title: anergic 5

description: FACS-sorted CD4+ T cells

source_name: CD73+FR4+CD4+ T cells

value: anergic


title: control 2

status: Public on Dec 18 2020

type: RNA

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

country: Germany

institute: LMU Munich

description: FACS-sorted CD4+ T cells

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse Gene ST 2.0 arrays containing about 35,000 probe sets.

scan_protocol: Staining and scanning using a GeneChip Scanner 3000 7G was done according to the Affymetrix expression protocol including minor modifications as suggested in the Encore Biotin protocol.

data_processing: R/Bioconductor, rma normalization, default parameters

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: CD73-FR4-CD4+ T cells

label_protocol: Total RNA (0.1-30 ng) was amplified and labeled using the Ovation Pico WTA System V2 in combination with the Encore Biotin Module (Nugen).

extract_protocol: The Trizol samples were thawed on ice, 300 µl chloroforn was added, shaken, incubated for 3 minutes at room temperature and spun at 12,000 x g and 4°C. The aqueous phase was transferred to new tubes, 1 volume of isopropanol and 1 µl of  linear polyachrylamide stock solution (25 µg/µl) was added. The samples were precipitated for 16 hours at -20°C and centrifuged for 10 minutes at 12,000 x g and 4°C. Supernatants were removed and RNA pellets washed with 70% ethanol. RNA pellets were resuspended in 100 µl RNAse-free water and purified with NucleoSpin RNA Clean-up XS columns as per manufacturer's instructions, from which the RNA was eluted with 12 µl water and stored at -80°C. RNAs were quantified with an Agilent 2100 Bioanalyzer. All samples had RNA integrity values > 8 and were use for amplification and microarray hybridizations.

tag: sample type

value: control


title: anergic 4

description: FACS-sorted CD4+ T cells


title: Patient 044

city: Buffalo

first: Song

last: Yao

state: NY

address: Elm and Carlton Streets

department: Cancer Prevention and Control

country: USA

institute: Roswell Park Comprehensive Cancer Center

hyb_protocol: Manufacturer protocol

scan_protocol: Manufacturer protocol

data_processing: NanoString nSolver with Advanced Analysis 2.0

organism: Homo sapiens

source_name: primary breast cancer

label_protocol: Manufacturer protocol

extract_protocol: Roche High Pure FFPET RNA Isolation Kit

tag: race

value: EA

tag: tissue

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

value: negative

tag: subtype

value: Luminal A


title: anergic 3

description: FACS-sorted CD4+ T cells


title: control 1

description: FACS-sorted CD4+ T cells


title: 51_TCGTTC: TMP195+TNFα  replicate3

type: SRA

library_source: transcriptomic

data_processing:
Sequenced reads were mapped to mm10 whole genome using STAR 2.6.1d with default parameters
STAR 2.6.1d was used to obtain read counts per gene based on ENSEMBL annotation Mus_musculus.GRCm38.95.gtf.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include STAR gene-based read counts for each sample

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophages (BMDM) were generated as established by flushing the bone marrow from femurs and tibiae with ice-cold PBS, resuspending in PBS by repeated pipetting and filtering through a 40 µm cell strainer (BD Biosciences). After centrifugation of the cell suspension at 500 g for 10 min, the pellet was resuspended in culture medium (RPMI 1640 containing 10% FCS, 15% L929-cell-conditioned medium (LCM) and 100 µl/ml gentamycin) and plated on 15 cm untreated culture plates (Greiner). 15 % fresh LCM was added again on day 1 and 2 of culturing. For the stimulation experiments, differentiated macrophages were harvested by gentle scraping, transferred onto untreated 6-well or 12-well plates (Greiner) on Day 7 of culturing and left in LCM-free medium for 24 hours, allowing cells to adhere. Cells were then stimulated in FCS-free medium with either 50 ng/ml mouse recombinant TNF-α at different time intervals or left untreated.

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were pretreated with either TMP195 (5 µM) or TPCA-1 (500 nM) for 1 h prior to stimulation with TNF-α (50 ng/ml) for 24 h.

tag: strain

value: Bone marrow-derived macrophages (BMDM)

tag: treament

tag: genotype


title: Patient 101

value: AA

value: Triple Negative


title: MBAL413

city: San Francisco

first: Aartik

last: Sarma

state: CA

address: 513 Parnassus Ave

institute: University of California, San Francisco

data_processing:
*** Raw data submission disallowed by submitter's IRB ***

Pseudoalignment with kallisto 0.46.1
Genome_build: ENSEMBL v.99

source_name: Tracheal aspirate

extract_protocol:
RNA was extracted with Zymo Pathogen Magbead Kit, treated with DNAse, and ribodeplted with FastSelect
NEBNext Ultra II RNAseq Kit

treatment_protocol: TA was collected and mixed 1:1 with DNA/RNA shield

value: Tracheal aspirate

tag: disease state

value: ARDS not due to COVID

tag: age

tag: gender

value: M

value: Caucasian

tag: hispanic ethnicity

value: N

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

tag: reason for intubation

value: ARDS


title: Patient 043

tag: race


title: 50_GACGAT: TNFα  replicate3

tag: tissue

value: TNFα


title: anergic 1

description: FACS-sorted CD4+ T cells

tag: sample type

value: anergic


title: MBAL411

value: Y


title: sc_AC1_266_sample_0011

city: Nijmegen

first: Ann

middle: Rose

last: Bright

address: Geert Grooteplein Zuid 30

department: Department of Molecular Biology

country: Netherlands

institute: RIMLS

data_processing:
samplename_reads.tab file is generated with STAR 2.5.0 with the option of  --quantMode GeneCounts
Genome_build: xt9

organism: Xenopus tropicalis

source_name: Tissue

extract_protocol:
Dissected embryo explants were dissociated into single cells using  Ca2+ and Mg2+ free media (Sive, Grainger, & Harland, 2007). 200 cells were picked for performing single-cell RNA-seq using the modified version of Tang et al protocol (Tang et al., 2008).
Amplified cDNA was purified with XP beads and the Zymo purification kit respectively and its concentration measured with Qubit® 2.0 Fluorometer (Q32866, Life Technologies). The quality of the amplified cDNA and distribution of DNA fragment size were assessed by Agilent 2100 Bioanalyzer (Agilent Technologies) with the High Sensitivity DNA Kit (5067-4626, Agilent). The sequencing libraries were prepared using the KAPA Hyper Pre Kit (KR0961 – v6.17, Kapa Biosystems). The concentrations of the fragments with the approximate indexed adapters were quantified by KAPA library quantification.

tag: cell line

tag: Stage

value: stage10 .5 (Gastrula)

tag: antibody


title: anergic 2

description: FACS-sorted CD4+ T cells


title: Patient 042

value: breast cancer

tag: age at diagnosis, years

tag: er

tag: pr

tag: subtype


title: 53_AGTTGA: DMSO  replicate4

tag: strain

tag: treament

value: DMSO

tag: genotype


title: MBAL409

tag: disease state

tag: age

tag: gender

value: Other

tag: hispanic ethnicity

tag: 30 day mortality

value: Staphylococcus

value: Bacterial


title: Patient 041

tag: race

value: AA

tag: tissue

value: negative


title: control 3

description: FACS-sorted CD4+ T cells

tag: sample type

value: control


title: naive 5

source_name: Unprimed CD4+ T cells

growth_protocol: AND TCR transgenic CD45.1+ Rag2o/o CD4+ T cells were adoptively transferred into iMCC recipients carrying two transgenes that allow for the dynamic regulation of the expression of an invariant chain cDNA which carries a moth cytochrome c (MCC) epitope instead of the CLIP sequence.

treatment_protocol: The recipients had been treated one day before the transfer with an anti-CD40 antibody to activate dendritic cells and with 100 µg/ml doycycline in the drinking water which induces the expression of the cDNA construct in dendritic cells. One group (none) was then withdrawn from doxycycline. We have seen before that the T cells in recipients undergoing this treatment will develop into Th1 memory cells (Obst et al., 2007). Another group (low) was switched to 10 µg/ml while a third (intermediate) was maintained on the 100 µg/ml dose. In addition, another strain of mice (cMCC) were used as recipients that expressed an invariant chain/MCC construct that is constitutively expressed in MHC-II+ cells at high levels (high). The adoptively transferred AND TCR tg T cells were sorted twice on day 10 as CD4+CD90.2+CD45.1+ cells directly into Trizol LS , mixed and stored at -80°C for processing. - A second series of sorts was done 30 days after transfer. Instead of the cMCC recipients, in which the AND T cells undergo apoptosis by then, iMCC animals were used which were taken off doxycycline on day 10 (off). Naive control AND T cells were transferred 3 days before the sort into non-transgenic recipients.

