title: Chun-3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to Sscrofa10.2  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: oavry

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

value: C57BL/6 J

value: ovary

tag: age

value: 8-weeks old


title: Chun-2

status: Public on Aug 31 2022

type: SRA

city: Hangzhou

first: Dan

last: Zhang

address: Yuhang Road 866

country: China

institute: Zhejiang University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue

tag: genotype


title: NAc, Caudate, and Putamen [1318N]

city: Pittsburgh

first: WEI

last: ZONG

state: PA

address: 130 De Soto St

country: USA

institute: UNIVERSITY OF PITTSBURGH

data_processing:
Quality control using FastQC
Trim data using Trimmomatic
Alignment with HISAT2
Read counts using HTSeq
Assembly: Ensembl GRh38
Supplementary files format and content: Matrix tables with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Nac

extract_protocol:
Total RNA was extracted from the tissue samples using a combination of Trizol (Invitrogen, Carlsbad, CA) and RNeasy Lipid Tissue Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepped for RNA-sequencing using the TruSeq Stranded Total RNA Sample Preparation Kit (Illumina, San Diego, CA). 75bp paired-end dual-indexed sequencing was performed using the NextSeq 500 platform (Illumina, San Diego, CA).

tag: gender

value: Male

value: Nac

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: C9: control7

city: Milwaukee

first: Rebecca

last: Klaper

state: WI

address: 600 E Greenfield Avenue

institute: University of Wisconsin - Milwaukee

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence data was quality-assessed using FastQC v0.11.5
Illumina TruSeq 3’-anchored primers were clipped using Cutadapt v1.18
Quality-controlled data was pseudoaligned and sample-quantified against the GCF_016745375.1 GenBank release of the fathead minnow reference genome using Kallisto v0.45.0
Genome_build: reference genome
Supplementary_files_format_and_content: estimated counts, tsv text

organism: Pimephales promelas

source_name: adult

growth_protocol: Fish were fed TetraMin Tropical Flakes twice a day and were maintained at a 16:8 h light:dark cycle. Tanks were kept at 19-23° C.

extract_protocol:
Brain tissues were homogenized in TRIzol and RNA-purified using the Direct-zol RNA MiniPrep (Zymo Research, R2051).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 96 h exposure 100 m upstream and 100 m downstream of effluent outfall

tag: Sex

value: male

value: WT

value: wild type

value: brain

tag: treatment

value: untreated

value: adult

tag: exposure


title: NAc, Caudate, and Putamen [13175N]

tag: age


title: NAc, Caudate, and Putamen [1326N]

tag: tissue


title: Chun-1

tag: strain

tag: genotype


title: C8: control6

value: female


title: C5: control4


title: C6: control5


title: WT SSU Processome rep_2 DMS

city: Jupiter

first: xin

last: liu

state: FL

address: 130 Scripps Way

institute: The Scripps Research

data_processing:
Library strategy: DMS-MaPseq
removing adaptors with skewer
trimming reads with seqtk
running shapemapper aligning to 35S rRNA
… S.c.35S_rRNA_profile.txt were extracted for further analysis.
Supplementary_files_format_and_content: Extract "Modified_effective_depth" and "modified_rate" of each nucleotide for further analysis.

organism: Saccharomyces cerevisiae

source_name: ribosome SSU Processome intermediate

growth_protocol: Cells were grown in YPD till mid-log phase before harvesting.

extract_protocol:
Phenol chloroform  precipitation
RNA-seq (DMS-MaPseq)

treatment_protocol: 1% DMS, 30°C, 5min

value: treated

tag: molecule subtype

value: ribosomal RNA


title: NAc, Caudate, and Putamen [13112N]

tag: gender

tag: race

value: Black

tag: pmi


title: WT-4

value: C57BL/6 J

value: ovary


title: NAc, Caudate, and Putamen [13149N]

value: Female

tag: disease state

tag: sequence id

tag: library size


title: WT SSU Processome rep_4 DMS


title: WT SSU Processome rep_3 NC


title: WT SSU Processome rep_2 NC


title: WT-7

value: 8-weeks old


title: WT-1


title: WT SSU Processome rep_1 DMS


title: C4: control3


title: C2: control2


title: NAc, Caudate, and Putamen [13071N]

value: Male

value: Nac

value: White

tag: rin

tag: bmi

tag: ph

value: Accidental


title: C1: control1

tag: Sex

value: WT


title: WT SSU Processome rep_3 DMS

tag: treatment


title: WT SSU Processome rep_1 NC


title: NAc, Caudate, and Putamen [13045N]

tag: tissuestoragetime

tag: manner of death

value: Undetermined


title: NAc, Caudate, and Putamen [13068N]

tag: age

tag: tissue

value: match control

value: Natural


title: RNA-seq RE3

city: Xuzhou

first: Jiaxin

last: Qin

address: Jiefang South Road, No. 199, Xuzhou, Jiangsu, China

institute: Department of Urology, Xuzhou Clinical College of Xuzhou Medical University, Xuzhou, Jiangsu, China

description: rawcounts.csv

data_processing:
Total RNA was extracted using the Quick-RNA MicroPrep Kit (Zymo Research, CA, USA).
The concentration and integrity of mRNA were measured by Nanodrop2000 (Thermofisher, Waltham, MA).
The cDNA library was prepared with the NEBNext Ultra RNA with Poly-A selection kit and sequenced on an Illumina Hi-Seq 4000.
Kallisto (https://pachterlab.github.io/kallisto/) was used for pseudo alignment of the mRNA raw counts.
A small RNA-seq library was constructed with NEBNext Multiplex Small RNA Library Prep Kit for Illumina (#7560S). Small RNA-seq data were analyzed with the sRNAnalyzer pipeline. Adapter sequences were input to the pipeline to remove adapter contamination. The cleaned reads were then mapped to the human miRNA database to generate a count matrix, and thereafter DEseq2 was used to identify differentially expressed miRNA.
Assembly: hg38
Supplementary files format and content: FASTA format was used to represent the nucleotide sequence of each sample

source_name: Bladder cancer tissues

extract_protocol:
Total RNA was extracted using the Quick-RNA MicroPrep Kit (Zymo Research, CA, USA).
The library was prepared with the NEBNext Ultra RNA with Poly-A selection kit and sequenced on an Illumina Hi-Seq 4000.

value: Bladder cancer tissues

value: partial cystectomy


title: RNA-seq RE11

description: rawcounts.csv

value: laparoscopic radical cystectomy


title: NAc, Caudate, and Putamen [13069N]


title: RNA-seq RE15

description: rawcounts.csv

value: transurethral resection of the bladder tumor


title: RNA-seq RE2

description: rawcounts.csv


title: NAc, Caudate, and Putamen [1296N]


title: RNA-seq RE1

description: rawcounts.csv


title: NAc, Caudate, and Putamen [13032N]


title: NAc, Caudate, and Putamen [13017N]


title: NAc, Caudate, and Putamen [1298N]


title: RNA-seq NEW8

description: rawcounts.csv


title: NAc, Caudate, and Putamen [1268N]

value: Black


title: THP-1_Cells_Exposed_rep4

type: RNA

city: NANCY

first: Laëtitia

last: CHEZEAU

address: Campus Artem, 2 allée André Guinier

department: Institut Jean Lamour

country: France

institute: Université de Lorraine

hyb_protocol: 600 ng of Cy3-CTP-labelled cRNA (Specific Activity > 10 pmol Cy3 per µg cRNA) were fragmented at 60°C for 30 min in a reaction volume of 25 µL containing 25X Agilent Fragmentation Buffer and 10X Agilent Blocking Agent following the manufacturer’s instructions. On cRNA fragmentation completion, 25 µL of 2X Agilent Hybridization Buffer were added to the fragmentation mixture. The subsequent purified labelled cRNAs were hybridized to Agilent G4851B SurePrint G3 Human Gene Expression 8*60 K v2 microarrays (Agilent Technologies) at 65°C overnight (17h) in a rotating hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with Agilent Gene Expression Wash Buffer 1 and 1 min with 37°C Agilent Gene Expression Wash buffer 2.

scan_protocol: Slides were scanned immediately after washing using Agilent high-resolution scanner (G2505C) by setting: (i) one color scan channel for 8x60k array slides, (ii) scan area of 61x21.6 mm, (iii) scan resolution of 3 µm, (iv) dye channel to Green, (v) Tiff file dynamic range of 20 bits and (vi) Green PMT to 100 %.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and data were quantile normalized using the software Solo (http://www-microarrays.u-strasbg.fr/Solo/index.html)

source_name: Human monocytic cell line THP-1, Exposed to KNbO3 powder (25 ug/mL)

label_protocol: For each of the 8 samples (4 control and 4 exposed rats per time group), 100 ng of RNA were labelled with Cyanine 3-CTP using Low Input Quick Amp Labelling kits (One-Color Microarray-Based Gene Expression Analysis, version 6.7, Agilent Technologies) and purified (RNeasy Plus Mini kit, QIAGEN) according to the manufacturer's instruction . Dye incorporation and cRNA yield and quality were checked by spectrophotometry (BioSpec-nano, Shimadzu) and by electrophoresis (Agilent 2100 Bioanalyser).

growth_protocol: THP-1 human monocyte cell line is derived from a blood sample of a one-year old child suffering from acute monocytic leukemia and was obtained from American Type Culture Collection (ATCC, TIB-202TM, Manassas, VA, USA). Cells were grown in RPMI 1640 Medium (Gibco™ Paisley, UK) supplemented with 2% L- Glutamine, 1% penicillin/streptomycin, 0.05% amphotericin B, and 10% FBS (Sigma-Aldrich® (Saint Quentin Fallavier, France)). Cells were cultured in humid atmosphere (37 °C, 5% CO2).

