title: Sample 736_Single mESC cell


title: Sample 741_Single mESC cell

status: Public on Jun 01 2020

type: SRA

city: Stanford

first: Alina

last: Isakova

state: CA

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

molecule: total RNA

organism: Mus musculus

source_name: Single mESC cell

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: Differentiated mESC

tag: day of differentiation

value: day 0


title: CIT_12_B

city: RTP

first: John

middle: S.

last: House

state: NC

address: 111 TW Alexander Drive

department: Biostatistics & Computational Biology Branch

institute: National Instititute of Environmental Health Sciences

description: HepG2 Cells

data_processing:
Reads Aligned against whole genome Manifest (BioSpyder) Human and counted
Raw Counts summed to Unique Gene
Raw Counts from Biospyder – removed features without at least 4 samples > 1 count across all samples
Remaining 13,133 unique features. Samples < 100 counts/gene removed

organism: Homo sapiens

source_name: HepG2 Cells

extract_protocol:
Cell lysates from plates were prepared using TempO-Seq lysis buffer (BioSpyder). After 10-min incubation at room temperature, lysates were stored at −80 °C until testing.
Sequencing libraries were prepared using  the TempO-Seq protocol (BioSpyder).

tag: exposure

value: Citrate

tag: treatment concentration

value: 1.2 ug/mL


title: CIT_12_A

description: HepG2 Cells


title: Sample 499_Single HEK293T cell

source_name: Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225357

type: RNA

city: South San Francisco

first: Radia

last: Johnson

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:
Blanks were not available for the AVAglio dataset, as a result background correction was implemented using 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) using the NanoStringQCPro package on Bioconductor.

label: Nucleotide/fluorophore barcode

growth_protocol: Not applicable

extract_protocol: Not applicable

treatment_protocol: Not applicable

tag: age

tag: Sex

value: Male

tag: corticosteroids

value: Off

tag: surgical status

value: Partial resection

tag: treatment

value: Placebo

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

value: Classical

tag: kps

tag: mmse

tag: rpa

value: Grade V

tag: os (diagnosis)

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

tag: mgmt status

value: Non-methylated


title: Sample 735_Single mESC cell

tag: cell line


title: AVAglio_GSM2225356

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

value: Female

value: Total resection

value: Bevacizumab

value: Proliferative


title: CIT_6_C

description: HepG2 Cells


title: AVAglio_GSM2225354

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

value: Grade IV

value: Methylated


title: CIT_6_A

description: HepG2 Cells

value: Citrate


title: CIT_12_C

description: HepG2 Cells

value: 1.2 ug/mL


title: Sample 733_Single mESC cell

value: Differentiated mESC

tag: day of differentiation

value: day 0


title: Sample 734_Single mESC cell


title: PEG_24_C

description: HepG2 Cells

tag: exposure

value: polyethylene glycol


title: Sample 496_Single HEK293T cell

value: HEK293T cell


title: Sample 497_Single HEK293T cell


title: AVAglio_GSM2225358

value: Male

value: On


title: PEG_24_B

description: HepG2 Cells

tag: treatment concentration


title: AVAglio_GSM2225353

tag: age

value: Partial resection

value: Placebo

value: Proneural

value: Grade III


title: Sample 495_Single HEK293T cell


title: Sample 737_Single mESC cell


title: Sample 732_Single mESC cell


title: Sample 731_Single mESC cell


title: PEG_24_A

description: HepG2 Cells


title: Sample 730_Single mESC cell


title: AVAglio_GSM2225351

tag: Sex

value: Off

value: Non-methylated


title: Sample 498_Single HEK293T cell


title: Sample 494_Single HEK293T cell


title: AVAglio_GSM2225350

tag: corticosteroids

value: Missing


title: AVAglio_GSM2225355

value: Female

tag: surgical status

value: Total resection

value: Bevacizumab

value: Mesenchymal

value: Grade IV


title: PEG_12_C

description: HepG2 Cells

value: 1.2 ug/mL


title: Sample 729_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 493_Single HEK293T cell

value: HEK293T cell


title: Sample 492_Single HEK293T cell


title: PEG_12_B

description: HepG2 Cells

value: polyethylene glycol


title: AVAglio_GSM2225348

value: Male

value: On

tag: treatment

value: Proliferative

value: Classical


title: Sample 728_Single mESC cell


title: PEG_12_A

description: HepG2 Cells


title: Sample 490_Single HEK293T cell


title: Sample 491_Single HEK293T cell


title: AVAglio_GSM2225352

value: Off

value: Partial resection

tag: phillips subtype


title: Sample 726_Single mESC cell


title: AVAglio_GSM2225347

value: Placebo

value: Proneural

tag: tcga subtype

value: Methylated


title: PEG_6_A

description: HepG2 Cells


title: Sample 489_Single HEK293T cell


title: Sample 725_Single mESC cell


title: Sample 488_Single HEK293T cell


title: BPEI_24_B

description: HepG2 Cells

value: branched polyethylenimine


title: Sample 724_Single mESC cell


title: AVAglio_GSM2225346

value: Bevacizumab

tag: kps

value: Grade V


title: Sample 487_Single HEK293T cell


title: AVAglio_GSM2225345

value: Female

value: Biopsy

tag: mmse


title: BPEI_24_A

description: HepG2 Cells

value: 1.2 ug/mL


title: AVAglio_GSM2225349

value: Mesenchymal

tag: rpa

value: Grade IV

value: Missing


title: Sample 723_Single mESC cell

value: Differentiated mESC

value: day 0


title: BPEI_12_C

description: HepG2 Cells


title: Sample 486_Single HEK293T cell

value: HEK293T cell


title: Sample 485_Single HEK293T cell


title: BPEI_12_B

description: HepG2 Cells


title: AVAglio_GSM2225344

value: Male

value: On

value: Total resection

tag: os (diagnosis)

value: Non-methylated


title: Sample 722_Single mESC cell


title: Sample 727_Single mESC cell


title: PEG_6_C

description: HepG2 Cells

value: polyethylene glycol


title: Sample 721_Single mESC cell


title: AVAglio_GSM2225343

value: Off

value: Proneural

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


title: BPEI_12_A

description: HepG2 Cells

value: branched polyethylenimine


title: Sample 484_Single HEK293T cell


title: AVAglio_GSM2225341

value: Female

value: Bevacizumab

value: Unclassified

value: Classical

tag: mgmt status

value: Methylated


title: Sample 720_Single mESC cell

tag: cell line


title: BPEI_6_C

description: HepG2 Cells

value: 1.2 ug/mL


title: Sample 483_Single HEK293T cell

tag: day of differentiation


title: Sample 482_Single HEK293T cell


title: BPEI_6_B

description: HepG2 Cells

tag: exposure


title: Sample 718_Single mESC cell

value: Differentiated mESC


title: Sample 719_Single mESC cell

value: day 0


title: Sample 481_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225340

value: Male

value: Placebo

value: Mesenchymal

value: Grade IV


title: AVAglio_GSM2225339

value: Partial resection

value: Non-methylated


title: NoNP_24_B

description: HepG2 Cells

value: No Treatment

tag: treatment concentration


title: BPEI_6_A

description: HepG2 Cells

value: branched polyethylenimine


title: Sample 716_Single mESC cell


title: AVAglio_GSM2225342

tag: age

value: Female

value: On

value: Proneural

value: Grade V


title: AVAglio_GSM2225338

tag: Sex

value: Total resection

value: Classical

value: Methylated


title: Sample 480_Single HEK293T cell


title: Sample 715_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 479_Single HEK293T cell

value: HEK293T cell


title: NoNP_24_A

description: HepG2 Cells


title: NoNP_12_C

description: HepG2 Cells


title: Sample 478_Single HEK293T cell


title: Sample 714_Single mESC cell


title: AVAglio_GSM2225337

value: Male

tag: corticosteroids

value: Bevacizumab


title: AVAglio_GSM2225336

value: Off

tag: surgical status

value: Placebo

value: Mesenchymal

value: Grade IV


title: Sample 713_Single mESC cell


title: AVAglio_GSM2225335

value: Partial resection

tag: treatment


title: NoNP_12_A

description: HepG2 Cells

value: No Treatment


title: Sample 476_Single HEK293T cell


title: NoNP_12_B

description: HepG2 Cells


title: Sample 712_Single mESC cell


title: AVAglio_GSM2225333

value: Female

value: On

value: Biopsy

tag: phillips subtype

value: Proliferative

value: Missing


title: Sample 475_Single HEK293T cell


title: Sample 717_Single mESC cell


title: Sample 711_Single mESC cell


title: NoNP_6_C

description: HepG2 Cells


title: AVAglio_GSM2225331

tag: tcga subtype


title: Sample 474_Single HEK293T cell


title: AVAglio_GSM2225332

value: Total resection

tag: kps

value: Non-methylated


title: Sample 473_Single HEK293T cell


title: NoNP_6_B

description: HepG2 Cells


title: Sample 710_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 709_Single mESC cell


title: NoNP_6_A

description: HepG2 Cells


title: Sample 477_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225330

value: Male

value: Proneural

tag: mmse

value: Grade V


title: Sample 708_Single mESC cell


title: Sample 472_Single HEK293T cell


title: AVAglio_GSM2225334

value: Bevacizumab

tag: rpa


title: AVAglio_GSM2225329

value: Off

value: Placebo

value: Mesenchymal

value: Grade IV

tag: os (diagnosis)


title: Sample 471_Single HEK293T cell


title: Sample 707_Single mESC cell


title: AVAglio_GSM2225328

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

value: Methylated


title: RNA-seq high risk T-ALL patient No. 2

city: Chicago

first: Yalu

last: Zhou

state: IL

address: 303 E. Superior St,

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
Diferential alternative splicing analysis was performed using rMATS.
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.

