit reticulocyte expression system.
sequencing libraries were constructed as described in Bartlett et al., 2017

tag: cultivar background

tag: tissue

value: 1-3cm maize ear

tag: fusion protein

tag: notes

value: fused leaves 1

tag: total read number

tag: mapped reads(>mapq30)


title: Glarius_GLARIUS_12_08

tag: Sex

value: Male

tag: treatment

value: BEVACIZUMAB+IRINOTECAN

tag: phillips subtype

value: Proliferative

value: Classical

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)


title: Glarius_GLARIUS_12_09

tag: age

value: Female

tag: surgical status

value: Proneural


title: QMa-25 mJ

description:
irradiated
human miRNA Card A

tag: cell type

value: melanocytes

tag: rna fraction

value: exosome

value: irradiated


title: UL74-High Replicate2

description: PDGFRA library sorted for receptor surface expression and high binding to CMV trimer in presence of 100 nM PDGF (Independent Replicate 2)

tag: protein

value: Top 15% of PDGFRα-expressing cells that bind trimer


title: iNK#2

city: Daejeon

first: Han-Seop

last: Kim

address: Gwahak-ro

department: Stem Cell Research Laboratory, Immunotherapy Convergence Research Center,

country: South Korea

institute: KRIBB

description: Gene expression data from iNK#2

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin

source_name: Human peripheral blood monocytes

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

extract_protocol: Total RNA were extracted from PBMC-NKs and iNK using an RNeasy Mini kit (Qiagen)

value: adult PBMC

value: induced NK cells


title: Glarius_GLARIUS_12_07

value: Partial resection

value: TEMOZOLOMIDE

value: Mesenchymal

tag: tcga subtype

tag: mgmt status

value: Non-methylated


title: QM-0 mJ-combo-A

description:
unirradiated
human miRNA Card A

value: unirradiated


title: UL74-High Replicate1

description: PDGFRA library sorted for receptor surface expression and high binding to CMV trimer in presence of 100 nM PDGF (Independent Replicate 1)

value: PDGFRA

tag: sort gate


title: iNK#1

description: Gene expression data from iNK#1

tag: tissue


title: Glarius_GLARIUS_12_06

value: BEVACIZUMAB+IRINOTECAN


title: Glarius_GLARIUS_13_03

value: Unclassified


title: 1533-ADC-2: HKC_wt_D0-2

tag: cell line

value: HKC

value: DMSO

tag: replicate

value: rep 2


title: Glarius_GLARIUS_12_05

value: Male

value: Total resection


title: PBMC-NK#2

description: Gene expression data from PBMC-NK#2

value: primary NK cells


title: Ulcerative Colitis rep 5

city: Boston

first: Kate

middle: L

last: Jeffrey

state: MA

address: 50 Blossom Street

institute: Massachusetts General Hospital

data_processing:
Transcriptome mapping was performed with STAR version 2.5.4a by using the NCBI37 assembly gene annotations
Read counts for individual genes were produced using the unstranded count feature in HTSeq 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read count for each sample

source_name: macrophage

growth_protocol: Peripheral blood mononuclear cells were isolated from the blood of healthy human donors using a Ficoll-based density gradient. Following isolation, adherent cells were cultured on tissue culture-treated plated plates in X-VIVO media containing 100ng/mL rhM-CSF and allowed to differentiate into mature macrophages for 7 days. At this point, cells were counted and replated overnight in fresh media for treatment.

extract_protocol:
Cells were lysed in 350µL buffer RLT and RNA was isolated using the Qiagen RNeasy Mini Kit with on-column DNase digest (all according to manufacturer's instruction).
100ng of total RNA from each sample was used for library preparation. First, poly(A)-tailed RNA was enriched for using the NEBnext Poly(A) mRNA magnetic isolation module (E7490; according to manufacturer's instructions). This poly(A)-enriched RNA was then used to construct libraries using the NEBnext Ultra II RNA Library Prep Kit for Illumina (E7770; according to manufacturer's instructions). To allow for multiplexed reads, libraries were dual indexed using indices from NEBnext Multiplex Oligos for Illumina (E6440). Sequencing was done on a NovaSeq S4 flow cell.

treatment_protocol: SM buffer or viral-like particle (VLP) preparation from non-IBD or IBD tissue or ileostomy was pre-treated for 30  minutes with polymixin B to ensure endotoxin-free conditions. Media was removed from the cells and SM buffer (for mock condition) or VLP preparation was added drop-wise onto the cells at a volume sufficient to cover the well surface. Treatment was left on cells for 1 hour at 37C with occasional rocking. After 1 hour, treatments were removed entirely, cells were gently washed with PBS, and media was replaced. Cells were collected 24 hours after the end of treatment.

tag: disease

value: Ulcerative Colitis


title: Glarius_GLARIUS_12_04

tag: Sex

value: Proneural


title: FOXP2 dhelix + CHIR rep5

city: Graz

first: Gesa

last: Richter

address: Neue Stiftingtalstrasse 6

country: Austria

institute: Medical University Graz

data_processing:
Alignment: Star 2.6.1a_08-27
Transcript Counts: featureCounts (subread package) 1.4.4
Raw RNA-Seq reads were aligned to the human hg19 genome using STAR.  considered differentially expressed.
Gene read counts are generated using featureCounts and differential expression was analyzed using DESeq2.
Genes with adjusted p-value lower than 0.05 and a log2 fold change of 1 or -1 were considered differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: read counts per gene

growth_protocol: Human Osteosarcoma Epithelial cells (U2OS) were maintained at 37°C under 5% CO2 in α-MEM medium (Invitrogen) supplemented with 5% (v/v) FCS (Gibco), 100 IU/ml penicillin and 100 µg/ml streptomycin.

