title: Patient 87

value: Patient 87

value: R

value: predictions/survival


title: Patient 86

status: Public on Aug 26 2022

type: RNA

city: Sydney

first: Susan

last: Ramus

state: NSW

address: L2, Lowy Cancer Research Centre

country: Australia

institute: UNSW Sydney

hyb_protocol: 700ng/uL RNA was mixed with hybridization buffer and hybridized at 65°C overnight.

data_processing: We used batch effects adjustment, quality control, and normalisation techniques that are applied one patient at a time, single-patient processing [Talhouk et al. 2016]. After quality control assessments, the count data were log2 transformed and centered by the arithmetic mean of the selected housekeeping genes, LDHA, MTG1, POLR1B, TBP.

label: barcode

molecule: total RNA

organism: Homo sapiens

source_name: Tumor tissue FFPE

label_protocol: Proprietary 'barcode' for each target sequence

extract_protocol: RNA was extracted from FFPE tumor samples using the Qiagen miRNeasy FFPE kit.

tag: tissue

value: Tumor tissue FFPE

tag: individual

value: Patient 86

tag: study

value: L

tag: stagegroup

tag: finalstatus

tag: diagnosis

value: MBOT

value: Ovary/presumed ovary

tag: analysis

value: All


title: Patient 78

value: Patient 78

value: I

value: MOC


title: human WBC, GB4030385 (iDNase-seq)

type: SRA

city: Bethesda

first: Keji

last: Zhao

state: MD

address: 10 Center Dr

department: Systems Biology Center

country: USA

institute: NHLBI

library_source: genomic

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

molecule: genomic DNA

source_name: WBC

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.

tag: cell type

value: WBC


title: human WBC, GB4030384 (iDNase-seq)


title: human WBC, GB4030396 (iDNase-seq)


title: human WBC, GB4030390 (iDNase-seq)


title: Patient 73

value: Patient 73

value: M

value: Expansile


title: Patient 74

value: Patient 74

value: D


title: Patient 72

value: Patient 72

value: V


title: human WBC, GB4030392 (iDNase-seq)


title: human WBC, GB4030380 (iDNase-seq)


title: human WBC, GB4030391 (iDNase-seq)


title: human WBC, GB4030389 (iDNase-seq)


title: human WBC, GB4030377 (iDNase-seq)


title: Patient 81

value: Tumor tissue FFPE

value: Patient 81


title: human WBC, GB4030381 (iDNase-seq)


title: human WBC, GB4030375 (iDNase-seq)


title: human WBC, GB4030376 (iDNase-seq)


title: human WBC, GB4030374 (iDNase-seq)


title: Patient 75

value: Patient 75


title: Patient 76

value: Patient 76

value: L

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: Patient 65

value: Patient 65

value: Ovary/presumed ovary

value: All


title: Patient 64

value: Patient 64

value: H

value: MOC


title: Patient 63

value: Patient 63


title: human WBC, GB4030386 (iDNase-seq)

value: WBC


title: human WBC, GB4030383 (iDNase-seq)


title: Patient 71

value: Patient 71

value: B

value: Expansile


title: human WBC, GB4030379 (iDNase-seq)


title: Patient 61

value: Tumor tissue FFPE

value: Patient 61

value: G


title: Patient 62

value: Patient 62

value: D

value: MBOT

value: predictions/survival


title: human WBC, GB4030382 (iDNase-seq)


title: human WBC, GB4030371 (iDNase-seq)


title: human WBC, GB4030387 (iDNase-seq)


title: Patient 79

value: Patient 79

value: Ovary/presumed ovary


title: human WBC, GB4030369 (iDNase-seq)


title: human WBC, GB4030378 (iDNase-seq)


title: Patient 77

value: Patient 77

value: W

value: All


title: Patient 68

value: Patient 68

value: S

value: Colon

value: Mets (CRC)

value: LGI

value: Omentum


title: Patient 69

value: Tumor tissue FFPE

value: Patient 69

value: V


title: human WBC, GB4030373 (iDNase-seq)

value: WBC


title: Patient 67

value: Patient 67

value: MOC


title: Patient 58

value: Patient 58

value: M

value: Expansile


title: Patient 70

value: Patient 70

value: MOC (anaplastic)

value: Infiltrative

value: Ovary/presumed ovary


title: Patient 66

value: Patient 66

value: F

value: Pancreas

value: Primary pancreatic

value: UGI

value: All


title: Patient 59

value: Tumor tissue FFPE

value: Patient 59

value: O


title: human WBC, GB4030372 (iDNase-seq)

value: WBC


title: human WBC, GB4030368 (iDNase-seq)


title: human WBC, GB4030366 (iDNase-seq)


title: human WBC, GB4030370 (iDNase-seq)


title: human WBC, GB4030367 (iDNase-seq)


title: human WBC, GB4030364 (iDNase-seq)


title: Patient 54

value: Patient 54

value: L

value: MOC


title: Patient 60

value: Patient 60

value: MBOT


title: Patient 57

value: Patient 57

value: W


title: Patient 53

value: Patient 53

value: V

value: Ovary/presumed ovary


title: human WBC, GB4030363 (iDNase-seq)


title: human WBC, GB4030362 (iDNase-seq)


title: human WBC, GB4030359 (iDNase-seq)


title: human WBC, GB4030361 (iDNase-seq)


title: human WBC, GB4030358 (iDNase-seq)


title: Patient 52

value: Patient 52

value: F

value: Pancreas

value: Primary pancreatic


title: Patient 51

value: Tumor tissue FFPE

value: Patient 51

value: M

value: All


title: human WBC, GB4030357 (iDNase-seq)

value: WBC


title: human WBC, GB4030365 (iDNase-seq)


title: Patient 50

value: Patient 50

value: U

value: MOC

value: predictions/survival


title: Patient 56

value: Patient 56

value: UGI


title: Patient 55

value: Patient 55

value: P

value: MBOT


title: human WBC, GB4030356 (iDNase-seq)


title: human WBC, GB4030355 (iDNase-seq)


title: human WBC, GB4030353 (iDNase-seq)


title: human WBC, GB4030354 (iDNase-seq)


title: Patient 47

value: Patient 47

value: R

value: Expansile

value: Ovary/presumed ovary


title: human WBC, GB4030360 (iDNase-seq)


title: human WBC, GB4030352 (iDNase-seq)


title: Patient 48

value: Tumor tissue FFPE

value: Patient 48

value: O

value: Infiltrative


title: Patient 49

value: Patient 49

value: V

value: Metastases (LGI)

value: Mets (Appendix)

value: LGI

value: All


title: human WBC, GB4030350 (iDNase-seq)

value: WBC


title: Patient 44

value: Patient 44

value: G

value: MOC


title: Patient 45

value: Patient 45

value: T

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030351 (iDNase-seq)


title: Patient 46

value: Tumor tissue FFPE

value: Patient 46

value: H

value: MBOT

value: Ovary/presumed ovary

value: predictions/survival


title: human WBC, GB4030348 (iDNase-seq)


title: Patient 42

value: Patient 42

value: Expansile


title: Patient 41

value: Patient 41

value: B

value: Benign mucinous neoplasm

value: survival


title: human WBC, GB4030347 (iDNase-seq)

value: WBC


title: human WBC, GB4030346 (iDNase-seq)


title: Patient 39

value: Patient 39

value: V

value: MOC

value: All


title: human WBC, GB4030349 (iDNase-seq)


title: Patient 38

value: Tumor tissue FFPE

value: Patient 38

value: C


title: human WBC, GB4030344 (iDNase-seq)


title: Patient 43

value: Patient 43

value: S

value: MBOT


title: human WBC, GB4030343 (iDNase-seq)


title: Patient 40

value: Patient 40

value: Ovary/presumed ovary


title: human WBC, GB4030345 (iDNase-seq)


title: human WBC, GB4030342 (iDNase-seq)


title: Patient 37

value: Patient 37

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Infiltrative


title: Patient 34

value: Patient 34

value: W


title: Patient 26

value: Patient 26

value: V

value: MOC

value: Expansile

value: All


title: human WBC, GB4030341 (iDNase-seq)

value: WBC


title: human WBC, GB4030338 (iDNase-seq)


title: human WBC, GB4030340 (iDNase-seq)


title: Patient 33

value: Tumor tissue FFPE

value: Patient 33

value: L

value: MBOT

value: predictions/survival


title: human WBC, GB4030336 (iDNase-seq)


title: human WBC, GB4030337 (iDNase-seq)


title: Nanopore_sequencing_Control_2

city: Amsterdam

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

department: Oncogenomics

country: Netherlands

institute: Netherlands Cancer Institute (NKI)

library_source: transcriptomic

data_processing:
Nanopore: FASTQ files were aligned to the genome GRCh37.p13.genome using minimap2 (2.17-r941). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Nanopore_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes. Also included is Nanopore_sequencing_Control_2.psl

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq. To inhibit RNA polymerase II transcription activity,

extract_protocol: For Nanopore samples, poly(A) selected RNA (500 ng) of control or TEX treated samples were prepared for nanopore direct RNA sequencing generally following the ONT SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. RNA sequencing on the MinION was performed using ONT R9 Flow Cells.

tag: treatment

value: Control for Nanopore sequencing


title: Nanopore_sequencing_TEX_2

data_processing:
Nanopore: FASTQ files were aligned to the genome GRCh37.p13.genome using minimap2 (2.17-r941). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Nanopore_Readcounts.txt is tab delimited txt file containing raw read counts obtaned with htseq over exons of protein coding genes. also included is Nanopore_sequencing_TEX_2.psl as psl file

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C. Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.

treatment_protocol:
Terminator phosphate-dependent TEX treatment:
For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: treatment:Nanopore sequencing + TEX


title: human WBC, GB4030334 (iDNase-seq)


title: Patient 35

value: Patient 35

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030333 (iDNase-seq)


title: Patient 32

value: Patient 32

value: W

value: Ovary/presumed ovary


title: Patient 29

value: Patient 29

value: A

value: Benign mucinous neoplasm

value: survival


title: Patient 30

value: Tumor tissue FFPE

value: Patient 30

value: R

value: MOC

value: Expansile

value: All


title: Patient 23

value: Patient 23

value: T


title: Patient 36

value: Patient 36

value: Pancreas

value: Primary pancreatic

value: Infiltrative


title: Nanopore_sequencing_Control_1.fastq.gz

data_processing:
Nanopore: FASTQ files were aligned to the genome GRCh37.p13.genome using minimap2 (2.17-r941). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Nanopore_Readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes. Also included is Nanopore_sequencing_Control_1.psl

source_name: U2OS cells

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.  Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq. To inhibit RNA polymerase II transcription activity,

value: Control for Nanopore sequencing


title: Patient 22

value: Patient 22

value: Ovary/presumed ovary


title: human WBC, GB4030335 (iDNase-seq)

value: WBC


title: human WBC, GB4030331 (iDNase-seq)


title: Patient 31

value: Patient 31

value: G

value: Metastases (LGI)

value: Mets (unk primary)

value: LGI


title: human WBC, GB4030339 (iDNase-seq)


title: Patient 24

value: Tumor tissue FFPE

value: Patient 24

value: K

value: Colon

value: Primary CRC


title: Patient 27

value: Patient 27

value: V

value: MBOT

value: All


title: pet2

city: Shenyang

first: Zhiyong

last: Liu

state: Liaoning Province

address: Dongling Road 120

country: China

institute: Shenyang Agriculral University

data_processing:
Illumina Casava1.8 software used for basecalling.
Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20) were removed.
We aligned reads of samples to the reference genome using HISAT2 package.
The mapped reads of each sample were assembled using StringTie, all transcriptomes were merged to reconstruct a comprehensive transcriptome.
Unmapped reads were still mapped to genome using tophat-fusion. CIRCExplorer2 was used to identify circRNAs.
Genome_build: BRAD：Brassica_rapa_v3.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each isoforms

organism: Brassica rapa

source_name: Chinese cabbage petiole

growth_protocol: Regular growth in the greenhouse

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Aglient 2100 Bioanalyzer and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 10 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of the Ribo-Zero™ rRNA removal kit (Illumina, San Diego, USA).Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the Truseq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).