source_name: T-cell acute lymphoblastic leukemia cells

growth_protocol: in vivo

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 50bp single-read method.

tag: cell type

tag: patient number

value: high risk 2


title: Sample 470_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: RNA-seq high risk T-ALL patient No. 4

value: T-cell acute lymphoblastic leukemia cells

value: high risk 4


title: AVAglio_GSM2225327

value: Total resection

value: Classical

tag: mgmt status


title: Sample 706_Single mESC cell

value: Differentiated mESC


title: RNA-seq high risk T-ALL patient No. 1

value: high risk 1


title: RNA-seq non-high risk T-ALL patient No. 10

value: non-high risk 10


title: Sample 705_Single mESC cell

value: day 0


title: AVAglio_GSM2225326

tag: age

value: Female

value: Non-methylated


title: Sample 468_Single HEK293T cell

value: HEK293T cell


title: Sample 704_Single mESC cell


title: RNA-seq non-high risk T-ALL patient No. 9

value: non-high risk 9


title: RNA-seq non-high risk T-ALL patient No. 8

value: non-high risk 8


title: AVAglio_GSM2225325

tag: Sex

value: On

value: Partial resection

value: Bevacizumab

value: Mesenchymal


title: AVAglio_GSM2225324

value: Male

tag: corticosteroids

value: Off

value: Proneural

value: Grade V

value: Methylated


title: RNA-seq high risk T-ALL patient No. 3

value: T-cell acute lymphoblastic leukemia cells

value: high risk 3


title: Sample 703_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 467_Single HEK293T cell


title: Sample 466_Single HEK293T cell


title: Sample 702_Single mESC cell


title: RNA-seq non-high risk T-ALL patient No. 7

value: non-high risk 7


title: Sample 701_Single mESC cell


title: RNA-seq non-high risk T-ALL patient No. 6

value: non-high risk 6


title: Sample 464_Single HEK293T cell

value: HEK293T cell


title: Sample 465_Single HEK293T cell


title: Sample 469_Single HEK293T cell


title: AVAglio_GSM2225323

tag: surgical status

value: Total resection

value: Grade IV

value: Missing


title: AVAglio_GSM2225322

value: On

value: Biopsy

tag: treatment

value: Bevacizumab

value: Proliferative


title: Sample 699_Single mESC cell


title: Sample 700_Single mESC cell


title: RNA-seq non-high risk T-ALL patient No. 4

value: non-high risk 4


title: AVAglio_GSM2225320

value: Male

value: Placebo

tag: phillips subtype

value: Mesenchymal

value: Non-methylated


title: RNA-seq non-high risk T-ALL patient No. 5

value: T-cell acute lymphoblastic leukemia cells

value: non-high risk 5


title: AVAglio_GSM2225321

value: Partial resection

tag: tcga subtype

value: Classical


title: Sample 463_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225319

value: Off

value: Proneural

tag: kps

value: Grade V


title: Sample 462_Single HEK293T cell


title: Sample 461_Single HEK293T cell


title: RNA-seq non-high risk T-ALL patient No. 3

value: non-high risk 3


title: RNA-seq non-high risk T-ALL patient No. 2

value: non-high risk 2


title: Sample 697_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 459_Single HEK293T cell


title: Sample 460_Single HEK293T cell


title: RNA-seq non-high risk T-ALL patient No. 1

value: non-high risk 1


title: Sample 696_Single mESC cell


title: AVAglio_GSM2225318

value: Female

value: Total resection

tag: mmse

value: Grade IV


title: Sample 695_Single mESC cell


title: AVAglio_GSM2225317

value: On

value: Placebo

value: Mesenchymal

tag: rpa

value: Non-methylated


title: Sample 458_Single HEK293T cell


title: AVAglio_GSM2225316

value: Male

value: Partial resection

tag: os (diagnosis)


title: Sample 457_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225314

value: Bevacizumab

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


title: Sample 694_Single mESC cell


title: Sample 693_Single mESC cell


title: Sample 698_Single mESC cell


title: Sample 456_Single HEK293T cell


title: Sample 455_Single HEK293T cell


title: Sample 454_Single HEK293T cell


title: Sample 691_Single mESC cell


title: Sample 690_Single mESC cell


title: Sample 453_Single HEK293T cell


title: AVAglio_GSM2225313

value: Off


title: AVAglio_GSM2225312

value: Grade III

value: Missing


title: Sample 689_Single mESC cell

value: Differentiated mESC


title: AVAglio_GSM2225311

value: Proneural


title: Sample 452_Single HEK293T cell


title: Sample 451_Single HEK293T cell


title: Sample 688_Single mESC cell

value: day 0


title: Sample 687_Single mESC cell


title: Sample 450_Single HEK293T cell


title: AVAglio_GSM2225315

value: Grade V


title: AVAglio_GSM2225309


title: AVAglio_GSM2225308

value: Female

value: Total resection

value: Methylated


title: Sample 692_Single mESC cell


title: A_TGFb_Inp_L_r2_R1

city: TALLAHASSEE

first: LAUREN

middle: A

last: COLE

state: Florida

address: 319 STADIUM DR

institute: FLORIDA STATE UNIVERSITY

description: Light MNase digest

library_source: genomic

data_processing:
Basecalls performed with CAVASA version v1.8.4
Sequencing data aligned to the HG19 genome using bowtie2 version 2.2.2, --wrapper basic -0 --end-to-end -p 23 --no-mixed --no-discordant -I 0 -X 500 -q -x  -S
Using samtools via the R package gyro (https://github.com/dvera/gyro), raw files converted from sam to bam files, minQual=10
Genome_build: hg19
Supplementary_files_format_and_content: Bed files were generated using bedtools via the R package travis (https://github.com/dvera/travis) and mat10 files were created using the package genmat (https://github.com/dvera/genmat). Nucleosome distributions were calculated by fragments per million for each bp in the 2kb surrounding each TSS.

molecule: genomic DNA

source_name: Human breast epithelial cells, immortalized

growth_protocol: MCF-10A and MCF-10Ca1a cell lines were grown in DMEM/Nutrient F12 (DMEM/F12) media supplemented with 5% Horse Serum, 14 mM NaHCO3, 10 µg/mL insulin, 2 mM L-glutamine, 20 ng/mL human EGF, 500 ng/mL Hydrocortisone and 100 ng/mL Cholera Toxin.

extract_protocol:
Nuclei were isolated in nucleus isolation buffer containing: 10 mM HEPES at pH 7.8, 2 mM MgOAc2, 0.3 M sucrose, 1 mM CaCl2, and 1% Nonidet P-40.  The nuclei were then pelleted by centrifugation at 1000g for 5 min at 4°C.
Using the NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB #E7370S/L), DNA sequencing libraries were prepared for the mononucleosomal-sized and sub-nucleosomal-sized fragments for each sample.  DNA was end-prepped using NEB Prep enzyme mix, end-repair reaction buffer (10X), and 30 ng of DNA for each samples, then held at 30 degrees Celsius for 30 minutes and then at 65 degrees Celsius for 30 minutes.  Adaptors were ligated onto the end-repaired samples by adding NEB Blunt/TA Ligase Master Mix, NEBNext Adaptor for Illumina, and Ligation Enhancer and incubating at 20 degrees Celsius for 15 minutes. The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted ligated products. The universal and indexed sequences were added by PCR using 23 ul of adaptor-ligated DNA fragments, NEBNext High Fidelity 2X PCR Master Mix, index primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina, and Universal PCR Primers provided in NEBNext Multiplex (NEB #E7335, #E7500) Oligos for Illumina. Then PCR was done for 8 cycles (not including the initial denaturation and final extension).  The adaptor-ligated DNA was cleaned up using AMPure XP beads to remove any unwanted products.  The libraries were quality-checked using Agilent 2100 Bioanalyzer High-Sensitivity. Across the libraries, the samples ranged between 200-400bp and there were no adapter or primer dimers.

treatment_protocol: For EMT induction, MCF-10A cells were treated with 5 ng/ml TGF-β1 (Redsystems) for 8 days. MCF-10A cells were transduced with the lentviral vector pLVTHM shH2A.Z as previously described (Domaschenz, 2017). GFP-positive cells were sorted 2 days post-transduction and further cultured for 8 days before being processed.