extract_protocol:
QIAshredder and RNeasy Mini Kit (Qiagen, UK) was used to isolate RNA from transfected U2OS cells according to the manufacturer’s protocol. Integrity of RNA was determined using a bioanalyzer instrument (Agilent Technologies, Santa Clara, CA, USA).
A cDNA library including 5 replicates per condition was prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina Inc., San Diego, CA) according to the manufacturer´s recommendation. Briefly, 1µg of total RNA was used for first-strand synthesis performed with a random hexamer and SuperScript II (Life Technologies, Carlsbad, CA, USA). Second-strand synthesis was performed using dUTP and the Illumina-specific Second Strand Marking Master Mix. After end repair and A-tailing indexed adaptors were ligated to the cDNA fragments. Fragments successfully ligated with adaptor molecules on both ends were enriched by PCR for 15 cycles and purified with AMPure XP Beads (Beckman Coulter Inc., Brea, CA). The final libraries were quality checked on an Agilent Bioanalyzer and quantified with qPCR using a commercially available PhiX-library (Illumina Inc., San Diego, CA) as a reference. All samples were run in five biological replicates and a total of 30 equimolarily pooled samples were sequenced two High Output flow cells on an Illumina NextSeq in a paired end run with 2x 75 cycles.

treatment_protocol: In a six-well plate, approx. 80% confluent U2OS cells were transfected with various FOXP2 construct plasmids (500 ng) in equal amount using Lipofectamin 3000 (Thermo Fisher Scientific) for 48h. In case of CHIR-treatment, 5µM CHIR 99021 was added in the medium 72h before transfection with FOXP2 construct plasmids.

value: osteosarcoma epithelial cells

tag: genotype

value: FOXP2 dhelix (lacking residue 264-272) overexpression + CHIR treatment


title: FOXP2 dhelix + CHIR rep4


title: Ulcerative Colitis rep 4


title: Glarius_GLARIUS_12_02

extract_protocol: Not applicable

value: Female

tag: treatment

value: TEMOZOLOMIDE

tag: phillips subtype


title: FOXP2 dhelix + CHIR rep3


title: Glarius_GLARIUS_12_01

value: Mesenchymal

tag: os (diagnosis)

tag: os cnsr (event = 1, censor = 0)

value: Non-methylated


title: FOXP2 dhelix + CHIR rep2


title: Ulcerative Colitis rep 2


title: Ulcerative Colitis rep 1


title: Glarius_GLARIUS_11_11

tag: age

tag: surgical status


title: Naive PDGFRA-D2D3 library

description:
Naive PDGFRA-D2D3 library
plasmid DNA

value: PDGFRA


title: mock rep 3

value: mock


title: mock rep 2


title: Glarius_GLARIUS_11_09


title: FOXP2 + CHIR rep5

tag: cell type

value: FOXP2 WT overexpression + CHIR treatment


title: Glarius_GLARIUS_11_08

value: BEVACIZUMAB+IRINOTECAN

value: Proliferative

value: Classical


title: FOXP2 + CHIR rep3


title: PBMC-NK#1

description: Gene expression data from PBMC-NK#1

value: adult PBMC


title: Ulcerative Colitis rep 3


title: FOXP2 + CHIR rep2


title: CR41_NSC_170905N_P7

city: Sevilla

first: Luis

last: Lopez Navas

state: Sevilla

address: c/ Americo Vespucio, 15, Ed. S-2

department: Preclinical Research

country: Spain

institute: Red Andaluza de diseño y traslación de Terapias Avanzadas

hyb_protocol: Hybridization was performed with independent Human Clarion-S Microarrays (Affymetrix) following Affymetrix protocol.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip Scanner 7G

data_processing: Data were analyzed with Affymetrix ® GeneChip® Command Console® 2.0 software.  Relevant Software parameters were the following: Anova Method: eBayes; DAGB threshold < 0.05; Pos/Neg AUC threshold: 0.7; Exploratory Grouping Analysis (all parameters): Default; Signal Space Transformation - Robust Microarray Analysis (SST-RMA) was used as the normalization method.

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_4_Passage_7

label_protocol: cDNA was synthetized and labelled with biotin following the instructions of the manufacturer (Affymetrix, WT PLUS)

growth_protocol: Cultured with FGF, EGF and LIF in a humidified incubator at 37°C and 5% CO2

extract_protocol: RNA was extracted with RNeasy® Mini kit (Qiagen) following the instructions of the manufacturer.