value: petiole

tag: genotype/variation

value: wild type


title: Nanopore_sequencing_TEX_1.fastq.gz

data_processing:
Nanopore: FASTQ files were aligned to the genome GRCh37.p13.genome using minimap2 (2.17-r941). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Genome_build: hg19
Supplementary_files_format_and_content: Nanopore_Readcounts.txt is tab delimited txt file containing raw read counts obtaned with htseq over exons of protein coding genes. also included is Nanopore_sequencing_TEX_1.psl as psl file

growth_protocol: HeLa, U2OS, HEK293 and MEF cell lines were grown in Dulbecco’s modified Eagle’s medium, supplemented with 10% fetal calf serum, 100 units/ml penicillin, and 100 μg/ml streptomycin at 37 °C.  Cell lines were regularly tested for Mycoplasma contamination. Cell lines were authenticated by expression analysis based on RNA-seq.

value: Nanopore sequencing + TEX


title: Patient 21

value: Patient 21

value: S


title: human WBC, GB4030332 (iDNase-seq)

value: WBC


title: leaf3

source_name: Chinese cabbage leaf

value: leaf


title: Patient 19

value: Patient 19

value: MOC

value: Infiltrative

value: Ovary/presumed ovary


title: human WBC, GB4030328 (iDNase-seq)


title: Patient 20

value: Tumor tissue FFPE

value: Patient 20

value: G


title: pet1


title: Patient 28

value: Patient 28

value: V


title: leaf2


title: Patient 25

value: Patient 25

value: Metastases (unknown)

value: Mets (CRC)

value: LGI

value: All


title: human WBC, GB4030330 (iDNase-seq)


title: pet3

value: petiole

value: wild type


title: human WBC, GB4030327 (iDNase-seq)

value: WBC


title: human WBC, GB4030326 (iDNase-seq)


title: human WBC, GB4030329 (iDNase-seq)


title: leaf1

value: leaf


title: Patient 18

value: Patient 18

value: MBOT


title: cry6_p10wt_192855

city: Kansas City

first: Congrong

middle: Ron

last: Yu

state: Missouri

institute: Stowers Insitute for Medical Research

description: polyA RNA extracted from mouse olfactory epithelia across different development stage

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: TPM table and count table.

molecule: polyA RNA

organism: Mus musculus

source_name: olfactory epithelium

extract_protocol:
Olfactory epithelium was dissected. RNA was extracted in TRIzol.
mRNA-Seq Sample Prep Kit (Illumina) was used to create libraries.

tag: strain

tag: development stage

value: olfactory epithelium


title: cry6_p10mut_192853


title: cry3_p7mut


title: cry3_p7wt


title: human WBC, GB4030324 (iDNase-seq)


title: human WBC, GB4030325 (iDNase-seq)


title: Patient 14

value: Tumor tissue FFPE

value: Patient 14

value: O

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Patient 15

value: Patient 15

value: V

value: Infiltrative


title: cry6_p10mut_192854


title: Patient 17

value: Patient 17

value: K

value: Colon

value: Primary CRC

value: LGI

value: All


title: cry6_p5mut_186074


title: cry6_p7wt_198727


title: Patient 16

value: Patient 16


title: cry6_p10wt_192852

value: olfactory epithelium


title: cry6_p5wt_186075


title: human WBC, GB4030323 (iDNase-seq)

value: WBC


title: cry6_p10mut_183676


title: Patient 13

value: Tumor tissue FFPE

value: Patient 13

value: G


title: human WBC, GB4030322 (iDNase-seq)


title: human WBC, GB4030321 (iDNase-seq)


title: human WBC, GB4030319 (iDNase-seq)


title: cry6_p10wt_192851


title: cry6_p5wt_186069


title: cry6_p5mut_186073


title: Patient 12

value: Patient 12

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: cry6_p7mut_181432


title: human WBC, GB4030320 (iDNase-seq)


title: cry6_p5mut_186072


title: Patient 11

value: Patient 11

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: cry4_p0wt2


title: human WBC, GB4030317 (iDNase-seq)


title: cry6_p5wt_186070


title: cry6_p7wt_181429


title: cry4_p21mut1


title: Patient 10

value: Patient 10

value: R

value: All


title: Patient 9

value: Patient 9

value: O


title: Patient 7

value: Tumor tissue FFPE

value: Patient 7

value: L

value: MBOT


title: cry4_p21wt2

value: olfactory epithelium


title: cry6_p10mut_192850


title: Patient 8

value: Patient 8


title: cry4_p14mut2


title: Patient 6

value: Patient 6


title: cry4_p14wt1


title: cry6_p7mut_198723


title: human WBC, GB4030315 (iDNase-seq)

value: WBC


title: cry4_p0wt1


title: human WBC, GB4030313 (iDNase-seq)


title: cry4_p21wt3


title: cry4_p3mut2


title: cry4_p14mut1


title: human WBC, GB4030314 (iDNase-seq)


title: Patient 5

value: Patient 5

value: G


title: Patient 4

value: Patient 4

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: cry4_p3mut3


title: human WBC, GB4030316 (iDNase-seq)


title: cry4_p14wt3


title: Patient 2

value: Patient 2

value: S

value: Appendix

value: Primary appendix

value: LGI

value: Expansile

value: All


title: Patient 3

value: Tumor tissue FFPE

value: Patient 3

value: C

value: MBOT

value: Ovary/presumed ovary


title: human WBC, GB4030312 (iDNase-seq)

value: WBC


title: cry4_p7wt1

value: olfactory epithelium


title: cry4_p3wt3


title: human WBC, GB4030311 (iDNase-seq)


title: Patient 1

value: Patient 1

value: V

value: MOC


title: cry4_p0mut1


title: cry4_p0wt4


title: human WBC, GB4030310 (iDNase-seq)


title: Patient 604

value: Patient 604

value: P

value: Infiltrative


title: cry4_p0mut3


title: human WBC, GB4030309 (iDNase-seq)


title: cry4_p21wt1


title: human WBC, GB4030308 (iDNase-seq)


title: cry4_p14wt2


title: cry4_p3mut1


title: cry4_p0mut4


title: cry4_p14mut3


title: human WBC, GB4030307 (iDNase-seq)


title: Patient 601

value: Patient 601

value: L


title: Patient 600

value: Patient 600

value: R

value: Expansile


title: cry4_p7mut1


title: human WBC, GB4030305 (iDNase-seq)


title: human WBC, GB4030306 (iDNase-seq)


title: cry4_p3wt2


title: cry4_p3wt1


title: Patient 599

value: Tumor tissue FFPE

value: Patient 599

value: predictions/survival


title: cry4_p0mut2


title: cry4_p21mut2


title: human WBC, GB4030303 (iDNase-seq)


title: human WBC, GB4030304 (iDNase-seq)


title: cry4_p0wt3


title: Patient 598

value: Patient 598

value: C

value: MBOT

value: Ovary/presumed ovary


title: Patient 603

value: Patient 603

value: V

value: All


title: Patient 596

value: Patient 596


title: human WBC, GB4030302 (iDNase-seq)

value: WBC


title: Patient 595

value: Patient 595

value: W

value: MOC


title: Patient 597

value: Patient 597


title: cry4_p21mut3

value: olfactory epithelium


title: human WBC, GB4030300 (iDNase-seq)


title: human WBC, GB4030299 (iDNase-seq)


title: Patient 594

value: Tumor tissue FFPE

value: Patient 594

value: Expansile


title: Patient 593

value: Patient 593


title: human WBC, GB4030298 (iDNase-seq)


title: Patient 592

value: Patient 592

value: L


title: human WBC, GB4030301 (iDNase-seq)


title: Patient 591

value: Patient 591

value: K

value: Colon

value: Primary CRC

value: LGI


title: human WBC, GB4030297 (iDNase-seq)

value: WBC


title: N8T-2

city: Berlin

first: Lars

last: Bullinger

address: Augustenburger Platz 1

department: Hematology, Oncology and Tumorimmunology

country: Germany

institute: Charité

description: Gene expression data from mouse germinal center B cells

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The data were normalized using RMA. Intensity values were log2 transformed

label: Biotin

source_name: Naive CD8T cells

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).

treatment_protocol: murine CD4T or CD8T cells

tag: foxo1 status

value: wt+/mt-


title: human WBC, GB4030318 (iDNase-seq)


title: Patient 590

value: Patient 590

value: M

value: Ovary/presumed ovary

value: All


title: Bisulfite-seq_Host tTregs, rep2

city: Regensburg

first: Philipp

last: Beckhove

address: Franz-Josef-Strauss-Allee 11

institute: Regensburg Center for Interventional Immunology

description: tTreg R2

data_processing:
Library strategy: Targeted Bisulfite-seq
Indexed reads were aligned to the respective gene region and the mouse mm10 genome, followed by CG methylation calling and raw data table exporting using a customized code. For Foxp3, following CG dinucleotides were analyzed and plotted CG1 X:7,583,950; CG2 X:7,583,986; CG3 X:7,584,002; CG4 X:7,584,036; CG5 X:7,584,063; CG6 X:7,584,068. For Il2ra, following CG dinucleotides were analyzed and plotted CG1 2:11,645,653; CG2 2:11,645,705; CG3 2:11,645,718; CG4 2:11,645,738. For Ikzf2, following CG dinucleotides were analyzed and plotted CG1 1:69,670,284; CG2 1:69,670,291; CG3 1:69,670,370; CG4 1:69,670,377; CG5 1:69,670,385. For Tnfrsf18, following CG dinucleotides were analyzed: CG1 4:156,028,566; CG2 4:156,028,568; CG3 4:156,028,605; CG4 4:156,028,648; For Ctla4, following CG dinucleotides were analyzed: CG1 1:60,912,472; CG2 1:60,912,521; CG3 1:60,912,536; CG4 1:60,912,573; CG5 1:60,912,684.
Genome_build: mouse mm10
Supplementary_files_format_and_content: txt

source_name: Lymphocytes

growth_protocol: Mice were housed at UKR central animal facility

extract_protocol: T cell subsets were sorted directly into FACS buffer and then lysed with buffer ATL and proteinase K (Qiagen QIAamp DNA Micro Kit #56304) for one hour at 56°C. Buffer ATL and AL with carrier RNA were added and sample stored at -80°C until further processing. To isolate genomic DNA, samples were heated to 90°C for 30 minutes followed by column-based DNA isolation according to manufacturer’s protocol (Qiagen QIAamp DNA Micro Kit #56304). DNA was eluted in 40 µl buffer AE and sodium bisulfite conversion was performed (Qiagen EpiTect Plus DNA Bisulfite Kit #59124). Bisulfite-converted DNA was used to amplify regions of interest56 with the following PCR conditions: 4 µl bisulfite-converted DNA, 0.5 µl forward primer (10 µM), 0.5 µl reverse primer (10 µM), 5 µl 2X PCR buffer, 0.1 µl dNTPs and 0.1 µl hot-start Taq polymerase (PCR buffer, dNTPs and Taq from: ZymoTaq DNA Polymerase Kit #E2002). To detect Foxp3 methylation at the Treg-specific demethylated region, we used a forward primer TGGGTTTTTTTGGTATTTAAGAAAG and a reverse primer AAAAAACAAATAATCTACCCCACAA. To detect Il2ra gene methylation, we used a forward primer TTTTAGAGTTAGAAGATAGAAGGTATGGAA and a reverse primer TCCCAATACTTAACAAAACCACATAT. For Ikzf2 gene methylation, we used a forward primer AGGATGGTTTTTATTGAAGGTGAT and a reverse primer ATACACACCAAACAAACACTACACC. For Ctla4 gene methylation, we used a forward primer TGGTGTTGGTTAGTAGTTATGGTGT and a reverse primer AAATTCCACCTTACAAAAATACAATC. For Tnfrsf18 gene methylation, we used a forward primer GAGGTGTAGTTGTTAGTTGAGGATGT and a reverse primer AACCCCTACTCTCACCAAAAATATAA. PCR was initiated with 95°C for 10 minutes, followed by 40 cycles with denaturation (95°C-30sec), annealing (56°C-30sec) and elongation (72°C-30sec) completed with a final elongation step (72°C for 7 minutes). PCR products were combined, pre-purified with AMPure XP beads (Beckman Coulter #463881) and indexed for Illumina-based sequencing (NEBNext Ultra II DNA Library Prep Kit for Illumina #E7645S with NEBNext Multiplex Oligos for Illumina #E7335S). Samples were pooled in an equimolar ratio and supplemented with an unindexed PhiX spike-in (50% spike-in, Illumina FC-110-3001). Sequencing was performed on an Illumina MiSeq with a reagent nano kit v2 and 500 cycles of PCR.