extract_protocol: Cells were centrifuged to eliminate KNbO3 powder and then were lysed with buffer RLT plus containing β-mercaptoethanol (Qiagen®). Total RNA was extracted and purified using a RNeasy Plus Mini Kit, Qiagen® (cat. No 74136). RNA purity was assessed by spectrophotometry using a BioSpecNano® (Shimadzu). RNA quality and integrity was assessed by microfluidic capillary  electrophoresis using an RNA 6000 Nano Kit and 2100 Bioanalyzer (Agilent). All RNA samples were of high purity and integrity, as demonstrated by A260/A280 ratios above 2, and RNA integrity number between 7.9 and 9.3. Total RNA were stored at −80 °C until further use.

treatment_protocol: 1,5 million of THP-1 cells (n = 4) were cultured without (control) or with 25 µg/mL of KNbO3 powder (Sigma Aldrich CAS number 12030-85-2) in RPMI medium (20 mL in Griner Petri dish, diameter 10 cm).

tag: cell line

value: monocyte THP-1

value: Exposed to KNbO3 powder (25 ug/mL)

value: male

value: 1 year infant with acute monocytic leukemia


title: RNA-seq NEW11

description: rawcounts.csv


title: RNA-seq NEW9

description: rawcounts.csv


title: THP-1_Cells_Exposed_rep3


title: F659_P_REP2

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG Brainarray Custom CDF EntrezG version 24

label: biotin

source_name: Gene expression data of Xenograft from bladder tumor sample F659_K

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: PDX models of muscle-Invasive bladder cancers (MIBC) were generated by engrafting tumor tissues directly obtained from patients. Viable tumor tissue was macro-dissected and tumor pieces were then prepared for implantation. Three immunodeficient mice strains were used for tissue implantation, including athymic nude Swiss (Crl:Nu(lco)-Foxn1nu), NMRI nude (Rj:NMRI-Foxn1nu/nu) and Shrn (NOD.Cg-PrkdcscidHrhr/NCrHsd) mice. Grafts were implanted into the interscapular fat pad. When s.c. xenograft tumors reached ~ 1000-1500 mm3, they were serially transplanted for expansion into new mice. In addition, harvested xenograft material was cryopreserved for future implantations and/or fixed in 4% formalin for 24h before paraffin embedding and/or stored at -80°C for subsequent analyses. A model was defined as established when stable growth over at least three passages and regrowth after a freeze-thaw cycle could be observed. Take rate and passage time were recorded for every models and every individual passage. Tumor growth was determined weekly by a two-dimensional measurement with a caliper. Animals were sacrificed when tumor volume reached 2000 mm3.

extract_protocol: Each frozen PDX fragment was ground to powder and subdivided for triple RNA, DNA and protein extraction. RNA isolation was performed using trizol while DNA isolation used Phenol/Chloroform/Isoamyl Alcohol extraction

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: yes

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

value: Cisplatin/Gemzar

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: BLCU-014_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-0014_T

tag: tissue type

tag: replicate

value: no

value: BCG

value: High grade non-infiltrating urothelial carcinoma


title: RNA-seq NEW7

description: rawcounts.csv

tag: tissue

value: Bladder cancer tissues

tag: treatment

value: transurethral resection of the bladder tumor


title: T525_P_REP2

source_name: Gene expression data of Xenograft from bladder tumor sample T525_K

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: tumor sample characteristics -variant (who)

value: Poorly differentiated Squamous differentiation

value: Yes

value: Poorly differentiated high grade invasive urothelial carcinoma partially associated with squamous cell carcinoma and Cis


title: THP-1_Cells_Exposed_rep2

tag: cell line

value: monocyte THP-1

value: Exposed to KNbO3 powder (25 ug/mL)

tag: gender

value: male

tag: age

value: 1 year infant with acute monocytic leukemia


title: THP-1_Cells_Control_rep3

source_name: Human monocytic cell line THP-1, control

value: control


title: NAc, Caudate, and Putamen [1247N]

value: Female

value: Nac

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: H1074_P

source_name: Gene expression data of Xenograft from bladder tumor sample H1074_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

tag: paired

tag: pair name

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

tag: patient characteristics -treatment  post-surgery

value: No

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

value: Squamous differentiation

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma with squamous cell inflexion

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: THP-1_Cells_Control_rep2

tag: cell line

value: monocyte THP-1

tag: treatment

tag: gender

tag: age


title: THP-1_Cells_Control_rep4

value: male


title: F456_P

source_name: Gene expression data of Xenograft from bladder tumor sample F456_K

tag: tissue type

tag: replicate

tag: paired

tag: pair name

tag: batch

tag: year of establishment

value: Male

value: Cisplatin/Gemzar Taxol Palliative treatment

tag: tumor sample characteristics -variant (who)

value: Glandular Squamous differentiation

value: urothelial carcinoma with glandular and squamous cell inflexion

value: Upper tract


title: NAc, Caudate, and Putamen [1244N]

tag: tissue

value: Nac

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Accidental


title: RNA-seq NEW6

description: rawcounts.csv

value: Bladder cancer tissues

tag: treatment

value: transurethral resection of the bladder tumor


title: BLCU-013_T

source_name: Gene expression data of bladder tumor sample BLCU-0013_T

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: Cisplatin + Gemcitabin

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: ypT3a N0 R1

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -associated cis

value: No

tag: tumor sample characteristics -classification

value: infiltrating papillary urothelial carcinoma

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: BLCU-013_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-0013_T

value: Xenograft from tumor

tag: pair name

tag: batch

tag: year of establishment

value: Male

value: Bladder

value: stable


title: NAc, Caudate, and Putamen [1255N]

tag: age

tag: gender

tag: tissue

value: Nac

tag: race

value: Black

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: miRNA-seq RE15

value: Bladder cancer tissues

tag: treatment


title: NAc, Caudate, and Putamen [1211N]

value: Female

value: White

value: Natural


title: THP-1_Cells_Exposed_rep1

tag: cell line

value: monocyte THP-1

value: Exposed to KNbO3 powder (25 ug/mL)

value: male

value: 1 year infant with acute monocytic leukemia


title: miRNA-seq RE13

value: laparoscopic radical cystectomy


title: miRNA-seq RE11


title: miRNA-seq RE8

value: transurethral resection of the bladder tumor


title: NAc, Caudate, and Putamen [1195N]


title: NAc, Caudate, and Putamen [1188N]


title: miRNA-seq RE9


title: NAc, Caudate, and Putamen [1196N]

value: Accidental


title: THP-1_Cells_Control_rep1

value: control


title: BLCU-011_T

source_name: Gene expression data of bladder tumor sample BLCU-0011_T

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: patient characteristics - gender

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: radiotherapy + Cisplatin + Gemcitabin

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: ypT4a N0 R0

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Plasmacytoid

tag: tumor sample characteristics -associated cis

value: No

tag: tumor sample characteristics -classification

value: transitional cell carcinoma, with independant cells contingent

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: no variant in PDX

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: Vessel_Disease model rat_male_rep4

city: Imabari

first: Masashi

last: Mukohda

state: Ehime

address: 1-3 Ikoinooka, Imabari

country: Japan

institute: Okayama University of Science

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol /ug ) was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL 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 65Â°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 37Â°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 (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1 (Agilent) using default parameters (Grid: 074036_D_F_2020909) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Rattus norvegicus

source_name: Vessel from disease model rat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA, United States).  Dye incorporation and cRNA yield were checked with the NanoDrop ONEc Spectrophotometer (Thermo Fisher Scientific, Waltham, MA, United States).

extract_protocol: Total RNA was prepared using Trizol, and RNA integrity was assessed using the 2200 TapeStation systems (Agilent Technologies, Santa Clara, CA, United States).

tag: tissue

value: Vessel

tag: disease state

value: Hypertensive Disease

tag: Sex

value: male

tag: strain

value: Wistar-Kyoto


title: Vessel_Disease model rat_male_rep3


title: NAc, Caudate, and Putamen [1207N]

tag: age

tag: gender

value: Nac

tag: race

value: White

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: Vessel_Disease model rat_male_rep1


title: BLCU-006_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-006_T

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: BCG

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: pT4a N2 R1

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: infiltrating urothelial carcinoma

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)


title: BLCU-011_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-0011_T

tag: tissue type

value: Male

value: radiotherapy + Cisplatin + Gemcitabin

value: ypT4a N0 R0

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Plasmacytoid

value: No

value: transitional cell carcinoma, with independant cells contingent

tag: pdx characteristics -latency  (days)


title: Vessel_Disease model rat_male_rep2

tag: tissue

value: Vessel

tag: disease state

value: Hypertensive Disease

tag: Sex

value: male

tag: strain

value: Wistar-Kyoto


title: NAc, Caudate, and Putamen [1178N]

source_name: Nac

tag: age

tag: gender

value: Female

value: Nac

tag: race

value: Black

tag: pmi

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: Vessel_Control rat_male_rep3

source_name: Vessel from control rat

value: Control


title: BLCU-006_T

source_name: Gene expression data of bladder tumor sample BLCU-006_T

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: BCG

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: pT4a N2 R1

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: infiltrating urothelial carcinoma