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: MBAL458

value: Tracheal aspirate

value: ARDS not due to COVID

value: M

tag: lrti pathogen

tag: lrti type

tag: reason for intubation


title: 48_ATATCC: TPCA-1+TNFα  replicate2

tag: strain

value: Bone marrow-derived macrophages (BMDM)

tag: treament


title: 47_ACAACG: TMP195+TNFα  replicate2

tag: genotype


title: MBAL337

tag: disease state

tag: age

value: Asian

value: N

value: HCOV-229E, Streptococcus

value: Viral + Bacterial

value: ARDS


title: MBAL414

tag: gender

value: Caucasian

tag: hispanic ethnicity

value: Y


title: Patient 040

tag: race

value: EA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype

value: Luminal A


title: naive 3

tag: cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3


title: naive 4

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: MBAL321

tag: tissue

value: Other

tag: 30 day mortality

tag: lrti pathogen

value: Influenza A

tag: lrti type

value: Viral

tag: reason for intubation


title: 46_AATGAA: TNFα  replicate2

tag: strain

tag: treament

value: TNFα

tag: genotype


title: Patient 039

tag: race

value: AA

value: negative

value: Triple Negative


title: MBAL334

value: Tracheal aspirate

tag: disease state

value: ARDS not due to COVID

tag: age

tag: gender

value: M

tag: hispanic ethnicity

value: N

value: Staphylococcus

value: Bacterial


title: 45_CGCCTG: DMSO replicate2

value: Bone marrow-derived macrophages (BMDM)

value: DMSO


title: 44_GGTATA: TPCA-1+TNFα  replicate1


title: MBAL314

value: African American

value: ARDS


title: naive 2

tag: cells

value: sorted CD4+ AND T cells


title: d30 off 5

source_name: CD4+ T cells primed in vivo, then exposed to different levels of persisting antigen

tag: days after transfer


title: Patient 036

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype

value: Luminal B


title: MBAL315

tag: tissue

value: Caucasian

tag: 30 day mortality

value: Y

tag: lrti pathogen

value: Influenza A + Streptococcus

value: Viral + Bacterial


title: MBAL311

value: Tracheal aspirate

value: ARDS not due to COVID

value: Asian

value: Influenza A + Streptococcus, Staphylococcus

tag: lrti type

tag: reason for intubation


title: 43_CACTAA: TMP195+TNFα  replicate1

tag: strain

tag: treament

tag: genotype


title: naive 1

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: 42_TCGAGG: TNFα replicate1

value: TNFα


title: 41_GTGCCA: DMSO replicate1

value: Bone marrow-derived macrophages (BMDM)


title: Patient 034

tag: race

value: EA


title: Patient 033


title: Patient 037

value: negative

value: Luminal A


title: Patient 038


title: MBAL234

tag: disease state

tag: age

tag: gender

value: F

tag: hispanic ethnicity

value: N

value: ARDS


title: genomic DNA from SCCOHT case 65 [9630789199_R05C01]

type: genomic

city: Hamburg

first: Dörthe

last: Holdhof

address: Martinistraße 52

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 BeadChip or the Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using the iScan System and standard recommended Illumina scanner setting.

data_processing:
Bioconductor (Version 3.10) package minifi (Version 1.32.0) using function 'preprocessNoob'
The Matrix_raw.txt.gz contains Unmethylated and methylated signal intensities

label: Cy3, Cy5

molecule: genomic DNA

source_name: primary SCCOHT sample

label_protocol: Standard Illumina Protocol

extract_protocol: For DNA isolation from FFPE tissue, 10 x 10 µm sections were cut and DNA isolated using the ReliaPrep™ FFPE gDNA Miniprep System (Promega) according to manufacturer’s instructions. About 100-500 ng DNA was used for bisulfite conversion by the EZ DNA Methylation Kit (Zymo Research). Afterwards, the DNA Clean & Concentrator-5 (Zymo Research) and the Infinium HD FFPE DNA Restore Kit (Illumina) were employed to clean and restore the converted DNA. Finally, either the HumanMethylation450 BeadChip array or the Infinium MethylationEPIC BeadChip Kit (both Illumina) were used to quantify the methylation status of 450,000 or 850,000 CpG sites, respectively, on an iScan device (Illumina).

tag: subject/case id

value: SCCOHT case 65

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: genomic DNA from SCCOHT case 66 [9630789199_R06C01]

value: SCCOHT case 66


title: Patient 031

tag: tissue

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype


title: MBAL229

value: Tracheal aspirate

value: ARDS not due to COVID

value: Caucasian

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

tag: reason for intubation


title: Patient 035

tag: race

value: Triple Negative


title: Patient 032

value: AA


title: genomic DNA from SCCOHT case 64 [9630789199_R03C01]

value: SCCOHT case 64


title: d30 off 1

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: MBAL251

tag: disease state

tag: age

tag: gender

value: M

value: Asian

tag: hispanic ethnicity

value: Klebsiella

value: Bacterial


title: d30 none 4


title: Patient 030

tag: tissue

tag: age at diagnosis, years

value: negative

value: Luminal A


title: MBAL288

value: F

value: N

value: Staphylococcus

value: ARDS


title: d30 none 5


title: d30 off 2


title: Patient 029

value: breast cancer

tag: er

value: positive

tag: pr

value: Luminal B


title: genomic DNA from SCCOHT case 62 [9630789199_R02C01]

tag: subject/case id

value: SCCOHT case 62

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: MBAL211

value: Tracheal aspirate

value: ARDS not due to COVID

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

tag: reason for intubation


title: genomic DNA from SCCOHT case 61 [9630789199_R01C02]

value: SCCOHT case 61


title: Patient 028

tag: race

value: AA

tag: subtype


title: Patient 027

value: EA

value: Triple Negative


title: genomic DNA from SCCOHT case 60 [10003885154_R06C01]

value: SCCOHT case 60


title: COMET1145-2

tag: disease state

value: COVID ARDS

value: M

value: Other

value: Y

value: SARS-CoV-2 + Klebsiella

value: Viral + Bacterial


title: MBAL227

tag: age

value: F

value: Caucasian

value: N

value: ARDS


title: genomic DNA from SCCOHT case 63 [9630789199_R02C02]

value: SCCOHT case 63

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

value: female


title: genomic DNA from SCCOHT case 59 [10003885154_R05C02]

value: SCCOHT case 59


title: COMET1122-2

value: Tracheal aspirate

tag: gender

value: Asian

value: Viral


title: d30 none 3

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: genomic DNA from SCCOHT case 58 [10003885154_R05C01]

value: SCCOHT case 58


title: Patient 024

value: EA

tag: tissue

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

value: Luminal B


title: Patient 025


title: Patient 026

value: negative

value: Triple Negative


title: COMET1115-3

value: COVID ARDS

value: M

value: Other

tag: hispanic ethnicity

value: Y

tag: 30 day mortality

value: N


title: d30 none 2


title: d30 off 3


title: genomic DNA from SCCOHT case 57 [10003885154_R04C02]

tag: subject/case id

value: SCCOHT case 57

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: d30 int 2


title: MBAL213

value: Tracheal aspirate

value: ARDS not due to COVID

tag: race

value: Caucasian

tag: lrti pathogen

value: Escherichia, Klebsiella

tag: lrti type

value: Bacterial

tag: reason for intubation

value: ARDS


title: d30 none 1

tag: cells

value: sorted CD4+ AND T cells


title: d30 int 3

tag: days after transfer


title: MBAL203

tag: disease state

tag: age

tag: gender

value: S. aureus, K. aerogenes


title: Patient 023

value: AA

tag: tissue

value: breast cancer

tag: age at diagnosis, years

value: negative

value: positive

tag: subtype


title: Patient 022

tag: er

tag: pr

value: Luminal A


title: d30 int 5

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: COMET1107-5

value: COVID ARDS

value: M

value: Other

tag: hispanic ethnicity

value: Y

tag: 30 day mortality

value: N

value: Viral


title: d30 int 1


title: d30 low 5


title: COMET1094-4

value: Tracheal aspirate

value: F

tag: race

tag: lrti pathogen


title: Patient 021

value: Triple Negative


title: genomic DNA from SCCOHT case 56 [10003885154_R04C01]

tag: subject/case id

value: SCCOHT case 56

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: genomic DNA from SCCOHT case 55 [10003885154_R03C02]

value: SCCOHT case 55


title: d30 off 4

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer


title: d30 int 4


title: genomic DNA from SCCOHT case 54 [10003885154_R03C01]

value: SCCOHT case 54


title: COMET1089-2

tag: disease state

tag: age

tag: gender

value: SARS-CoV-2 + HMPV

tag: lrti type

value: Viral + Viral

tag: reason for intubation

value: ARDS


title: Patient 020

value: AA

tag: tissue

value: breast cancer

tag: age at diagnosis, years

tag: er

value: negative

tag: pr

value: positive

tag: subtype


title: d30 low 4

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: COMET1114-4

value: COVID ARDS

tag: race

value: Asian

tag: hispanic ethnicity

value: N

tag: 30 day mortality

value: Y

tag: lrti pathogen

value: SARS-CoV-2 + Pseudomonas

value: Viral + Bacterial


title: d30 low 3

tag: cells

tag: days after transfer


title: Patient 019

value: Luminal B


title: COMET1078-2

value: Tracheal aspirate

tag: disease state

tag: age

value: M

value: Other

value: Viral


title: genomic DNA from SCCOHT case 51 [10003885154_R01C02]

tag: subject/case id

value: SCCOHT case 51

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: genomic DNA from SCCOHT case 52 [10003885154_R02C01]

value: SCCOHT case 52


title: COMET1077-1

tag: tissue

tag: gender

value: SARS-CoV-2 + HMPV

tag: lrti type

value: Viral + Viral

tag: reason for intubation

value: ARDS


title: Patient 018

value: EA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

value: negative

tag: subtype

value: Luminal A


title: genomic DNA from SCCOHT case 50 [10003885154_R01C01]

value: SCCOHT case 50


title: COMET1072-1

value: Tracheal aspirate

value: COVID ARDS

tag: race

tag: hispanic ethnicity

value: N

tag: 30 day mortality

value: SARS-CoV-2 + Influenza B


title: Patient 017

value: AA

value: Triple Negative


title: Patient 016


title: genomic DNA from SCCOHT case 49 [10003885129_R06C01]

value: SCCOHT case 49

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

value: female


title: COMET1059-1

value: M

value: Other

value: Y

tag: lrti pathogen

value: SARS-CoV-2 + Proteus

value: Viral + Bacterial


title: genomic DNA from SCCOHT case 53 [10003885154_R02C02]

value: SCCOHT case 53


title: COMET1053-1

tag: disease state

value: F

value: Viral

value: ARDS


title: d30 low 2

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: Patient 015

tag: tissue

value: breast cancer

value: negative


title: Patient 014

value: EA


title: genomic DNA from SCCOHT case 48 [10003885129_R05C02]

tag: subject/case id

value: SCCOHT case 48

tag: subject status

tag: Sex


title: genomic DNA from SCCOHT case 47 [10003885129_R05C01]

value: SCCOHT case 47


title: d30 low 1


title: d10 none 4


title: d10 none 5


title: COMET1043-1

value: Tracheal aspirate

value: COVID ARDS

tag: age

tag: gender

value: Asian

value: N

value: SARS-CoV-2 + Klebsiella

tag: lrti type

tag: reason for intubation


title: Patient 012

tag: race

tag: age at diagnosis, years

tag: er

value: positive

tag: pr

tag: subtype

value: Luminal B


title: genomic DNA from SCCOHT case 45 [10003885129_R04C01]