value: Balb/c

value: T cell

tag: sorting markers


title: Bisulfite-seq_Host pTregs, rep2

description: pTreg R2


title: N4T d25CM-2

source_name: Induced EBV specific memory from naive CD4T cells


title: Bisulfite-seq_Host pTregs, rep3

description: pTreg R3


title: N4T d25EF-2

source_name: Induced EBV specific effector from naive CD4T cells

value: wt-/mt+


title: N8T d25EF-1

source_name: Induced EBV specific effector from naive CD8T cells

value: wt-/mt-


title: human WBC, GB4030296 (iDNase-seq)


title: N4T d25CM-1


title: N4T-2

source_name: Naive CD4T cells

value: wt+/mt+


title: N4T d25EF-1


title: N4T-1


title: N8T-1


title: human WBC, GB4030295 (iDNase-seq)


title: Bisulfite-seq_Host tTregs, rep3

description: tTreg R3


title: Patient 602

value: Tumor tissue FFPE

value: Patient 602

value: V

value: MBOT


title: Bisulfite-seq_in vitro-induced Tregs, rep3

description: iTreg R3


title: human WBC, GB4030294 (iDNase-seq)


title: Bisulfite-seq_in vitro-induced Tregs, rep1

description: iTreg R1


title: N8T d25EF-2


title: Bisulfite-seq_Donor 6.5TCR T cells which were converted to Tregs, rep3

description: BM Treg R3


title: Bisulfite-seq_Host pTregs, rep1

description: pTreg R1


title: Bisulfite-seq_Donor 6.5TCR T cells which were converted to Tregs, rep2

description: BM Treg R2


title: Patient 589

value: Patient 589


title: Patient 587

value: Patient 587

value: MOC

value: Expansile


title: Patient 588

value: Patient 588

value: T

value: Pancreas

value: Primary pancreatic

value: UGI


title: Bisulfite-seq_Donor 6.5TCR T cells which were converted to Tregs, rep1

description: BM Treg R1

value: Balb/c

value: T cell


title: Bisulfite-seq_Donor 6.5TCR T cells which were not converted to Tregs, rep2

description: BM Tconv R2


title: human WBC, GB4030292 (iDNase-seq)

value: WBC


title: Patient 585

value: Patient 585

value: F

value: All


title: Bisulfite-seq_Donor 6.5TCR T cells which were not converted to Tregs, rep3

description: BM Tconv R3


title: Patient 586

value: Tumor tissue FFPE

value: Patient 586

value: S

value: Stomach

value: Primary gastric


title: Bisulfite-seq_Donor 6.5TCR T cells which were not converted to Tregs, rep1

description: BM Tconv R1


title: Bisulfite-seq_in vitro-induced Tregs, rep2

description: iTreg R2


title: human WBC, GB4030291 (iDNase-seq)


title: human WBC, GB4030287 (iDNase-seq)


title: human WBC, GB4030288 (iDNase-seq)


title: human WBC, GB4030290 (iDNase-seq)


title: Patient 582

value: Patient 582

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Patient 580

value: Patient 580

value: B

value: MBOT

value: predictions/survival


title: Bisulfite-seq_Host tTregs, rep1

description: tTreg R1

value: Balb/c

value: T cell


title: Patient 581

value: Patient 581

value: Colon

value: Mets (CRC)

value: LGI

value: Omentum

value: All


title: human WBC, GB4030293 (iDNase-seq)

value: WBC


title: human WBC, GB4030285 (iDNase-seq)


title: human WBC, GB4030289 (iDNase-seq)


title: Patient 583

value: Tumor tissue FFPE

value: Patient 583

value: M


title: Patient 584

value: Patient 584

value: K

value: Primary CRC


title: human WBC, GB4030283 (iDNase-seq)


title: human WBC, GB4030284 (iDNase-seq)


title: Patient 578

value: Patient 578

value: T

value: Pancreas

value: Primary pancreatic

value: UGI

value: Expansile


title: Patient 579

value: Patient 579

value: Colon


title: Patient 577

value: Patient 577

value: D

value: MOC

value: MBOT

value: Ovary/presumed ovary

value: predictions/survival


title: human WBC, GB4030281 (iDNase-seq)

value: WBC


title: human WBC, GB4030280 (iDNase-seq)


title: Patient 576

value: Tumor tissue FFPE

value: Patient 576

value: G

value: All


title: human WBC, GB4030278 (iDNase-seq)


title: human WBC, GB4030286 (iDNase-seq)


title: human WBC, GB4030279 (iDNase-seq)


title: Testes, High-plane of nutrition, 73759

city: Co. Meath

first: Kate

last: Keogh

address: Dunsany

department: Animal and Bioscience Department

country: Ireland

institute: Teagasc Grange

description:
High-plane of nutrition
T36_L

data_processing:
FASTQC software (v0.11.8) was used to check the quality of the raw sequencing reads.
Sequencing indexing adapters were removed using Cutadapt (v2.6)
Input reads were then aligned to the bovine reference genome (ARS1.2) using the miRDeep2 package (version 2.00.8), the miRDeep2 quantifier module was used to quantify all expressed miRNAs in the sequence data, producing read counts for each individual sample.
The R (v3.4) Bioconductor package, EdgeR (v3.5), was applied to identify statistically significant differentially expressed genes.
Genome_build: ARS1.2
Supplementary_files_format_and_content: Tab delimited txt file of merged miRNA read counts

organism: Bos taurus

source_name: Testes

growth_protocol: Holstein-Friesian bull calves were fed differentially either a High plane of nutrition (n=15) or a Moderate plane of nutrition (n=15)  from 2-12 weeks of age. Calves on the High plane of nutrition were expected to grow at 1.0 kg/day, with the Moderate plane of nutrition expected to gain 0.5 kg/day.

extract_protocol:
total RNA was  precipitated and purified from testes samples using the Qiagen RNeasy Plus Universal kit (Qiagen, UK) according to the manufacturer’s guidelines, which included a step to remove any contaminating genomic DNA.
small RNA libraries were prepared from high quality RNA using the Illumina TruSeq small RNA sample prep kit (Illumina, San Diego, CA, USA), following the manufacturer’s instructions.

treatment_protocol: Calves on the High-plane of nutrition received 1.5 kg of milk replacer (10 liters) per day and ad libitum concentrates. The Moderate plane of nutrition group received 0.5 kg of milk replacer (4 litres) per day and 0.5 kg of concentrates.

tag: diet

value: Moderate

value: Testes

tag: breed

value: Holstein-Friesian

tag: developmental stage

value: calf


title: human WBC, GB4030282 (iDNase-seq)


title: Patient 573

tag: tissue

value: Patient 573

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 572

tag: individual

value: Patient 572

value: V

value: MBOT


title: human WBC, GB4030277 (iDNase-seq)

value: WBC


title: human WBC, GB4030276 (iDNase-seq)


title: Patient 570

value: Tumor tissue FFPE

value: Patient 570

tag: study

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Patient 574

value: Patient 574

value: J

tag: stagegroup

value: predictions/survival


title: Patient 569

value: Patient 569

value: C

tag: finalstatus

value: All


title: human WBC, GB4030274 (iDNase-seq)


title: Testes, Moderate-plane of nutrition, 31979

description:
Moderate-plane of nutrition
T33_H

value: High

value: Testes

value: Holstein-Friesian

value: calf


title: Patient 571

value: Patient 571

value: H

tag: diagnosis


title: SW480 cells, CPEB3, biological rep3

city: Guangzhou

first: Qun

last: Yan

address: NO.1838 Guangzhou Avenue

institute: Nanfang Hospital

description: Gene expression data from CPEB3 overexpressing SW480 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software.Raw data were normalized and perfect matches summarized through median polish using the Robust Multi-array Average algorithm.

label: biotin

source_name: CPEB3 overexpressing SW480 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

growth_protocol: The transfected cells were maintained in Dulbecco’s modified Eagle’s medium containing 10% fetal calf serum, 100 IU/mL penicillin, and 100 µg/mL streptomycin.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: SW480-NC and SW480-CPEB3 cells were rinsed with PBS and placed on ice in the Trizol solution.

tag: cell line

value: colorectal cancer cells

tag: genotype

value: CPEB3 overexpressing


title: Testes, High-plane of nutrition, 61965

description:
High-plane of nutrition
T34_L

value: Moderate


title: SW480 cells, NC, biological rep3

description: Gene expression data from negative control SW480 cells

source_name: Negative control SW480 cells

tag: cell type

value: control


title: SW480 cells, NC, biological rep1


title: human WBC, GB4030275 (iDNase-seq)

value: WBC


title: SW480 cells, NC, biological rep2


title: Testes, Moderate-plane of nutrition, 37840

description:
Moderate-plane of nutrition
T35_H


title: SW480 cells, CPEB3, biological rep2


title: SW480 cells, CPEB3, biological rep1


title: Patient 567

value: Tumor tissue FFPE

value: Patient 567

value: G

value: MOC

value: MBOT

value: Ovary/presumed ovary

tag: analysis


title: Patient 568

value: Patient 568

value: F

value: Pancreas

value: Primary pancreatic

value: UGI

value: All


title: human WBC, GB4030273 (iDNase-seq)


title: Patient 575

value: Patient 575

value: T

value: Unknown


title: Testes, High-plane of nutrition, 37824

description:
High-plane of nutrition
T32_H

value: High

value: Testes

value: Holstein-Friesian

value: calf


title: Testes, Moderate-plane of nutrition, 27848

description:
Moderate-plane of nutrition
T31_H


title: Testes, High-plane of nutrition, 47874

description:
High-plane of nutrition
T28_L

value: Moderate


title: human WBC, GB4030271 (iDNase-seq)

value: WBC


title: human WBC, GB4030272 (iDNase-seq)


title: human WBC, GB4030270 (iDNase-seq)


title: Patient 565

value: Tumor tissue FFPE

value: Patient 565

value: V

value: MBOT


title: Patient 566

value: Patient 566

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: human WBC, GB4030269 (iDNase-seq)


title: human WBC, GB4030268 (iDNase-seq)