value: Hemorrhagic cerebrospinal fluid

value: Neural Stem Cells


title: Glarius_GLARIUS_11_06

value: Male

value: Partial resection

value: Unclassified


title: mock rep 1


title: CR39_NSC_181129N_P3

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_5_Passage_3


title: CR38_NSC_170905N_P3

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_4_Passage_3


title: Glarius_GLARIUS_11_05

value: Total resection


title: FOXP2 dhelix + CHIR rep1

value: osteosarcoma epithelial cells

value: FOXP2 dhelix (lacking residue 264-272) overexpression + CHIR treatment


title: FOXP2 + CHIR rep1

value: FOXP2  overexpression + CHIR treatment


title: CR42_NSC_181129N_P8

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_5_Passage_7


title: CR35_CD133+

source_name: CD133+ purified Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case 2

growth_protocol: CD133+ cells purified by MACS


title: CR34_CD133+

source_name: CD133+ purified Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case 1


title: CHIR rep5

value: CHIR treatment to activate WNT signaling


title: FOXP2 + CHIR rep4


title: Healthy Control rep 4

value: Healthy Control


title: Glarius_GLARIUS_11_10

value: Proneural

value: Non-methylated


title: Glarius_GLARIUS_11_04

value: Female

value: BEVACIZUMAB+IRINOTECAN

value: Mesenchymal


title: Healthy Control rep 3


title: Glarius_GLARIUS_11_03

value: TEMOZOLOMIDE


title: CR31_CB-C_CD34+_3

source_name: Umbilical Cord Blood derived CD34 positive cells. Biological Replicate_3

growth_protocol: Mononuclear cells isolated  by density gradient centrifugation and CD34+ cells purified by MACS

value: Umbilical Cord Blood

value: CD34 positive cells


title: Glarius_GLARIUS_11_02


title: CHIR rep4


title: Healthy Control rep 2


title: CHIR rep3


title: CR36_CD133+

source_name: CD133+ purified Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case 3

value: Hemorrhagic cerebrospinal fluid

value: Neural Stem Cells


title: Healthy Control rep 5


title: Crohn's Disease rep 5

value: Crohn's Disease


title: CHIR rep1


title: Healthy Control rep 1


title: Glarius_GLARIUS_11_01

value: Male

value: Total resection


title: CHIR rep2

value: osteosarcoma epithelial cells


title: Glarius_GLARIUS_10_11


title: FOXP2 dhelix rep4

value: FOXP2 dhelix (lacking residue 264-272) overexpression


title: Crohn's Disease rep 3


title: Crohn's Disease rep 4


title: FOXP2 dhelix rep5


title: Glarius_GLARIUS_10_12

value: Partial resection


title: CR30_CB-B_CD34+_2

source_name: Umbilical Cord Blood derived CD34 positive cells. Biological Replicate_2


title: Glarius_GLARIUS_10_08

value: Classical


title: Glarius_GLARIUS_10_10


title: CR27_iPSC_Cbips_L5

source_name: induced Pluripotential Stem cells. Biological Replicate_2

growth_protocol: Cultured over MEFs. Manual picking

value: CD133 + umbilical cord cells

value: induced Pluripotential Stem cells


title: Glarius_GLARIUS_10_07

value: Female

value: Unclassified

value: Non-methylated


title: Crohn's Disease rep 2


title: CR28_iPSC_IpsEl_L6

source_name: induced Pluripotential Stem cells. Biological Replicate_3

value: Adult Dermal Fibroblasts


title: CR29_CB-A_CD34+_1

source_name: Umbilical Cord Blood derived CD34 positive cells. Biological Replicate_1

value: Umbilical Cord Blood


title: FOXP2 dhelix rep3


title: Crohn's Disease rep 1


title: FOXP2 dhelix rep2


title: CR22_iPSC-NSCs_IpsEl_L6

source_name: induced Pluripotential Stem-derived Neural Stem Cells. Biological Replicate_6

growth_protocol: EB-based protocol. Caudalized with RA

value: iPSC-NSC (episomal from adult fibroblasts)


title: Glarius_GLARIUS_10_06

value: BEVACIZUMAB+IRINOTECAN

value: Proneural


title: Panc1_ABCG2_B

city: Huntsville

first: Sara

last: Cooper

state: AL

address: 601 Genome Wau

institute: HudsonAlpha Institute

data_processing:
adapter trimming using trimgalore v0.4.1
fastqc v0.11.7 for quality score assessment
star version v2.4.2a for alignment
ht-seq-gene v 0.5.3 to consoldiate reads to features
Genome_build: hg38
Supplementary_files_format_and_content: xlsx spreadsheet containing raw count data for each of the four samples across all measured genes.

molecule: polyA RNA

source_name: Panc-1 cell line

growth_protocol: Panc 1 cells were grown in DMEM with 10% FBS, 0.5% PenStrep, 0.5% Glutamax. They were maintained at 37C and 5%CO2

extract_protocol:
3x10^5 cells were suspended in RL buffer with BME. Total RNA was extracted with the Norgen Total RNA extraction kit, including DNAse kit.
NEBNext Ultra RNA Library Prep Kit for Illumina with polyA selection

treatment_protocol: All cells were grown under the same conditions. Each of three pools of cells were infected with a plastmid containing a sgRNA targeting a random genomic segment or the ABCG2 gene. Cells were selected for integration of the plasmid using blasticidin (10ug/ml)

value: Panc-1 cell line

tag: crispr guide

value: Activating guide B for ABCG2 gene

tag: cell line modification

value: Stable integration of Lenti-dCas9-VP46-Blast (Addgene $61425) and lenti-MS2-p65-HSF1-Hygro (Addgene #61425)