value: SCCOHT case 45

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

value: female


title: d10 high 4

tag: cells


title: d10 none 2

tag: days after transfer


title: PC-3-KQ, RNA-seq

city: Shenzhen

first: Jin-Tang

last: Dong

state: Guangdong

address: 1088 Xueyuan Blvd

department: Human Cell Biology and Genetics

country: China

institute: Southern University of Science and Technology

data_processing:
DU 145 libraries were sequenced using single-end 50 bp reads on a BGISEQ-500 at BGI (Shenzhen, Guangzhou, China) and PC-3 libraries were sequenced at Novogene (Sacramento, CA) using paired-end 150 bp reads on a NovaSeq.
FASTQ files from sequencing were quality controlled and adapter trimmed using FASTQC (v0.11.5) and mapped to HG19 reference genome using the STAR aligner (v2.5.0a)
Putative PCR duplicates were marked and removed with SAMtools (v1.7) for downstream analysis
Genome_build: UCSC HG19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

source_name: Prostate cancer

extract_protocol:
DU 145 and PC-3 cells expressing different forms of KLF5 were collected freshly in Trizol reagent for RNA isolation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: genotype

value: acetylation mimicking mutant KLF5K369Q (KQ)


title: Patient 011

tag: tissue


title: d10 none 3

value: sorted CD4+ AND T cells

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: d10 none 1


title: PC-3-KR, RNA-seq

value: acetylation deficient mutant KLF5K369R (KR)


title: genomic DNA from SCCOHT case 44 [10003885129_R03C02]

tag: subject/case id

value: SCCOHT case 44

tag: subject status

tag: Sex


title: genomic DNA from SCCOHT case 46 [10003885129_R04C02]

value: SCCOHT case 46


title: PC-3-KLF5, RNA-seq

value: wildtype KLF5


title: d10 high 3


title: COMET1002-2

tag: disease state

tag: age

tag: gender

value: M

value: Other

tag: hispanic ethnicity

tag: 30 day mortality

tag: lrti pathogen

tag: lrti type

value: Viral

value: ARDS


title: Patient 009

tag: race

value: AA

value: breast cancer

tag: age at diagnosis, years

tag: er

tag: pr

tag: subtype


title: Patient 010

tag: tissue

value: positive

value: negative

value: Luminal A


title: genomic DNA from SCCOHT case 42 [10003885129_R02C02]

value: SCCOHT case 42

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)


title: COMET1001-4

value: Tracheal aspirate

value: COVID ARDS

value: F

value: Caucasian

value: N

tag: reason for intubation


title: PC-3-EV, RNA-seq

tag: cell line

tag: genotype

value: KLF5 null


title: d10 high 2

tag: cells

value: sorted CD4+ AND T cells

tag: days after transfer

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: genomic DNA from SCCOHT case 41 [10003885129_R02C01]

tag: subject/case id

value: SCCOHT case 41

tag: subject status

tag: Sex

value: female


title: Patient 008

value: Triple Negative


title: d10 int 4


title: Patient 007

value: AA


title: 49_AAGCTC: DMSO  replicate3

tag: strain

value: Bone marrow-derived macrophages (BMDM)

tag: treament

value: DMSO


title: IMR-32_rep3

city: Moscow

first: Tatiana

last: Portseva

address: Vavilova street 32

country: Russia

institute: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences

data_processing:
Sequencing on the Illumina NovaSeq6000 SP on one side, reading length 100 bp.
After control Illumina NovaSek (101 cycle with end of fragments) using NovaSeq SP reagents. FASTQ files were obtained using bcl2fastq v2.20 Conversion Software (Illumina).
Recording format quality data strings - Phred 33.
Data were generated by deep sequencing, in triplicate, using Illumina NovaSeq. Mapping reads to the human genome (hg38) using hisat program.  The htseq-count utility calculated the number of reads that were mapped to known genes (ncbi - entrezID). The obtained values (cpm - countpermillion) for each gene for each library were combined into one matrix for further analysis.
Filtration, normalization by the method (TMM), variance estimation and evaluation of differentially expressed genes were performed in the edgeR module. Genes in which cpm did not exceed 1 in any three libraries were considered low-expressing. After filtering the low-expressing genes, 15,108 entries remained. RNA-Seq data confirmed that approximately 8% of the transcripts showed differential expression between the WT and Oct-1 overexpressed differentiating neuroblastoma cells, with FDR<0.01 (p-value adjusted for multiple testing).
Genome_build: hg38
Supplementary_files_format_and_content: edgeR output

source_name: neuroblastoma cell line IMR32

growth_protocol: IMR32 cells growth in the MEM medium, 10% FCS, 5% CO2

extract_protocol:
differentiation in vitro with 2.5 mkM BrdU in the MEM medium, 10 % FCS during 16 days
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) was used with 3 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: IMR32 total RNA was harvested using Trizol reagent.

value: neuroblastoma cell line IMR32

value: pLenti 5 - Empty Vector stably overexpressed

tag: treatment

value: untreated


title: IMR-32_rep2


title: genomic DNA from SCCOHT case 40 [10003885129_R01C02]

value: SCCOHT case 40

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)


title: d10 high 5


title: d10 int 2


title: IMR-32_rep1


title: genomic DNA from ATRT case 11 [3999510017_R05C01]

source_name: primary ATRT  sample (FFPE)

value: ATRT case 11

value: Atypical teratoid/rhabdoid tumors (ATRTs)

value: male


title: d10 int 3


title: Patient 006

tag: race

value: EA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: negative


title: d10 int 1

value: sorted CD4+ AND T cells


title: genomic DNA from ATRT case 07 [9829119185_R06C01]

value: ATRT case 07


title: d10 low 4


title: d10 low 5


title: genomic DNA from ATRT case 06 [9611519030_R05C02]

value: ATRT case 06

value: female


title: IMR-32 dEV_rep3

value: neuroblastoma cell line IMR32 differentiating in vitro during 16 days

value: treated with 2.5 mkM BrdU for 16-days


title: genomic DNA from ATRT case 05 [9611519030_R02C02]

value: ATRT case 05


title: Patient 003

tag: tissue

tag: pr

value: positive

tag: subtype


title: Patient 004

value: Luminal B


title: IMR-32 dEV_rep2

tag: cell line

tag: genotype

value: pLenti 5 - Empty Vector stably overexpressed


title: IMR-32 dEV _rep1


title: genomic DNA from ATRT case 04 [9611519030_R03C02]

value: ATRT case 04


title: Patient 002

value: AA


title: Patient 001

value: Triple Negative


title: d10 low 2

tag: cells

tag: days after transfer


title: Patient 005


title: 18_P_putida_E3665_1hr_CRE_3_25_20_12

status: Public on Dec 17 2020

city: Burlington

first: Matthew

middle: J

last: Wargo

state: VT

address: 95 Carrigan Dr

department: Department of Microbiology and Molecular Genetics

institute: University of Vermont

data_processing:
Basecalls performed with bcl2fastq v2.17.1.4
Reads were trimmed to remove adapters and low quality bases using Trim Galore! (v0.6.4) removing Illumina adapters, reads <Q20, and a minimum length of 35 bp.
Read mapping and counting was performed using Rockhopper2, with default parameters and verbose output.  Reads from each sample were mapped to the reference genome of Pseudomonas putida strain KT2440 pre-packed with the program.
Raw counts from Rockhopper2 were anlayzed using the DESeq2 package in R. Counts were adjusted for library size and genes with fewer than 10 counts in at least 2 samples were removed from further analysis. Normalization was performed using the default settings of DESeq2 with independent filtering and alpha (FDR) set to <0.05.
Genome_build: NC_002947.3
Supplementary_files_format_and_content: comma-separated (.csv) files containing the raw counts

organism: Pseudomonas putida

source_name: Bacterial cells

growth_protocol: - 2 mM creatine. Each strain was cultured in technical duplicate and biological triplicate per condition for 1 hr at 30 ˚C while shaking at 170 RPM. Technical duplicates were pooled and the data are presented from three inductions on different days.

extract_protocol:
Cells were collected via centrifugation and immediately resuspended in 600 µl of ~60 C RNAzol. Total RNA was then extracted from these samples using Qiagen's RNeasy Miniprep Kit. Residual genomic DNA was removed from each sample through DNaseI treatment (NEB), and the RNA was re-purified using Qiagen’s RNeasy kit.
Following RNA extraction and purification using the RNeasy miniprep kit, RNA was percipitated overnight and enriched for mRNA using the Microbexpress protocol. Libraries of the mRNA enriched samples were constructed using the BIOO Scientific NEXTFlex mRNA-Seq protocol. Library concentrations were measured via Qubit and Bioanalyzer and pooled libraries were submitted for RNA-Seq analysis.

treatment_protocol: Cells were treated with or without 2 mM creatine as described in the growth protocol.

tag: clinical status

value: reference

tag: growth condition

value: 20mM pyruvate, 2mM creatine


title: 13_P_putida_E3665_1hr_PYR_6_17_20_7

value: 20mM pyruvate


title: 6_P_putida_WT_1hr_CRE_3_25_20_6

value: KT2440 WT


title: 16_P_putida_E3665_1hr_CRE_6_17_20_10


title: 2_P_putida_WT_1hr_PYR_3_25_20_2


title: 14_P_putida_E3665_1hr_PYR_3_25_20_8


title: 5_P_putida_WT_1hr_CRE_3_25_20_5


title: 1_P_putida_WT_1hr_PYR_6_17_20_1


title: d10 low 3

value: sorted CD4+ AND T cells

tag: doxycycline [ug/ml]  day -1 to 3

tag: doxycycline [ug/ml]  day 3 to 10 or 30


title: 17_P_putida_E3665_1hr_CRE_3_25_20_11

tag: strain


title: 4_P_putida_WT_1hr_CRE_6_17_20_4


title: 3_P_putida_WT_1hr_PYR_3_25_20_3


title: 15_P_putida_E3665_1hr_PYR_3_25_20_9


title: d10 low 1


title: N1dE_PKM2_PTEN_enhancer_rep3

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

library_source: genomic

data_processing:
Library strategy: 4C-Seq
The first nucleotides in each read (corresponding to barcode) and the nucleotides corresponding to theHindIII primer were trimmed from the 5' of the read
Mapping was performed using Bowtie2 to a reduced genome consisting of all unique 24 nucleotide-long regions surrounding DpnII sites allowing for zero mismatches.
Analysis of 4C-Seq signal was performed by building successive 25kb windows with 90% overlap and calculating the total number of reads per window.
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: bedgraph files show total read count per 25kb window. Windows show 90% overlap.