title: Testes, High-plane of nutrition, 61973

description:
High-plane of nutrition
T27_L


title: Testes, Moderate-plane of nutrition, 81983

description:
Moderate-plane of nutrition
T26_H


title: Patient 563

value: Patient 563

value: F

value: Pancreas

value: Primary pancreatic

value: UGI

value: All


title: Patient 562

value: Patient 562

value: Q

value: predictions/survival


title: Patient 564

value: Tumor tissue FFPE

value: Patient 564

value: L


title: human WBC, GB4030266 (iDNase-seq)

value: WBC


title: Testes, Moderate-plane of nutrition, 27864

description:
Moderate-plane of nutrition
T25_H

value: High

value: Testes

value: Holstein-Friesian

value: calf


title: Testes, High-plane of nutrition, 37865

description:
High-plane of nutrition
T22_L

value: Moderate


title: Patient 560

value: Patient 560

value: M

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: Testes, Moderate-plane of nutrition, 42931

description:
Moderate-plane of nutrition
T20_H


title: Patient 559

value: Patient 559

value: O

value: MBOT


title: human WBC, GB4030267 (iDNase-seq)


title: Testes, Moderate-plane of nutrition, 77860

description:
Moderate-plane of nutrition
T19_H


title: human WBC, GB4030265 (iDNase-seq)


title: Patient 561

value: Tumor tissue FFPE

value: Patient 561

value: C

value: All


title: Patient 558

value: Patient 558

value: B


title: human WBC, GB4030264 (iDNase-seq)

value: WBC


title: human WBC, GB4030263 (iDNase-seq)


title: Testes, High-plane of nutrition, 17855

description:
High-plane of nutrition
T18_H

value: High

value: Testes

value: Holstein-Friesian

value: calf


title: Testes, High-plane of nutrition, 41971

description:
High-plane of nutrition
T17_L

value: Moderate


title: human WBC, GB4030261 (iDNase-seq)


title: human WBC, GB4030262 (iDNase-seq)


title: Patient 557

value: Patient 557

value: A

value: MOC

value: predictions/survival


title: human WBC, GB4030260 (iDNase-seq)


title: Patient 555

value: Patient 555

value: V

value: Expansile

value: Ovary/presumed ovary


title: Patient 556

value: Tumor tissue FFPE

value: Patient 556

value: Q

value: MBOT


title: Patient 554

value: Patient 554

value: H

value: All


title: human WBC, GB4030259 (iDNase-seq)

value: WBC


title: Patient 553

value: Patient 553

value: C


title: Testes, Moderate-plane of nutrition, 51980

description:
Moderate-plane of nutrition
T15_L

value: Moderate

value: Testes

value: Holstein-Friesian

value: calf


title: Patient 552

value: Patient 552

value: MOC


title: Testes, Moderate-plane of nutrition, 97854

description:
Moderate-plane of nutrition
T14_L


title: Testes, High-plane of nutrition, 27823

description:
High-plane of nutrition
T13_H

value: High


title: human WBC, GB4030258 (iDNase-seq)


title: Testes, High-plane of nutrition, 13745

description:
High-plane of nutrition
T11_H


title: human WBC, GB4030257 (iDNase-seq)


title: Testes, Moderate-plane of nutrition, 21978

description:
Moderate-plane of nutrition
T12_L


title: Testes, Moderate-plane of nutrition, 97821

description:
Moderate-plane of nutrition
T10_L


title: Testes, Moderate-plane of nutrition, 93744

description:
Moderate-plane of nutrition
T9_H


title: human WBC, GB4030254 (iDNase-seq)


title: human WBC, GB4030255 (iDNase-seq)


title: human WBC, GB4030256 (iDNase-seq)


title: Testes, Moderate-plane of nutrition, 47825

description:
Moderate-plane of nutrition
T8_L


title: Patient 550

value: Tumor tissue FFPE

value: Patient 550

value: B

value: Ovary/presumed ovary


title: Testes, Moderate-plane of nutrition, 92928

description:
Moderate-plane of nutrition
T6_H


title: human WBC, GB4030251 (iDNase-seq)


title: Patient 547

value: Patient 547

value: A

value: MBOT

value: predictions/survival


title: human WBC, GB4030252 (iDNase-seq)

value: WBC


title: Patient 549

value: Patient 549

value: V

value: Expansile

value: All


title: Patient 545

value: Patient 545


title: Patient 551

value: Patient 551

value: R


title: Patient 546

value: Patient 546

value: C

value: Metastases (GIT)

value: Mets (UGI)

value: UGI

value: Infiltrative


title: Testes, High-plane of nutrition, 12937

description:
High-plane of nutrition
T3_L

value: Moderate

value: Testes

value: Holstein-Friesian

value: calf


title: Patient 544

value: Tumor tissue FFPE

value: Patient 544

value: M

value: MOC

value: Ovary/presumed ovary


title: Testes, High-plane of nutrition, 93760

description:
High-plane of nutrition
T2_H

value: High


title: human WBC, GB4030253 (iDNase-seq)

value: WBC


title: human WBC, GB4030249 (iDNase-seq)


title: Patient 548

value: Patient 548

value: MOC (anaplastic)

value: All


title: Patient 543

value: Patient 543

value: D

value: MBOT

value: predictions/survival


title: Testes, High-plane of nutrition, 57826

description:
High-plane of nutrition
T7_L

value: Moderate

value: Testes


title: human WBC, GB4030248 (iDNase-seq)


title: Testes, High-plane of nutrition, 47858

description:
High-plane of nutrition
T16_H

value: Holstein-Friesian

value: calf


title: Patient 542

value: Tumor tissue FFPE

value: Patient 542

value: V

value: Infiltrative


title: Occipital cortex, PSEN1-E280A + APOEch carrier

city: Santa Barbara

first: Kenneth

middle: S

last: Kosik

state: CA

address: 5165 Biology II

department: Molecular, Cellular, and Developmental Biology

institute: University of California Santa Barbara

description:
10X Genomics
C402_C17 (sample 3)

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the 10x Genomics CellRanger pipeline (version 3.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Downstream analysis was performed using Seurat 4.0 (https://satijalab.org/seurat/index.html) in RStudio Version 4.1.0. Data was imputed for missing values using single-cell RNA-Seq Gene Expression Recovery package SAVER (v1.1.2).
Assembly: GRch38-3.0.0
Supplementary files format and content: comma separated values file include meta.data information and cell type annotation
Supplementary files format and content: comma separated values file include processed count matrix for all 3 samples: sample 1 - frontal cortex, sample 2 - hippocampus and sample 3 - occipital cortex.

source_name: Brain

extract_protocol:
Hippocampal formation (HIP), frontal cortex (FC) or occipital cortex (OL) were dissociated, and nuclei isolation was performed separately for each of these regions using the Nuclei Isolation Kit: Nuclei EZ Prep (Sigma, #NUC101) as described in (https://doi.org/10.1038/nmeth.4407).  Briefly, tissue samples were dounce homogenized in 2 ml of ice-cold EZ PREP and incubated on ice for 5 min. Following initial dounce homogenization, an additional 2ml of EZ PREP was added and the samples were incubated for 5 min. Nuclei suspension was centrifuged (500 × g, 5 min and 4°C) washed 1X in ice-cold EZ PREP buffer, and 1X in Nuclei Suspension Buffer (NSB; consisting of 1× PBS, 1% (w/v) BSA and 0.2 U/μl RNase inhibitor (Clontech, #2313A), resuspended in 1 ml of NSB and filtered through a 40 μm cell strainer. Nuclei were stained with SYTOX green (1:1000) and counted twice. A final concentration of 1000 nuclei per µl was used for loading onto the 10X Chromium (10X Genomics).
Library construction was performed using the Chromium Single Cell 3′ Library & Gel Bead Kit v3.1 (10X Genomics) using manufacturer instructions.

value: Brain

value: diverse brain cell types

value: Occipital cortex

value: PSEN1-E280A +APOEch

tag: treatment

value: no treatment


title: Testes, Moderate-plane of nutrition, 87886

description:
Moderate-plane of nutrition
T1_L


title: Testes, High-plane of nutrition, 57867

description:
High-plane of nutrition
T5_L


title: Hippocampus, PSEN1-E280A + APOEch carrier

description:
10X Genomics
C402_C12 (sample 2)

value: Hippocampus


title: Patient 540

value: Patient 540

value: W

value: MOC

value: Ovary/presumed ovary

value: All


title: Frontal cortex, PSEN1-E280A + APOEch carrier

description:
10X Genomics
C402_C01 (sample 1)

value: Frontal cortex


title: Patient 541

value: Patient 541

value: M

value: Expansile


title: human WBC, GB4030246 (iDNase-seq)

value: WBC


title: human WBC, GB4030245 (iDNase-seq)


title: human WBC, GB4030250 (iDNase-seq)


title: human WBC, GB4030244 (iDNase-seq)


title: human WBC, GB4030243 (iDNase-seq)


title: Patient 538

value: Tumor tissue FFPE

value: Patient 538

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: Patient 539

value: Patient 539

value: A


title: 231260, peripheral blood, RNA-seq

city: shanghai

first: xuebing

last: Shi

address: 225 Changhai Road

institute: Eastern Hepatobiliary Surgery Institute, Second Military Medical University

description:
10x genomics
paired tissues from patient with GBC

data_processing:
Cell Ranger software (Version 2.0) was applied to convert Illumina base call files to FASTQ files with the ‘cellranger mkfastq’ command, which were subsequently aligned to the hg19 human genome. Meanwhile, Cell Ranger carried out default quality control, and generate files containing raw unique molecular identifier (UMI) counts matrix. Downstream analyses were performed using the “Seurat” package (3.1.1) form R software (4.0.3). Cells with lower than 200 identified genes were removed during quality control process. Of note, quality-control parameters also included UMI counts, proportion of UMIs derived from mitochondrial and dissociation or sorting associated genes. After exclusion of low-quality cells, UMI counts were normalized by the function ‘NormalizeData’, in which normalization method was set as ‘logNormalize’ with the scale factor of 10000 total UMIs per cell. Thereafter, ‘FindVariableGenes’ function was performed with default parameters to detect 2000 highly variable genes, in which ribosome as well as heat shock response related genes were regressed out due to potential confounding effect. Principal component analysis (PCA) was subsequently conducted based on the processed expression matrix containing highly variable genes, followed by secondary UMAP visualization on selected PCA using the ‘RunUMAP’ function at a perplexity value of 30. Differentially expressed genes across clusters were calculated and identified using function “FindAllMarkers”.
Assembly: mm10
Supplementary files format and content: RNA-seq: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: TCR-seq: contig_annotations.csv

source_name: peripheral blood

extract_protocol:
Fresh surgical resected samples were rinsed with Hank’s balanced salt solution (HBSS), which were subsequently minced and digested with digestive buffer, followed by incubation for 60 min at 37 °C with gentle shaking. The digestive buffer was conFigured by dissolving digestive enzyme into RPMI with 10% serum, including deoxyribonuclease type I, collagenase IV, and hyaluronidase type V. After digestion, the mixture was filtered using 300-mesh filter screen, and was then collected in the centrifuge tubes. Thereafter, leukocytes were isolated form tissues via density gradient centrifugation in line with manufacturer’s instructions. Filtered cell suspensions were centrifuged with 450 g for 8 min, and the re-suspended precipitates were subsequently centrifuged with 50 g for 1 min. Washed cell suspensions were carefully layered on the surface of lymphoprep liquid, followed by centrifugation of 450 g for 25 min at room temperature. Tissue derived leukocytes were obtained by collecting the middle layer of the mixture.
CountessII Automated Cell Counter (Thermo Fisher Scientific, USA) was applied to determine viability and density of mononuclear cells from tumor, lymph node and peripheral blood. Single cell suspensions were then processed for single-cell gene expression (scRNA-seq) as well as single cell T cell receptor (TCR) clonotypes (scTCR-seq) using Chromium Controller. Single cells were adjusted to an ideal concentration of 5×10^5 to 1×10^6 cells/mL with a viability higher than 70%. Single-cell library was prepared in line with the protocol of 10X Genomics for Single Cell V(D)J and 5′ Gene Expression (10X Genomics, Pleasanton, CA, USA). In brief, single-cell suspensions were then loaded onto the Chromium Controller combined with the reverse transcription (RT) master mix and Gel beads containing barcode information. Following single-cell gel bead-in-emulsions reverse transcription, PCR amplification was carried out to generate adequate cDNAs for the construction of scRNA-seq as well as TCR V(D)J libraries. Thereafter, the libraries were sequenced on HiSeq4000 (Illumina) following the manufacturer’s specification.