title: FOXP2 dhelix rep1

value: osteosarcoma epithelial cells


title: FOXP2 over rep5

value: FOXP2 WT overexpression


title: Panc1_ABCG2_A

value: Activating guide A for ABCG2 gene


title: Glarius_GLARIUS_10_05

growth_protocol: Not applicable

value: Partial resection

value: TEMOZOLOMIDE

value: Proliferative

tag: tcga subtype

value: Mesenchymal

tag: mgmt status


title: Glarius_GLARIUS_10_04

value: Female


title: CR21_iPSC-NSCs_Cbips_L5

source_name: induced Pluripotential Stem-derived Neural Stem Cells. Biological Replicate_5

tag: tissue

value: iPSC-NSC (Sendai V from CD133+ Cord cells)


title: Panc1_NTC2

tag: cell line

value: Non-targeting guide 2


title: FOXP2 over rep4


title: Panc1_NTC1

value: Non-targeting guide 1


title: FOXP2 over rep3


title: CR17_iPSC-NSCs_H9_L1

source_name: Embryonic Stem-derived Neural Stem Cells. Biological Replicate_1

value: ESC-NSC

value: Embryonic stem cells


title: CR19_iPSC-NSCs_IMR90_L3

source_name: induced Pluripotential Stem-derived Neural Stem Cells. Biological Replicate_3

value: iPSC-NSC (retrovirus from fetal fibroblasts)


title: CR18_iPSC-NSCs_MRC5_L2

source_name: induced Pluripotential Stem-derived Neural Stem Cells. Biological Replicate_2

value: iPSC-NSC (retrovirus from fetal lung fibroblasts)


title: TSS-Scramble_map_1

city: Los Angeles

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Plasmid DNA
processed data file: endo_scramble_combined_controls_bc_map.txt

data_processing:
Counts for each unique barcode in the census files were complete in Unix as follows: Raw sequences were extracted from each fastq file and the first 20 bp (corresponding to the barcode) was extracted. This sequence was reverse complemented and the entire file was sorted before counting the number of counts of each barcode. Counts were normalized as a proportion of totals reads per sample and all samples aggregated together in R.
Barcode mapping was completed as follows: Demultiplexed reads were paired using Paired-End reAd mergeR (PEAR v0.9.1, default settings). Custom python code was used to identify reads corresponding to perfectly synthesized promoters and their respective barcodes. Briefly, this code searched the first 150 bp of each read for perfect matches to library variants. For reads with perfect matches, the last 20 bp of each read (the barcode) was extracted and a list was compiled mapping each barcode to the most frequently associated library variant. A single barcode appears many times in the sequencing data, and we took steps to ensure a barcode consistently mapped to the same variant. We required that all variants mapped to a single barcode be within an edit distance (Levenshtein distance) of 5 from one another (five single bp changes between the two sequences). We determined this number by bootstrapping a distribution of the edit distance between any two random sequences in our variant library, and setting the threshold to the first percentile (1%) of this bootstrapped distribution. Additionally, each barcode had to appear at least three times in order to be considered for downstream analysis. This step hopefully eliminates barcodes which contained sequencing errors.
Promoter variant expression was calculated in R by assigning barcodes to their mapped promoter, and for each promoter, dividing the sum of all RNA counts for all of its barcodes by the sum of all DNA counts for all of its barcodes.
Genome_build: U00096.2
Supplementary_files_format_and_content: *txt: Tab-delimited text files

organism: Escherichia coli DH5[alpha]

source_name: Escherichia coli

growth_protocol: Luria-Bertani (LB) Rich Media

extract_protocol: Qiagen Plasmid Plus Maxi Kit

tag: strain/background


title: CR16_NSCs-Fetal_PC-1

source_name: Neural Stem Cells derived from the forebrain of 15-22 weeks (EGA) fetuses that had undergone natural, spontaneous in utero death.

growth_protocol: Cultured with FGF and EGF in a humidified incubator at 37°C, 5% O2 and 5% CO2

value: Fetal forebrain

value: Neural Stem Cells


title: TSS-Scramble_map_2


title: FOXP2 over rep1

value: osteosarcoma epithelial cells


title: FOXP2 over rep2

value: FOXP2 WT overexpression


title: CR20_iPSC-NSCs_MSU-Epi_L4

source_name: induced Pluripotential Stem-derived Neural Stem Cells. Biological Replicate_4

value: iPSC-NSC (episomal from adult fibroblasts)


title: CR12_NSCs-Fetal_PL-4


title: Glarius_GLARIUS_10_01

first: Radia

last: Johnson

address: 1 DNA Way

institute: Genentech

data_processing:
Raw data were preprocessed using functions from NanoStringQCPro R package in particular positive control normalisation, background correction (using both water samples and negative control probes) and RNA content normalisation (median normalisation). Prior to clustering analysis, sample-wise normalization was performed by transforming counts to the log2 scale and subtracting the sample-wise mean of housekeeping genes.
Water samples (used for the normalisation) using the NanoStringQCPro package on Bioconductor.