tag: tissue

value: Human breast epithelial cells

tag: cell type

value: TGF-beta-1 added to growth medium


title: Sample 449_Single HEK293T cell

tag: cell line


title: A_TGFb_Inp_L_r1_R1

description: Light MNase digest


title: Sample 685_Single mESC cell

tag: day of differentiation


title: Sample 448_Single HEK293T cell


title: Sample 684_Single mESC cell


title: A_TGFb_Inp_H_r2_R1

description: Heavy MNase digest


title: AVAglio_GSM2225305

value: On

value: Placebo

value: Mesenchymal

tag: mgmt status

value: Non-methylated


title: A_TGFb_Inp_H_r1_R1

description: Heavy MNase digest


title: AVAglio_GSM2225310

tag: age

value: Male

value: Partial resection

value: Grade IV


title: Sample 447_Single HEK293T cell

value: HEK293T cell


title: AVAglio_GSM2225304

tag: Sex

value: Missing


title: Sample 683_Single mESC cell

value: Differentiated mESC


title: A_TGFb_H2AZ_L_r2_R1

description: Light MNase digest


title: Sample 682_Single mESC cell

value: day 0


title: Sample 445_Single HEK293T cell


title: AVAglio_GSM2225303

tag: corticosteroids

value: Off


title: AVAglio_GSM2225307

tag: surgical status


title: Sample 686_Single mESC cell


title: AVAglio_GSM2225306

tag: treatment

value: Bevacizumab

value: Proliferative

value: Classical


title: AVAglio_GSM2225302

tag: phillips subtype

value: Proneural


title: Sample 444_Single HEK293T cell


title: Sample 680_Single mESC cell


title: A_TGFb_H2AZ_H_r2_R1

description: Heavy MNase digest

value: Human breast epithelial cells

value: TGF-beta-1 added to growth medium


title: A_TGFb_H2AZ_H_r1_R1

description: Heavy MNase digest


title: Sample 443_Single HEK293T cell


title: Sample 679_Single mESC cell


title: AVAglio_GSM2225301

tag: tcga subtype


title: AVAglio_GSM2225299

value: Total resection

tag: kps


title: A_shH2AZ_Inp_L_r2_R1

description: Light MNase digest

value: shRNA targeting H2A.Z, retroviral transduction


title: Sample 442_Single HEK293T cell


title: Sample 678_Single mESC cell


title: AVAglio_GSM2225298

value: Placebo

tag: mmse


title: Sample 441_Single HEK293T cell


title: Sample 677_Single mESC cell


title: A_shH2AZ_Inp_H_r2_R1

description: Heavy MNase digest


title: A_shH2AZ_Inp_L_r1_R1

description: Light MNase digest


title: AVAglio_GSM2225297

value: Male

value: On

tag: rpa

value: Grade V


title: Sample 440_Single HEK293T cell

value: HEK293T cell


title: A_TGFb_H2AZ_L_r1_R1

description: Light MNase digest


title: Sample 681_Single mESC cell


title: Sample 446_Single HEK293T cell


title: AVAglio_GSM2225295

value: Partial resection

value: Mesenchymal

value: Grade III

tag: os (diagnosis)

value: Missing


title: A_shH2AZ_Inp_H_r1_R1

description: Heavy MNase digest


title: Sample 439_Single HEK293T cell


title: Sample 676_Single mESC cell

value: Differentiated mESC

value: day 0


title: Sample 675_Single mESC cell


title: Sample 674_Single mESC cell


title: Sample 438_Single HEK293T cell


title: Sample 436_Single HEK293T cell


title: Sample 673_Single mESC cell


title: AVAglio_GSM2225293

value: Classical

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


title: Sample 672_Single mESC cell


title: Sample 435_Single HEK293T cell


title: AVAglio_GSM2225292

value: Off

value: Non-methylated


title: AVAglio_GSM2225294

value: Biopsy

value: Proneural


title: AVAglio_GSM2225290

value: Bevacizumab


title: AVAglio_GSM2225291

value: Proliferative

value: Grade IV


title: Sample 671_Single mESC cell


title: Sample 670_Single mESC cell


title: Sample 669_Single mESC cell


title: Sample 433_Single HEK293T cell


title: Sample 432_Single HEK293T cell


title: Sample 668_Single mESC cell


title: AVAglio_GSM2225289

value: Male

value: On

value: Placebo


title: Sample 431_Single HEK293T cell

value: HEK293T cell


title: Sample 667_Single mESC cell


title: Sample 430_Single HEK293T cell


title: AVAglio_GSM2225288

value: Total resection

value: Mesenchymal


title: RSK2KO rep2

city: Nashville

first: Deborah

last: Lannigan

state: TN

address: 2220 Pierce Ave

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads were aligned to human geneome (hg38) using CLC Workbench 10.0 (Qiagen).
Differential gene expression analysis was performed using CLC Workbench 10.0 (Qiagen).
Genome_build: hg38
Supplementary_files_format_and_content: CLC Workbench generated Excel files containing Gene Name, Chromosome Region, Identifier (ENSEMBLE), Max. Group Means, Fold-change, Log fold change, p-value, FDR-pvalue, and total counts, RPKM, TPM, CPM values for each sample.

extract_protocol:
Rneasy Mini Kit (Qiagen)
Library constructions were performed using TruSeq RNA Library Prep Kit (Illumina)

treatment_protocol: Cells were serum starved for 12-15h and treated with EGF(10nM)/E2(1nM) for 8h before RNA purified

value: ER+ breast cancer cells

tag: genotype/variation

tag: treated with


title: AVAglio_GSM2225287

value: Partial resection


title: AVAglio_GSM2225286

value: Grade III

value: Methylated


title: Sample 666_Single mESC cell

tag: cell line

value: Differentiated mESC

value: day 0


title: Sample 437_Single HEK293T cell

tag: day of differentiation


title: RSK2KO rep1

tag: cell type


title: WT rep2

source_name: MCF-7_wild type

value: wild type


title: AVAglio_GSM2225285

tag: age

value: Female

value: Off

value: Unclassified

value: Classical

value: Grade V

tag: mgmt status

value: Non-methylated


title: Sample 664_Single mESC cell


title: Sample 665_Single mESC cell


title: Sample 428_Single HEK293T cell


title: Sample 429_Single HEK293T cell


title: Sample 427_Single HEK293T cell


title: Sample 663_Single mESC cell


title: Sample 434_Single HEK293T cell


title: UHR Control 04

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.

source_name: UHR Control 04

tag: sample type

value: UHR control


title: WT rep1


title: UHR Control 03

source_name: UHR Control 03


title: Sample 662_Single mESC cell


title: Sample 426_Single HEK293T cell

value: HEK293T cell


title: Sample 425_Single HEK293T cell


title: UHR Control 07

source_name: UHR Control 07


title: UHR Control 02

source_name: UHR Control 02


title: Sample 661_Single mESC cell


title: UHR Control 06

source_name: UHR Control 06


title: UHR Control 01

source_name: UHR Control 01


title: Sample 660_Single mESC cell


title: Sample 423_Single HEK293T cell


title: UHR Control 05

source_name: UHR Control 05


title: Sample 659_Single mESC cell


title: UHR Control 11

source_name: UHR Control 11


title: Sample 422_Single HEK293T cell


title: Sample 658_Single mESC cell


title: Sample 421_Single HEK293T cell


title: Sample 657_Single mESC cell


title: Sample 420_Single HEK293T cell


title: UHR Control 09

source_name: UHR Control 09


title: Sample 656_Single mESC cell


title: UHR Control 08

source_name: UHR Control 08


title: Sample 655_Single mESC cell


title: Sample 424_Single HEK293T cell


title: Sample 418_Single HEK293T cell


title: Sample 654_Single mESC cell


title: Sample 417_Single HEK293T cell


title: Sample 653_Single mESC cell


title: G081 2082KD

city: Boston

first: Kamil

last: Krawczynski

state: MA

address: 60 Fenwood Rd

department: Neurosurgery

institute: Brigham and Womens Hospital

description: Gene expression after 72 hr in transfected cells

hyb_protocol: 1 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a final reaction volume of 100 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: glioblastoma patient derived cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: 3D culture in Neurobasal medium supplemented with glutamine, B27, EGF and FGF

extract_protocol: Total RNA was extracted from cells using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. The purity and concentration of RNA was evaluated with the NanoDrop ND-1000 (Thermo Fisher Scientific, Wilmington, DE).

treatment_protocol: Cells were transfected with either control or antisense oligos targeting circ2082 and harvested after 72h.

tag: disease state

value: glioblastoma

tag: tissue

value: brain

value: circ2082 KD


title: Sample 416_Single HEK293T cell


title: Sample 652_Single mESC cell

source_name: Single mESC cell


title: UHR Control 10

source_name: UHR Control 10


title: G088 control

tag: treatment

value: control


title: G062 control


title: G088 2082KD


title: Sample 415_Single HEK293T cell

source_name: Single HEK293T cell


title: Sample 419_Single HEK293T cell


title: EORTC_Patient_93526

tag: Sex

value: Male

tag: corticosteroids

value: On

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Proneural

tag: tcga subtype

value: Missing

tag: who category

tag: dataset

value: EORTC


title: G816 2082KD


title: Sample 651_Single mESC cell

value: Differentiated mESC

value: day 0


title: G081 control


title: EORTC_Patient_85886

value: Off

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)