growth_protocol: We performed cell culture of cell lines in standard conditions in a humidified atmosphere at 37°C under 5% CO2. DND41 (ACC 525), JURKAT (ACC 282), HPB-ALL (ACC 483) cells were obtained from Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ). T-ALL cells were cultured in HyClone RPMI 1640 Media (SH3002701, Fisher Scientific) supplemented with 10% FBS (900-108, Gemini Bio-Products) and 1% penicillin-streptomycin (45000-652, VWR).

extract_protocol:
4C-Seq was prepared using HindIII and DpnII digestions.
The following primers were used for amplification (human PTEN promoter viewpoint: FW-AAATATCAACACTGAAGCTT and RV- GCCTCCAGTTGATTTCCAGA; human PE viewpoint FW- CAGCTTCTCCTTTTAAGCTT and RV- CACAGACATAATGCTGGGAA; mouse Pten promoter viewpoint FW- GTTCATCCTGAGTAAAGCTT and RV- CAAAAGATAATTGGTGAGCA; mouse PE viewpoint: FW- CCTCTATATGAGAGAAGCTT and RV- AAGAGCTGGCCACATGGTGA)

treatment_protocol: All samples were collected under same treatment conditions as described in growth protocol

tag: cell type

value: deltaE-NOTCH1 induced mouse leukemia

tag: bait


title: sessile_4h_2

city: Freiburg i. Br.

first: Sabrina

last: Oeser

address: Schänzlestraße 1

department: Institute of Biology III

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 2 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software, programme G3-GX_1Color and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. After background correction the median signal intensity was cyclic loess normalized.

organism: Synechocystis sp. PCC 6803

source_name: sessile 4h #2

label_protocol: RNA was labelled with Cy3 (ULSTM Fluorescent Labeling Kit for Agilent Arrays (EA-023), Kreatech, Germany)

growth_protocol: Planktonic cultures were grown in modified 1 x BG11 (Rippka et al., 1979) substituted with 0.3 % (w/v) sodium thiosulphate and 10 mM (w/v) (N-[tris-(hydroxymethyl)-methyl]-2-aminoethane sulphonic acid) buffer (TES) pH 8.0. Cultures were grown photoautotrophically with orbital shakers at 140 rpm at 30°C under continuous white light illumination (Philips TLD Super 80/840) of 50 µmol photons m-2 s-1. Sessile cultures were grown on 0.75% agar plates (Bacto-Agar) using the same medium and growth conditions without shaking as described for planktonic cultures.

extract_protocol: For planktonic cultures, cells were collected by vacuum filtration through 0.8 µm polyethersulphone filter disks (Pall, Germany). Filters were immediately transferred to 1.6 ml PGTX solution (Pinto et al., 2009), vortexed, frozen in liquid nitrogen and stored at -80°C until further use. For sessile cultures, cells were scratched from the agar plates and directly suspended in 1.6 ml PGTX solution, vortexed, frozen in liquid nitrogen and stored at -80°C. RNA was then extracted according to Pinto et al. (2009) with modifications as described in Wallner et al. (2020).

treatment_protocol: A planktonic preculture was grown in BG11 medium to OD750nm 0.6-0.8. Then, 35 ml were centrifuged at 4000 x g for 10 min at room temperature. For planktonic cultures, pellets were resuspended in 35 ml BG11 medium and incubated as described above in the culture conditions section. For sessile cultures, pellets were resuspended in 300 µl BG11 medium, plated onto BG11 agar plates and incubated.

tag: lifestyle

value: sessile

tag: timepoint


title: sessile_4h_1

source_name: sessile 4h #1


title: N1dE_PKM2_PTEN_enhancer_rep2


title: planktonic_8h_2

source_name: planktonic 8h #2

value: planktonic


title: N1dE_PKM2_PTEN_promoter_rep2


title: sessile_8h_2

source_name: sessile 8h #2


title: CD40-activated B cells, biological rep 2

city: Boston

first: Baochun

last: Zhang

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from CD40-activated B cells

hyb_protocol: Fragmented, biotinylated cDNA was hybridized to Mouse Gene 2.0 ST arrays for 16 hours at 45oC and 60rpm in a Affymetrix GeneChip™ Hybridization Oven 645. Mouse GeneChip ST arrays were washed/stained using the Affymetrix FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 7G scanner with autoloader.

data_processing: The microarray data were normalized using RMA method from the R package oligo.

label: Biotin

source_name: Anti-CD40-treated B cells

label_protocol: Total RNA was processed using the Affymetrix GeneChip™ WT PLUS Reagent Kit.  The kit generates amplified and biotinylated sense-stranded DNA targets for hybridization.

growth_protocol: B cells were isolated from spleens of YFPflSTOP/+ and LMP1flSTOP/YFPflSTOP mice, by CD43 depletion using magnetic-activated cell sorting (Miltenyi Biotec); the cells were treated with TAT-Cre; two days posttreatment, reporter (YFP)+ cells were purified by FACS sorting for RNA extraction. Naive B cells were isolated from spleens of B6/J mice by CD43 depletion, and either directly subjected to RNA extraction or treated with anti-CD40 for two days followed by RNA extraction.

extract_protocol: Total RNA was extracted with TRIzol reagent (Invitrogen) according to manufacturer’s instructions.

tag: breed

tag: gender

value: Male

value: Spleen

value: B cells


title: N1dE_PKM2_PTEN_enhancer_rep1


title: planktonic_4h_1

source_name: planktonic 4h #1


title: LMP1-B cells, biological rep 2_re-analyzed

description:
Gene expression data from LMP1-expressing B cells
GSM2901338 (LMP1-2)

source_name: LMP1-expressing B cells

value: (C57BL6XBALBc) F1

value: Female

tag: tissue


title: HDdPEST_PTEN_enhancer_rep3

source_name: HDdPEST

value: HDdPEST-NOTCH1 induced mouse leukemia

value: HDdPEST


title: N1dE_PKM2_PTEN_promoter_rep1


title: planktonic_4h_2

source_name: planktonic 4h #2


title: Naive control B cells, biological rep 2

description: Gene expression data from naive control B cells

source_name: Naive B cells


title: Naive control B cells, biological rep 1


title: sessile_8h_1

source_name: sessile 8h #1


title: CD40-activated B cells, biological rep 1


title: LMP1-B cells, biological rep 1_re-analyzed

description:
Gene expression data from LMP1-expressing B cells
GSM2901337 (LMP1-1)


title: YFP control B cells, biological rep 2_re-analyzed

description:
Gene expression data from YFP-expressing control B cells
GSM2901336 (control2)

source_name: YFP-expressing B cells

value: YFPflSTOP/+


title: HDdPEST_PTEN_enhancer_rep1


title: HDdPEST_PTEN_enhancer_rep2


title: HDdPEST_PTEN_promoter_rep2


title: YFP control B cells, biological rep 1_re-analyzed

description:
Gene expression data from YFP-expressing control B cells
GSM2901335 (control1)


title: planktonic_8h_1

source_name: planktonic 8h #1


title: N1dE_PKM2_PTEN_promoter_rep3


title: HDdPEST_PTEN_promoter_rep1


title: S40A-S133A_8h_rep1

city: Pasadena

first: Elizabeth

middle: Hwang

last: Jensen

address: 1200 E California Blvd, MC 164-30

department: CCE

institute: Caltech

description: DIV7 neurons treated with HSV expressing S40A-S133A-CREB for 8h, depolarized 2h

data_processing:
Illumina Casava 1.7 and BCLConverter 1.7.1 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Raw fastq data files were imported to Galaxy and concatenated end-to-end.  Then, the Fastq groomer program was used followed by Fastq trimmer for reads that were longer than 50.  The Fastq Groomer data was then aligned to the mm10 mouse transcriptome from UCSC using Bowtie in Galaxy.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a Cufflinks protocol. In short, exons from all isoforms of a gene were merged using Cuffmerge to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library using Cufflinks.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: E16.5 cortical neurons (DIV7)

growth_protocol: Mouse cortical neurons were prepared as described previously (Kim, et al. Nature, 2010, 465(7295):182-187). Briefly, we dissected E16.5 neurons by separating embryos and then using 1X TrypLE (ThermoFisher, 12605028) to trypsinize individual cortices. Following 20 minutes of trypsinization, 1X Defined Trypsin Inhibitor (ThermoFisher, R007100) was added to the neurons to quench trypsinization.  Next, DMEM, high glucose, GlutaMAX Supplement (ThermoFisher, 10566024) with 10% fetal bovine serum, heat-inactivated (ThermoFisher, 10082147) was added to the mixture followed by trituration using a flame-tipped glass pipette with washing in clean 1X HBSS, no calcium, no magnesium, phenol red (ThermoFisher, 14170161). Then, neurons were plated at approximately 2 x 106 cells in 6 cm dishes.  Prior to plating, the dishes were coated for at least 2 hours in poly-D-lysine hydrobromide MW 70,000-150,000 (ThermoFisher, P6407-5MG) in 0.2 µm filter-sterilized PBS (10 mM PO4, 137 mM NaCl, 2.7 mM KCl), pH 7.4 at 37oC and 5% CO2 and then washed twice with sterile-filtered water and allowed to dry. The neurons were cultured in 5 ml of neuronal medium (Neurobasal Medium (ThermoFisher, 21103049) supplemented with GS21 Neural Supplement (Amsbio, GSM-3100), Penicillin-Streptomycin (ThermoFisher, 15070063), and GlutaMAX Supplement (ThermoFisher, 35050061)). Two hours after plating all the media was removed and replaced with warmed media.

extract_protocol:
Total RNA from DIV7 cortical neurons were prepared using Qiagen RNeasy Plus Mini Kit. Illumina mRNA sequencing sample preparation guide (Cat # RS-930-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 4 days in vitro (DIV), half of the media was replaced with fresh media. Following 6DIV, half of the media was replaced with fresh media supplemented with a final concentration of 1 μM tetrodotoxin (TTX) (Tocris Biosciences, 1078) and 100 µM D-(-)-2-amino-5-phosphonopentanoic acid (D-AP5) (Tocris Biosciences, 0106-1mg). At 12-16 hours following silencing, we added herpes simplex virus for 4 hours or 8 hours and then depolarized neurons for 2 hours using 55 mM KCl.