value: patient 231260

tag: disease state

value: GBC

value: peripheral blood

value: immune cell

value: RNA

value: surgery


title: 231260, lymph node, RNA-seq

source_name: lymph node

value: lymph node


title: Patient 537

source_name: Tumor tissue FFPE

value: Patient 537

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary

value: All


title: human WBC, GB4030247 (iDNase-seq)

source_name: WBC

value: WBC


title: Patient 535

value: Tumor tissue FFPE

value: Patient 535

value: MBOT


title: Patient 533

value: Patient 533

value: Infiltrative


title: 231260, primary focus, TCR-seq

data_processing:
Cell Ranger software (Version 2.0) was applied to convert Illumina base call files to FASTQ files with the ‘cellranger mkfastq’ command, which were subsequently aligned to the hg19 human genome. Meanwhile, Cell Ranger carried out default quality control, and generate files containing raw unique molecular identifier (UMI) counts matrix. Downstream analyses were performed using the “Seurat” package (3.1.1) form R software (4.0.3). Cells with lower than 200 identified genes were removed during quality control process. Of note, quality-control parameters also included UMI counts, proportion of UMIs derived from mitochondrial and dissociation or sorting associated genes. After exclusion of low-quality cells, UMI counts were normalized by the function ‘NormalizeData’, in which normalization method was set as ‘logNormalize’ with the scale factor of 10000 total UMIs per cell. Thereafter, ‘FindVariableGenes’ function was performed with default parameters to detect 2000 highly variable genes, in which ribosome as well as heat shock response related genes were regressed out due to potential confounding effect. Principal component analysis (PCA) was subsequently conducted based on the processed expression matrix containing highly variable genes, followed by secondary UMAP visualization on selected PCA using the ‘RunUMAP’ function at a perplexity value of 30. Differentially expressed genes across clusters were calculated and identified using function “FindAllMarkers”.
Assembly: mm10
Supplementary files format and content: RNA-seq: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: TCR-seq: contig_annotations.csv
Library strategy: scTCR-seq

source_name: primary focus

value: patient 231260

value: GBC

value: primary focus


title: human WBC, GB4030240 (iDNase-seq)


title: 231260, peripheral blood, TCR-seq

value: peripheral blood

value: immune cell

value: RNA

value: surgery


title: 231260, primary focus, RNA-seq


title: Patient 534

value: Patient 534

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: human WBC, GB4030241 (iDNase-seq)

value: WBC


title: Patient 532

value: Tumor tissue FFPE

value: Patient 532

value: P

value: MOC

value: Ovary/presumed ovary

value: predictions/survival


title: 230723, peripheral blood, TCR-seq

value: patient 230723

value: GBC


title: human WBC, GB4030238 (iDNase-seq)


title: human WBC, GB4030237 (iDNase-seq)


title: human WBC, GB4030236 (iDNase-seq)


title: 230723, peripheral blood, RNA-seq

value: peripheral blood

value: immune cell


title: Patient 531

value: Patient 531

value: T

value: Infiltrative

value: All


title: Patient 529

value: Patient 529

value: W


title: human WBC, GB4030235 (iDNase-seq)

value: WBC


title: Patient 530

value: Tumor tissue FFPE

value: Patient 530

value: H

value: MBOT


title: Patient 536

value: Patient 536

value: M

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: 231260, lymph node, TCR-seq

value: patient 231260

value: GBC

value: lymph node

value: immune cell

value: RNA

value: surgery


title: human WBC, GB4030242 (iDNase-seq)


title: 230723, lymph node, RNA-seq

value: patient 230723


title: human WBC, GB4030239 (iDNase-seq)

value: WBC


title: human WBC, GB4030234 (iDNase-seq)


title: human WBC, GB4030233 (iDNase-seq)


title: 230723, liver metastasis, TCR-seq

source_name: liver metastasis

value: liver metastasis


title: Patient 528

value: Tumor tissue FFPE

value: Patient 528

value: S

value: Benign mucinous neoplasm

value: survival


title: human WBC, GB4030232 (iDNase-seq)


title: 230723, primary focus, TCR-seq

value: primary focus


title: 230723, liver metastasis, RNA-seq


title: 230723, primary focus, RNA-seq


title: 230723, lymph node, TCR-seq


title: Patient 526

value: Patient 526

value: G

value: MOC

value: MBOT

value: predictions/survival


title: human WBC, GB4030230 (iDNase-seq)


title: Patient 527

value: Patient 527

value: V

value: Ovary/presumed ovary

value: All


title: 357818, metastasis, TCR-seq

description:
10x genomics
paired tissues from patient with iCCA

value: patient 357818

value: iCCA

value: immune cell

value: RNA

value: surgery


title: human WBC, GB4030231 (iDNase-seq)

value: WBC


title: human WBC, GB4030229 (iDNase-seq)


title: human WBC, GB4030228 (iDNase-seq)


title: 357818, metastasis, RNA-seq

value: liver metastasis


title: Patient 523

value: Tumor tissue FFPE

value: Patient 523

value: L


title: Patient 524

value: Patient 524

value: MOC

value: Expansile


title: 357818, primary focus, TCR-seq

value: primary focus


title: 357818, peripheral blood, RNA-seq

value: peripheral blood


title: 357818, peripheral blood, TCR-seq


title: human WBC, GB4030226 (iDNase-seq)


title: Patient 520

value: Patient 520

value: A

value: MBOT

value: Ovary/presumed ovary


title: Patient 525

value: Patient 525

value: B

value: predictions/survival


title: human WBC, GB4030227 (iDNase-seq)

value: WBC


title: 230498, peripheral blood, TCR-seq

description:
10x genomics
paired tissues from patient with Dcca

value: patient 230498

value: Dcca

value: immune cell

value: RNA

value: surgery


title: human WBC, GB4030225 (iDNase-seq)


title: 357818, primary focus, RNA-seq

value: patient 357818

value: iCCA


title: Patient 521

value: Tumor tissue FFPE

value: Patient 521

value: G

value: MOC


title: 230498, peripheral blood, RNA-seq

value: peripheral blood


title: human WBC, GB4030224 (iDNase-seq)


title: Patient 517

value: Patient 517

value: Expansile

value: Ovary/presumed ovary

value: All


title: Patient 518

value: Patient 518

value: B

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: Patient 516

value: Patient 516

value: N

value: predictions/survival


title: Patient 522

value: Tumor tissue FFPE

value: Patient 522

value: I


title: human WBC, GB4030223 (iDNase-seq)

value: WBC


title: HK2, HIF1, Hypoxia

city: Tokyo

first: Imari

last: Mimura

address: 7-3-1 Hongo Bunkyo-ku

department: Div. Nephrol and Endocrinol.

country: Japan

institute: The University of Tokyo

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v1.3.7.1 with the significance cut-off q-value <=0.01
Assembly: UCSCv37,hg19

source_name: Kidney

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using an ultrasonicator.
ChIP-seq libraries were prepared using the Truseq v5 Library Preparation Kit. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified on the thermocycler. Post amplification libraries were size selected at 250-450bp in length. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: 1% hypoxia

value: Kidney

value: Human Kidney-2

value: immortalized

value: 1% hypoxia 24 hours


title: HK2, HIF1, Normoxia

value: normoxia


title: human WBC, GB4030222 (iDNase-seq)


title: 230498, lymph node, TCR-seq

value: patient 230498

value: Dcca

value: lymph node

value: immune cell

value: RNA

value: surgery


title: Patient 519

value: Patient 519

value: Q

value: MOC

value: MBOT

value: Ovary/presumed ovary


title: 230498, lymph node, RNA-seq


title: Patient 515

value: Tumor tissue FFPE

value: Patient 515

value: L

value: Expansile

value: All


title: human WBC, GB4030220 (iDNase-seq)

value: WBC


title: Patient 514

value: Patient 514

value: V


title: human WBC, GB4030219 (iDNase-seq)


title: Patient 513

value: Patient 513

value: F

value: Pancreas

value: Primary pancreatic

value: UGI


title: 3D aggregates - Replica 2

city: Aachen

first: Mohamed Hamdy Elsafi

last: Mabrouk

state: NRW

address: pauwelsstraße 20

department: Helmholtz Institute of Biomedical Engineering

institute: RWTH-Aachen

description:
EB8n2
191114_scRNASeq_GF_191113_1_01_4_S4

data_processing:
demultiplexing raw base call (BCL) and generation of FASTQ files:  cellranger mkfastq v3.1.0
alignment, filteration, counting: cellranger count v3.1.0
Genome_build: refdata-cellranger-GRCh38-3.0.0
Supplementary_files_format_and_content: barcodes.tsv which corrsponds to the specific barcodes of each GEM droplet for each sample.
Supplementary_files_format_and_content: features.tsv which contains both gene names and ensembl IDs for the genes expressed in each sample.
Supplementary_files_format_and_content: the expression matrix.mtx which is a sparse matrix containg the expression data for each sample.

source_name: hiPSCs_3D aggregates

growth_protocol: Five iPSC-lines were generated from mesenchymal stromal cells (iPSC-102, iPSC-104, and iPSC-106) or blood (PT4-WT4, PT18-WT18) by reprogramming with episomal plasmids or sendai virus, respectively. The study was approved by the local ethic committee and all samples were taken after written consent (EK206/09). The iPSC lines were cultured on tissue culture plastic coated with vitronectin (0.5 µg/cm2) in StemMACS iPS-Brew XF (Miltenyi Biotec). Pluripotency was validated by three lineage differentiation potential and Epi-Pluri-Score analysis, as described in our previous work (Lenz et al., 2015; doi.org/10.1038/srep08973). Micro-contact printing (µCP) was carried out to generate circular adhesion islands with different diameters that facilitate attachment of iPSCs. PDMS pillars were coated with vitronectin (10 µg/mL) for 45 minutes and then used as stamps on pretreated substrates. Stamps were brought into conformal contact with the substrate for at least 1 minute. Cells were seeded on the patterned substrates at 10,000 cells/cm2. Self-detaching EBs formed spontaneously from micro-contact printed substrates after 6-7 days in culture.