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


title: G062 2082KD


title: G146 2082KD


title: rLP6_TSS_RNA2_2

city: Los Angeles

first: Guillaume

last: Urtecho

address: 607 Charles E. Young Drive

department: Molecular Biology

institute: University of California, Los Angeles

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.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 str. K-12 substr. MG1655

source_name: Escherichia coli

growth_protocol: Luria-Bertani (LB) Rich Media

extract_protocol: Qiagen RNeasy Midi Kit

tag: strain/background


title: G044 control


title: G816 control


title: EORTC_Patient_93524

tag: age

value: LOMUSTINE

value: Mesenchymal

tag: mgmt status


title: EORTC_Patient_85884

value: Proliferative


title: G044 2082KD

tag: disease state

tag: tissue


title: rLP6_TSS_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt


title: Sample 414_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: G146 control

value: glioblastoma

tag: treatment


title: Sample 650_Single mESC cell


title: Sample 413_Single HEK293T cell


title: Sample 649_Single mESC cell


title: rLP6_TSS_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt


title: EORTC_Patient_85888

tag: Sex

value: Female

tag: corticosteroids

tag: surgical status

tag: phillips subtype


title: EORTC_Patient_85882

tag: tcga subtype

tag: kps

tag: who category

tag: dataset


title: Sample 412_Single HEK293T cell


title: rLP6_TSS_RNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt


title: Sample 648_Single mESC cell


title: EORTC_Patient_84984

tag: mmse

tag: rpa

tag: os (diagnosis)

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


title: Sample 647_Single mESC cell


title: Sample 411_Single HEK293T cell


title: Sample 410_Single HEK293T cell


title: Sample 409_Single HEK293T cell


title: rLP6_TSS_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt

extract_protocol: Qiagen Puregene Yeast/Bact. Kit 2

tag: strain/background


title: EORTC_Patient_84558

tag: age

value: Unclassified

tag: mgmt status


title: EORTC_Patient_84366

value: Non-methylated


title: Sample 645_Single mESC cell

tag: cell line

tag: day of differentiation


title: Sample 644_Single mESC cell


title: rLP6_TSS_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt


title: Sample 408_Single HEK293T cell


title: EORTC_Patient_84364

tag: Sex

value: Male

tag: treatment


title: Sample 407_Single HEK293T cell


title: rLP6_TSS_DNA1_1


title: EORTC_Patient_84362

tag: corticosteroids

tag: surgical status


title: fLP3_TSS_RNA2_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: Sample 643_Single mESC cell


title: Sample 406_Single HEK293T cell


title: EORTC_Patient_84360

value: On

tag: phillips subtype

tag: tcga subtype


title: Sample 642_Single mESC cell


title: fLP3_TSS_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: rLP6_TSS_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: rLP6_Endo2_lb_expression_formatted_std.txt


title: Sample 405_Single HEK293T cell


title: Sample 641_Single mESC cell


title: Sample 646_Single mESC cell


title: fLP3_TSS_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: Sample 404_Single HEK293T cell


title: Sample 403_Single HEK293T cell


title: fLP3_TSS_RNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: Sample 640_Single mESC cell


title: Sample 639_Single mESC cell


title: EORTC_Patient_84282

value: BEVACIZUMAB+LOMUSTINE

tag: kps

tag: who category


title: Sample 402_Single HEK293T cell


title: Sample 638_Single mESC cell


title: EORTC_Patient_84278

tag: mmse

tag: dataset


title: fLP3_TSS_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: Sample 637_Single mESC cell


title: Sample 401_Single HEK293T cell


title: Sample 400_Single HEK293T cell


title: EORTC_Patient_84286

value: Classical

tag: rpa

tag: os (diagnosis)


title: EORTC_Patient_84274

value: Proneural

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

value: Missing


title: EORTC_Patient_84276

tag: age

value: EORTC


title: Sample 636_Single mESC cell

value: Differentiated mESC

value: day 0


title: EORTC_Patient_84270

tag: mgmt status


title: EORTC_Patient_84284


title: fLP3_TSS_DNA1_1

tag: strain/background


title: Sample 399_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: rLP5_TSS_RNA_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: rLP5_Endo2_lb_expression_formatted_std.txt


title: Sample 635_Single mESC cell


title: EORTC_Patient_84268

tag: Sex

tag: treatment


title: Sample 634_Single mESC cell


title: EORTC_Patient_84266

tag: corticosteroids

tag: surgical status

value: LOMUSTINE

value: Methylated


title: fLP3_TSS_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: Sample 397_Single HEK293T cell


title: rLP5_TSS_DNA_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: rLP5_Endo2_lb_expression_formatted_std.txt


title: Mettl3 WT fetal liver J2 RIP rep 2

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

description:
J2-RIP from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 2
Mettl3_J2_RNAseq_counts.txt
J2_WT_2

data_processing:
bulk RNA-seq: reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of differentially expressed genes were performed with the edgeR package in Bioconductor.
CUT&RUN: reads were aligned to the mouse genome (GRCm38.p5) with Bowtie2 v2.2.9, (--local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700). Duplicated reads were removed with Picard tools v2.9.0. Using the Gencode M15 annotation and bedtools coverage function (v2.26.0), the number of reads aligned around known transcription start sites (TSS) was determined considering a window of 3k nucleotides. Differential changes in H3K4me3 occupancy between WT and Mettl3-deficient LSK cells were identified with edgeR.
J2-RIP RNA-seq: duplicated reads were removed with FastUniq (v1.1). Reads generated from J2 RIP and INPUT samples were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a, –quantMode GeneCounts), using the Gencode M15 transcript annotation as transcriptome guide. Normalization with the TMM method and identification of J2 Mettl3-deficient enriched genes were performed with the edgeR package in Bioconductor.
single cell RNA-seq: single cell expression measurements (digital counts) were obtained from raw sequence data with Drop-seq tools v1.12. Reads were aligned to the mouse genome (GRCm38.p5) with STAR (version 2.5.3a) using the Gencode M15 transcript annotation as transcriptome guide. The final digital expression matrix was obtained selecting cells with at least 500 identified genes. Single cell expression data analysis was performed with Seurat 3.0.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Mettl3_bulk_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (bulk RNA-seq, Mettl3 depleted and wild type).  Mettl3_H3K4me3_TSS_3k_counts.txt: tab-delimited text file including transcript annotations (columns 1-6) and sample specific counts of H3K4me3 CUT&RUN reads aligned in the TSS region, considering a window of 3kb (Mettl3 depleted and wild type).  Mettl3_J2_RNAseq_counts.txt: tab-delimited text file including gene annotations (columns 1-4) and sample-specific counts of aligned reads (for both J2-RIP and INPUT samples, Mettl3 depleted and wild type).  Mettl3_singlecell_RNAseq_counts.txt: tab-delimited text file containing gene-specific and cell-specific counts (single cell RNA-seq, Mettl3 depleted and wild type).

source_name: Fetal Liver E14.5

growth_protocol: Mice were bred and maintained under specific-pathogen-free conditions at the animal facility of Yale University School of Medicine. One male and one female mice were put in one cage for mating. The pregnant female mice were sacrificed at E14.5 for fetal liver analysis.

extract_protocol:
bulk RNA-seq: RNA were extracted from E14.5 LSK cells following QIAGEN RNeasy Plus Micro Kit protocol.
CUT&RUN: Nuclei from E14.5 LSK cells were isolated with NE buffer, captured with Bio-Mag Plus Concanavalin A coated beads (Polysciences) and incubated with primary antibody for 2 hours at 4°C. After washing away unbound antibody with wash buffer, protein A-MNase was added to a final concentration of 700 ng/ml and incubated for 1 hour at 4 °C. The nuclei were washed again and placed in a metal block at 0°C. To activate protein A-MNase, CaCl2 was added to a final concentration of 2 mM. The reaction was carried out for 45 min and stopped by addition of an equal volume of 2XSTOP buffer. The protein-DNA complex was released by incubation for 10 min at 37 °C and centrifugation. DNA was extracted by QIAGEN PCR MiniElute Kit.
J2-RIP RNA-seq: Fresh E14.5 fetal livers were harvested. One part of the fetal liver was extracted by TRIzol Reagent for input RNA, the other part of the fetal liver was lysed in dsRIP lysis buffer. The fetal liver lysate was incubated with 5 ug SCICONS J2 antibody for 2 hours at 4 ℃. Protein G Dynabeads were washed in dsRIP lysis buffer and added to the lysate to allow J2-RNA complex formation for 1 hour at 4 ℃. Beads were washed four times with dsRIP lysis buffer, and J2 antibody pull-down RNA was extracted with TRIzol Reagent.
single cell RNA-seq: Microfluidic devices were infused with PBS and pressurized to remove air bubbles inside the microwells using a manually operated syringe with a closed outlet. E14.5 LSK single cell suspensions with 20,000 cells/50 µl in PBS + 1%BSA were pipetted on the inlet and drawn into the device. Once the channel was completely filled with cell solution, the fluid flow was stopped, and cells were allowed to settle by gravity. Excess cells were washed out with PBS, and mRNA capture beads at concentrations of 30,000–120,000 beads/50–150 µl were similarly loaded into the cell-loaded wells. Microwells were sealed with fluorinated oil (Fluorinert FC-40), the tubing at the outlet was disconnected, and the microfluidic devices were exposed to three freeze-thaw cycles with 5 min freezing (–80°C) alternating with 5 min thawing at room temperature. Following lysis, the microfluidic device was incubated for one hour inside a wet chamber for mRNA capture onto beads. After incubation, beads were collected into 6x saline-sodium citrate (SSC) buffer and washed twice with 6x SSC buffer prior to reverse transcription.
Bulk RNA-seq: polyA RNA selection
CUT&RUN: NEBNext Ultra II DNA Library Prep Kit
J2-RIP RNA-seq: rRNA depletion
single cell RNA-seq: Library preparation steps follow the same steps as in the DropSeq and SeqWell methods

tag: sequencing method

tag: mouse genotype

value: METTL3 wild type

tag: rip antibody

value: RIP antibody:SCICONS J2

tag: mouse model

value: Mettl3fl/fl mice without Vav-Cre

tag: tissue

value: liver


title: fLP3_TSS_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: fLP3_Endo2_lb_expression_formatted_std.txt


title: rLP5_TSS_DNA_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: rLP5_Endo2_lb_expression_formatted_std.txt


title: EORTC_Patient_84262

value: Off

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: who category

tag: dataset


title: Sample 396_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: rLP5_TSS_RNA_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: rLP5_Endo2_lb_expression_formatted_std.txt

tag: strain/background


title: EORTC_Patient_84264

tag: age

tag: Sex

value: Male

tag: corticosteroids

tag: treatment

tag: os (diagnosis)