value: cortical neurons

tag: age


title: S40A-S133A_8h_rep2


title: HDdPEST_PTEN_promoter_rep3

tag: cell line


title: S133A_8h_rep2

description: DIV7 neurons treated with HSV expressing S133A-CREB for 8h, depolarized 2h

tag: genotype


title: GFP_8h_rep4

description: DIV7 neurons treated with HSV expressing GFP for 8h, depolarized 2h


title: GFP_4h_rep2

description: DIV7 neurons treated with HSV expressing GFP for 4h, depolarized 2h


title: S40A_8h_rep4

description: DIV7 neurons treated with HSV expressing S40A-CREB for 8h, depolarized 2h


title: GFP_8h_rep1


title: GFP_8h_rep2


title: S40A_4h_rep2

description: DIV7 neurons treated with HSV expressing S40A-CREB for 4h, depolarized 2h


title: GFP_8h_rep3


title: WT_4h_rep2

description: DIV7 neurons treated with HSV expressing WT CREB for 4h, depolarized 2h


title: WT_4h_rep1


title: WT_8h_rep4

description: DIV7 neurons treated with HSV expressing WT CREB for 8h, depolarized 2h


title: S40A_4h_rep1


title: WT_8h_rep1


title: S40A_8h_rep2


title: S40A_8h_rep1


title: S40A_8h_rep3


title: WT_8h_rep3


title: WT_8h_rep2


title: GFP_4h_rep1


title: S133A_8h_rep1


title: Prdm9 Set-KO H3K4me3-ChIP

city: Bar Harbor

first: Hui

last: Tian

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

data_processing:
H3K4me3 and H3K36me3 ChIP-Seq reads were aligned to the mm10 genome assembly using BWA (v.0.5.10-tpx). For DMC1 ChIP, Fastq files  were trimmed using Trimmomatic (v0.32) and subsequently parsed for detection and selection of paired reads having homology at the 5’ and 3’ ends.
H3K4me3 and H3K36me3 ChIP-Seq reads were filtered to keep only uniquely mapped reads. DMC1 files were aligned to mm10 genome using BWA (v.0.5.10-tpx) and bam files were parsed for detection and selection of reads containing true genomic sequence versus fill-in sequence at the homologous region.
H3K4me3 ChIP-Seq peaks were called using MACS1.4.DMC1 reads were selected from the original paired-end fastq files and single-ended fastq files were created containing only the true genomic sequences of single strand DNA reads.
The filtered DMC1 reads were then aligned to the mouse mm10 genome using BWA (v.0.5.10-tpx).
DMC1 peaks were called using MACS1.4.
Genome_build: mm10
Supplementary_files_format_and_content: peak and bedgraph

source_name: spermatocytes

extract_protocol:
For H3K4me3 and H3K364me3 ChIP, nuclei were isolated from cells using hypotonic lysis. Nuclei were fixed with 1% formaldehyde, and chromatin was fragmented by Mnase digestion. After high-speed spin soluble chromatin was removed and used for ChIP. For DMC1 ChIP, spermatocytes were isolated and fixed by 1% paraformaldehyde solution. The chromatin was sheared to ~1000 bp by sonication and used for ChIP.
H3K4me3 and H3K36me3 ChIP libraries were prepared for sequencing using standard Illumina protocols. For DMC1 library preparation,  DNA was firstly end repaired by incubation with T4 DNA Ligase Reaction Buffer with dNTP, T4 DNA polymerase, Klenow Enzyme and T4 PNK, followed by addition of 3’-A overhangs using Klenow Fragment 3’-5’ exo-. After denaturation of DNA , the adapters from TruSeq Nano DNA LD Library Prep Kit (set A, Illumina, FC-121-4001) were ligated with Quick Ligation kit. The libraries then were amplified using PCR Enhancer mix and primer cocktail (Illumina, FC-121-4001) for 12 cycles.

value: spermatocytes

value: 14 days post-partum

tag: antibody

value: H3K4me3 (Millipore, 07-473)


title: Prdm9 Set-KO H3K4me3-input


title: Ewsr1-H3K36me3-input

value: Ewsr1-CKO with Stra8-iCre


title: Ewsr1-H3K36me3-ChIP rep2

value: H3K36me3 (Active Motif, 61101)


title: Ewsr1-H3K36me3-ChIP rep1


title: Ewsr1-H3K4me3-ChIP rep1


title: Ewsr1-H3K4me3-ChIP rep2


title: Prdm9 Set-KO DMC1-input


title: Prdm9 Set-KO DMC1-ChIP rep1

value: DMC1 (Santa Cruz, sc-8973)


title: cpsf30-1 rep2

city: Perpignan

first: Thierry

last: Lagrange

address: 58 Avenue Paul Alduy

country: France

institute: CNRS

data_processing:
Filtering out of reads corresponding to chloroplastic, mitochondrial and rRNA genes was performed with Bowtie 2 v2.3.4 in sensitive local mode (Langmead and Salzberg, 2012).
Remaining reads were mapped against the TAIR 10 genome using gtf annotation file and default parameters of TopHat2 v2.0.7 (Kim et al, 2013).
Assembly and transcript quantification were performed with Cufflinks v2.2.1 (Trapnell et al, 2010). Finally, the low expressed transcripts - less than 1 rpkm (reads per kilobase per million mapped reads) in one of the libraries are filtered out.
The differential analysis  was conducted by Cuffdiff software, belonging to the Trapnell suite.

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol:
Total RNA were extracted from 9 day-old seedlings for Col0, nerd-1 and cpsf30-1 plants using the RNeasy Plant Mini Kit and treated onto the column with the RNase-Free DNase Set. Two replicates were performed per line. PolyA purification, library preparation using the Illumina TruSeq stranded mRNA kit and library quality controls were performed by Fasteris SA.
RNA libraries were prepared for sequencing by Fasteris SA using standard Illumina protocols. Sequencing was performed using Illumina procedure with paired-end reads,21x 125bp and 37-53x106 reads per library

tag: ecotype

value: 9 day-old seedlings

tag: genotype/variation


title: Prdm9 Set-KO DMC1-ChIP rep2


title: cpsf30-1 rep1


title: WT rep2

value: WT


title: Prdm9 het DMC1-ChIP rep1


title: nerd-1 rep1


title: Ewsr1-CKO DMC1-ChIP rep2


title: B6 DMC1-ChIP rep2


title: Prdm9 het DMC1-input


title: Ewsr1-CKO DMC1-input


title: Prdm9 het DMC1-ChIP rep2


title: Ewsr1-CKO DMC1-ChIP rep1


title: H. pylori P12 (CagA-KO)-infected AGS cells - rep1

city: Athens

first: Eleftherios

last: Kontizas

address: Vasilissis Sofias 127

department: Microbiology

country: Greece

institute: Hellenic Pasteur Institute

data_processing:
Sequencing was performed on Ion PI Hi-Q Sequencing 200 Kit utilizing Ion Proton PI chips (Thermo Fisher Scientific), according to manufacturer’s protocol.
Alignment was performed on the human reference genome hg19, using TopHat2, according to suggested parameters and exploiting transcript annotation from Illumina iGenomes.
Non-aligned reads were resubmitted for alignment on genome assembly hg19 using Bowtie2 (parameter “very-sensitive” activated), and merged with the initial alignments.
Read counts per gene were estimated using GenomicRanges.
metaseqR tool was employed to perform sample quality control, biotype quantification per sample, differential expression analysis and visualization of results. Via metaseqR, read counts were filtered for possible artifacts and discrepancies; genes presenting any of the following were excluded from further analysis: (i) genes with length less than 500, (ii) genes whose average reads per 100 bp was less than the 25th quantile of the total normalized distribution of average reads per 100 bp, (iii) genes with read counts below the median read counts of the total normalized count distribution. The resulting gene counts table was subjected to differential expression analysis, utilizing edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample (metadata columns chromosome, start, end, gene_id, gc_content, strand, gene_name, biotype).

molecule: polyA RNA

source_name: AGS gastric epithelial cells

growth_protocol: Human gastric epithelial cell lines AGS (ATCC CRL-1739) were cultured in 75 cm2 flasks (Corning) in RPMI-1640 medium (Gibco), supplemented with 10% FBS (Gibco), including antibiotics (penicillin 10 U/ml, streptomycin 10 mg/ml) at 37°C in a humidified chamber supplemented with 5% CO2.

extract_protocol:
Total RNA was extracted from 24 hour H. pylori-infected and uninfected AGS cells, using TRIzol Reagent (Invitrogen) and purified utilizing DNAaseI (Promega) and RNAeasy Mini kit (Qiagen). PolyA-containing transcripts were purified using Dynabeads mRNA DIRECT Micro Kit (Thermo Fisher Scientific).
Sequencing libraries were prepared using Ion Total RNA-Seq Kit v2 according to manufacturer’s protocol (Thermo Fisher Scientific). Template preparation was implemented on Ion Chef using Ion PI Hi-Q OT2 200 Kit.

treatment_protocol: Gastric epithelial cells were infected with H. pylori at a MOI of 100. 4e05 cells were seeded in 6-well plates (Corning) and were left to adhere and grow overnight. Two hours prior to infection, cells were rinsed twice with PBS (1x) and the medium was replaced with 2 ml of antibiotic-free RPMI-1640 supplemented with 10% FBS.