value: Male

value: Partial resection

value: BEVACIZUMAB+IRINOTECAN

value: Proneural

value: Classical

value: Non-methylated


title: PeakTiling_map_1

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Plasmid DNA
processed data file: peak_tile_combined_controls_bc_map.txt


title: Control rep5

value: Mock-transfected cells as control


title: Control rep4


title: Glarius_GLARIUS_1_11

value: Total resection

value: TEMOZOLOMIDE


title: frag_map_2

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Plasmid DNA
processed data file: frag_stats.txt


title: CR11_NSCs-Fetal_PL-3


title: CR9_NSCs-Fetal_PC-2


title: Glarius_GLARIUS_10_03

value: Female


title: Control rep3


title: Glarius_GLARIUS_1_10

value: Proliferative


title: Glarius_GLARIUS_10_02

value: Mesenchymal


title: CR6_NSCs-csf_P7-8_3

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_3_Passage_7

value: Hemorrhagic cerebrospinal fluid


title: Glarius_GLARIUS_1_09


title: frag_map_1


title: PeakTiling_map_2


title: CR5_NSCs-csf_P7-8_2

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_2_Passage_7

value: Neural Stem Cells


title: CR23_iPSC_H9_L1

source_name: induced Pluripotential Stem cells. Biological Replicate_1

value: Embryonic Stem Cells

value: Embryonic stem cells


title: Glarius_GLARIUS_1_12


title: Control rep2

value: osteosarcoma epithelial cells


title: Glarius_GLARIUS_1_08

value: Male


title: cDNA of TTYH2 mutants from degenerate donor rep1

first: Jin

last: Li

address: M341, 300 Pasteur Dr.

department: Genetics

institute: Stanford University

description:
random mutagenesis
TTYH2_deg_editinglevel.txt

data_processing:
Library strategy: amplicon sequencing
genome with designed mutations was built using GMAP
alignment using GSNAP with parameter -m 12 -i 1000000
mutant isoforms with less than 50 reads were filtered out
RNA editing level were measured at target sits by calculating G in total reads
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including editing level, reads coverage of each isoform

molecule: nuclear RNA

source_name: HEK293T cells

extract_protocol:
nuclear fraction was extracted using Cell Biolabs kit (AKR-171), DNA was extracted using Zymo kit (D3020) and RNA was extracted using Trizol reagent.
gene specific primers with partial Illumina adapter were used to amplify each targets and then a second round of PCR was included to add barcodes.

value: HEK293T cells

tag: extraction

value: nuclear fraction


title: cDNA of TTYH2 mutants from degenerate donor rep2


title: Control rep1


title: Glarius_GLARIUS_1_07

tag: Sex

value: Partial resection

value: Unclassified


title: Glarius_GLARIUS_1_05

value: Non-methylated


title: cDNA of NEIL1 mutants from degenerate donor rep2

description:
random mutagenesis
NEIL1_deg_editinglevel.txt

value: total RNA


title: CR3_NSCs-csf_P3-4_3

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_3_Passage_3


title: Glarius_GLARIUS_1_06

value: Total resection

value: BEVACIZUMAB+IRINOTECAN


title: Glarius_GLARIUS_1_04

value: Proneural


title: CR1_NSCs-csf_P3-4_1

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_1_Passage_3


title: Glarius_GLARIUS_1_03

value: Classical


title: cDNA of AJUBA mutants in editng stem rep2

description:
targeted mutagenesis
AJUBA_editinglevel.txt


title: cDNA of NEIL1 mutants from degenerate donor rep1


title: cDNA of AJUBA mutants in editng stem rep1


title: Glarius_GLARIUS_1_02

value: Female

value: Proliferative


title: Czf1-PBase_Cecum

city: San Francisco

first: Suzanne

middle: M

last: Noble

address: 513 Parnassus Ave., Box 0414

institute: UCSF

description: processed data file: Table S2.Wor1-PBase,Efg1-PBase,Czf1-PBase in host data.xlsx

data_processing:
library strategy: calling card-seq
Reads were aligned to whole genome using bowtie
Custom software was used to collapse PCR duplicates into single insertions and only include those that originally had more than 50 reads mapping
Custom software was used to cluster insertions within 1000 base pair windows and assign genes closest to the cluster with bedtools closest-feature
Poisson and hypergeometric statistical tests were performed by comparing insertions for strains of interest against a background insertion set
Genome_build: C. albicans Assembly 22
Supplementary_files_format_and_content: Excel - binding enrichment data, MochiView - read coverage aligned to whole genome

organism: Candida albicans

source_name: C. albicans cells

extract_protocol:
phenol-chloroform
Genomic DNA was digested with MspI, RsaI or Taq1α, precipitated, and resuspended in nuclease-free water. Fragments were self-ligated using T4 ligase overnight. A PCR reaction was then performed to add Illumina adapter sequences to the insert. Libraries were size selected to between 250 and 500 base pairs.

tag: strain

tag: growth condition

value: Murine cecum, 5-15 days combined

tag: selection

value: SD-his-leu-arg, 30C, 2 days


title: cDNA of TTYH2 mutants in editing complementary sequence rep1

description:
targeted mutagenesis
TTYH2_editinglevel.txt


title: Glarius_GLARIUS_1_01

city: South San Francisco

tag: treatment

value: TEMOZOLOMIDE

tag: phillips subtype

tag: os (diagnosis)


title: Wor1-PBase_Cecum

value: Murine cecum, 10-20 days combined


title: CR2_NSCs-csf_P3-4_2

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_2_Passage_3

value: Hemorrhagic cerebrospinal fluid

value: Neural Stem Cells


title: WT(Cy5) vs MUT (Cy3)_pair4

city: New Orleans

first: Samir

middle: S

last: El-Dahr

state: Louisiana

address: 1430 Tulane Avenue

department: Pediatric Nephrology

institute: Tulane University

description: WT and MUT pair 4

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2505C US45102949 scanner

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Mus musculus

source_name: E14.5 Embryonic kidneys

label_protocol: Fluorescently labeled (Cy3-CTP or Cy5-CTP) cRNA was generated from 100 ng of total RNA using the Low input quick amp labeling protocol from Agilent.The labeled cRNA was hybridized to Agilent’s 4X 44K whole mouse genome microarray slide. The arrays were scanned using a dual-laser DNA microarray scanner (Agilent). To prevent bias from signal detection with different color dyes (Cy5, Cy3), we applied dye-swap strategy to this experiment, in which identical sample pairs were reverse labeled.