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)


title: Vessel_Control rat_male_rep4

tag: tissue

value: Vessel

tag: disease state

tag: Sex

tag: strain


title: miRNA-seq RE6

source_name: Bladder cancer tissues

value: Bladder cancer tissues

tag: treatment

value: transurethral resection of the bladder tumor


title: NAc, Caudate, and Putamen [1171N]

tag: age

tag: gender

value: Male

tag: race

value: White

tag: pmi

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: miRNA-seq RE5

value: partial cystectomy


title: Vessel_Control rat_male_rep2

value: male

value: Wistar-Kyoto


title: miRNA-seq RE7


title: NAc, Caudate, and Putamen [1159N]

value: Nac

value: Natural


title: miRNA-seq RE4


title: BLCU-001_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-001_T

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: pT3b N2 M1 R1

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Poorly differentiated Sarcomatoid

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: poorly differentiated urothelial carcinoma with sarcomatoid contingent

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: miRNA-seq RE3

tag: tissue

value: Bladder cancer tissues

tag: treatment


title: NAc, Caudate, and Putamen [1121N]

tag: age

tag: gender

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: Vessel_Control rat_male_rep1

value: Vessel

value: Control

tag: Sex

tag: strain


title: NAc, Caudate, and Putamen [1105N]

value: Male

value: White


title: miRNA-seq RE2

value: laparoscopic radical cystectomy


title: B1032_P3

source_name: Gene expression data of Xenograft from bladder tumor sample B1032_K

tag: tissue type

tag: replicate

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: BCG

tag: patient characteristics -treatment  post-surgery

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

value: Yes

tag: tumor sample characteristics -classification

value: urothelial carcinoma

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: P977_P3

source_name: Gene expression data of Xenograft from bladder tumor sample P977_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

value: MVAC

tag: tumor sample characteristics -variant (who)

value: Micropapillary

value: No

value: urothelial carcinoma with micropapillary component


title: miRNA-seq RE1

tag: tissue

value: Bladder cancer tissues

tag: treatment


title: UCB-exosome_GA≥37w_4

city: Changzhou

first: huaiyan

last: Wang

state: Jiangsu

address: Dingxiang Road

department: Department of Neonatology

institute: Changzhou Maternity and Child Health Care Hospital of Nanjing Medical University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml 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 65Â°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 37Â°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 9.1 (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: umbilical cord blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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.

extract_protocol: Then, Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes from preterm newborn with and without BPD.

treatment_protocol: UCB specimens were obtained from the umbilical vein right after fetal delivery. Then, Microarray analysis was performed to compare the RNA profiles of UCB-derived exosomes.

tag: gestational age

tag: gender

value: female


title: BLCU-003_P

source_name: Gene expression data of Xenograft from bladder tumor sample BLCU-003_T

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Female

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: pT4a Rx

value: Urothelial carcinoma

value: Squamous differentiation

value: infiltrating transitional cell carcinoma


title: UCB-exosome_GA≥37w_3


title: NAc, Caudate, and Putamen [1092N]

tag: age

value: Nac

tag: race

value: Black

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: UCB-exosome_GA≥37w_2

tag: gestational age

tag: gender


title: miRNA-seq NEW13

tag: tissue

tag: treatment

value: transurethral resection of the bladder tumor


title: R1056_P3

source_name: Gene expression data of Xenograft from bladder tumor sample R1056_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -treatment  post-surgery

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -variant (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma with squamous (focal) differentiation

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: More Squamous variant

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: NAc, Caudate, and Putamen [1069N]

tag: age

tag: gender

value: Male

tag: tissue

tag: race

value: White

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: L987_P3

source_name: Gene expression data of Xenograft from bladder tumor sample L987_K

tag: tissue type

tag: replicate

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Squamous cell carcinoma

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: squamous cell carcinoma

tag: tumor sample characteristics -primary site

value: stable


title: NAc, Caudate, and Putamen [1099N]

tag: age

tag: gender

value: Female

tag: tissue

value: Nac

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime


title: NAc, Caudate, and Putamen [1044N]

tag: manner of death

value: Natural


title: M1030_P3

source_name: Gene expression data of Xenograft from bladder tumor sample M1030_K

tag: tissue type

tag: replicate

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Sarcomatoid

value: High grade invasive urothelial carcinoma with sarcomatoid differentiation

value: Upper tract

tag: pdx characteristics - histology (pdx)

value: No variant in PDX

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: A54_P7

source_name: Gene expression data of Xenograft from bladder tumor sample A54_K

value: Xenograft from tumor

value: no

value: yes

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: high grade papillary urothelial carcinoma

tag: tumor sample characteristics -primary site


title: NAc, Caudate, and Putamen [1067N]

tag: age

tag: gender

value: Male

tag: tissue

tag: race

value: White

tag: pmi

tag: disease state

value: match control

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death


title: miRNA-seq NEW11

value: Bladder cancer tissues

tag: treatment

value: laparoscopic radical cystectomy


title: miRNA-seq NEW14


title: W787_P3

source_name: Gene expression data of Xenograft from bladder tumor sample W787_K

tag: tissue type

tag: replicate

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: Cisplatin + Gemcitabin

tag: patient characteristics -treatment  post-surgery

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -variant (who)

value: Poorly differentiated

tag: tumor sample characteristics -associated cis

value: No

value: poorly differentiated urothelial carcinoma

value: Bladder

tag: pdx characteristics - histology (pdx)

value: stable

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: NAc, Caudate, and Putamen [1088N]

tag: age

tag: gender

tag: tissue

value: Nac

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Accidental


title: miRNA-seq NEW9

tag: treatment

value: transurethral resection of the bladder tumor


title: UCB-exosome_GA≥32w_4

tag: gestational age

value: male


title: B1032_K

source_name: Gene expression data of bladder tumor sample B1032_K

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: BCG

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -associated cis

value: Yes

tag: tumor sample characteristics -classification

value: urothelial carcinoma

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)


title: UCB-exosome_GA≥32w_2

tag: gestational age

tag: gender

value: female


title: UCB-exosome_GA＜32w_2


title: F753_P3

source_name: Gene expression data of Xenograft from bladder tumor sample F753_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

tag: paired

value: Male

value: Cisplatin/Gemzar

value: high grade urothelial carcinoma

tag: pdx characteristics -latency  (days)


title: UCB-exosome_GA≥32w_3


title: UCB-exosome_GA＜32w_3


title: A981_P3

source_name: Gene expression data of Xenograft from bladder tumor sample A981_K

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: No

value: Carboplatin/Gemzar Taxotere

value: Bladder

value: stable


title: A981_K

source_name: Gene expression data of bladder tumor sample A981_K

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm


title: miRNA-seq NEW12

tag: tissue

value: Bladder cancer tissues

tag: treatment

value: transurethral resection of the bladder tumor


title: UCB-exosome_GA≥37w_1

value: male


title: NAc, Caudate, and Putamen [10025N]

source_name: Nac

tag: age

value: Nac

tag: race

value: Black

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Natural


title: UCB-exosome_GA＜32w_4

tag: gestational age

tag: gender


title: miRNA-seq NEW8

value: partial cystectomy


title: miRNA-seq NEW7


title: P977_K

source_name: Gene expression data of bladder tumor sample P977_K

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: MVAC

tag: patient characteristics -treatment  post-surgery

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Micropapillary

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma with micropapillary component

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: NAc, Caudate, and Putamen [10023N]

tag: age

tag: gender

value: Female

tag: tissue

tag: race

tag: pmi

tag: disease state

tag: sequence id

tag: library size

tag: rin

tag: bmi

tag: ph

tag: tissuestoragetime

tag: manner of death

value: Suicide


title: UCB-exosome_GA≥32w_1

tag: gestational age


title: NAc, Caudate, and Putamen [1034N]

value: White

value: match control


title: NAc, Caudate, and Putamen [10003N]

value: Male

value: Accidental


title: miRNA-seq NEW6

source_name: Bladder cancer tissues

value: Bladder cancer tissues

tag: treatment

value: transurethral resection of the bladder tumor


title: miRNA-seq NEW5


title: R1056_K

source_name: Gene expression data of bladder tumor sample R1056_K

tag: tissue type

tag: replicate

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -variant (who)

value: Squamous differentiation

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma with squamous (focal) differentiation

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

value: More Squamous variant

tag: pdx characteristics -inclusion rate (percent)


title: MDA134-shFOXA1-ND-WM-E2-ER input

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

library_source: genomic

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

molecule: genomic DNA

source_name: Breast carcinoma cell line

growth_protocol: MDA134 containing a Dox inducible shFOXA1 were cultured for 3 days in presence of Dox

extract_protocol:
Chromatin was extracted with a sarkosyl based buffer and sonicated to a size range of 200-300 bp
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep Kit (Takara Bio USA)

treatment_protocol: Cells were treated with 10nM E2 for 45 minutes

tag: cell line

value: MDA_MB134 breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: ER (Ab10 Thermo Fisher Scientific, SC-543 Santa cruz)


title: MDA134-shFOXA1-ND-WM-Tam-ER rep2

value: Tamoxifen


title: miRNA-seq NEW4

tag: tissue

tag: treatment


title: miRNA-seq NEW3


title: W787_K

source_name: Gene expression data of bladder tumor sample W787_K

tag: tissue type

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Cisplatin + Gemcitabin

value: Urothelial carcinoma

value: Poorly differentiated

value: poorly differentiated urothelial carcinoma

value: stable

tag: pdx characteristics -latency  (days)


title: miRNA-seq NEW2

value: Bladder cancer tissues

value: transurethral resection of the bladder tumor


title: MDA134-shFOXA1-ND-WM-E2-ER rep2


title: F753_K

source_name: Gene expression data of bladder tumor sample F753_K

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

value: Cisplatin/Gemzar

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: high grade urothelial carcinoma


title: M1030_K

source_name: Gene expression data of bladder tumor sample M1030_K

value: Female

tag: tumor sample characteristics -variant (who)