value: AGS

tag: infection status

value: infected

tag: caga status

value: knock-out


title: H. pylori P12 (CagA-KO)-infected AGS cells - rep2


title: H. pylori P12 (phosphorylation-defective)-infected AGS cells  - rep1

value: phosphorylation-defective


title: H. pylori P12 (wild-type)-infected AGS cells - rep1

value: wild-type


title: Naïve AGS cells - rep1

value: non-infected


title: 3_DLD1_siVPS37C#1

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

data_processing:
torrent mapper, version 5.0.4
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
removal of features with less then 100 counts based on the sum of normalized counts across all samples, removal of non-protein coding features
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized count matrix

growth_protocol: Human colorectal carcinoma cell line DLD1 was obtained fom American Type Culture Collection (ATCC). DLD1 were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Sigma-Aldrich, M2279) supplemented with 10% (v/v) fetal bovine serum (FBS, Sigma-Aldrich, F7524) and 2 mM L-Glutamine (Sigma-Aldrich, G7513). Cells were cultured in an incubator at 37°C in a humidified atmosphere containing 5% CO2. During the study, cells were regularly tested for mycoplasma and the identities of DLD1 and RKO were confirmed by short tandem repeat (STR) profiling performed by the ATCC Cell Authentication Service.

extract_protocol:
Total RNA was isolated with RNeasy Mini Kit (Qiagen, 74104) followed by on-column DNase  digestion according to manufacturer’s protocol.
Library was prepared with the Ion AmpliSeq Transcriptome Human Gene Expression Panel (Thermo Fisher, USA)

treatment_protocol: Cells were plated in 12-well plate format at the density 60,000 cells/ml in 1 and 2 ml of medium, respectively. After 16-24 h cells were left non-transfected or differentially transfected according to the forward transfection protocol with combinations of siRNA molecules specified in Table S4. The following PreDesigned or Validated Ambion Silencer Select siRNAs (Thermo Fisher Scientific) were used: Negative Control No. 1 (siNC#1, 4390843), on-target siVPS37A#1 (s44037), siVPS37B#1 (s36177), and siVPS37C#1 (s30059). Additionally, two custom-ordered Silencer Select duplexes were used: Negative Control No. 3 (NC3, sense strand 5’->3’ UACGACCGGUCUAUCGUAGtt, antisense strand 5’->3’ CUACGAUAGACCGGUCGUAtt) and Negative Control No. 4 (NC4, sense strand 5’->3’ UUCUCCGAACGUGUCACGUtt, antisense strand 5’->3’ ACGUGACACGUUCGGAGAAtt). 72h later, cells were washed with PBS and cell pellet was collected.

tag: sirna

tag: batch


title: Patient 013

source_name: primary breast cancer

tag: race

value: EA

value: breast cancer

tag: age at diagnosis, years

tag: er

value: negative

tag: pr

tag: subtype

value: Triple Negative


title: nerd-1 rep2


title: WT rep1


title: genomic DNA from SCCOHT case 43 [10003885129_R03C01]

source_name: primary SCCOHT sample

tag: subject/case id

value: SCCOHT case 43

tag: subject status

value: small cell carcinoma of the ovary hypercalcemic type (SCCOHT)

tag: Sex

value: female


title: H. pylori P12 (phosphorylation-defective)-infected AGS cells - rep2

tag: cell line


title: 3_DLD1_siVPS37B#1


title: 3_DLD1_siVPS37ABC#1


title: 3_DLD1_siVPS37A#1


title: 3_DLD1_siVPS37AC#1


title: H. pylori P12 (wild-type)-infected AGS cells - rep2


title: 3_DLD1_siCTRL#1


title: 2_DLD1_siVPS37B#1


title: 2_DLD1_siVPS37BC#1


title: 2_DLD1_siVPS37C#1


title: 3_DLD1_NT

value: NT


title: 2_DLD1_NT


title: 2_DLD1_siCTRL#1


title: 2_DLD1_siVPS37A#1


title: 1_DLD1_siVPS37C#1


title: 2_DLD1_siVPS37ABC#1


title: 1_DLD1_siVPS37B#1


title: 1_DLD1_siVPS37AC#1


title: 1_DLD1_siVPS37ABC#1


title: 1_DLD1_siVPS37BC#1


title: 2_DLD1_siVPS37AB#1


title: B6 DMC1-ChIP rep1

tag: cell type

value: spermatocytes

tag: age

value: 14 days post-partum

tag: strain

value: DMC1 (Santa Cruz, sc-8973)


title: 1_DLD1_siVPS37AB#1


title: Naïve AGS cells - rep2

value: AGS


title: 1_DLD1_siVPS37A#1


title: 1_DLD1_siCTRL#1


title: 1_DLD1_NT


title: Hyp-PDT 10h rep2

city: Leuven

first: Nicole

last: rufo

address: Herestraat 49

country: Belgium

institute: KU Leuven

data_processing:
base quality per cycle was calculated by the ShortRead 1.24.0, low quality ends (Phred quality score <20) were trimmed by FastX 0.0.14 and reads shorter than 35 bp were removed
adapters were trimmed (at least 10bp overlap and 90% match) with cutadapt 1.7.1 and reads shorter than 35 bp are removed
polyA-reads (more than 90%  of the bases equal to A), ambiguous reads (containing N), low quality reads (more than 50% of the bases with a Phred quality score <25) and artifact reads (all but 3 bases in the read equal one base type) were removed using FastX 0.0.14 and ShortRead 1.24.0. Using bowtie 2.2.4, we identify reads that align to phix illumina and remove them.
The reads are aligned to the reference genome with STAR 2.4.1d. As parameter options we used: --outSAMprimaryFlag OneBestScore --twopassMode  Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate. With samtools 1.1 we remove reads from the alignment that are non-primary mappings or  have a mapping quality   =<20. With samtools 1.1 we sort the reads from the alignment according to the chromosomes and index the resulting bam-files.
Gene counts were generated with featureCounts 1.4.6 with parameters -Q 0 -s 2 -t exon -g gene id.
Genome_build: GRCh3773
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample,

growth_protocol: A375 were cultured in DMEM (Sigma) supplemented with 2mM glutamine (Sigma) and 10% fetal bovine serum (PAN-Biotech)

extract_protocol:
RNA was harvested using TriSure reagent (Bioline) followed by phenol/chloroform extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A375 cells were incubated with 1 μM mitoxantrone (MTX, Sigma) or 50 μM Cisplatin (CDDP, Sigma).For hypericin-based photodynamic therapy (Hyp-PDT) conditions, A375 cells were incubated for 16 hr with 150 nM hypericin (Enzo Life Sciences) in full medium followed by removal of hypericin and irradiation with fluence=2.70 J/cm2

value: Human melanoma

tag: treatment

value: Hypericin (150nM), irradiation fluence 2.70 J/cm2

tag: recovery time

value: 10 hours


title: Hyp-PDT 10h rep3


title: Hyp-PDT 4h rep2

value: 4 hours


title: Hyp-PDT 4h rep1


title: Hyp-PDT 4h rep3


title: Hyp-PDT 20h rep3

value: 20 hours


title: Hyp-PDT 20h rep2


title: Hyp-PDT 10h rep1


title: MTX 20h rep2

value: MTX 1uM


title: MTX 20h rep1


title: MTX 20h rep3


title: MTX 10h rep3


title: MTX 4h rep1


title: MTX 10h rep1


title: MTX 4h rep2


title: MTX 4h rep3


title: MTX 10h rep2


title: CDDP 20h rep1

value: CDDP 50uM


title: CDDP 10h rep2


title: CDDP 20h rep3


title: CDDP 20h rep2


title: CDDP 10h rep3


title: CDDP 10h rep1


title: CDDP 4h rep2


title: CDDP 4h rep3


title: 3_DLD1_siVPS37BC#1


title: Hyp-PDT 20h rep1


title: CTRL 20h rep3

value: untreated


title: CTRL 20h rep2


title: CTRL 20h rep1


title: CTRL 10h rep3


title: CTRL 4h rep1


title: CTRL 4h rep3


title: CTRL 4h rep2


title: CTRL 0h rep2

value: 0 hours


title: CTRL 0h rep1


title: CTRL 10h rep1


title: INPUT Drug Treated Rep 2

city: Houston

first: Jarey

middle: Hao

last: Wang

state: Texas

address: 1 Baylor Plaza, 304B, Anderson Building

institute: Baylor College of Medicine

data_processing:
Raw read of fastq format were obtained after adapter removal in BaseSpace. Index of the mm10 mouse or hg38 human genome was built using hisat2-v2.0.4.
Proper paired-end reads were aligned to the reference genome using hisat2-v2.0.4.
The pysam python module was used to compute number of reads mapping to introns (in gtf format); reads mapping to features were then RPKM normalized.
Genome_build: hg38
Supplementary_files_format_and_content: gtf files for introns, along with two additional columns 1) number of reads mapped to the intron 2) number of reads mapped to or spanning the intron and 3) rpkm based on intronic reads

growth_protocol: SUM159 cells grown in media as described in manuscript.

extract_protocol:
dsRNA RNA immunoprecipitation was performed as described in manuscript.
~300 bp insert strand specific library with polyA selection (TruSeq Stranded mRNA kit, Illumina).

treatment_protocol: Cells treated with 8800 or DMSO prior to collection in RNA lysis buffer.

tag: tissue

value: Immortalized cell line

tag: antibody

value: INPUT

value: Drug Treated


title: J2-enriched Veh Treated Rep 2

value: J2 Enriched

value: Vehicle Control


title: INPUT Drug Treated Rep 1


title: INPUT Veh Treated Rep 1


title: CDDP 4h rep1


title: SUM159 Cytoplasmic 8800 Sample 1

description: Cytoplasmic

extract_protocol:
Cytoplasmic RNA isolated via subcellular fractionation as described in manuscript.
~300 bp insert strand specific library with polyA selection (TruSeq Stranded mRNA kit, Illumina).