extract_protocol: Total RNA was isolated from E14.5 kidneys using the RNeasy Mini Kit (Qiagen)

tag: genotype

value: Wild Type

value: Mutant


title: cDNA of TTYH2 mutants in editing complementary sequence rep2

city: Stanford

tag: cell type

value: HEK293T cells

value: nuclear fraction


title: Efg1-PBase_Cecum


title: WT(Cy5) vs MUT (Cy3)_pair3

description: WT and MUT pair 3


title: WT(Cy5) vs MUT (Cy3)_pair1

description: WT and MUT pair 1


title: cDNA of TTYH2 mutants in editing stem rep1


title: WT(Cy5) vs MUT (Cy3)_pair2

description: WT and MUT pair 2


title: WT(Cy3) vs MUT (Cy5)_pair3

description: WT and MUT pair 3


title: cDNA of NEIL1 mutants from Crick strand donor knockin rep2

description:
targeted mutagenesis
NEIL1_editinglevel.txt


title: cDNA of TTYH2 mutants in editing stem rep2


title: T11 [3 dpi]

city: Guiyang

first: Huiqing

last: Yan

state: Guizhou

address: Guizhou Normal University

department: School of Life Science

country: China

institute: Guizhou Normal University

data_processing:
Clean data were obtained from raw reads by filtering low-quality tags (those that contained ambiguous bases), and low-quality reads (reads containing more than 50% bases with Q-value≤10.
Using TopHat2 based on Bowtie2, we aligned all distinct clean data to the reference genome database of P. patens (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA_000002425.1_V1.1). Data that mapped multigene were removed. The number of clean tags for each gene was calculated and then normalized. Saturation analysis was performed to check whether the data was satisfied for further analysis.
To compare the expression levels of transcripts in the different samples, FPKM fragments per kilobase of ranscript per million mapped reads) was used to normalize the gene expression according to the formula: FPKM = (106 × C × 103)/NL. C represents the number of reads uniquely aligned to a certain unigene, N indicates the total number of reads uniquely aligned to all unigenes, and L is the base number of this unigene.
Genome_build: GCA_000002425.1_V1.1
Supplementary_files_format_and_content: the text files include FPKM values for each Sample

organism: Physcomitrium patens

source_name: 3 days post inoculation

extract_protocol:
The total RNA of Mock plants, 0.5, 1, 2, and 3 dpi were extracted using TAKARA Trizol Reagent according to the protocol of manufacture.
The total RNA was treated with RNase-free DNase I to eliminate DNA contamination.The enrichment of mRNA was performed with Oligo (dT)-attached magnetic beads,and fragmentation was performed using divalent cations under high temperature in NEBNext First Strand Synthesis Reaction Buffer (5×) to randomly interrupt mRNA. The first-strand cDNA chain was synthesized by random hexamers and M-MuLV Reverse Transcriptase (RNase H) with the mRNA template. Subsequently, the second-strand cDNA chain was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. The the double stranded cDNA was purified using AMPure XP beads. Following end-pair and single nucleotide A (adenine) addition for the purified cDNA, adapters were used to distinguish the different samples by selection with AMPure XP beads for PCR amplification, following which the cDNA library was obtained.

value: wild type

value: Botrytis cinerea stress

tag: time point

value: 3 days post inoculation


title: TDH3promoter-PBase_YEPD

value: YEPD + BPS, 30C, overnight


title: cDNA of NEIL1 mutants from Crick strand donor knockin rep1


title: T10 [2 dpi]

source_name: 2 days post inoculation

value: 2 days post inoculation


title: WT(Cy3) vs MUT (Cy5)_pair1

description: WT and MUT pair 1


title: cDNA of NEIL1 mutants from double strand donor knockin rep2


title: T05 [2 dpi]


title: czf1_YPD_1

data_processing:
Reads In fastq files were aligned to C. albicans transcriptome using kallisto with default parameters
Estimated counts generated from kallisto for each fastq were extracted and pair-wise comparisons between biological conditions was performed with limma using growth condition and batch as parameters in the design matrix
Supplementary_files_format_and_content: White_opaque_regulator_RNA_expression.xlsx contains log2 fold changes and adjusted p-values of pair-wise comparisons performed in limma; White_opaque_regulator_estimated_counts.xlsx contains estimated counts generated by kallisto that were used as input to limma

source_name: in vitro culture

growth_protocol: Candida albicans strains were grown in YEPD media overnight, then diluted to OD=0.1 and grown for 4 hours to an OD=1. These log phase cultures were either pelleted and snap frozen or used for oral gavage of mice. For mouse colonization, mice were given autoclaved food and water with penicillin and streptomycin ad libitum throughout the colonization. C. albicans colonization in mice was maintained for 10 days until the euthanization of the animals.