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

tag: mgmt status


title: EORTC_Patient_84260

value: On

tag: surgical status

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

value: Unclassified


title: EORTC_Patient_84258

tag: tcga subtype

tag: kps

value: Missing


title: Sample 394_Single HEK293T cell


title: Sample 395_Single HEK293T cell


title: Sample 398_Single HEK293T cell


title: Sample 393_Single HEK293T cell


title: Mettl3 WT fetal liver J2 RIP rep 1

description:
J2-RIP from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 1
Mettl3_J2_RNAseq_counts.txt
J2_WT_1

tag: sequencing method

tag: mouse genotype

tag: rip antibody

tag: mouse model

tag: tissue


title: Mettl3 KO fetal liver J2 RIP rep 1

description:
J2-RIP from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 1
Mettl3_J2_RNAseq_counts.txt
J2_KO_1

value: METTL3 deficient

value: Vav-Cre Mettl3fl/fl mice


title: Sample 392_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: EORTC_Patient_84254

tag: age

tag: Sex

value: Female

value: Proneural

tag: mmse

tag: rpa

tag: who category

tag: dataset

value: EORTC


title: Mettl3 WT fetal liver J2 INPUT rep 2

description:
INPUT RNA-seq from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 2
Mettl3_J2_RNAseq_counts.txt
INPUT_WT_2

value: METTL3 wild type

value: RIP antibody:none


title: EORTC_Patient_84256

tag: corticosteroids

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: os (diagnosis)

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

tag: mgmt status


title: Mettl3 WT fetal liver J2 INPUT rep 1

description:
INPUT RNA-seq from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 1
Mettl3_J2_RNAseq_counts.txt
INPUT_WT_1

tag: sequencing method

tag: mouse genotype

tag: rip antibody

value: Mettl3fl/fl mice without Vav-Cre

value: liver


title: Sample 391_Single HEK293T cell

tag: cell line


title: EORTC_Patient_84252

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Non-methylated


title: Sample 390_Single HEK293T cell

value: HEK293T cell

tag: day of differentiation


title: Mettl3 KO fetal liver J2 INPUT rep 1

description:
INPUT RNA-seq from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 1
Mettl3_J2_RNAseq_counts.txt
INPUT_KO_1

tag: age

tag: mouse model

tag: tissue


title: Mettl3 KO fetal liver J2 INPUT rep 2

description:
INPUT RNA-seq from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 2
Mettl3_J2_RNAseq_counts.txt
INPUT_KO_2


title: Sample 389_Single HEK293T cell


title: EORTC_Patient_84250

tag: Sex

value: Male

tag: corticosteroids

value: Off

value: Classical

tag: mmse

tag: rpa

tag: who category

tag: dataset


title: EORTC_Patient_84176

value: On

tag: surgical status

tag: treatment

value: Mesenchymal

tag: os (diagnosis)

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

tag: mgmt status


title: Mettl3 KO fetal liver J2 RIP rep 2

description:
J2-RIP from E14.5 fetal liver of a Mettl3 deficient mouse, biological replicate 2
Mettl3_J2_RNAseq_counts.txt
J2_KO_2

tag: sequencing method

tag: mouse genotype

value: METTL3 deficient

tag: rip antibody

value: RIP antibody:SCICONS J2


title: Sample 388_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: Sample 387_Single HEK293T cell


title: EORTC_Patient_84174

tag: age

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Missing


title: C2B6_5M

city: Clemson

first: William

middle: S

last: Baldwin

state: South Carolina

address: 230 Parkway Dr

department: Biological Sciences

institute: Clemson University

data_processing:
Illumina Control Software/Real-Time Analysis (RTA) was used for base-calling.
Samples were sequenced to an average sequencing depth of 20,000,000 read pairs with a 2 x 150 paired-end module.
Quality metrics were checked using FastQC on all samples sequenced, and Trimmomatic was used to trim low quality bases.
Trimmed reads were aligned to the Mus musculus reference genome (GCF_000001635.25_GRCm38.p6) using GSNAP.  Subread feature counts software finds reads that aligned with known genes.
Raw read counts and EdgeR were used to determine differential gene expression.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Tab-deliminated text file includes raw counts for each sample.

source_name: liver

extract_protocol:
Livers were removed and stored at -80 degrees C. RNA was extracted from each treatment group (n=4) using Trizol.
Libraries were prepared using NEB Next Ultra RNA Library Prep kit.

treatment_protocol: Cyp2b-null and hCYP2B6-Tg mice were fed a high-fat diet (60% fat) for 16 weeks.

tag: strain

tag: genotype

tag: Sex


title: C2B6_4M


title: EORTC_Patient_84172

tag: corticosteroids

tag: surgical status

tag: mmse

tag: rpa

tag: who category

tag: dataset

value: EORTC


title: C2B6_3M


title: rLP5_TSS-Scramble_RNA2_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt

tag: strain/background


title: s10_22107_N

city: Shanghai

first: Jian

last: Wu

address: 138 Yixue Yuan Road

country: China

institute: Fudan University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: affymetrix-algorithm-name = ExpressionStat  affymetrix-algorithm-version = 5.0

label: biotin

source_name: precarcinoma-NASH-HCC liver tissues

label_protocol: Affymetrix protocol

extract_protocol: Paraffin-embedded paired tumor and peri-carcinoma tissues (n=4) were obtained from the Biorepository of Fudan University Institute of Liver Cancer.

value: female

tag: tissue

value: non-completely divided cirrhosis in the pre-carcinoma tissue


title: EORTC_Patient_82148

tag: treatment

value: LOMUSTINE

value: Proneural

tag: os (diagnosis)

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

tag: mgmt status


title: s10_29261_T

source_name: NASH-HCC liver tissues

tag: age

value: male

value: tumor tissue

tag: differentiation degree

value: differentiation degree II-III


title: s10_29261_N

value: pre-carcinoma tissue has no cirrhosis but 50% steatosis


title: Sample 385_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: s09_946_2_T

tag: Sex

value: differentiation degree II accompanying with obvious steatosis


title: s09_946_2_N

value: surounding liver tissue (pre-carcinoma tissue) without cirrhosis


title: EORTC_Patient_82146

value: Female

tag: corticosteroids

value: On

tag: phillips subtype

value: Proliferative

tag: tcga subtype

value: Classical

tag: kps


title: s11_17936_N

value: 40% steatosis in the pre-carcinoma tissue


title: Sample 386_Single HEK293T cell


title: rLP5_TSS-Scramble_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt


title: Sample 384_Single HEK293T cell


title: rLP5_TSS-Scramble_RNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt


title: s10_22107_T

value: differentiation degree II


title: Sample 383_Single HEK293T cell


title: EORTC_Patient_82144

value: Off

tag: surgical status

value: Mesenchymal

tag: mmse

tag: rpa

value: Methylated

tag: who category

value: EORTC


title: NULL_2M

tag: strain

tag: genotype

value: Male


title: Sample 382_Single HEK293T cell


title: NULL_1M


title: rLP5_TSS-Scramble_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt

tag: strain/background


title: NULL_3M


title: s11_17936_T

value: male

tag: tissue

value: tumor tissue


title: C2B6_2M


title: rLP5_TSS-Scramble_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt


title: rLP5_TSS-Scramble_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt


title: EORTC_Patient_82142

tag: age

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

tag: os (diagnosis)

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

tag: mgmt status

value: Missing

tag: dataset


title: EORTC_Patient_82140

tag: Sex

tag: corticosteroids

value: LOMUSTINE

tag: phillips subtype

value: Non-methylated


title: EORTC_Patient_82136

tag: surgical status

tag: tcga subtype

tag: kps


title: NULL_4M


title: Sample 381_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: rLP5_TSS-Scramble_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: endo_scramble_expression_formatted_std.txt


title: Sample 380_Single HEK293T cell


title: rLP5_TSS-Scramble_DNA1_1


title: Sample 379_Single HEK293T cell


title: EORTC_Patient_82132

tag: mmse

tag: rpa

tag: who category


title: Sample 378_Single HEK293T cell


title: rLP5_PeakTiling_RNA2_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: peak_tile_expression_formatted_std.txt

tag: strain/background


title: C2B6_2F

tag: strain

tag: genotype

value: Female


title: rLP5_PeakTiling_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: peak_tile_expression_formatted_std.txt


title: C2B6_1F


title: EORTC_Patient_82128

tag: age

tag: treatment

tag: os (diagnosis)