value: Sarcomatoid

value: High grade invasive urothelial carcinoma with sarcomatoid differentiation

tag: tumor sample characteristics -primary site

value: Upper tract

tag: pdx characteristics - histology (pdx)

value: No variant in PDX

tag: pdx characteristics -inclusion rate (percent)


title: miRNA-seq NEW1

tag: tissue

tag: treatment


title: T505_P3

source_name: Gene expression data of Xenograft from bladder tumor sample

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

tag: paired

tag: pair name

tag: batch

value: MVAC

value: poorly differentiated urothelial carcinoma (G2-3)

value: Bladder

value: PDX stable but no original accessible tumor


title: T525_K

source_name: Gene expression data of bladder tumor sample T525_K

value: Tumor

value: yes

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: Urothelial carcinoma

value: Poorly differentiated Squamous differentiation

value: Yes

value: Poorly differentiated high grade invasive urothelial carcinoma partially associated with squamous cell carcinoma and Cis

value: stable

tag: pdx characteristics -latency  (days)


title: MDA134-shFOXA1-ND-WM-Tam-ER rep1

tag: cell line

value: MDA_MB134 breast carcinoma cell line

tag: agent

value: Tamoxifen

tag: chip antibody

value: ER (Ab10 Thermo Fisher Scientific, SC-543 Santa cruz)


title: UCB-exosome_GA＜32w_1

source_name: umbilical cord blood

tag: gestational age

tag: gender

value: male


title: UCB-exosome_BPD_4

value: female


title: UCB-exosome_BPD_2


title: UCB-exosome_BPD_1


title: MDA134-shFOXA1-DOX-WM-Tam-ER rep2

value: Tamoxifen + DOX


title: MDA134-shFOXA1-DOX-WM-E2-ER rep2

value: Estrogen + DOX


title: THP1_RV_rep3

city: DongGuan

first: JiaJun

address: No. 1 Xincheng Road

institute: Guangdong Medical University

data_processing:
Illumina Casava1.8 software used for base calling.
The Trim-Galore software was used to remove adapters in the sequence, which sequences with low quality and N and the sequences shorter than the length threshold.
The HISAT2 software (version 2.2.0) was used to compare the sequence with the reference genome.
Read count extraction and normalization were quantitatively analyzed by using the Stringtie software.
We perform expression level for mRNAs by calculating FPKM and estimate the expression levels of all transcripts by using the software StringTie (version 2.1.2).
Assembly: mm9

growth_protocol: The human THP-1 monocyte cell line was maintained in RMPI 1640 supplemented with 1% Penicillin-Streptomycin Solution and 10% heat-inactivated foetal bovine serum (FBS; Life Technologies, Carlsbad, CA, USA) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated from THP-1 cells and H37Rv infected cell using Trizol reagent according to the manufacturer′s instructions. The total RNA were then subjected to accurate detection of RNA integrity using Agilent 2100 BioAnalyzer. To obtain mRNA, mRNA with polyadenylate tails can be enriched by magnetic beads with oligo-thymine beads attached. At last, Illumina sequencing is performed after pooling of different libraries according to the requirements of effective concentration and target unload data amount.
RNA libraries for RNA-seq were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Before mycobacterium tuberculosis infection, the THP-1 cells were treated with 50ng/ml PMA for 24 hours, so that THP-1 cell can be induced into macrophages. The cells was then washed with PBS at 37 ℃ for 3 times for subsequent experiments.  Then, mycobacterium tuberculosis H37Rv(MOI=1) suspension was added into macrophages and mixed evenly. After incubating for 6 h in the incubator, the supernatant was discarded and the cells were washed with PBS at 37 ℃ for 3 times before subsequent experiments.

value: H37Rv infected


title: THP1_RV_rep2


title: HS-5, NOMO KO-3

city: Salamanca

first: Rogelio

last: González-Sarmiento

state: Salamanca

address: Alfonso X el Sabio, sn

department: Medicine

country: Spain

institute: University of Salamanca

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip ClariomS human Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw microarray data were quantile normalized, background corrected and log2 transformed by the Robust Multi-array Average (RMA) procedure in the oligo R package (v.1.54.1) using a custom cdf reference from BrainArray (v.25.0.0). Differential gene expression analyses were carried out with the limma package (v.3.46.0). Microarray batch-effects were adjusted through the ComBat function from the sva package.

label: Biotin

source_name: stromal cell line HS-5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The colorectal cancer cell lines HT-29 and HCT-116 and the human stromal cell line HS-5 were acquired from ATCC (American Type Culture Collection). The cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma-Aldrich) supplemented with 10% of fetal bovine serum (FBS) (Sigma-Aldrich) and 1% penicillin/streptomycin (Gibco Life Technologies, Grand Island, NY). All cells were incubated at 37°C in a 5% CO2. The presence of mycoplasma was routinely checked with MycoAlert kit (Lonza, Basel, Switzerland) and only mycoplasma free cells were used in all subsequent experiments.

extract_protocol: Total RNA was extracted from the NOMO wild type and knockout HT-29, HCT-116 and HS-5 clones using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. DNA was removed from the samples using RNase-free DNase Set (Qiagen, Hilden, Germany). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

treatment_protocol: CRISPR/cas9 technology was used to deleted endogenous NOMO1.

tag: tissue

value: Bone marrow

tag: cell type

value: Non tumoral

tag: genotype

value: NOMO KO


title: T525_P3_REP1

source_name: Gene expression data of Xenograft from bladder tumor sample T525_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

value: no

value: yes

value: Male

value: No

tag: patient characteristics -treatment  post-surgery

value: Cisplatin/Gemzar

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -variant (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

tag: tumor sample characteristics -primary site

value: Bladder

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)


title: MDA134-shFOXA1-DOX-WM-E2-ER rep1

tag: cell line

value: MDA_MB134 breast carcinoma cell line

tag: agent

tag: chip antibody


title: HS-5, NOMO KO-1

tag: tissue


title: S225_K

source_name: Gene expression data of bladder tumor sample S225_K

value: Tumor

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: Palliative treatment

value: Urothelial carcinoma

value: Squamous differentiation

value: urothelial carcinoma with focal squamous differentiation

value: stable

tag: pdx characteristics -latency  (days)


title: THP1_RV_rep1

tag: treatment

value: H37Rv infected


title: HS-5, NOMO KO-2

value: Bone marrow

tag: cell type

value: Non tumoral

tag: genotype


title: S225_P2

source_name: Gene expression data of Xenograft from bladder tumor sample S225_K

tag: tissue type

value: Xenograft from tumor

tag: replicate

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -variant (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)


title: T47D-WM-E2-H3K27ac Rep2

growth_protocol: Ductal and Lobular cells were grown in estrogen deprived media for 3 days

tag: cell line

value: T47D breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: H3K27ac (C15410196, Diagenode)


title: T47D-WM-E2-H3K27ac Rep1


title: HS-5, PX458-3

tag: tissue

value: NOMO WT


title: S162_P3

value: no

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: Squamous cell carcinoma

value: No

value: squamous cell carcinoma

value: Upper tract

value: PDX stable but no original accessible tumor

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: THP1_NC_rep3

tag: treatment

value: normal


title: THP1_NC_rep2


title: SUM44-WM-E2-H3K27ac Rep2

value: SUM44PE breast carcinoma cell line


title: M425_P2

source_name: Gene expression data of Xenograft from bladder tumor sample M425_K

tag: tissue type

tag: replicate

value: yes

value: BCG

tag: patient characteristics -treatment  post-surgery

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: urothelial carcinoma

value: Bladder

value: stable


title: HS-5, PX458-2

tag: tissue

value: Bone marrow

tag: cell line

tag: cell type

value: Non tumoral

tag: genotype

value: NOMO WT


title: THP1_NC_rep1


title: M559_P3

source_name: Gene expression data of Xenograft from bladder tumor sample M559_K

value: Xenograft from tumor

value: no

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Male

value: Carboplatin/Gemzar

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)


title: HCT-116, NOMO KO-2

source_name: colorectal cancer cell line HCT-116

value: Colon

value: Tumoral

value: NOMO KO


title: MDA134-WM-E2-H3K27ac Rep2

value: MDA_MB134 breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: H3K27ac (C15410196, Diagenode)


title: HS-5, PX458-1


title: M559_K

source_name: Gene expression data of bladder tumor sample M559_K

tag: tissue type

value: Tumor

tag: replicate

value: yes

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: Urothelial carcinoma

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: K661_P3

source_name: Gene expression data of Xenograft from bladder tumor sample K661_K

tag: paired

value: Cisplatin/Gemzar

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: high grade urothelial carcinoma

value: Bladder

value: stable


title: M425_K

source_name: Gene expression data of bladder tumor sample M425_K

value: no

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: BCG

value: Palliative treatment

value: urothelial carcinoma


title: HCT-116, NOMO KO-1

tag: tissue

value: Colon

tag: cell line

tag: cell type

value: Tumoral

tag: genotype


title: H3R17me2a, DMSO, HeLa

city: Xiamen

first: Guosheng

last: Hu

state: Fujian

address: Xiang'an South Road, Xiang'an District

department: School of Pharmaceutical Sciences

institute: xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Bowtie version 2.2.6 with the default options.
The bigwig files were generated by using HOMER 4.9, in which the total tags are normalized to 1.00e+07.
Peaks are called by using Homer findPeaks script
Assembly: hg19
Supplementary files format and content: bigWig