title: SUM159 Cytoplasmic DMSO Sample 2

description: Cytoplasmic


title: SUM159 Cytoplasmic 8800 Sample 2

description: Cytoplasmic


title: INPUT Veh Treated Rep 2


title: J2-enriched Drug Treated Rep 2


title: J2-enriched Veh Treated Rep 1


title: J2-enriched Drug Treated Rep 1


title: iPSC, PEmut - polyclonal, Cech-991-1051_22_S22 (ChIP-seq)

city: Boulder

first: Thomas

last: Cech

state: CO

address: 3415 Colorado Ave., Jennie Smoly Caruthers Biotech BLDG

institute: University of Colorado Boulder

description:
Flag_SUZ12_count.csv
column header in *count.csv: 22_S22_R1_cat_trimmed_nodups

data_processing:
[ChIP-seq]  Reads containing Illumina indexes were trimmed with trimmomatic/0.36 (Bolger et al., 2014), aligned to the hg38 genome with bowtie/2.2.9 (Langmead and Salzberg, 2012) using --very-sensitive, and duplicates were marked and removed with picard/2.6.0. Peak calling was performed with MACS/2.1.1 (Zhang et al., 2008) on merged replicates using the --broad setting and a false-discovery rate of 0.01. Consensus peak sets were generated by merging peak sets and removing ENCODE blacklist genomic regions with bedtools/2.25.0 (Quinlan and Hall, 2010). Metapeak plots and heatmaps were generated with deeptools/3.0.1 (Ramirez et al., 2016) using the computeMatrix function on the consensus peaks sets. ChIP-seq signal intensity plots over genomic regions were curated using CPM normalized bigwig files generated by deeptools and visualized with the Integrative Genomics Viewer (igv/2.8.0) (Robinson et al., 2011; Thorvaldsdottir et al., 2013).
Rstudio packages were used for gene centric analysis. To include promoter proximal reads, the slop function within bedtools/2.25.0 was used to add 2,500 base-pairs onto the upstream region of the 60,609 genes within the gencode hg38 annotation. Reads were counted over these annotated regions using featureCounts (Liao et al., 2014) within the Rsubread/1.32.4 package (Liao et al., 2019). P-values and fold change were calculated using DEseq2/1.26.0 (Love et al., 2014). Plotting was performed with ggplot2/3.2.1.
[RNA-seq]  Paired-end reads containing Illumina indexes were trimmed with trimmomatic/0.36 (Bolger et al., 2014), aligned to the hg38 genome with HISAT2/2.1.0 (Kim et al., 2015) using --very-sensitive, and duplicates were marked and removed with picard/2.6.0. RNA-seq signal intensity plots over genomic regions were curated using RPKM normalized bigwig files generated by deeptools/3.0.1 (Ramirez et al., 2016) and visualized with the Integrative Genomics Viewer (igv/2.8.0) (Robinson et al., 2011; Thorvaldsdottir et al., 2013). Reads were counted over gencode annotated genes in the hg38 genome with HTseq/0.9.1 (Anders et al., 2015). P-values and fold change were calculated using DEseq2/1.26.0 (Love et al., 2014). Plotting was performed with ggplot2/3.2.1.
Genome_build: hg38
Supplementary_files_format_and_content: Comma seperated file has the read counts for every gene in the GENCODE (v27) gene annotation. Bigwig files are also provided for ChIP-seq data files

source_name: iPSC

growth_protocol: All experiments were performed in the human iPSC line GM25256 (WTC-11) purchased from the Coriell Institute (https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM25256). Unless otherwise noted, cells were maintained on Vitronectin coated plates in Essential 8 Flex medium supplemented with 50 U/mL penicillin and 50 μg/mL streptomycin at 37C/5%CO2. Cell splitting was performed using gentle conditions by incubating cells at 37C/5%CO2 for 5 min in PBS/0.5mM EDTA.

extract_protocol:
Total RNA was extracted with Trizol following manufactuer's protocol. DNA samples in ChIP-seq were extracted using phenol-chloroform.
KAPA RNA Hyperprep kit with riboerase (RNA-seq and fRIP-seq), KAPA HyperPlus Kit (ChIP-seq)

treatment_protocol: Refer to main text for complete ChIP-seq and RNA-seq methods

tag: differentiation state

value: undifferentiated

tag: clone

value: PEmut - polyclonal

tag: genotype

value: PEmut

value: iPSC

tag: chip antibody

value: Flag (Sigma-Aldrich F1804)

tag: fraction

value: DNA pulldown by Flag

tag: biological replicate


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_24_S24 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 24_S24_R1_cat_trimmed_nodups

value: A2J2mut2 - polyclonal


title: CTRL 10h rep2

value: Human melanoma

value: 10 hours


title: CTRL 0h rep3


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_19_S19 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 19_S19_R1_cat_trimmed_nodups

value: A2J2mut1 - polyclonal


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_20_S20 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 20_S20_R1_cat_trimmed_nodups


title: SUM159 Cytoplasmic DMSO Sample 1

description: Cytoplasmic


title: iPSC, PEmut - polyclonal, Cech-991-1051_21_S21 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 21_S21_R1_cat_trimmed_nodups


title: iPSC, WT - polyclonal, Cech-991-1051_17_S17 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 17_S17_R1_cat_trimmed_nodups

value: WT - polyclonal

value: WT


title: iPSC, WT - polyclonal, Cech-991-1051_18_S18 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 18_S18_R1_cat_trimmed_nodups


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_15_S15 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 15_S15_R1_cat_trimmed_nodups

value: SUZ12 (Cell Signaling Technology #3737)

value: DNA pulldown by SUZ12


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_12_S12 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 12_S12_R1_cat_trimmed_nodups


title: iPSC, PEmut - polyclonal, Cech-991-1051_13_S13 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 13_S13_R1_cat_trimmed_nodups


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_11_S11 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 11_S11_R1_cat_trimmed_nodups


title: iPSC, WT - polyclonal, Cech-991-1051_9_S9 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 9_S9_R1_cat_trimmed_nodups


title: iPSC, WT - polyclonal, Cech-991-1051_10_S10 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 10_S10_R1_cat_trimmed_nodups


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_23_S23 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 23_S23_R1_cat_trimmed_nodups


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_7_S7 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 7_S7_R1_001_trimmed_nodups

value: DNA input


title: iPSC, PEmut - polyclonal, Cech-991-1051_6_S6 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 6_S6_R1_001_trimmed_nodups


title: iPSC, PEmut - polyclonal, Cech-991-1051_5_S5 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 5_S5_R1_001_trimmed_nodups


title: iPSC, A2J2mut2 - polyclonal, Cech-991-1051_16_S16 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 16_S16_R1_cat_trimmed_nodups


title: iPSC, PEmut - polyclonal, Cech-991-1051_14_S14 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 14_S14_R1_cat_trimmed_nodups


title: 2_DLD1_siVPS37AC#1

tag: sirna

tag: batch


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_3_S3 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 3_S3_R1_001_trimmed_nodups


title: iPSC, WT - polyclonal, Cech-991-1051_2_S2 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 2_S2_R1_001_trimmed_nodups


title: smallRNA_TBSx2_72h_rep1

city: Baltimore

first: Margaret

middle: R

last: Starostik

state: MD

address: 3400 Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
snpc-1.3(2xtbs) gravid adult (72h) replicate 1
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

data_processing:
Raw small RNA-seq reads were trimmed for Illumina adapters and quality (SLIDING WINDOW: 4:25) using Trimmomatic 0.39 (Bolger et al., 2014).
Trimmed reads were then filtered using bbmap 38.23 (http://jgi.doe.gov/data-and-tools/bb-tools) to retain reads that were 15-30 nucleotides in length.
These filtered reads were aligned to the C. elegans WBcel235 (Cunningham et al., 2018) reference genome using Bowtie 1.1.1 (Langmead et al., 2009) with parameters -v 0 -k 5 --best --strata --tryhard.
Mapped reads were assigned to genomic features using featureCounts from Subread 1.6.3 (Liao et al., 2014), taking into account overlapping and multi-mapping reads (-O -M).
Raw counts were normalized within DESeq2 1.26.0 (Love et al., 2014).
For SNPC-1.3 and TRA-1 ChIP seq data, reads were trimmed for adapters and filtered for sequencing quality score > Q25 using Trim Galore! 0.5.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
Filtered reads were aligned to C. elegans reference genome WBcel235 (Cunningham et al., 2018) using Bowtie2 2.3.4.2 (Langmead and Salzberg, 2012) with default parameters.
Post-alignment filtering was then performed to remove PCR duplicates using the MarkDuplicates utility within Picard 2.22.1 (http://broadinstitute.github.io/picard/).
In addition, SAMtools 1.9 was applied to remove unmapped reads and reads that mapped with MAPQ 30 but were not of primary alignment or failed sequence platform quality checks (SAMtools -F 1804 -q 30) (Li et al., 2009).
To identify DNA binding sites for SNPC-1.3, mapped and filtered SNPC-1.3 ChIP-seq reads were extended to 200 base pairs to account for the average length of ChIP fragments.
We then partitioned the genome into consecutive, non-overlapping 1,000 base pair bins and calculated read coverage, normalized by sequencing depth of each library, based on the total read count in each bin.
Bins with read coverages in the IP sample that fell below the median read coverage of piRNA-depleted regions on chromosome IV in the relevant input control were excluded from further analysis.
TRA-1 ChIP-seq peaks were called by callpeak within MACS 2.1.2 (Zhang et al., 2008) (--pvalue 0.05) with filtered TRA-1 ChIP-seq reads and relevant input controls.
Genome_build: WBcel235

organism: Caenorhabditis elegans

source_name: whole worms, gravid adult (72 h, 20°C )

growth_protocol: Worms were grown on NGM plates at 20°C and fed E. coli strain OP50.

extract_protocol:
Worms were collected in TriReagent (Thermo Fisher Scientific) and underwent three freeze-thaw cycles. Following addition of 1-bromo-3-chloropropane (BCP), the aqueous phase was then precipitated with isopropanol at -80°C for 2 hrs. To pellet RNA, samples were spun at 21,000 x g for 30 min at 4°C. After three washes in 75% ethanol, the pellet was resuspended in water. RNA concentration and integrity was measured using a TapeStation (Agilent Technologies). 16-30 nt small RNAs were size-selected from 5 ug total RNA on 17% denaturing polyacrylamide gels. Small RNAs were treated with 5’ polyphosphatase (Illumina) to reduce 5’ triphosphate groups to monophosphates to enable 5’ adapter ligation.
Small RNA-sequencing libraries were prepared using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina (NEB). Small RNA amplicons were size-selected on 10% polyacrylamide gels and quantified using qRT-PCR. Samples for each developmental time point were pooled into a single flow cell and single-end, 75 nt-long reads were generated on a Illumina NextSeq 500 (Illumina).