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


title: EORTC_Patient_82130

tag: Sex

tag: corticosteroids

value: On

value: Proliferative

tag: mgmt status

tag: dataset


title: Sample 377_Single HEK293T cell


title: rLP5_PeakTiling_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: peak_tile_expression_formatted_std.txt


title: EORTC_Patient_82126

tag: surgical status

tag: phillips subtype

tag: tcga subtype

tag: kps


title: Sample 376_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: rLP5_PeakTiling_RNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: peak_tile_expression_formatted_std.txt

tag: strain/background


title: NULL_4F

tag: strain


title: NULL_5F

tag: genotype


title: NULL_3F


title: Sample 374_Single HEK293T cell


title: rLP5_PeakTiling_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: peak_tile_expression_formatted_std.txt


title: NULL_1F


title: C2B6_5F


title: EORTC_Patient_82116

tag: age

value: Proneural

tag: mmse

tag: rpa

tag: who category


title: EORTC_Patient_82114

tag: Sex

tag: treatment

tag: os (diagnosis)

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


title: C2B6_4F


title: Sample 373_Single HEK293T cell


title: EORTC_Patient_82110

tag: corticosteroids

tag: surgical status

tag: mgmt status

tag: dataset


title: rLP5_PeakTiling_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: peak_tile_expression_formatted_std.txt


title: rLP5_PeakTiling_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: peak_tile_expression_formatted_std.txt


title: PyMT ChOVA assay 2

city: Houston

first: Kenneth

middle: H

last: Hu

state: Texas

address: 7455 Fannin Street

department: Immunology

institute: MD Anderson

data_processing:
Library strategy: ZipSeq
Base-calling using CellRanger v3.0.2 mkfastq
Demultiplexing using i7 index using CellRanger v3.0.2 mkfastq
Alignment using CellRanger v3.0.2 count to mouse reference assembly
Filter out cells below nUMI threshold
Genome_build: mm10 from 10X with added fluorophores
Supplementary_files_format_and_content: Raw count files with cell barcodes and gene names in .tsv and counts in .mtx

source_name: CD45+ immune cells from pymt chova tumor

extract_protocol:
10X Chromium v3 encapsulation and RT
10X recommended library construction

tag: cell type

tag: setting

value: live tumor microenvironment (TME)


title: Sample 372_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: EORTC_Patient_82108

tag: phillips subtype

tag: tcga subtype

tag: kps


title: PyMT ChOVA assay 1

value: CD45+ immune cells from pymt chova tumor


title: rLP5_PeakTiling_DNA1_1

tag: strain/background


title: Sample 371_Single HEK293T cell


title: Sample 375_Single HEK293T cell


title: EORTC_Patient_82104

tag: age

value: Off

value: Mesenchymal

tag: mmse

tag: rpa

tag: who category


title: Sample 370_Single HEK293T cell


title: B508_KO

city: Schwerzenbach

first: Katrien

last: De Bock

state: Zürich

address: Schorenstrasse 16

department: D-HEST

country: Switzerland

institute: ETH Zurich

data_processing:
Reads were aligned with STAR aligner with the options --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif
Alignments were counted with the featureCounts function
Genome_build: GRCm38
Supplementary_files_format_and_content: text files holding match counts per gene

source_name: adult brain MACS isolated mouse endothelial cells

growth_protocol: Brain endothelial cells were isolated from GLUT1EC-/- mice and WT littermates using MACS sorting from adult mice. ECs were sorted directly into RNA lysis buffer.

extract_protocol:
RNA was extracted immediately using PureLink™ RNA Mini Kit PureLink™ RNA Mini Kit (#12183020, Invitrogen, Merelbeke, Belgium).  RNA was stored  in -80 freezer till further processing for RNA-sequencing.   RNA was stored  in -80 freezer till further processing for RNA-sequencing.
The libraries were prepared following Illumina TruSeq stranded mRNA protocol. The quality of the RNA and final libraries was determined using an Agilent 4200 TapeStation System. The libraries were pooled equimolecularly and sequenced in an Illumina NovaSeq sequencer (single-end 100 bp) with a depth of around 20 Mio reads per sample.
Illumina TruSeq stranded mRNA protocol

value: Brain endothelial cells

tag: passages

value: primary uncultured endothelial cells

tag: strain

value: 8-weeks old mice

tag: genotype


title: EORTC_Patient_82100

tag: Sex

value: Male

tag: corticosteroids

tag: surgical status

tag: treatment

value: Classical

tag: os (diagnosis)

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

tag: mgmt status

value: EORTC


title: B505_KO

tag: cell type


title: rLP5_Frag_M9_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt

growth_protocol: M9 Minimal Media + .2% Glucose


title: rLP5_Frag_M9_RNA2_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt


title: EORTC_Patient_82112

value: BEVACIZUMAB+LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

value: Missing

tag: dataset


title: EORTC_Patient_82098

tag: age

value: Unclassified

tag: mmse

tag: rpa


title: rLP5_Frag_M9_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt

tag: strain/background


title: Sample 368_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: Sample 367_Single HEK293T cell


title: B506_WT

tag: passages

tag: strain

tag: genotype

value: WT


title: Sample 369_Single HEK293T cell


title: EORTC_Patient_82084

tag: Sex

tag: corticosteroids

value: On

tag: surgical status

tag: treatment

value: LOMUSTINE

tag: os (diagnosis)

value: Methylated

tag: who category


title: EORTC_Patient_82096

tag: phillips subtype

tag: tcga subtype

tag: kps

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

tag: mgmt status

value: Non-methylated


title: EORTC_Patient_82088

tag: age

tag: mmse

tag: rpa

tag: dataset


title: Sample 366_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: rLP5_Frag_M9_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt

tag: strain/background


title: B239_WT

tag: cell type

tag: passages

tag: strain

tag: genotype


title: Sample 365_Single HEK293T cell


title: rLP5_Frag_M9_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt


title: Sample 364_Single HEK293T cell


title: B240_KO


title: rLP5_Frag_M9_DNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt


title: Sample 363_Single HEK293T cell


title: EORTC_Patient_81648

tag: Sex

value: Female

tag: corticosteroids

tag: surgical status

tag: treatment

value: Proneural

tag: os (diagnosis)

tag: who category


title: rLP5_Frag_M9_RNA1_1


title: EORTC_Patient_81646

tag: age

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

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

tag: mgmt status


title: Sample 362_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: rLP5_frag_RNA2_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt

tag: strain/background


title: rLP5_frag_RNA2_1

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt


title: B241_WT

tag: cell type

value: Brain endothelial cells

tag: passages

value: primary uncultured endothelial cells

tag: strain


title: EORTC_Patient_81638

tag: Sex

tag: corticosteroids

value: Off

tag: mmse

tag: rpa

tag: dataset


title: rLP5_frag_RNA1_2

description:
Sequencing RNA barcode counts. Total RNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt


title: EORTC_Patient_81644

tag: age

value: Male

tag: surgical status

tag: treatment

tag: os (diagnosis)

tag: who category


title: EORTC_Patient_81650

tag: phillips subtype

tag: tcga subtype

value: Classical

tag: kps

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

tag: mgmt status

value: EORTC


title: EORTC_Patient_81642

value: BEVACIZUMAB+LOMUSTINE


title: rLP5_frag_RNA1_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt

tag: strain/background


title: Sample 361_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 36 h

city: Beijing

first: Keqian

last: Yang

address: NO.1 Beichen West  Road, Chaoyang District

institute: IMCAS

description: 36 h has A04_532.pair and A04_635.pair

hyb_protocol: Array hybridization, washing, scanning and data analysis were carried out according to NimbleGen Expression user’s guide and performed by CapitalBio Corporation (Beijing, China). The labeled samples were dried and resuspended according to hybridization kit manual (Roche NimbleGen). The transcription arrays were hybridized on a 12-bay Hybridization System (Roche NimbleGen) at 42°C for 14h, and then washed with NimbleGen wash buffers I, II and III supplied by NimbleGen, and finally dried in NimbleGen Microarray Dryer.

scan_protocol: The arrays were scanned using MS200 scanner (NimbleGen) with 2 µm resolution.

data_processing: The probe intensities were subjected to background correction, quantile normalization, and gene expression data were generated using Robust Multi-Array Analysis algorithm as implemented in the NimbleScan Software, version 2.6 (Roche NimbleGen, Inc.).

organism: Streptomyces coelicolor

source_name: Cells of streptomyces coelicolor M145-OA harvested at 18 h after fermentation, 18hA

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Streptomyces coelicolor M145-OA were cultivated at 28°C and shaken in 250 Erlenmeyer flasks containing 100 ml liquid supplemented minimum medium at 250 rpm.

extract_protocol: RNA was isolated by using Ambion RiboPure bacteria kit (Life Technologies, USA) according to the manufacturer’s protocol. Total RNA was purified by NucleoSpin® RNA clean-up kit (MACHEREY-NAGEL, Germany). RNA integrity and quantity were checked by denaturing agarose gel eletrophoresis and NanoDropND-1000 spectrophotometer (NanoDrop Technologies, USA).

treatment_protocol: Cell pellets were quickly harvested by fast filtration and flash frozen in liquid nitrogen, and then ground into powder.