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM medium supplemented with 10% FBS and 1%penicillin and streptomycin

extract_protocol:
Cells were fixed with 1% formaldehyde (Sigma) for 10 min at RT. Fixation was stopped by adding glycine (0.125 M) and incubated for 5 min at RT, followed by washing with PBS twice. Cells were lysed in lysis buffer (1% SDS, 50 mM Tris-HCl pH 7.8, 10 mM EDTA, and 1 x complete protease inhibitor cocktail (Roche)) and chromatin DNA was sheared to 200-500 bp average in size through sonication. Resultant was diluted in dilution buffer (1% Triton X-100, 150 mM NaCl, 20 mM Tris-HCl pH 7.8, 2 mM EDTA, and 1 x complete protease inhibitor cocktail) and immunoprecipitated with specific antibody overnight at 4 °C, followed by incubation with protein G magnetic beads (Bio-Rad) for an additional 2 h. The bound fractions were sequentially washed for 15 min at 4 °C with TSE I buffer (0.1% SDS, 1% Triton X-100, 150 mM NaCl, 20 mM Tris-HCl pH 7.8, 2 mM EDTA, and 1 x complete protease inhibitor cocktail), TSE II buffer (0.1% SDS, 1% Triton X-100, 400 mM NaCl, 20 mM Tris-HCl pH 7.8, 2 mM EDTA, and 1 x complete protease inhibitor cocktail), and TE buffer (20 mM Tris-HCl pH 7.4, and 1mM EDTA). After washing and elution, the protein-DNA complex was reversed by heating at 65 °C℃ overnight. Immunoprecipitated DNA was purified by using QIAquick spin columns (Qiagen) and subjected to high throughput sequencing.
The libraries were constructed following Illumina ChIP-seq Sample prep kit. Briefly, ChIP DNA was end-blunted and added with an ‘A’ base so the adaptors from Illumina with a ‘T’ can ligate on the ends. Then 200-400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: HeLa cells were treated with or without iJMJD6 before ChIP-seq.

value: HeLa

tag: chip antibody

value: Anti-Histone H3 (asymmetric di methyl R17) antibody, Abcam ab8284

tag: treatment

value: DMSO


title: SUM44-WM-E2-H3K27ac Rep1

value: SUM44PE breast carcinoma cell line

tag: agent

value: Estrogen

value: H3K27ac (C15410196, Diagenode)


title: H3R17me2a, iJMJD6, HeLa


title: HT-29, NOMO KO-2

source_name: colorectal cancer cell line HT-29

value: NOMO KO


title: K661_K

source_name: Gene expression data of bladder tumor sample K661_K

tag: tissue type

value: Tumor

tag: replicate

value: yes

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

value: Cisplatin/Gemzar

tag: patient characteristics -tnm

value: Urothelial carcinoma

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

tag: pdx characteristics -inclusion rate (percent)


title: HCT-116, PX458-1

value: NOMO WT


title: MCF7-WM-E2-H3K27ac Rep2

value: MCF7 breast carcinoma cell line


title: H4R3me2s, iJMJD6, HeLa

value: Anti-Histone H4 (symmetric di methyl R3) antibody, Abcam ab5823


title: HCT-116, WT

value: Colon

value: Tumoral


title: HT-29, NOMO KO-1


title: MDA134-WM-E2-H3K27ac Rep1

value: MDA_MB134 breast carcinoma cell line


title: T47D-WM-E2-GATA3 Rep2

value: T47D breast carcinoma cell line

value: GATA3 (D13C9, Cell Signaling Technology )


title: H106_P4

source_name: Gene expression data of Xenograft from bladder tumor sample H106_K

value: Xenograft from tumor

value: no

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Female

value: Palliative treatment

tag: tumor sample characteristics -tumor type (who)

value: Squamous cell carcinoma

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: Invasive squamous cell carcinoma

value: Bladder

value: stable

tag: pdx characteristics -latency  (days)


title: H4R3me2s, DMSO, HeLa

tag: cell line

value: HeLa

tag: chip antibody

tag: treatment

value: DMSO


title: LM shWDR5 Replicate 3

city: New Haven

first: Qin

last: Yan

email: qin.yan@yale.edu, craig.wilen@yale.edu

address: 310 Cedar St.

department: Pathology

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.8.2
Raw reads were aligned using STAR 2.7.0 to hg38 using standard parameters
Counts were obtained to GENCODEv96 transcripts
DEseq2 was used to determine differential expression using counts.
Genome_build: hg38
Supplementary_files_format_and_content: txt (DESeq2 results comparing shWDR5 and shControl), txt (raw counts)

source_name: MDA-MB-231 breast cancer cell line lung metastatic variant

growth_protocol: Cells were grown in monolayer in DMEM + 10% FBS + Penicillin-streptomycin at 37ºC, 5% CO2 for 3 days

extract_protocol:
Cells from knockdown control or shWDR5 group were harvested with QIAzol Lysis Reagent (Qiagen) and homogenized using QIAshredder tubes (Qiagen). For each cell line, shRNA expression was induced with doxycycline (1 ug/mL) for 3 days and 3 biological replicates were harvested at different passages. RNA isolation was performed using miRNeasy with on-column DNase digestion. ERCC spike-in RNA was added in proportion to the number of cells obtained during cell counts.
Library generation was performed using TruSeq stranded mRNA library prep kit (Illumina). Paired-end sequencing was performed using an Illumina HiSeq4000 sequencer, generating an average of 59 million reads per library.
TruSeq stranded RNA-seq

value: MDA-MB-231 LM2

tag: cell type

value: mammary gland/breast epithelial cell


title: MCF7-WM-E2-H3K27ac Rep1

value: MCF7 breast carcinoma cell line

tag: agent

value: Estrogen

value: H3K27ac (C15410196, Diagenode)


title: LM shWDR5 Replicate 2


title: LM shWDR5 Replicate 1

source_name: MDA-MB-231 breast cancer cell line brain metastatic variant


title: SUM44-WM-E2-GATA3 Rep2

value: SUM44PE breast carcinoma cell line


title: Chlorops oryzae, female adults

city: Changsha

first: Ailin

last: Zhou

address: 1 Nongda Road, Furong District, Changsha City, Hunan Province

institute: Agricultural University Of Hunan

data_processing:
Align cleaned reads with the bowtie 2 end-to-end algorithm
Detect the ligation site with an exact matching program and to align the 5’ segment read on the genome with HiC-Pro (v2.7.8)
Merged into a single alignment file of each mapping step
Lachesis, the assembly package, was used to cluster, order and orient reads
Cut the chromosomes predicted by Lachesis into equal-length bins, such as 1Mb or 500Kb, and constructed a heatmap according to the interaction signals revealed by the effective mapping between bins
Assembly: Reference sequence used for read alignment
Supplementary files format and content: A “.gff3” file
Supplementary files format and content: A “fasta” file

organism: Chlorops oryzae

source_name: adult

extract_protocol:
DNA was extracted from adults using an Ezup Column Animal Genomic DNA Extraction Kit as per the manufacturer’s instructions (Sangon Biotech, Shanghai, China)
Samples were crosslinking, then prepared and sequenced on the Illumina Novaseq platform with 2 × 150bp reads at Annoroad Gene Technology Co. Ltd.

tag: tissue

value: adult


title: SUM44-WM-E2-GATA3 Rep1

value: GATA3 (D13C9, Cell Signaling Technology )


title: H633_K

source_name: Gene expression data of bladder tumor sample H633_K

tag: tissue type

value: Tumor

tag: replicate

value: no

value: yes

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

tag: patient characteristics -tnm

value: Urothelial carcinoma

value: high grade urothelial carcinoma

tag: tumor sample characteristics -primary site

value: Upper tract

tag: pdx characteristics - histology (pdx)


title: LM shCtrl Replicate 2

source_name: MDA-MB-231 breast cancer cell line bone metastatic variant


title: LM shCtrl Replicate 3


title: H633_P3

source_name: Gene expression data of Xenograft from bladder tumor sample H633_K

value: Xenograft from tumor

tag: paired

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Palliative treatment

tag: tumor sample characteristics -tumor type (who)

tag: tumor sample characteristics -associated cis

value: stable

tag: pdx characteristics -inclusion rate (percent)


title: K4

city: Luzhou

last: yang

address: Longmatan District Xianglin Road 1 section 1, Luzhou city

institute: Southwest Medical University

data_processing:
RNA-seq was performed using the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150-bp read length) by Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China).
The raw paired end reads were processed with SeqPrep and Sickle.
Then clean reads were aligned to the reference genome using HISAT2 software.
Transcripts were assembled with StringTie
Assembly: GRCh38

source_name: control

growth_protocol: K562 cells were cultured with RPMI 1640 medium (Gibico, Invitrogen Corporation, Carlsbad, CA) supplemented with 10% FBS (Thermo Fisher Scientific, Waltham, MA, USA), 100 U/ml of penicillin, and 100 mg/ml of streptomycin at 37°C, with 5% CO2 and saturated humidity.

extract_protocol:
The K562 cells were treated with CPM (80 µg/mL) for 3 days. Total RNA of cells was extracted using TRIzol® Reagent (Invitrogen, USA) based on the manufacturer’s instructions.  RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA.
RNA libraries for RNA-seq were prepared using TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA).