extract_protocol:
For colonies harvested at day 5, the cell culture medium was aspirated, 800 µL of Accutase were added on top of the cells, and they were incubated for 5 minutes at 37 °C After that, 1 mL of pre-warmed KO-DMEM were added to each sample and the cell were pipetted several time to create single cell suspension. Cells were then transferred to 15-mL falcon tubes. For processing of 3D aggregates, they were collected at day 8 from cell seeding into15 mL falcon tube and centrifuged at 100 g for 3 minutes. The supernatant was aspirated, and 1 mL of pre-warmed Accutase were added to each falcon tube for 9 mins at 37 °C. The aggregates were pipetted up and down several time to create single cell suspension. Falcons containing single cells were centrifuged again at 1000 RPM for 4 minutes. Then, they were re-suspended in 1 mL of PBS + 1 µL Y-27632 ROCK Inhibitor + 0.04% BSA. The suspension were filtered through 40 µm cell strainer to remove cell clumps. The cells were counted and centrifuged again, and the cells density was adjusted to 500-1000 cells/µL. Cells were kept on ice until further processing.
The cell suspension was processed by the chromium platform (V3) from 10X Genomics according to the manufacturer’s 3' protocol to obtain a sequencing library. The cells were deposited into the microfluidic platform provided by 10X Genomics. Chromium controller was used to partition cells into Gel Bead-In-EMulsions (GEMs). Cell lysis was carried out in the GEMs, which included a unique barcode for each bead. The Read1 was added during the GEMs lysis and cDNA construction. The barcoded cDNA was then purified using Dynabeads and amplified using PCR and random primers. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and Read 2 primers are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina amplification. The library was then sequenced using Nextseq 550 to get paired-ended reads.

value: induced pluripotent stem cells (iPSCs)

tag: day

tag: dimensionality


title: 2D colonies- Replica 2

description:
EB5n2
191114_scRNASeq_GF_191113_1_01_2_S2

source_name: hiPSCs_2D colonies


title: 230498, primary focus, RNA-seq

value: patient 230498

value: Dcca

value: primary focus

value: immune cell

value: RNA

value: surgery


title: 3D aggregates - Replica 1

description:
EB8n1
191114_scRNASeq_GF_191113_1_01_3_S3


title: 230498, primary focus, TCR-seq


title: human WBC, GB4030218 (iDNase-seq)


title: Patient 512

data_processing: We used batch effects adjustment, quality control, and normalisation techniques that are applied one patient at a time, single-patient processing [Talhouk et al. 2016]. After quality control assessments, the count data were log2 transformed and centered by the arithmetic mean of the selected housekeeping genes, LDHA, MTG1, POLR1B, TBP.

value: Tumor tissue FFPE

value: Patient 512

value: R

value: MOC

value: Expansile

value: Ovary/presumed ovary


title: 2D colonies- Replica 1

description:
EB5n1
191114_scRNASeq_GF_191113_1_01_1_S1


title: 230093, peritonneal metastasis, TCR-seq

source_name: peritonneal metastasis

value: patient 230093

value: iCCA

value: peritonneal metastasis


title: human WBC, GB4030217 (iDNase-seq)

data_processing:
Basecalls performed
The raw fastq files are read and separated into 480 files corresponding to 96 pairs of cell barcodes over 5 replicates. The 480 pairs are shown in barcode_480.txt. A read is considered as belonging to one of the barcodes if the beginning of read 1 or read 2 contains the same pair of barcodes in the left and right column respectively.  After separting each set of fastq files into 480 files, some base pairs starting from 5' are trimmed and the remaining reads are mapped to the human genome using bowtie2.
The top 30 barcodes are selected from each well based on read count, so 30 nuclei are sorted for each well with doublets removed, where the number removed was calculated based on the collision rate like in (Science. 2015 May 22; 348(6237): 910–914). These are denoted as single cells because of the low likelihood of two cells in the same well having the same barcode. We required that qualifying cells have more than 100 reads and a FRiP greater than 0.1. With these requirements, 4489 cells were obtained, and we were able to identify 218,042 DHSs. For each cell, we calculated the reads that were located within the DHS and stored the results in a matrix.
Genome_build: hg18
barcode_480.txt: two columns, the left column refers to a DNA barcode starting from the 5' end while the right column refers to a DNA barcode starting from the 3' end
peaks_218042_WBC.txt: first column is for chromsome, second column is for DHS start site, and third column is for DHS end site
iDNase_4489_cells_218042_peaks_counts_at_WBC.mtx: This file contains read count data for single cells in MatrixMarket format. Each row corresponds to a non-zero entry with the row, column, and then value specified. Reading the matrix results in a 218042 x 4489 matrix of peaks by cells where each element represents the number of reads located within a DHS site for some single cell.

value: WBC


title: 230093, PBMC, RNA-seq

source_name: PBMC

value: PBMC


title: human WBC, GB4030216 (iDNase-seq)


title: 230093, peritonneal metastasis, RNA-seq


title: Patient 511

value: Patient 511

value: G

value: MBOT

value: All


title: human WBC, GB4030221 (iDNase-seq)


title: 230093, PBMC, TCR-seq

value: immune cell

value: RNA


title: Patient 508

value: Tumor tissue FFPE

value: Patient 508

value: V


title: Patient 510

value: Patient 510

value: M

value: MOC


title: Patient 509

value: Patient 509

value: P

value: Infiltrative

value: Ovary/presumed ovary


title: Patient 507

value: Patient 507

value: C

value: predictions/survival


title: 230093, primary focus, TCR-seq

value: patient 230093

value: iCCA

value: primary focus

value: surgery


title: Well, Top, veh, D7, RP13

city: Boston

first: Lorna

last: Ewart

state: MA

address: 27 Drydock Avenue

institute: Emulate Inc.

description: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line from the brain side of the transwell

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted
Supplementary files format and content: counts

source_name: Transwell Top Channel Day 7 - Vehicle

growth_protocol: Brain-Chip and cell seeding: A mixture of glutamatergic and GABAergic neurons, astrocytes, microglia, and pericytes were seeded in the brain channel of the Brain-Chips at the following concentrations: 4 million cells/mL for Glutamatergic neurons, 2 million cells/mL for GABAergic neurons, 2 million cells/mL for astrocytes, 0.2 million cells/mL for microglia, and 0.15 million cells/mL for pericytes. After cell seeding, the upper channel of the Brain-Chip was maintained in NeuCyte maintenance medium and incubated overnight at 37°C (Day 0). The following day (Day 1), the vascular channel was rinsed with human serum-free endothelial medium supplemented with 2% platelet-poor plasma-derived serum, 10 μM Y27632. Then BMECs were seeded at a concentration of 16 million cells/mL to ensure the very tight endothelial monolayer found in the human blood-brain barrier, and the chips were flipped immediately to allow  BMECs to adhere to the ECM-coated part of the membrane. After 2 h incubation, the chips were flipped back to let the rest of the BMECs sit on the bottom and sides of the channel to form a capillary lumen. The vascular channel of the Brain-Chip was maintained overnight. On Day 2, the Brain-Chips were connected to the Zoë® culture module and perfused continuously through the brain and vascular channel at a flow rate of 60 μl hr-1 and 60 μl hr-1, respectively, using each channels' respective media. Brain Transwell model. The conventional cell cultures (transwells) and the Brain-Chips were seeded using the same ECM composition as well as cell composition, media formulations, and seeding density. At the first experimental day (D0), the cortical (Glutamatergic and GABAergic subtypes) neurons, astrocytes, microglia, and pericytes were seeded on the apical side, followed by the seeding of the endothelial cells (D1) on the basolateral side of the 0.47 cm2 Transwell-Clear permeable inserts (0.4-μm pore size). For the apical compartment, we used NeuCyte medium, while for the basolateral compartment, we used hESFM with 5% human serum from platelet-poor human plasma. The cells were maintained under static conditions throughout the duration of the experiment (D8). The culture medium was replaced daily in both compartments.

extract_protocol:
RNA was extracted using TRIzol (Life Technologies) according to manufacturer’s guidelines
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: applied mechanostimulation

value: flow (60 µl/hr)

value: brain

tag: air liquid interface

value: vehicle

tag: time

value: day 7

tag: growth protocol

value: conventional cell cultures (transwells)


title: human WBC, GB4030214 (iDNase-seq)

value: WBC


title: human WBC, GB4030213 (iDNase-seq)


title: Patient 505

tag: tissue

value: Tumor tissue FFPE

tag: individual

value: Patient 505

value: B

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: human WBC, GB4030212 (iDNase-seq)


title: Well, Top, veh, D7, RP15

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line


title: 230093, primary focus, RNA-seq

value: patient 230093

value: immune cell

value: RNA


title: Patient 504

value: Patient 504

tag: study

value: L

tag: stagegroup

value: MOC

value: Ovary/presumed ovary

value: predictions/survival


title: Patient 506

value: Patient 506

value: W

tag: finalstatus

tag: diagnosis

value: All


title: HC7

first: Bernd

last: Denecke

address: Pauwelsstrasse 30

department: IZKF Aachen

institute: RWTH Aachen University

hyb_protocol: Following fragmentation, 5.5 µg of fragmented biotin labelled cDNAs were hybridized for 16 hrs at 45°C and 60 rpm on HTA 2.0 ST Arrays. Gene Chips were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics Program FS450_0001.

scan_protocol: Gene Chips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Raw image data were analysed with  Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized with SST-RMA algorithm (Affymetrix).

source_name: CD34+ cells

label_protocol: Fragmented, biotinylated cDNAs were prepared according according to the Affymetrix Gene Chip WT Pico Reagent Kit according to the manufactorers instructions: input each 6.6 ng total RNA

extract_protocol: Blood and bone marrow mononuclear cells from MPN patients were isolated using Ficoll density gradient centrifugation. Enrichment of the CD34+ cell population was performed by magnetic cell separation (MACS) with the CD34 MicroBead Kit, human (Miltenyi). RNA was isolated using the RNeasy Micro Kit (QIAGEN).

value: peripheral blood (PB) mononuclear cells

tag: genotype

value: non-mutated

tag: age

tag: Sex

value: M

value: healthy


title: HC9

value: F


title: Patient 503

value: Tumor tissue FFPE

value: Patient 503

value: MBOT

tag: analysis


title: HC6


title: human WBC, GB4030211 (iDNase-seq)

tag: cell type

value: WBC


title: HC5


title: human WBC, GB4030215 (iDNase-seq)


title: HC8


title: HC4


title: Well, Top, veh, D7, RP11

value: flow (60 µl/hr)

value: brain

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line

tag: treatment

value: vehicle

value: day 7

value: conventional cell cultures (transwells)


title: human WBC, GB4030207 (iDNase-seq)


title: human WBC, GB4030208 (iDNase-seq)


title: human WBC, GB4030210 (iDNase-seq)


title: Well, Top, veh, D7, RP9


title: Well, Top, veh, D5, RP7

source_name: Transwell Top Channel Day 5 - Vehicle

value: day 5


title: human WBC, GB4030209 (iDNase-seq)


title: human WBC, GB4030206 (iDNase-seq)


title: PV10

value: bone marrow (BM)

value: PV


title: Patient 502

value: Patient 502

value: V

value: MOC

value: Expansile

value: Ovary/presumed ovary

value: All


title: PV12

value: F


title: human WBC, GB4030205 (iDNase-seq)

value: WBC


title: PV9

value: peripheral blood (PB) mononuclear cells

value: M


title: Patient 499

value: Tumor tissue FFPE

value: Patient 499

value: B

value: MBOT


title: Well, Top, veh, D5, RP5

value: flow (60 µl/hr)

value: brain

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line

value: vehicle

value: day 5

value: conventional cell cultures (transwells)


title: Patient 500

value: Patient 500

value: G

value: MOC

value: predictions/survival


title: PV11

value: PV


title: Patient 501

value: Patient 501

value: Metastases (LGI)

value: Mets (Appendix)

value: LGI

value: Expansile

value: Ovary/presumed ovary

value: All


title: human WBC, GB4030204 (iDNase-seq)

value: WBC


title: human WBC, GB4030203 (iDNase-seq)


title: Well, Top, veh, D5, RP1

value: flow (60 µl/hr)