tag: strain

value: An engineered M145-OA strain

source_name: Cells of streptomyces coelicolor M145-OA harvested at 36 h after fermentation, 36hB


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 60 h

description: 60 h has A07_532.pair and A07_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 60 h after fermentation, 60hB


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 42 h

description: 42 h has A05_532.pair and A05_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 42 h after fermentation, 42hB


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 48 h

description: 48 h has A06_532.pair and A06_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 48 h after fermentation, 48hB


title: Sample 360_Single HEK293T cell

value: HEK293T cell


title: Sample 359_Single HEK293T cell


title: EORTC_Patient_81500

tag: Sex

tag: corticosteroids

tag: mmse


title: rLP5_Frag_M9_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_M9_expression.txt


title: rLP5_frag_DNA2_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt


title: Sample 358_Single HEK293T cell


title: rLP5_frag_DNA2_1

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 1st technical replicate of the 2nd biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 30 h

description: 30 h has A03_532.pair and A03_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 30 h after fermentation, 30hB


title: cont3

city: Erzurum

first: Selçuk

last: Özdemir

address: Atatürk University Faculty of Veterinary Medicine

country: Turkey

institute: Atatürk University

data_processing:
Bowtie v2.0.6 (Langmead and Salzberg, 2012) was used to generate index of the reference genome and aligment of paired-end clean reads to the reference genome was perfomed with TopHat v2.0.9 (Trapnell et al., 2009).
The assembly of mapped transcripts for each sample was performed with Scripture (beta2) (Guttman et al., 2010) and Cufflinks (v2.1.1) (Trapnell et al., 2009; Trapnell et al., 2010) in a reference-based approach.
The calculation of protein coding potency of transcipts was performed using four sofware: CNCI (Coding-Non-Coding-Index) (score < 0) (Sun et al., 2013), CPC (Coding Potential Calculator) (score < 0) (Kong et al., 2007), Pfam-scan (E-value < 0.001) (Punta et al., 2012), and PhyloCSF (Lin et al., 2011). Predicted transcripts with coding potential in any/all of the four tools were filtered out.
FPKMs (fragments per kilo-base of exon per million fragments mapped) of both lncRNAs and coding genes in each sample were calculated with Cuffdiff (v2.1.1) (Trapnell et al., 2010). The summing the FPKMs of transcripts in each gene group was used to compute gene FPKMs.
Cuffdiff was used to determine differential expression in lncRNA transcript or gene expression data (Trapnell et al., 2010).
Genome_build: UMD3.1
Supplementary_files_format_and_content: FPKM

organism: Bos taurus

source_name: mammary gland

extract_protocol:
Mammary gland tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. The RNA sample was preparated by using total of 2 µg RNA. Firstly, Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA) was used to remove ribosomal RNA, and ethanol precipitation was perfomed to clean the rRNA free residue. Subsequently, the rRNA-depleted RNA by NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina® (NEB, USA) was used to generate sequencing cDNA libraries following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: mammary gland tissue

tag: agent


title: EORTC_Patient_81496

tag: age

value: On

tag: surgical status

tag: treatment

tag: rpa

tag: dataset


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 24 h

description: 24 h has A02_532.pair and A02_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 24 h after fermentation, 24hB


title: Sample 357_Single HEK293T cell


title: rLP5_frag_DNA1_2

description:
Sequencing DNA barcode counts. Genomic DNA extracted from an E. coli population with single barcoded promoter variants integrated into the nth-ydgr intergenic region. This is the 2nd technical replicate of the 1st biological replicate.
processed data file: U00096.2_frag-rLP5_LB_expression.txt


title: cont2


title: Global gene expression profile of Streptomyces coelicolor M145-OA at 18 h

description: 18 h has A01_532.pair and A01_635.pair

source_name: Cells of streptomyces coelicolor M145-OA harvested at 18 h after fermentation, 18hB


title: cont1


title: EORTC_Patient_81494

value: LOMUSTINE

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: os (diagnosis)

tag: who category


title: Sample 354_Single HEK293T cell

source_name: Single HEK293T cell

tag: cell line

tag: day of differentiation


title: infected2

value: Mycoplasma bovis


title: rLP5_frag_DNA1_1

source_name: Escherichia coli

tag: strain/background


title: Sample 355_Single HEK293T cell


title: EORTC_Patient_81492

tag: Sex

tag: corticosteroids

value: Proliferative

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

tag: mgmt status

value: Methylated


title: infected3

tag: tissue

tag: agent


title: Sample 353_Single HEK293T cell


title: Adjacent5

city: Taiyuan

first: Deping

last: Wang

address: 56 Xinjiannanlu Rd

institute: ShanXi Medical University

data_processing:
Quality control, fastp, 0.17.0
Alignment, HISAT, 2
Differential expression analysis, DESeq, 2
Genome_build: hg38
Supplementary_files_format_and_content: fpkm, gene expression level, Gene IDs are NCBI Gene IDs.

source_name: Adjacent normal tissue

extract_protocol:
Frozen gastric tissues were washed with pre-cold phosphate buffer solution (PBS) to remove residual blood. Total RNA was extracted using RNAiso Plus regent (TaKaRa, Osaka, Japan).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The harvested tissues were frozen in LN2 and stored at ultra-low temperature freezer for the following experiments

value: Adjacent normal gastric tissue

tag: subject id


title: EORTC_Patient_81486

tag: age

value: Female

tag: surgical status

tag: treatment

value: Mesenchymal

tag: mmse

tag: rpa


title: EORTC_Patient_81488

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: os (diagnosis)

value: Missing

tag: dataset


title: EORTC_Patient_81490

tag: Sex

value: Male

value: Off

tag: who category


title: EORTC_Patient_81498

tag: corticosteroids

value: Classical

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

value: Non-methylated

value: EORTC


title: Adjacent6

tag: tissue


title: Sample 351_Single HEK293T cell

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

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: HEK293T cell

tag: day of differentiation


title: Sample 352_Single HEK293T cell


title: Sample 350_Single HEK293T cell


title: Adjacent4

tag: subject id


title: EORTC_Patient_81484

tag: age

tag: surgical status

tag: mgmt status


title: Sample 356_Single HEK293T cell


title: Adjacent3


title: M4

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

data_processing:
Mapping with STAR_2.4.0a versus Sscrofa10.2 and Pseudomonas_aeruginosa_PAK_518 genome
Read counting with featureCounts (subread-1.4.6-p1-Linux-x86_64) with "--primary -g gene_name -p -s 1 -M " options
Statistical analysis performed on Sus scrofa  genes only. Genes which did not have at least 5 counts in at least 2 samples were filtered out.
Normalization performed with DESeq2
Genome_build: Scrofa10.2
Supplementary_files_format_and_content: Matrix of normalized counts with genes as rows and sample as columns.

organism: Sus scrofa

source_name: tracheal carina

growth_protocol: All experiments were conducted in accordance with the guidelines of the Institutional Animal Care and Use Committee at INRA. The protocol was approved by the French “Ministère de l’éducation nationale, de l’enseignement supérieur et de la recherche” (n° 1166-2015071615392426). Male and female CFTR+/- transgenic pigs were provided by the LMU Munich, Germany (Klymiuk, Mundhenk et al., 2012), transferred to INRA, Nouzilly (France) and mated to generate CFTR+/+, CFTR+/- and CFTR-/- (CF) piglets. Piglets were allowed to suckle colostrum and genotype was confirmed by multiplex PCR as described below. All experiments were performed within 12 hours of birth. Non-infected newborn piglets were sacrificed by electronarcosis followed by exsanguination in the experimental slaughterhouse. Newborn piglets infected by P. aeruginosa were sacrificed by an i.v. overdose of pentobarbital (Dolethal, Vétoquinol, France) and exsanguinated before collection of post-mortem samples.

extract_protocol:
1 µg of total RNA were depleted from ribosomal RNA with the Ribozero kit (Illumina Kit)
Illumina TruSeq Stranded Total RNA Sample Preparation.

treatment_protocol: Infection protocol: CFTR-/- and CFTR+/+ weighing 1 ± 0.2 kg were anesthetized with isoflurane (Vetflurane®). The trachea of each pig was then intubated and ventilated mechanically with a Fabius® Tiro® Ventilator (Dräger, Telford, USA). The ventilator settings were: volume controlled mode, tidal volume = 8-10 mL.kg-1, positive end-expiratory pressure = 5 cmH2O, respiratory rate = 15 breath.min-1, and inspiratory/expiratory ratio = 0.5, 50% oxygen in air. Piglets were inoculated with 2 mL of a suspension of luminescent P. aeruginosa strain PAKlux (5 x 10^6 cfu/mL) into the carina of trachea using an esophageal probe. Piglets were ventilated mechanically and monitored during the whole procedure and sacrificed 6 hours after infection.