treatment_protocol: K562 cells were treated with 80 μg/ml CPM for 3 days

tag: cell line

tag: cell type

value: The human chronic myeloid leukemia (CML) cell line

tag: treatment

value: treated without CPM


title: D4

source_name: treated with CPM

value: treated with CPM(80ug/ml) for 3 days


title: HT-29, PX458-1

tag: tissue

value: Colon

value: Tumoral

tag: genotype

value: NOMO WT


title: K5


title: H106_K

source_name: Gene expression data of bladder tumor sample H106_K

tag: tissue type

value: Tumor

tag: replicate

value: Female

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

tag: patient characteristics -treatment  post-surgery

value: Squamous cell carcinoma

tag: tumor sample characteristics -classification

value: Invasive squamous cell carcinoma

value: Bladder

tag: pdx characteristics -latency  (days)


title: T47D-WM-E2-GATA3 Rep1

value: T47D breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: GATA3 (D13C9, Cell Signaling Technology )


title: HT-29, WT


title: C704_P3

source_name: Gene expression data of Xenograft from bladder tumor sample C704_K

value: Xenograft from tumor

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Male

value: No

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Squamous differentiation

value: invasive urothelial carcinoma associated with squamous differentiation

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

value: minimal variation of the squamous component


title: F659_K

source_name: Gene expression data of bladder tumor sample F659_K

tag: tissue type

value: Tumor

tag: replicate

tag: patient characteristics -age ( years)

value: Cisplatin/Gemzar

tag: tumor sample characteristics -associated cis

value: urothelial carcinoma

value: stable

tag: pdx characteristics -inclusion rate (percent)


title: B521_P3

source_name: Gene expression data of Xenograft from bladder tumor sample B521_K

tag: patient characteristics -prior therapy

value: laser therapy

tag: patient characteristics -treatment  post-surgery

value: Poorly differentiated

tag: tumor sample characteristics -classification

value: poorly differentiated urothelial carcinoma

value: Upper tract

tag: pdx characteristics -latency  (days)


title: BrM shWDR5 Replicate 2

tag: cell line

value: MDA-MB-231 BrM2

tag: cell type

value: mammary gland/breast epithelial cell


title: F659_P3_REP1

source_name: Gene expression data of Xenograft from bladder tumor sample F659_K

value: Xenograft from tumor

value: no

tag: paired

value: yes

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

value: Bladder


title: K3

value: The human chronic myeloid leukemia (CML) cell line

tag: treatment

value: treated without CPM


title: D2

value: treated with CPM(80ug/ml) for 3 days


title: C704_K

source_name: Gene expression data of bladder tumor sample C704_K

tag: tissue type

value: Tumor

value: Male

value: No

value: Palliative treatment

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: Urothelial carcinoma

tag: tumor sample characteristics -variant (who)

value: Squamous differentiation

value: invasive urothelial carcinoma associated with squamous differentiation

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)

value: minimal variation of the squamous component


title: MCF7-WM-E2-GATA3 Rep1

value: MCF7 breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: GATA3 (D13C9, Cell Signaling Technology )


title: BrM shWDR5 Replicate 1

value: MDA-MB-231 BrM2

value: mammary gland/breast epithelial cell


title: Pleural-Effusion-FOXA1

value: FOXA1 (ab5089 Abcam, ab23738 Abcam)


title: D3

value: The human chronic myeloid leukemia (CML) cell line


title: MDA134-WM-E2-GATA3 Rep2

value: MDA_MB134 breast carcinoma cell line


title: MDA134-WM-E2-GATA3 Rep1


title: BrM shCtrl Replicate 3


title: D1

value: treated with CPM(80ug/ml) for 3 days


title: BrM shWDR5 Replicate 3


title: K2

value: treated without CPM


title: MCF7-WM-E2-GATA3 Rep2


title: si-RAB23-9-2

city: Tianjin

first: Gang

last: Ma

email: horsegang@163.com, horsegang@tmu.edu.cn

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District

department: Department of Gastric Surgery

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
Raw reads quality report was generated using FastQC.
The adapter sequences were remove from the 3’ end of reads with software Trimmomatic(v0.36). Then the filtered reads were mapped to the human (Homo sapiens) genome (version hg19) and transcriptome (gencode v19) using the software STAR (v2.5.1b).
Gene abundance estimation was conducted with the software RSEM (v1.2.29).
The library normlized factor and CPM values were calculated with R package edgeR (v3.8.5). Genes with CPM value greater than 1 in at least two samples were considered to further analysis.
R package edgeR (v3.8.5) was used to compare expression levels between sample pairs. Fold change > 2 and FDR < 0.05 as thresholds to define DEGs.
Assembly: hg19

source_name: esophagus

growth_protocol: KYSE30 cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) (HyClone, South Logan, UT, USA), penicillin (100 U/ml), and streptomycin (100 U/ml) at 37℃ in a humidified 5% CO2 incubator.

extract_protocol:
When cells grew to approximately 80% confluence, they were washed twice with pre-chilled PBS, and then total RNAs were harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: KYSE30 cells were transfected with si-NC, si-RAB23-1 and si-RAB23-9 using HiPerFect Transfection Reagent (Qiagen). The final concentration of siRNA was 100 nM. The knockdown efficiency was tested using immunoblot assay.

tag: tissue

value: esophagus

value: cells transfected with siRNA9


title: LM shCtrl Replicate 1

tag: cell line

value: MDA-MB-231 LM2


title: si-RAB23-9-1

tag: cell type


title: SUM44-WM-E2-FOXA1 Rep2

value: SUM44PE breast carcinoma cell line


title: LW90

city: Jinan

first: Tao

last: Su

state: Shandong

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

data_processing:
By removing adapter reads, reads containing over 0.2% of poly-N, and low quality paired reads (>50% of bases whose Phred scores were<5%) to filter raw reads.
Clean reads for subsequent analysis were obtained by filtering the raw data, checking the Phred score (Q20 and Q30) and GC content.
The clean data were compared and analyzed by Hisat2 (https://daehwankimlab.github.io/hisat2/) using default parameters
Assembly: Sus scrofa reference genome 11.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: longissimus dorsi muscle, low intramuscular fat content

extract_protocol:
Total RNA was isolated from the longissimus dorsi muscles of the selected six pigs using TRIzol reagent (Invitrogen). 3 ug of total RNA was used for the construction of sequencing libraries.
A chain-specific library was constructed by removing ribosomal RNA.

value: longissimus dorsi muscle


title: B521_K

source_name: Gene expression data of bladder tumor sample B521_K

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: laser therapy

tag: patient characteristics -treatment  post-surgery

value: No

value: Urothelial carcinoma

value: Poorly differentiated

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

value: poorly differentiated urothelial carcinoma

value: Upper tract

value: stable

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: BrM shCtrl Replicate 1

value: MDA-MB-231 BrM2

value: mammary gland/breast epithelial cell


title: BoM shWDR5 Replicate 3

source_name: MDA-MB-231 breast cancer cell line lung metastatic variant

value: MDA-MB-231 BoM


title: B296_P3

source_name: Gene expression data of Xenograft from bladder tumor sample B296_K

tag: tissue type

value: Xenograft from tumor

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: low and high grade papillary urothelial carcinoma

value: Bladder


title: SUM44-WM-E2-FOXA1 Rep1

tag: cell line

value: SUM44PE breast carcinoma cell line

tag: agent

value: Estrogen

tag: chip antibody

value: FOXA1 (ab5089 Abcam, ab23738 Abcam)


title: UCB-exosome_BPD_3

source_name: umbilical cord blood

tag: gestational age

tag: gender

value: male


title: T47D-WM-E2-FOXA1 Rep2

value: T47D breast carcinoma cell line


title: BoM shWDR5 Replicate 2

tag: cell type


title: BrM shCtrl Replicate 2


title: LW70

source_name: longissimus dorsi muscle, high intramuscular fat content

tag: tissue

value: longissimus dorsi muscle


title: BoM shCtrl Replicate 3

source_name: MDA-MB-231 breast cancer cell line brain metastatic variant


title: MDA134-WM-E2-FOXA1 Rep1

value: MDA_MB134 breast carcinoma cell line


title: si-NC-1

value: esophagus

value: control cells


title: T47D-WM-E2-FOXA1 Rep1


title: LW88


title: B296_K

source_name: Gene expression data of bladder tumor sample B296_K

value: Tumor

tag: replicate

value: no

tag: paired

value: yes

value: Male

tag: patient characteristics -age ( years)

tag: patient characteristics -prior therapy

value: No

tag: patient characteristics -treatment  post-surgery

value: Urothelial carcinoma

tag: tumor sample characteristics -associated cis

tag: tumor sample characteristics -classification

tag: tumor sample characteristics -primary site

tag: pdx characteristics - histology (pdx)


title: A54_K

source_name: Gene expression data of bladder tumor sample A54_K

tag: tissue type

tag: pair name

tag: batch

tag: year of establishment

tag: patient characteristics - gender

tag: patient characteristics -tnm

tag: tumor sample characteristics -tumor type (who)

value: high grade papillary urothelial carcinoma

tag: pdx characteristics -inclusion rate (percent)

tag: pdx characteristics -latency  (days)


title: WT_Mock_A

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

country: Germany

institute: University Münster

description: Mock

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91  and to Influenza KAN1 virus genome, using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)).
Human and virus raw reads were combined before normalization.
Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)) and batch corrected for donor using LIMMA (version 3.42.2).
Assembly: ENSEMBL hg38 release 91
Supplementary files format and content: txt matrix with log2 normalized values per sample.

molecule: polyA RNA

extract_protocol:
Total RNA was isolated using the RNeasy kit following the manufactures protocol. Quality and integrity of total RNA was controlled on Agilent Technologies 2100, Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols.

treatment_protocol: A549-control or A549-TRIM28-KO cells were infected with MOI 0.01 for 24h with IAV strain KAN-1 (H5N1). Total RNA was isolated and used for sequencing.