value: brain

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line


title: Patient 498

value: Tumor tissue FFPE

value: Patient 498

value: L

value: MBOT

value: Benign mucinous neoplasm

value: survival


title: Patient 497

value: Patient 497

value: S

value: Appendix


title: Chip, Top, veh, D7, R13

description: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line from the brain channel of the Brain-Chip

source_name: Chip Top Channel Day 7 - Vehicle

value: vehicle

value: day 7

value: Brain-Chip


title: human WBC, GB4030202 (iDNase-seq)


title: Chip, Top, veh, D7, R11


title: PV5

value: bone marrow (BM)

value: M

value: PV


title: Chip, Top, veh, D7, R9

value: flow (60 µl/hr)

value: brain


title: PV2


title: PV8

value: F


title: human WBC, GB4030201 (iDNase-seq)

value: WBC


title: PV7


title: Patient 495

value: Tumor tissue FFPE

value: Patient 495

value: Q

value: MOC

value: Ovary/presumed ovary

value: predictions/survival


title: human WBC, GB4030200 (iDNase-seq)


title: Chip, Top, veh, D5, R7

source_name: Chip Top Channel Day 5 - Vehicle

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line

value: day 5


title: Chip, Top, veh, D5, R5

value: vehicle


title: Patient 493

value: Patient 493

value: MBOT


title: human WBC, GB4030199 (iDNase-seq)


title: PV1

value: peripheral blood (PB) mononuclear cells

value: M


title: Chip, Top, veh, D5, R3

value: flow (60 µl/hr)

value: Brain-Chip


title: PMF10

value: bone marrow (BM)

value: PMF


title: Patient 496

value: Tumor tissue FFPE

value: Patient 496

value: V

value: All


title: PMF9

value: F


title: Patient 492

value: Patient 492

value: W

value: MOC

value: Ovary/presumed ovary


title: human WBC, GB4030197 (iDNase-seq)

value: WBC


title: Patient 494

value: Patient 494

value: O

value: Expansile


title: Patient 491

value: Patient 491

value: C

value: MBOT


title: PMF7

value: bone marrow (BM)

value: M

value: PMF


title: Cord-isolated HUVEC donor 5 ATAC-seq

city: Tucson

first: Casey

middle: E

last: Romanoski

state: AZ

address: 1657 E. Helen St.

department: Cellular & Molecular Medicine

institute: University of Arizona

data_processing:
demultiplexed ATAC-seq fastq data were aligned to hg19 using Bowtie2.
Aligned sam files were made into tagDirectories in HOMER. Reads mapping to mitochondiral DNA were discarded for ATAC seq.
ATAC peaks were identified using the findPeaks function.
Genome_build: hg19
Supplementary_files_format_and_content: peak files are in the original HOMER output format (http://homer.salk.edu/homer/)

source_name: Human Umbilical Vein Endothelial Cell

extract_protocol: For ATAC-seq, nuclei were extracted with nuclear isolation buffer and DNA was size-selected for 125-175 bp fragments on a TBE gel

value: human endothelial cells (HUVECs)

tag: assayed

value: ex-vivo (cord)


title: Chip, Top, veh, D5, R1

tag: applied mechanostimulation

value: flow (60 µl/hr)

value: brain

value: Human (iPSC)-derived glutamatergic and GABAergic neurons, commercially available human astrocytes, pericytes, and human microglial cell line

value: vehicle

value: day 5

value: Brain-Chip


title: Cord-isolated HUVEC donor 4 ATAC-seq


title: PMF5


title: human WBC, GB4030196 (iDNase-seq)

value: WBC


title: human WBC, GB4030198 (iDNase-seq)


title: human WBC, GB4030195 (iDNase-seq)


title: Chip, Top, veh, D7, R15

tag: air liquid interface

value: day 7


title: Cultured HUVEC donor 3 ATAC-seq

value: cultured


title: Well, Top, veh, D5, RP3

tag: time

value: conventional cell cultures (transwells)


title: human WBC, GB4030193 (iDNase-seq)


title: Cultured HUVEC donor 2 ATAC-seq


title: human WBC, GB4030192 (iDNase-seq)


title: PMF2


title: PMF1


title: s_97_771061_tetfzd1_het_p0_neg10dox

description: DOX from P0 to P10

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18.
Reads were aligned to UCSC genome mm10 with STAR aligner (version STAR_2.6.1c ), using Ensembl 91 gene models.
TPM values were generated using RSEM (version v1.3.0 ).
Genome_build: mm10
Supplementary_files_format_and_content: csv, STAR count table and TPM table

source_name: olfactory epithelium

extract_protocol:
TRIzol
TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold

value: olfactory epithelium

tag: development stage


title: Cultured HUVEC donor 1 ATAC-seq


title: s_96_771060_tetfzd1_het_p0_neg10dox

description: DOX from P0 to P10

tag: tissue


title: Organoid-805F-Pat-D217-noAAV-3

first: Zachary

middle: A

last: Batz

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

institute: NIH

description:
Raw_Transcript_Counts.tsv
Raw_Gene_Counts.tsv
Normalized_Filtered5CPM_Gene_Counts.tsv

data_processing:
Reads passing filter were aligned to the Ensembl v94 transcriptome and quantified using Kallisto v0.44.0
Transcript-level counts were collapsed to the gene-level using TxImport v1.8.0
Only genes with >5 CPM in all samples for at least one condition were retained.
Genes were TMM normalized using EdgeR v3.10.5
Assembly: hg38

source_name: Organoid derived from human iPSCs

extract_protocol:
RNA was isolated from 3 frozen organoids per sample using the QIAGEN RNeasy Kit according to manufacturer’s manual (n=3 individual organoids per sample). RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA samples with RIN more than 7 were used for library generation using the TruSeq Library Preparation Kit (Illumina Inc.) following manufacturer’s instructions.

tag: patient

value: Patient

tag: media

value: FBS

value: Organoid derived from human iPSCs


title: human WBC, GB4030191 (iDNase-seq)

extract_protocol:
DNase-seq human 1.25M 2-step crosslink human healthy T/B/NK/monocyte, final 0.1U/μl DNase digestion 37°C 5 minutes, T cell split #1-15 wells, B cell split #16-30 wells, NK cell split #31-45 wells, monocyte split #46-61 wells, TdT&T4 methods adding P7 barcode adaptor (12.5μl volumn/well 37°C 60 minutes), pool, dilution, counting and redistribute into 96-well plate, total 20 nuclei per well seal completely, 65°C overnight; direct PCR1 (12 cycles), pool all the DNA, EXO I 30 minutes, A-tailing and P5 ligation(rt overnight) , column purification and PCR2(16 cycles), run-e-gel and cut from 200-500bp rc#1 i5-01
The isolated 50M of PBMC suspended by 50ml PBS /MgCl2 are firstly fixed by adding 400μl freshly prepared 0.25M Disuccinimidyl glutarate (DSG, ThermoFisher Scientific, catalog no.20593) and incubate at room temperature for 45 minutes with rotation. After protein-protein fixation by DSG and washing three times by PBS, cells suspended by culture medium DMEM supplemented with 10% FBS are further fixed by the addition of 1:15 volume of 16% (w/v) methanol-free formaldehyde solution (Thermo Fisher Scientific) and incubate at room temperature for 10 minutes. The fixing reaction is terminated by a 1:10 volume of 1.25 M glycine and incubate at room temperature for 5 minutes. The fixed cells are collected by centrifugation at 1320rpm for 7 minutes and washed with PBS. The cells are stored in aliquots (1 × 10e6 cells per tube) at −80°C until use.


title: s_94_770702_tetfzd1_het_p0_neg3dox

description: DOX from P0 to P3


title: pPV-MF1

value: peripheral blood (PB) mononuclear cells

value: F

value: pPV-MF


title: human WBC, GB4030194 (iDNase-seq)


title: Organoid-805F-Pat-D217-noAAV-2


title: human WBC, GB4030190 (iDNase-seq)


title: s_95_770702_tetfzd1_het_p0_neg3dox

description: DOX from P0 to P3


title: Organoid-805F-Pat-D217-noAAV-1


title: pPV-MF2

value: bone marrow (BM)


title: ET1

value: ET


title: Organoid-804B-Ctrl-D208-3

value: Control


title: s_92_770701_tetfzd1_het_p0_neg1dox

description: DOX from P0 to P1


title: human WBC, GB4030188 (iDNase-seq)


title: human WBC, GB4030187 (iDNase-seq)


title: human WBC, GB4030189 (iDNase-seq)


title: Organoid-804B-Ctrl-D208-2


title: s_91_770700_tetfzd1_het_p0_neg1dox

description: DOX from P0 to P1


title: s_90_770699_tetfzd1_het_p0_neg1dox

description: DOX from P0 to P1


title: Organoid-804B-Ctrl-D208-1


title: Organoid-806A-Pat-D200-AAVNPHP5Myc-3


title: AMA pool OxBS 2

type: genomic

city: Leuven

first: Bernard

last: Thienpont

state: Vlaams-Brabant

address: Herestraat 49

department: Human Genetics

country: Belgium

institute: KU Leuven Association

description: periosteal cell DNA from mouse treated with AMA

hyb_protocol: DNA was hybridized following manufacturers instructions of the Infinium Mouse Methylation BeadChip

scan_protocol: Infinium Mouse Methylation BeadChips were scanned at Life & Brain following standard procedures.

data_processing: Inter-array quantile normalization, low-quality and sample removal and background correction.

label: Cy5 and Cy3

source_name: periosteum

label_protocol: DNA was labelled following manufacturers instructions of the Infinium Mouse Methylation BeadChip

growth_protocol: Periosteal cells were expanded 1 week after isolation and seeded at 5500 cells/cm2. Three days after seeding, DNA was extracted using DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).

extract_protocol: DNA was extracted using the Dneasy blood and tissue prep kit, followed by an RNAse H and protienase K treatment

treatment_protocol: Periosteal cells were cultured in the presence of 10µM Antimycin A (AMA) or vehicle as control. The inhibitor was added the day after cell isolation.

value: periosteal cells

tag: method

value: Oxidative bisulfite sequencing

tag: group

value: treated

tag: agent

value: antimycin a


title: SD20 elevated temperature

city: Nathan

first: Tessa

middle: M

last: Page

state: QLD

address: 170 Kessels Road

department: Science and Environment

institute: Griffith University

data_processing:
Customised sequencing was performed on a single lane of an Illumina NovaSeq 6000, sequencing 26 bp on read 1, and 100 bp on read 2.
Raw sequence data were processed using Illumina BCL2FASTQ.
Quality control was performed with FastQC.
CEL-Seq-pipeline (https://github.com/yanailab/CEL-Seq-pipeline) for demultiplexing and mapping.
Assembly: Reference transcriptomes were created using transcriptomes for P. onkodes and S. durum (NCBI BioProject PRJNA518156, accession numbers GHIN00000000.1 and GHIO00000000.1 for S. cf. durum and P. cf. onkodes, respectively).
Supplementary files format and content: csv matrix of counts data for Porolithon onkodes
Supplementary files format and content: csv matrix of counts data for Sporolithon durum

organism: Sporolithon durum

source_name: pigmented tissue

growth_protocol: Coralline algae were cultured for three months in flow through aquarium where temperature and pH were altered.