extract_protocol:
Acid phenol extraction followed by phenol-chloroform extraction, isopropanol preciptation, followed by SPRI bead cleanup
Followed standard protocol for NEBNext Ultra Directional Library Preparation

tag: time post inoculation

value: 4 hours

value: YEPD, 30C


title: cDNA of NEIL1 mutants from Watson strand donor knockin rep2


title: T04 [1  dpi]

source_name: 1  day post inoculation

value: 1  day post inoculation


title: cDNA of NEIL1 mutants from double strand donor knockin rep1


title: cDNA of NEIL1 mutants from Watson strand donor knockin rep1


title: EFG1promoter-PBase_Lees

description: processed data file: Table S1.Efg1-PBase in vitro data.xlsx

value: Lee's pH 6.8, 37C, 7 days

value: SD-his-arg, 30C, 2 days


title: czf1_YPD_2


title: CR4_NSCs-csf_P7-8_1

source_name: Neural Stem Cells derived from cerebrospinal fluid obtained from 27-36 weeks (EGA) preterm infants. Case_1_Passage_7


title: T08 [0.5 dpi]

source_name: 0.5 day post inoculation

value: 0.5 day post inoculation


title: WT(Cy3) vs MUT (Cy5)_pair4

description: WT and MUT pair 4


title: DNA of NEIL1 mutants from Crick strand donor knockin rep2

description:
targeted mutagenesis
178Neilcrick2g_counts

value: total genomic DNA


title: efg1wor1_YPD_2


title: T03 [0.5 dpi]


title: DNA of NEIL1 mutants from Crick strand donor knockin rep1

description:
targeted mutagenesis
177Neilcrick1g_counts


title: Efg1-PBase_Lees


title: ∆SO_3096_Flow_4 (expt 2)

city: Hachioji

first: Atsushi

last: Kouzuma

state: Tokyo

address: 1432-1 Horinouchi

country: Japan

institute: Tokyo University of Pharmacy and Life Sciences

description: Gene expression in AFP-expressing ∆SO_3096 grown under an electrolyte-flow condition

hyb_protocol: For each array, 19 µL of the purified Cy3-labeled cRNA (600 ng) was mixed with 5 µL of 10× Blocking Agent, 1 µL of 25× Fragmentation Buffer, and 25 µL of 2× GE Hybridization Buffer HI-RPM. The resultant mixtures were hybridized to the arrays at 65ºC for 17 h. After hybridization, each microarray slide was washed with Gene Expression wash buffer 1 at room temperature for 1 min, followed by Gene Expression wash buffer 2 at 37ºC for 1min.

scan_protocol: Slides were air dried for 1 min and scanned using an Agilent DNA Microarray Scanner at 5-µm resolution.

data_processing: Gene expression data (fluorescent intensities) were extracted from the scanned image using the Feature Extraction Software version 8.1 (Agilent Technologies) and normalized and statistically analyzed using the limma software package (version 3.36.2; https://www.bioconductor.org/packages/release/bioc/html/limma.html)

organism: Shewanella oneidensis

source_name: AFP-expressing ∆SO_3096 grown under a flow condition replicate 4

label_protocol: Cyanine3 (Cy3)-labeled cRNA was synthesized from 25 ng of total RNA using the Low Input Quick Amp WT Labeling Kit (Agilent Technologies) and purified using a RNeasy Mini Kit (Qiagen). The labeled cRNA was quantified using NanoDrop ND-1000 Spectrophotometer (Thermo Scientific).

growth_protocol: An electrochemical flow cell (EFC) was filled with lactate minimal medium (LMM) containing gentamicin (Gm) and was purged with pure nitrogen gas (99.999%) for anaerobic operation. After inoculation with AFP-expressing MR-1 or SO_3096 pregrown in LB medium supplemented with Gm, the electrodes were connected to a potentiostat (VMP3; Bio-Logic Science Instruments, Seyssinet-Pariset, France), and the potential of the working electrode (WE) was poised at +0.2 V (versus the standard hydrogen electrode). After inoculation, medium (electrolyte) was not supplied to the EFC for approximately 1 h, to allow S. oneidensis cells to attach to the WE. After inoculation, LMM containing Gm was supplied to the EFC at a constant linear velocity of 5.5 mm min-1. The EFC was operated for 48 h until the WE-associated cells reached the early stationary growth phase.

extract_protocol: Total RNA was extracted using a Trizol reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions and subsequently purified using an RNeasy Mini Kit and an RNase-Free DNase Set (Qiagen, Valencia, CA). The quality of total RNA was evaluated using an Agilent 2100 Bioanalyzer with RNA 6000 Pico reagents and RNA Pico Chips (Agilent Technologies) according to the manufacture’s instruction.

treatment_protocol: Cells associated with the WE were suspended in LMM with vigorous pipetting. After vortex-mixing, the cell suspension was centrifuged at 15,000 g for 5 min to precipitate the cells.