tag: cell line

tag: genotype

value: WT

tag: treatment

value: Mock


title: si-RAB23-1-2

tag: tissue

tag: cell type

value: cells transfected with siRNA1


title: BoM shCtrl Replicate 1

source_name: MDA-MB-231 breast cancer cell line bone metastatic variant

value: MDA-MB-231 BoM

value: mammary gland/breast epithelial cell


title: LW82


title: LW63


title: Virus stock P2

city: Berlin

first: Emanuel

last: Wyler

address: Robert Roessle Str 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

description: total RNA

data_processing:
For bulk RNA-sequencing, alignments were done using hisat2 (Kim et al, 2015)
Sequencing reads were aligned to the hg19 version of the human genome
Reads were then quantified using quasR (Gaidatzis et al, 2015).
For generating the viral genome sequences in the fasta files provided here, sequencing reads were aligned to the rubella virus sequence NC_001545.2 and differences recursively corrected. See JF727654.2 (Ervevax) and JN635289.1 (MA17) for previously available genome sequences.
Genome_build: hg19
Genome_build: Rubella virus NC_001545.2
Supplementary_files_format_and_content: tab-separated values
Supplementary_files_format_and_content: fasta

organism: Rubivirus rubellae

source_name: Rubella virus stock

growth_protocol:
Human umbilical vein cells (HUVEC) from three donors (Promocell) were maintained in Endothelial Cell Growth Medium 2 (Promocell) and supplemented with 10% (v/v) Supplement Mix and 100 units/ml penicillin. The cells were cultivated in a humidified atmosphere with 5% CO2 at 37°C
Viruses were propagated on Vero E6 cells. After 6 days viral supernatant was concentrated by ultrafiltration through a 30 kDa filter and stored at −80°C. For every virus stock, a mock sample from uninfected cells was processed in parallel, which was then used as the mock control for the infections.

extract_protocol:
Illumina Truseq stranded
adapter sequence: GATCGGAAGAGCACACGT
For RNA extraction, medium was removed and cells were lysed in Trizol (Thermo Fisher). Virus stocks were diluted 1:3 in Trizol LS (Thermo Fisher). RNA was extracted using the clean and concentrator kit 25 (Zymo) according to manufacturer's instruction.
RNA-sequencing library were prepared with polyA enrichment, or using the RiboZero kit (Illumina) for rRNA depletion, before continuing with the TruSeq stranded kit (Illumina)
rRNA depleted total RNA
polyA RNA-seq
total RNA from virus stocks

treatment_protocol: Cells were infected with a MOI of 5.

tag: infection

tag: rubella virus strain

tag: sampling timepoint


title: Virus stock P1

description: total RNA


title: BoM shWDR5 Replicate 1


title: LW119


title: MDA134-WM-E2-FOXA1 Rep2

tag: agent

value: Estrogen

tag: chip antibody

value: FOXA1 (ab5089 Abcam, ab23738 Abcam)


title: T47D-WM-E2-Input

value: T47D breast carcinoma cell line


title: si-NC-2

value: esophagus


title: WT_Mock_C

description: Mock


title: Experiment 2, polyA RNA, WB12, 24hpi, replicate 1

description: polyA+ RNA

source_name: HUVEC


title: Virus stock WB12

description: total RNA


title: WT_KAN1_B


title: MCF7-WM-E2-FOXA1 Rep2

value: MCF7 breast carcinoma cell line


title: MCF7-WM-E2-FOXA1 Rep1


title: WT_Mock_B

description: Mock


title: si-RAB23-1-1


title: BoM shCtrl Replicate 2


title: Virus stock HPV77

description: total RNA


title: Experiment 2, polyA RNA, WB12, 24hpi, replicate 2

description: polyA+ RNA


title: Experiment 2, polyA RNA, mock for WB12, 24hpi, replicate 1

description: polyA+ RNA


title: PE1B-INPUT


title: SUM44-WM-E2-Input

value: SUM44PE breast carcinoma cell line


title: WT_KAN1_C


title: MCF7-WM-E2-Input


title: MDA134-WM-E2-Input

value: MDA_MB134 breast carcinoma cell line


title: Virus stock MA17

description: total RNA


title: Experiment 2, polyA RNA, mock for WB12, 24hpi, replicate 2

description: polyA+ RNA

value: no


title: TRIM28KO_Mock_B

description: Mock


title: MDA134-WM-Tam-ER-batch2 Rep2

value: Tamoxifen

value: ER (Ab10 Thermo Fisher Scientific, SC-543 Santa cruz)


title: Virus stock Ervevax

description: total RNA

value: Ervevax


title: Experiment 2, polyA RNA, mock for HPV77, 24hpi, replicate 2

description: polyA+ RNA


title: TRIM28KO_Mock_C

description: Mock


title: WT_KAN1_A


title: Experiment 2, polyA RNA, mock for MA17, 24hpi, replicate 2

description: polyA+ RNA


title: TRIM28KO_KAN1_C


title: Pleural-Effusion-ER

source_name: Pleural-Effusion-ER


title: MDA134-WM-E2-ER-batch2 Rep2


title: Experiment 2, polyA RNA, mock for MA17, 24hpi, replicate 1

description: polyA+ RNA


title: TRIM28KO_Mock_A

description: Mock


title: MDA134-WM-Tam-ER-batch2 Rep1


title: MCF7-WM-Tam-ER-batch2 Rep2


title: Experiment 2, polyA RNA, mock for Ervevax, 24hpi, replicate 2

description: polyA+ RNA


title: TRIM28KO_KAN1_B


title: TRIM28KO_KAN1_A


title: Experiment 2, polyA RNA, MA17, 24hpi, replicate 2

description: polyA+ RNA

value: yes


title: MDA134-WM-E2-ER-batch2 Rep1


title: MCF7-WM-Tam-ER-batch2 Rep1


title: CRISPR_CTRL_Mock_B

description: Mock


title: Experiment 2, polyA RNA, mock for Ervevax, 24hpi, replicate 1

description: polyA+ RNA


title: Experiment 2, polyA RNA, MA17, 24hpi, replicate 1

description: polyA+ RNA


title: Experiment 2, polyA RNA, mock for HPV77, 24hpi, replicate 1

description: polyA+ RNA


title: Experiment 2, polyA RNA, HPV77, 24hpi, replicate 1

description: polyA+ RNA


title: CRISPR_CTRL_Mock_A

description: Mock


title: CRISPR_CTRL_KAN1_C


title: CRISPR_CTRL_Mock_C

description: Mock


title: Experiment 2, polyA RNA, HPV77, 24hpi, replicate 2

description: polyA+ RNA


title: MCF7-WM-E2-ER-batch2 Rep1


title: Experiment 2, polyA RNA, Ervevax, 24hpi, replicate 1

description: polyA+ RNA


title: CRISPR_CTRL_KAN1_A


title: CRISPR_CTRL_KAN1_B


title: T47D-WM-E2-ER Rep1


title: T47D-WM-E2-ER Rep2


title: SUM44-WM-E2-ER Rep2


title: SUM44-WM-E2-ER Rep1


title: Experiment 2, polyA RNA, basal, replicate 1

description: polyA+ RNA


title: WT_PR8_C

data_processing:
Reads were quality checked with package FastQC (version 0.11.4,), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome ENSEMBL hg38 release 91  and to Influenza PR8 virus genome, using STAR aligner (Dobin and Gingeras, 2015) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)).
Human and virus raw reads were combined before normalization.
Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)) and batch corrected for donor using LIMMA (version 3.42.2).
Assembly: ENSEMBL hg38 release 91
Supplementary files format and content: txt matrix with log2 normalized values per sample.

extract_protocol:
Total RNA was isolated using the RNeasy kit following the manufactures protocol. Quality and integrity of total RNA was controlled on Agilent Technologies 2100, Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 100 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols.
Bioanalyzer (Agilent Technologies; Waldbronn, Germany).

treatment_protocol: A549-control or A549-TRIM28-KO cells were infected with MOI 0.01 for 24h with IAV strain PR8 (H1N1) or mock-infected. Total RNA was isolated and used for sequencing

value: WT


title: WT_PR8_B


title: WT_PR8_A


title: MDA134-WM-E2-ER Rep2


title: MCF7-WM-E2-ER-batch2 Rep2


title: WT_Mock_C

value: Mock


title: MCF7-WM-E2-ER Rep2


title: MCF7-WM-E2-ER Rep1


title: Experiment 1, rRNA depleted, WB12, 6hpi, replicate 1

description: rRNA depleted total RNA


title: MDA134-WM-E2-ER Rep1


title: Experiment 2, polyA RNA, Ervevax, 24hpi, replicate 2

description: polyA+ RNA


title: WT_Mock_A


title: WT_Mock_B


title: Experiment 1, rRNA depleted, WB12, 24hpi, replicate 2

description: rRNA depleted total RNA


title: Experiment 2, polyA RNA, basal, replicate 2

description: polyA+ RNA


title: Experiment 1, rRNA depleted, mock for WB12, 6hpi, replicate 1

description: rRNA depleted total RNA


title: TRIM28KO_PR8_C


title: MDA134-shFOXA1-WM-plus-E2-No-Dox-ATAC Rep2

growth_protocol: MDA134 cells with Dox inducible shFOXA1 were maintained in their media in presence of puromicin

extract_protocol:
Cells were lysate with RSB buffer containing 0.1% NP40, 0.1%, Tween-20, and 0.01% Digitonin followed by transposition mixture
Transposed DNA library preparation was performed with Customized Nextera PCR primers and SYBR green, amplifying for 5 + 20 cycles total


title: Experiment 1, rRNA depleted, mock for WB12, 6hpi, replicate 2

description: rRNA depleted total RNA


title: Experiment 1, rRNA depleted, WB12, 6hpi, replicate 2

description: rRNA depleted total RNA


title: TRIM28KO_PR8_B


title: TRIM28KO_Mock_B


title: TRIM28KO_Mock_C


title: MDA134-shFOXA1-WM-plus-E2-Dox-ATAC Rep2

growth_protocol: MDA134 cells with Dox inducible shFOXA1 were maintained in their media in presence of puromicin and treated with DOX for 3 days