extract_protocol:
Fragments of CCA were thoroughly cleaned prior to sampling for molecular analysis under a microscope and all epiphytes, as far as possible, were removed. CCA were rinsed with filtered seawater and RNAlater® and then blotted with a kimwipe to remove bacterial film. RNA was extracted following a modified TRIzol protocol.
cDNA synthesis, library preparation, and sequencing followed the single-cell sequencing (CEL-Seq2) protocol detailed in Hashimonshony et al. 2016

treatment_protocol: Fragments of CCA (20 per species) were divided across four treatments [“control” (unmanipulated seawater conditions, 27.2 ºC, 8.0 pH/450 µatm pCO2), “T” (elevated temperature and ambient pH, 29.5 ºC, 8.0 pH/450 µatm pCO2), “pH” (reduced pH and ambient temperature, 27.2 ºC, 7.7 pH/1000 µatm pCO2), or “T+pH” (elevated temperature and reduced pH, 29.5 ºC, 7.7 pH/1000 µatm pCO2)] with five biological replicates (n = 5) per treatment for a duration of three months.

value: pigmented tissue

value: elevated temperature


title: s_89_770694_fzd1_negko_neghomo_p14

description: no DOX

tag: genotype


title: human WBC, GB4030184 (iDNase-seq)

first: Keji

last: Zhao

address: 10 Center Dr

institute: NHLBI

source_name: WBC

value: WBC


title: human WBC, GB4030183 (iDNase-seq)


title: ET2

tag: age

tag: diagnosis


title: SD19 elevated temperature + reduced pH

value: elevated temperature + reduced pH


title: s_88_770693_fzd1_negko_neghomo_p14

description: no DOX

value: olfactory epithelium


title: human WBC, GB4030186 (iDNase-seq)


title: human WBC, GB4030185 (iDNase-seq)


title: s_93_770702_tetfzd1_het_p0_neg3dox

description: DOX from P0 to P3


title: AMA pool OxBS 3


title: Organoid-806A-Pat-D200-AAVNPHP5Myc-2

value: Patient


title: human WBC, GB4030182 (iDNase-seq)


title: Vehicle pool OxBS 3

description: periosteal cell DNA from mouse treated with vehicle

value: control

value: vehicle


title: Vehicle pool OxBS 1


title: Organoid-806A-Pat-D200-noAAV-3

value: Organoid derived from human iPSCs


title: s_86_770492_tetfzd1_wt_p0_neg14dox

description: DOX from P0 to P14

value: Omp-IRES-tTA


title: Vehicle pool BS 3

value: Bisulfite sequencing


title: human WBC, GB4030181 (iDNase-seq)


title: s_87_770392_fzd1_negko_neghomo_negp14

description: no DOX


title: Organoid-806A-Pat-D200-noAAV-2


title: AMA pool OxBS 1


title: SD15 elevated temperature + reduced pH


title: Vehicle pool OxBS 2


title: human WBC, GB4030180 (iDNase-seq)


title: s_85_770491_tetfzd1_wt_p0_neg14dox

description: DOX from P0 to P14


title: Organoid-806A-Pat-D200-noAAV-1


title: AMA pool BS 1


title: s_84_770490_tetfzd1_wt_p0_neg14dox

description: DOX from P0 to P14


title: human WBC, GB4030179 (iDNase-seq)


title: Organoid-804B-Ctrl-D200-3


title: SD13 control


title: SD14 reduced pH

value: reduced pH


title: s_83_770496_tetfzd1_wt_p0_neg10dox

description: DOX from P0 to P10


title: human WBC, GB4030178 (iDNase-seq)


title: SD18 elevated temperature


title: SD12 elevated temperature + reduced pH


title: s_82_770495_tetfzd1_wt_p0_neg10dox

description: DOX from P0 to P10


title: Vehicle pool BS 2


title: Vehicle pool BS 1


title: human WBC, GB4030177 (iDNase-seq)


title: Organoid-804B-Ctrl-D200-1

value: Control


title: AMA pool BS 2

value: periosteal cells


title: SD11 reduced pH


title: s_81_770494_tetfzd1_wt_p0_neg10dox

description: DOX from P0 to P10


title: s_80_770585_tetfzd1_wt_p14

description: no DOX


title: SD10 control


title: Organoid-804B-Ctrl-D200-2


title: human WBC, GB4030175 (iDNase-seq)


title: human WBC, GB4030176 (iDNase-seq)


title: AMA pool BS 3


title: human WBC, GB4030174 (iDNase-seq)


title: s_79_770584_tetfzd1_wt_p14

description: no DOX


title: AMO_morpholino_U1_TEX_1.fastq.gz

first: Pierre-Rene

last: Körner

address: Plesmanlaan 121

institute: Netherlands Cancer Institute (NKI)

data_processing:
FASTQ files were aligned to the human hg19 genome using STAR (STAR_2.5.0a). File conversions were done using samtools. Reads on exons were counted using HTSEQ (0.5.4p3).
Assembly: hg19
Supplementary files format and content: bigwig file .bw

source_name: HeLa

extract_protocol: RNA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment.  PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit.  for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

treatment_protocol: U1 and control morpholino oligonucleotide sequences were 5ʹ-GGTATCTCCCCTGCCAGGTA AGTAT-3ʹ, and 5ʹ-TGATAAGAA CAGATACTACACTTGA-3ʹ, respectively. Oligonucleotides were transfected into 15cm dish for 24h (12 millions of cells -190 pmole).

value: HeLa

value: U1 morpholino + TEX


title: AMO_morpholino_TEX_2.fastq.gz

value: AMO morpholino control + TEX


title: SD8 elevated temperature

value: pigmented tissue


title: SD9 reduced pH


title: s_78_770583_tetfzd1_wt_p14

first: Congrong

last: Yu

institute: Stowers Insitute for Medical Research

description: no DOX


title: human WBC, GB4030173 (iDNase-seq)


title: AMO_morpholino_TEX_1.fastq.gz


title: Organoid-806A-Pat-D200-AAVNPHP5Myc-1


title: SD7 elevated temperature + reduced pH


title: human WBC, GB4030172 (iDNase-seq)


title: s_77_770582_fzd1_negko_neghomo_p10

description: no DOX


title: SD6 elevated temperature + reduced pH


title: AMO_morpholino_U1_TEX_2.fastq.gz


title: human WBC, GB4030171 (iDNase-seq)


title: AMO_morpholino_U1_2.fastq.gz

value: U1 morpholino


title: AMO_morpholino_U1_1.fastq.gz


title: s_76_770581_fzd1_negko_neghomo_p10

description: no DOX


title: SD5 reduced pH


title: s_75_770580_fzd1ko_neghomo_negp10

description: no DOX


title: AMO_morpholino_Control_1.fastq.gz

value: AMO morpholino control


title: human WBC, GB4030168 (iDNase-seq)

value: WBC


title: AMO_morpholino_Control_2.fastq.gz


title: human WBC, GB4030169 (iDNase-seq)


title: human WBC, GB4030170 (iDNase-seq)


title: human WBC, GB4030167 (iDNase-seq)


title: SD3 reduced pH


title: s_73_770578_fzd1_negko_neghomo_p7

description: no DOX

value: olfactory epithelium


title: s_74_770579_fzd1_negko_neghomo_p7

description: no DOX


title: s_53_764554_tetfzd1_het_p7

description: no DOX


title: SD1 elevated temperature

value: elevated temperature


title: s_54_764553_tetfzd1_het_p7

description: no DOX


title: human WBC, GB4030166 (iDNase-seq)


title: RNA_sequencing_ALKBH5_KD_TEX_1

data_processing: FASTQ files were aligned to the human hg19 genome using either STAR (STAR_2.5.0a) or TopHat (v.2.0.13) (Kim et al., 2013). Mouse FASTQ files were aligned with the same tools to the mm10 genome. TopHat aligned reads were aligned allowing up to 3 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 8. Peaks were called using mapped reads from all samples, using findPeaks (Homer package, v.3.12)(Heinz et al., 2010) with “-region -size 200 -minDist 250 -strand” parameters. Peaks found within transcripts or up to 5 kb downstream of promoters were included in a GTF file and processed by the DESeq package. Exon-aligned reads were counted using HTSEQ (0.5.4p3). Supplementary_files_format_and_content: TotalRNAs_readcounts.txt is a tab delimited txt file containing raw read counts obtained with htseq over exons of protein coding genes.

extract_protocol: RNA was extracted from U2OS and HEK293 cells using QIAzol Reagent (Qiagen; 79306) and Trizol reagent for HeLa cells (15596-018, Ambion life technologies) according to the manufactures protocol followed by DNase I treatment. PolyA selected RNA was isolated using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490) for U2OS and HEK293 and Oligotex kit (QIAGEN) for HeLa cells and further processed with the NEBNext Ultra Directional RNA Library Prep Kit (NEB; E7420S) for U2OS and HEK293 or SMARTer® Stranded RNA-Seq Kit (Takara; 634839) and illumina Truseq Stranded mRNA Library Prep kit. for HeLa cells or 3′–3′-mRNA-Seq Library Prep Kit (lexogen; 015UG009V0211).

treatment_protocol: siRNAs against ALKBH5 were purchased from Life Technologies ( ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687; Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h. For RNA-seq analysis DNase I-treated, poly(A) selected RNA was treated with Terminator 5′-Phosphate-Dependent Exonuclease (Epicentre; TER51020) according to the manufacturer’s instructions followed enzyme deactivation.

value: RNA sequencing of ALKBH5 KD plus TEX treatment


title: RNA_sequencing_ALKBH5_KD_TEX_2


title: RNA_sequencing_ALKBH5_KD_2

treatment_protocol: siRNAs against ALKBH5 were purchased from Life Technologies ( ALKBH5 siRNA catalogue number 4392420, ID s29686 and s29687; Cells were transfected for using Dharmafect I reagent (Dharmacon) following the manufacturer’s instructions (2 siRNAs per target gene) for 72h.

value: RNA sequencing of ALKBH5 KD


title: s_49_764549_tetfzd1_het_p3

description: no DOX


title: MAC1_Input_MWZ7484

city: Memphis

first: Brian

middle: J

last: Abraham

state: TN

address: 262 Danny Thomas Blvd

department: Computational Biology

institute: St. Jude Children's Research Hospital

data_processing:
Single-end data were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 with parameters -k 2 -m 2 --best.
Paired-end data were aligned to the hg19 revision of the human reference genome using bowtie v1.2.2 in paired-end mode with parameters -k 2 -m 2 --best -X 600.
Paired-end alignments were converted into fragments using samtools view, samtools sort, and bedtools bamtobed.
Single-end read coverage was calculated using MACS v1.4 with parameters -w -S --space=50 --nomodel --shiftsize=200.
Paired-end fragment coverage was calculated in 50bp bins genome-wide using bedtools makewindows and bedtools intersect and were normalized to the millions of mapped reads.
Assembly: hg19
Supplementary files format and content: Paired-end bigWig files contain reads-per-million-normalized coverage of fragments in 50bp bins.
Supplementary files format and content: Single-end bigWig files contain reads-per-million-normalized coverage of reads in 50bp bins.

growth_protocol: Cells were grown in T75 flasks in RPMI media containing 10% FBS and 1% pen-strep.

extract_protocol:
For each target, 5 μg of antibody coupled to 2 μg of magnetic Dynabeads (Life Technologies) was added to 3 ml of sonicated nuclear extract from formaldehyde-fixed cells. Chromatin was immunoprecipitated overnight, cross-links were reversed, and DNA was purified by precipitation with phenol:chloroform:isoamyl alcohol. DNA pellets were resuspended in 25 μl of TE buffer.
Swift 2S automated library prep (manufacturer's instructions).

tag: cell line

value: ALCL

tag: antibody


title: human WBC, GB4030164 (iDNase-seq)

city: Bethesda

tag: cell type


title: s_52_764552_tetfzd1_het_p3

description: no DOX


title: human WBC, GB4030165 (iDNase-seq)