value: AFP-expressing ∆SO_3096

value: deltaSO

tag: growth protocol


title: ∆SO_3096_Flow_3 (expt 2)

source_name: AFP-expressing ∆SO_3096 grown under a flow condition replicate 3

value: grown under an electrolyte-flow condition


title: T01 [3 dpi]


title: WT(Cy3) vs MUT (Cy5)_pair2

description: WT and MUT pair 2

value: Wild Type

value: Mutant


title: T02 [mock treatment]

source_name: mock treatment

value: wild type

value: mock treatment


title: efg1wor1_YPD_3


title: T09 [1 dpi]

source_name: 1 day post inoculation

value: Botrytis cinerea stress

value: 1 day post inoculation


title: DNA of NEIL1 mutants from double strand donor knockin rep1

description:
targeted mutagenesis
175Neilds1g_counts

value: HEK293T cells


title: efg1_YPD_2

value: 4 hours


title: czf1_YPD_3

value: YEPD, 30C


title: TSS_map_2

description:
Determining promoter-barcode associations. After barcoding promoters, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Plasmid DNA
processed data file: endo_lb_bc_map.txt

source_name: Escherichia coli


title: ∆SO_3096_Flow_1 (expt 2)

source_name: AFP-expressing ∆SO_3096 grown under a flow condition replicate 1


title: DNA of NEIL1 mutants from Watson strand donor knockin rep2

description:
targeted mutagenesis
174Neilwatson2g_counts

source_name: HEK293T cells


title: DNA of NEIL1 mutants from Watson strand donor knockin rep1

description:
targeted mutagenesis
173Neilwatson1g_counts


title: efg1_YPD_1


title: efg1wor1_YPD_1


title: TSS_map_1


title: GUT_YPD_3


title: GUT_YPD_2


title: T06 [mock treatment]


title: WT_Flow_3 (expt 2)

description: Gene expression in AFP-expressing MR-1 grown under an electrolyte-flow condition

source_name: AFP-expressing MR-1 grown under a flow condition replicate 3

value: AFP-expressing MR-1

value: WT


title: WT_Flow_4 (expt 2)

source_name: AFP-expressing MR-1 grown under a flow condition replicate 4


title: ∆SO_3096_Flow_2 (expt 2)

source_name: AFP-expressing ∆SO_3096 grown under a flow condition replicate 2


title: SD3_1

city: 天津市

first: peixia

last: wang

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203

institute: 天津大学

data_processing:
Basecalls performed using BGISEQ-500
SOAPnuke was used to get the "clean reads".
Mapping clean reads to ControlSYN3_1 whole genome using BWA.
Bowtie2 was used to get the mapping ratio.
Fragments Per Kilobase Million (FPKM) was calculated based on the RSEM.
Genome_build: R64
Supplementary_files_format_and_content: tab-delimited text files include fpkm values for each Sample ...

organism: Saccharomyces cerevisiae

source_name: Fungus

extract_protocol:
Strains were quickly frozen on dry ice, ground to powder with liquid nitrogen, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: SD


title: SD2_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: efg1_YPD_3


title: WT_Flow_2 (expt 2)

source_name: AFP-expressing MR-1 grown under a flow condition replicate 2


title: RNA-seq of miR396_L_2

city: Qingdao

first: Lingyan

last: Wang

address: No.72 Binhai Road Jimo

institute: Shandong University

description: biological replicate 2

data_processing:
The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software, and differential gene expression was analyzed using Noiseq software.
Genome_build: tair 10
Supplementary_files_format_and_content: XLS file for two sample comparison testing if a gene is differentially expressed

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana Hypocotyl

growth_protocol: The seedlings of wild type Col-0 and 35S:miR396a were grown on ½ MS medium containing 1% sucrose for 4 days in the dark, and treated with or without light for 3 hrs.

extract_protocol:
Total RNA was extracted with Trizaol RNA extraction kit (Transgene)
the mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Geonomics institute(BGI)

treatment_protocol: The seedlings grown in the dark were treated with or without light for 3 hrs

tag: ecotype

value: Columbia

value: hypocotyl

tag: development stage

value: 4day-dark growth seedling


title: WT_Flow_1 (expt 2)

source_name: AFP-expressing MR-1 grown under a flow condition replicate 1


title: RNA-seq of miR396_L_1

description: biological replicate 1

tag: tissue


title: wor1_YPD_3

source_name: in vitro culture


title: SD1_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: GUT_YPD_1


title: RNA-seq of miR396_D_3

description: biological replicate 3


title: RD6_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203

value: RD


title: WT_Flow_4 (expt 1)

growth_protocol: An electrochemical flow cell (EFC) was filled with lactate minimal medium (LMM) containing gentamicin (Gm) and was purged with pure nitrogen gas (99.999%) for anaerobic operation. After inoculation with AFP-expressing MR-1 pregrown in LB medium supplemented with Gm, the electrodes were connected to a potentiostat (VMP3; Bio-Logic Science Instruments, Seyssinet-Pariset, France), and the potential of the working electrode (WE) was poised at +0.2 V (versus the standard hydrogen electrode). After inoculation, medium (electrolyte) was not supplied to the EFC for approximately 1 h, to allow MR-1 cells to attach to the WE. For operation under the electrolyte-flow conditions, LMM containing Gm was supplied to the EFC at a constant linear velocity of 5.5 mm min-1. The EFC was operated for 48 h (for the flow condition) or 78 h (for the non-flow condition) until the WE-associated cells reached the early stationary growth phase.

value: grown under an electrolyte-flow condition


title: RNA-seq of miR396_L_3

description: biological replicate 3


title: RNA-seq of miR396_D_2

description: biological replicate 2


title: WT_Flow_3 (expt 1)


title: wor1_YPD_1


title: RNA-seq of miR396_D_1

description: biological replicate 1


title: RD1_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: RD5_1

address: 天津市津南区海河教育园区雅观路135号天津大学北洋园校区54教203


title: RNA-seq of Col-0_L_3

description: biological replicate 3