value: Estrogen + Dox


title: MDA134-shFOXA1-WM-plus-E2-Dox-ATAC Rep1


title: Experiment 1, rRNA depleted, mock for WB12, 24hpi, replicate 2

description: rRNA depleted total RNA


title: MDA134-shFOXA1-WM-plus-E2-No-Dox-ATAC Rep1


title: Experiment 1, rRNA depleted, mock for WB12, 24hpi, replicate 1

description: rRNA depleted total RNA


title: TRIM28KO_PR8_A


title: TRIM28KO_Mock_A


title: T47D-WM-E2-ATAC Rep1


title: T47D-WM-E2-ATAC Rep2


title: SUM44-WM-E2-ATAC Rep2


title: Experiment 1, rRNA depleted, WB12, 24hpi, replicate 1

description: rRNA depleted total RNA


title: Experiment 1, rRNA depleted, mock for HPV77, 6hpi, replicate 2

description: rRNA depleted total RNA


title: CRISPR_CTRL_PR8_C


title: CRISPR_CTRL_PR8_B


title: PDA4b

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were filtered using fastp v0.21.0 using default parameters.
Trimmed reads were mapped to the Trichoderma asperelloides T203 v1.0 genome from GenBank with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Assembly: Trichoderma asperelloides T203 v1.0
Supplementary files format and content: CSV and tab delimited text files including raw counts and LOX output. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals

organism: Trichoderma asperelloides

source_name: hyphae

growth_protocol: Conidia of T. asperelloides strain T203 were harvested from 5-7 day old cultures. Conidia were harvested from three 90mm diameter petri dishes by adding 5 ml of cold sterile double deionized water (DDW) to each dish. Conidia were released by brief shaking with glass beads and collected by filtration through a gauze pad layered over a funnel. The conidial suspension was centrifuged at 4000 RPM for 5 minutes, and the conidial pellet was washed twice with 30 ml cold DDW. Conidial suspensions were incubated overnight at 4°C and then conidial density was calculated using a hemocytometer and adjusted to a concentration of 5×106 conidia/ml. To facilitate the harvesting of conidia and germlings cultured on PDA, presterilized cellulose membranes (Life Technologies, Carlsbad, CA) were placed over the solid medium prior to spreading the inoculum. Plates were inoculated by spreading 50 μl of the adjusted conidial suspension and incubated at 28°C for the required periods.

extract_protocol:
Total RNA was extracted from homogenized tissue with TRI REAGENT (Molecular Research Center). Messenger RNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen).
Preparation of cDNA for sequencing followed the Illumina mRNA Sequencing Sample Preparation Guide. Complementary DNA was prepared using N6 primers for samples of all time-points.
Sequencing libraries were produced from purified total RNA samples by the Illumina TruSeq stranded protocol. The libraries underwent 76 bp single-end sequencing using Illumina HiSeq 2500 in Rapid Run Model according to Illumina protocols.

treatment_protocol: Trichoderma asperelloides strain T203 was  cultured on Potato Dextrose agar at 28°C

tag: strain

tag: development points

value: first hyphal branching

tag: morphology

value: branched hyphae


title: PDA4c


title: Experiment 1, rRNA depleted, mock for HPV77, 24hpi, replicate 2

description: rRNA depleted total RNA


title: PDA3c

value: doubling of the long axis

value: germinating tube extention


title: MDA134-WM-E2-ATAC Rep2

value: Estrogen


title: SUM44-WM-E2-ATAC Rep1


title: PDA4a


title: PDA3a


title: MDA134-WM-E2-ATAC Rep1


title: CRISPR_CTRL_PR8_A


title: Experiment 1, rRNA depleted, mock for Ervevax, 6hpi, replicate 2

description: rRNA depleted total RNA


title: MCF7-WM-E2-ATAC Rep2


title: Experiment 1, rRNA depleted, mock for HPV77, 24hpi, replicate 1

description: rRNA depleted total RNA


title: CRISPR_CTRL_Mock_A


title: PDA3b


title: Experiment 1, rRNA depleted, mock for Ervevax, 6hpi, replicate 1

description: rRNA depleted total RNA


title: PDA1c

source_name: conidia

value: fresh condia

value: condia


title: Experiment 1, rRNA depleted, mock for Ervevax, 24hpi, replicate 1

description: rRNA depleted total RNA


title: CRISPR_CTRL_Mock_C


title: CRISPR_CTRL_Mock_B


title: PDA1b

value: fresh conidia

value: conidia


title: Experiment 1, rRNA depleted, HPV77, 6hpi, replicate 2

description: rRNA depleted total RNA

value: no


title: PDA2a

value: polar growth

value: germinating conidia


title: Experiment 1, rRNA depleted, mock for Ervevax, 24hpi, replicate 2

description: rRNA depleted total RNA


title: Experiment 1, rRNA depleted, mock for HPV77, 6hpi, replicate 1

description: rRNA depleted total RNA


title: MDA134-WM-Tam RNA-seq rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using STAR
For peak calling STAR was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using STAR using the VIPER pipeline

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: Cells were maintained in their original media and harvested for RNA extraction.

value: MDA_MB134VI breast carcinoma cell line

value: Tamoxifen

tag: genotype/growth protocol

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm Tamoxifen for 12hrs


title: Experiment 1, rRNA depleted, HPV77, 6hpi, replicate 1

description: rRNA depleted total RNA

value: yes


title: fragile x, day 23, rep 2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Raw sequencing data was trimmed and filtered using fastp 0.19.6
Trimmed reads were aligned and quantified using STAR 2.7.1a
Taxonomic classification of contaminants was performed using Kraken 2.0.9.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited, raw gene counting data. Per sample, with Ensemble gene Ids

source_name: Lis_FX6 clone #8A

growth_protocol: hESC were cultured on Geltrex-coated plates in mTeSR1 medium supplemented with 100 μg/mL Primocin. hESC were passaged using Accutase and medium was supplemented with 5μM ROCK inhibitor Y-27632 for 24 h to increase survival. hESCs were frozen using CryoStem.

extract_protocol:
Total mRNA samples were extracted from hESCs (day 0), at 13 and 23 DIV of their differentiation into cortical neurons, using the mirVana miRNA Isolation Kit according to manufacturer’s protocol. Extraction was performed in three biological experiments.
illumina TruSeq Stranded mRNA Library construction (stranded, polyA enrichment) and RNA sequencing were performed on Illumina NovaSeq 6000, at a commercial laboratory (Macrogen Inc., Europe).

treatment_protocol: hESCs were differentiated into cortical neurons by an accelerated dual SMAD inhibition protocol as previously described by Qi et al., 2017. Briefly, hESCs were plated on Geltrex with mTeSR1 to confluence. From day 0 cells were cultured in KSR media in the presence of small chemical inhibitors of the TGF, SMAD, and Wnt pathways till day 6. From day 2 cells were cultured also in the presence of MEK, FGF and Notch signaling inhibitors to trigger cortical precursors for cortical neuron differentiation. N2/B27 medium was added in increasing 1/3 increment every other day from day 4, until reaching 100% Neurobasal at day 8. The WNT agonist CHIR99021 was added at days 8-15 as it exerted a strong pro-survival effect on cultures. After MACS, cortical neurons were cultured on Poly-L-ornithine hydrobromide/Laminin I/Fibronectin coated wells in NB/B27 supplemented with 1% Pen/Strep, BDNF, dbcAMP and ascorbic acid.

value: Lis_FX6 clone #8A

value: neuorns, day 23 of neuronal differentiation

value: Fragile X

value: neuronal differentiation


title: PDA1a


title: fragile x, day 13, rep 1

value: day 13 of neuronal differentiation


title: MDA134-WM-E2-batch2 RNA-seq rep1

value: Estrogen

value: Ductal and Lobular cells were grown in estrogen deprived media for 3 days and treated with 10nm E2 for 12hrs


title: MCF7-WM-Tam RNA-seq rep2

value: MCF7 breast carcinoma cell line


title: fragile x, day 23, rep 1


title: fragile x, day 23, rep 3


title: fragile x, day 13, rep 2


title: MCF7-WM-E2-ATAC Rep1


title: Experiment 1, rRNA depleted, HPV77, 24hpi, replicate 2

description: rRNA depleted total RNA


title: Experiment 1, rRNA depleted, Ervevax, 6hpi, replicate 2

description: rRNA depleted total RNA

value: Ervevax


title: MDA134-WM-E2-batch2 RNA-seq rep2


title: MCF7-WM-E2-batch2 RNA-seq rep1


title: fragile x, day 0, rep 1

value: hESCs


title: MCF7-WM-Tam RNA-seq rep1


title: fragile x, day 13, rep 3


title: fragile x, day 0, rep 2


title: Experiment 1, rRNA depleted, HPV77, 24hpi, replicate 1

description: rRNA depleted total RNA


title: Experiment 1, rRNA depleted, Ervevax, 24hpi, replicate 2

description: rRNA depleted total RNA


title: fragile x, day 0, rep 3


title: MDA134-WM-Tam RNA-seq rep2


title: MDA134-siCTR RNA-seq rep2

value: Full Media

value: MDA134 were transfected with siRNA and cultured for 48-72 hrs


title: isogenic control, day 23, rep 3

source_name: Lis_FX6 clone #7B

value: Lis_FX6 clone #7B

value: isogenic control


title: Experiment 1, rRNA depleted, Ervevax, 24hpi, replicate 1

description: rRNA depleted total RNA


title: isogenic control, day 23, rep 2