tag: genotype

value: CFTR+/+

tag: infection

value: non infected

value: M

value: tracheal carina


title: M11

value: Non infected


title: M6


title: Female patient

city: Poznan

first: Ewelina

last: Bukowska-Olech

address: Rokietnicka 8

country: Poland

institute: Univeristy of Medical Sciences

hyb_protocol: according to standard Agilent protocol

scan_protocol: according to standard 8x60k manufacters' protocol using SureScan Dx Microarray Scanner

data_processing: Agilent gProcessedSignal

source_name: peripheral blood

label_protocol: according to standard Agilent protocol

extract_protocol: RNA and miRNA isolation protocol with the use of TRIreagent and chloroform

tag: gender

value: female

tag: disease state

value: Craniosynostosis

value: peripheral blood


title: EORTC_Patient_81480

extract_protocol: Not applicable

value: Female

value: On

tag: treatment

value: LOMUSTINE

tag: phillips subtype

value: Mesenchymal

tag: tcga subtype

tag: kps

tag: mmse

tag: rpa

tag: os (diagnosis)


title: F5

tag: Sex

value: F

tag: tissue


title: Sample 349_Single HEK293T cell

city: Stanford

first: Alina

last: Isakova

address: 318 Campus drive

institute: Stanford University

tag: cell line

tag: day of differentiation


title: Adjacent2

value: Adjacent normal gastric tissue

tag: subject id


title: Female control

value: control


title: Sample 348_Single HEK293T cell


title: F4


title: Adjacent1


title: EORTC_Patient_81472

city: South San Francisco

first: Radia

last: Johnson

address: 1 DNA Way

institute: Genentech

tag: age

value: Male

tag: corticosteroids

tag: surgical status

value: Classical

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

tag: mgmt status

value: Non-methylated

tag: who category

tag: dataset

value: EORTC


title: M7

tag: genotype

value: CFTR+/+

tag: infection

value: Infected with Pseudomonas aeruginosa

value: M


title: GC6

source_name: Gastric cancer tissue

value: Gastric cancer tissue


title: Sample 346_Single HEK293T cell

value: HEK293T cell


title: M10

value: tracheal carina


title: F8


title: Sample 347_Single HEK293T cell


title: EORTC_Patient_81482

value: Female

tag: treatment

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: mmse


title: EORTC_Patient_81470

tag: Sex

value: Off

value: BEVACIZUMAB+LOMUSTINE

value: Proneural

tag: rpa

tag: os (diagnosis)

value: Methylated


title: F1

value: F

tag: tissue


title: GC5

tag: subject id


title: GC7


title: Sample 343_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: Sample 344_Single HEK293T cell


title: Sample 345_Single HEK293T cell


title: EORTC_Patient_81462

tag: age

tag: corticosteroids

value: On

tag: surgical status

value: LOMUSTINE

value: Mesenchymal

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

tag: mgmt status

value: Missing


title: EORTC_Patient_81468

tag: treatment

value: Proliferative

value: Classical

value: Non-methylated

tag: who category

tag: dataset

value: EORTC


title: EORTC_Patient_81460

value: Male

tag: phillips subtype

tag: tcga subtype

tag: kps


title: Sample 342_Single HEK293T cell

value: HEK293T cell


title: EORTC_Patient_81458

tag: Sex

tag: mmse

tag: rpa


title: M5

tag: genotype

value: CFTR-/-

tag: infection

value: Non infected

value: M

tag: tissue

value: tracheal carina


title: GC3

value: Gastric cancer tissue

tag: subject id


title: M3

value: non infected


title: EORTC_Patient_81406

tag: age

tag: corticosteroids

value: Unclassified

tag: os (diagnosis)

value: Methylated


title: Sample 341_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: GC2


title: EORTC_Patient_81404

value: On

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

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

tag: mgmt status

tag: who category


title: EORTC_Patient_81402

tag: Sex

tag: phillips subtype

value: Proneural

tag: tcga subtype

tag: kps

tag: dataset


title: GC4

tag: tissue


title: M12

tag: genotype

tag: infection


title: Sample 339_Single HEK293T cell


title: MCF-7 RNA-seq

city: panjin

first: bo

middle: yu

last: liu

state: liaoning

address: Dagong Road 2

institute: Dalian University of Technology

data_processing:
base-calling: in-house BGISEQ-500 software
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene
peak-calling: MACS2 for ChIP-Seq; FPKM method was used in calculated RNA-seq expression level.
ChIPseeker for the annotation of peaks.
Genome_build: Genome_build: ChIP-Seq: hg19; RNA-Seq: hg19;
Supplementary_files_format_and_content: Supplementary_files_format_and_content: bigwig (bw): The signal intensity of binding.

source_name: human breast cancer cell MCF-7

extract_protocol:
MCF-7 and MCF-7/ADR cells were maintained in RPMI-1640 medium with 10% fetal calf serum. Approximately 2 x 10e7 cells were used for each COGC-seq or sWGA-seq assay. O-GlcNAz chromatin DNAs enriched by Streptavidin-magnetic beads were purified with the Qiagen PCR purification kit. For sWGA-seq, O-GlcNAc protein bound chromatin DNAs were enriched by sWGA-agarose beads. For RNA-seq, total RNA was extracted from the MCF-7 and MCF-7/ADR cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA). RNA libraries were prepared for sequencing using standard BGI protocols.
DNA-end repair, 3'-dA overhang and ligation of methylated sequencing adaptor. PCR amplification and size selection (usually 100-300bp, including adaptor sequence. Qualified library for sequencing. RNA-seq libraries were constructed using SMARTer cDNA library construction kit (Clontech, Takara Bio, CA, USA).

treatment_protocol: MCF-7 and MCF-7/ADR cells were cultured in RPMI-1640 medium with 10% fetal calf serum. MCF-7/ADR cells were cultured in the presence of a low concentration of Dox (1 µg/ml) and passaged for 1 week in drug-free medium before the experiments. For labeling, media was aspirated and the cells were washed with PBS. DMSO stocks of GalNAz was added to achieve the final treatment conditions and incubated for 48 h, with vehicle-only controls always included. ~2x107 S2 cells were used as a unit of cells for each experiment.

tag: morphology type

value: epithelial type of breast cancer cell


title: F3

value: F


title: EORTC_Patient_81398

tag: age

tag: corticosteroids

value: Off

value: LOMUSTINE

value: Mesenchymal

tag: mmse

tag: rpa

tag: os (diagnosis)


title: M8

value: Infected with Pseudomonas aeruginosa


title: ADR RNA-seq

source_name: human breast cancer cell MCF-7/ADR

growth_protocol: RPMI-1640 medium with 10% fetal calf serum.


title: sWGA-MCF-7 IP

tag: chip antibody/selection

value: sWGA Agarose beads


title: sWGA-ADR IP


title: Sample 337_Single HEK293T cell

tag: cell line

value: HEK293T cell

tag: day of differentiation


title: EORTC_Patient_81396

tag: Sex

value: Female

tag: surgical status

tag: treatment

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

tag: mgmt status

value: Missing

tag: who category

value: EORTC


title: M9

tag: genotype

value: CFTR-/-

value: M

tag: tissue

value: tracheal carina


title: M2

tag: infection


title: Sample 336_Single HEK293T cell


title: GC1

value: Gastric cancer tissue

tag: subject id


title: Sample 335_Single HEK293T cell


title: F7


title: EORTC_Patient_81392

tag: age

value: Male

tag: corticosteroids

tag: phillips subtype

tag: tcga subtype

tag: kps

tag: dataset


title: F2


title: EORTC_Patient_81386

value: Classical

tag: mmse

tag: rpa

tag: os (diagnosis)

value: Methylated


title: Sample 334_Single HEK293T cell

tag: cell line

tag: day of differentiation


title: F6

value: Non infected

tag: Sex

value: F


title: Sample 340_Single HEK293T cell


title: EORTC_Patient_81382

value: Off

tag: surgical status

tag: treatment

value: BEVACIZUMAB+LOMUSTINE

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

tag: mgmt status

value: Non-methylated

tag: who category


title: EORTC_Patient_81384

tag: age

value: Proneural


title: Sample 338_Single HEK293T cell

value: HEK293T cell


title: EORTC_Patient_81380

tag: corticosteroids

value: On

value: LOMUSTINE

value: Mesenchymal


title: sWGA-ADR-Input

tag: morphology type

value: epithelial type of breast cancer cell

tag: chip antibody/selection

value: sWGA Agarose beads


title: Sample 333_Single HEK293T cell


title: COGC-seq MCF_7-R2

value: GalNAz feeding, Click reaction, and streptavidin purification


title: Mettl3 WT fetal liver LSK single-cell RNA-seq rep 1

description:
single cell RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 1
Mettl3_singlecell_RNAseq_counts.txt
scRNAseq_WT_1

molecule: polyA RNA

source_name: Fetal Liver E14.5, Lin-Sca-1+c-Kit+ sorted cells

tag: sequencing method

value: single cell RNA-seq

tag: mouse genotype

value: METTL3 wild type

tag: mouse model

value: Mettl3fl/fl mice without Vav-Cre

tag: tissue

value: liver

tag: cell type

value: Lin-Sca-1+c-Kit+ sorted cells


title: COGC-seq MCF_7-R1


title: Mettl3 WT fetal liver LSK single-cell RNA-seq rep 2

description:
single cell RNA-seq from LSK cells sorted from E14.5 fetal liver of a Mettl3 wild type mouse, biological replicate 2
Mettl3_singlecell_RNAseq_counts.txt
scRNAseq_WT_2


title: Sample 332_Single HEK293T cell

tag: cell line


title: Sample 331_Single HEK293T cell

tag: day of differentiation


title: sWGA-MCF-7-Input