value: whole worm

value: gravid adult (72h)

tag: replicate


title: smallRNA_N2_72h_rep3

description:
N2 gravid adult (72h) replicate 3
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt


title: 3_DLD1_siVPS37AB#1

tag: cell line


title: smallRNA_SNPC13_48h_rep2

description:
snpc-1.3(-) L4 (48h) replicate 2
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

source_name: whole worms, L4 (48 h, 20°C )


title: smallRNA_N2_72h_rep1

description:
N2 gravid adult (72h) replicate 1
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

source_name: whole worms, gravid adult  (72 h, 20°C )


title: B3: brain_ GBM patients_rep3

city: zhengzhou

first: zhao

middle: cheng

last: bin

address: jianshe road

institute: zhengzhou university

description: lncRNA, mRNA and circRNAs expression in primary glioblastoma tissues

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: GBM_ surg patients_rep1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the mirVana RNA RNA Isolation Kit，(AM1561)following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The STRG samples included the standard resection of GBM performed on these patients and treatment with a 150 mg / (m2 d) dose of temozolomide was applied for the postoperative period. These patients underwent surgery again owing to GBM recurrence, and the daily dose of temozolomide was increased to 200 mg / (m2 d), postoperatively

value: brain

tag: gender

value: male

tag: disease state

value: Glioblastoma multiforme (GBM)

tag: molecule subtypes

value: lncRNA, mRNA and circRNAs


title: HUASMC spheroids (SMC_1)

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description:
Gene expression data from human umbilical artery smooth muscle cells
SMC

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of Human HuGene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: human umbilical artery smooth muscle cells were cultured in DMEM +15% FCS and propagated 1:3, human umbilical vein endothelial cells were cultured in EASY Endothelial Cell Medium (Pelo Biotech, without hydrocortisone) +10% FCS

extract_protocol: RNA was extracted from spheroids by utilizing the Qiagen mini RNA extraction kit  following man. instr.

treatment_protocol: Spheroids were cultured for 48h before RNA extraction

value: Control spheroids without endothelial cells


title: HUASMC spheroids (SMC_3)

source_name: human umbilical artery smooth muscle cells


title: smallRNA_TBSx2-72h-rep3

description:
snpc-1.3(2xtbs) gravid adult (72h) replicate 3
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

tag: age


title: HUASMC spheroids (SMC_2)


title: iPSC, WT - polyclonal, Cech-991-1051_1_S1 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 1_S1_R1_001_trimmed_nodups

value: undifferentiated

tag: cell type

value: iPSC


title: iPSC, A2J2mut2 - polyclonal, Cech-1079-5_S5 (ChIP-seq)

value: A2J2mut2 - polyclonal

value: H3K27me3 (Abcam Ab6002)

value: DNA pulldown by H3K27me3


title: smallRNA_SNPC13_48h_rep1

description:
snpc-1.3(-) L4 (48h) replicate 1
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

tag: tissue


title: B2: brain_ GBM patients_rep2


title: A1: brain_STRG patients_rep1

description: lncRNA, mRNA and circRNAs expression in secondary temozolomide-resistant glioblastom

source_name: GBM_TMZ,surg, patients_rep1


title: smallRNA_N2_48h_rep3

description:
N2 L4 (48h) replicate 3
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt


title: B1: brain_ GBM patients_rep1


title: denuded HUVEC/HUASMC spheroids (SMC_EC_2)

description:
Gene expression data from human umbilical artery smooth muscle cells cocultured with human umbilical vein endothelial cells
SMC+EC

value: 3D vascular organoids upon removal of the HUVEC surface layer


title: smallRNA_N2_48h_rep2

description:
N2 L4 (48h) replicate 2
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt


title: iPSC, A2J2mut2 - polyclonal, Cech-1079-6_S6 (ChIP-seq)


title: smallRNA_N2_48h_rep1

description:
N2 L4 (48h) replicate 1
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt


title: iPSC, WT - polyclonal, Cech-1079-3_S3 (ChIP-seq)

value: WT - polyclonal

value: WT


title: iPSC, A2J2mut2 - polyclonal, Cech-1079-4_S4 (ChIP-seq)


title: A2: brain_STRG patients_rep2


title: denuded HUVEC/HUASMC spheroids (SMC_EC_3)

source_name: human umbilical artery smooth muscle cells cocultured with human umbilical vein endothelial cells


title: iPSC, WT - polyclonal, Cech-1079-2_S2 (ChIP-seq)


title: Rat Spg Chip-Seq_Sample 4

city: Dallas

first: F. Kent

last: Hamra

address: 5323 Harry Hines Blvd.

department: Obstetrics and Gynecology

institute: UT Southwestern Medical Center

description:
USg_2 Anti-Foxa2 antibody_Rep
0 Hr in SD Medium

data_processing:
RNAseq fastq files were mapped to reference rn6 using STAR/v2.5.3a and Chipseq fastq files were mapped to rn5 using bowtie2/v2.2.3
Gene counts were calculated using featureCounts (subread/v1.4.6)
Normalized read counts and differentially expressed genes found using edgeR/v3.2.4
For chipseq duplicates were removed using picard/v1.127
Chipseq peaks were called using MACS/v2.1.0.20160309
Bigwig files were made using HOMER/v3
Genome_build: rn5 and rn6
Supplementary_files_format_and_content: for RNAseq: tab delimited text file with raw gene counts per sample
Supplementary_files_format_and_content: for Chipseq: bigwig files

organism: Rattus norvegicus

source_name: Culture in SG Medium

growth_protocol: Rat spermatogonial stem cell line/rat undifferentiated spermatogonia (USg) cultured in SG Medium containing GDNF and FGF as growth factors.

extract_protocol:
Chip-Seq samples were extracted on d0 (prior to plating on laminin) or d7 post-plating on laminin (d5 in SD Medium), and ~4 million Brown Norway rat laminin-non-binding spermatogenic cells, using the RNAqueous Kit (Ambion, Inc.). RNA concentration in each isolated sample was measured using the RiboGreen Kit (Invitrogen, Inc.).
Rat USg DNA (50 μg) was pretreated with protein G agarose beads (ThermoFisher) and Foxa2-DNA binding motifs co-precipitated using 5 μg of goat anti-human FOXA2 antibody sc-6554 (Santa Cruz Biotechnology) that was used to define the FOXA2 cistrome in the endometrium of the human uterus (Kelleher et al., 2019). Precipitates were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Cross-links were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation (Kelleher et al., 2019). Single end reads of 75 bp were generated. After mapping reads to rat genome Rnor6.0 by bowtie2 (v2.2.3) with parameter “--sensitive”, we perform filtering by (1) removing alignments with mapping quality less than 10, (2) removing duplicate reads identified by Picard MarkDuplicates (v1.127) http://broadinstitute.github.io/picard. Then enriched regions (peaks) were identified using MACS2 (v2.0.10)(Zhang et al., 2008), with a q-value cut-off of 0.05 for broad peaks. Peak regions were annotated by HOMER (Ross-Innes et al., 2012).

treatment_protocol: Replicate samples of rat USg after subculture in SG Medium following treatement with isotype control IgG and Chip-Seq verified Goat anti-Foxa2 IgG sc-6554 (Santa Cruz Biotechnology)

value: Undifferentiated Spermatogonia

tag: strain

value: Brown Norway

tag: culture type

value: Cell Line

tag: treatment

value: SG Medium

value: Primary Rat Germline


title: LNB_Sample-2

description:
Spc_2 Rep
2.5d in 10% FBS in DMEM:Ham's F12 Medium (1:1)

source_name: Laminin Non-Binding Germ Cells Purified from Testis Cell Culture

growth_protocol: Rat spermatogonial stem cell line before and after being induced to differentiate in culture on laminin using SD Medium (contains all-trans-retinoic acid and neuregulin-1)

extract_protocol:
Total RNA samples were extracted on d0 (prior to plating on laminin) or d7 post-plating on laminin (d5 in SD Medium), and ~4 million Brown Norway rat laminin-non-binding spermatogenic cells, using the RNAqueous Kit (Ambion, Inc.). RNA concentration in each isolated sample was measured using the RiboGreen Kit (Invitrogen, Inc.).
Standard RNA Sequencing Protocols used for analyses on rat spermatogonial transcripts were conducted by The McDermott Center Next Generation Sequencing (NGS) Core at UT Southwestern Medical Center as describe by (Kollipara and Kittler, 2015).

treatment_protocol: Replicate cultures maintained in SG Medium before and after culture for 120hr in SD Medium to induce formation of differentiting spermatogonial syncitia.

value: Primary Spermatocytes Enriched

value: Primary Culture

value: Negative selection in culture on plastic, collogen-I and laminin matrices


title: denuded HUVEC/HUASMC spheroids (SMC_EC_1)


title: T120plusRAplusN_Sample 2

description:
DSg_2 Rep
120 Hr in SD Medium

source_name: Spermatogonial Line Differentiated Culture in SD Medium

value: Differentiating Spermatogonia

value: SD Medium


title: T120plusRAplusN_Sample 1

description:
DSg_1 Rep
120 Hr in SD Medium


title: iPSC, WT - polyclonal, Cech-1079-1_S1 (ChIP-seq)

tag: differentiation state

value: undifferentiated

tag: clone

tag: genotype

value: iPSC


title: T120plusG_Sample 2

description:
USg_2 Rep
0 Hr in SD Medium

source_name: Spermatogonial Line Expanded Culture in SG Medium


title: T120plusG_Sample 1

description:
USg_1 Rep
0 Hr in SD Medium


title: iPSC, PEmut.10, 975_6_S16 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_6_S6_nodups

value: PEmut

tag: fraction

value: rRNA-depleted RNA

tag: biological replicate


title: iPSC, PEmut.4, 975_5_S15 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_5_S5_nodups


title: iPSC, PEmut.2, 975_4_S14 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_4_S4_nodups


title: healthy tumor-surrounding mucosa of sample CRC.76

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

data_processing:
Library strategy: amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2020crc)

source_name: Colonic mucosa

growth_protocol: Tissue samples were stored at -80°C

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerLyzer PowerSoil Kit (Qiagen, Hilden, Germany)  162 Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

tag: diagnosis

value: Surrounding healthy tissue

tag: Sex

value: M


title: colorectal mucosa of sample CRC.76

value: Colorectal adenocarcinoma tissue

tag: tnm classification

value: pT1 N0

tag: colorectal cancer stadium

value: I

tag: tumor localization

value: Rectosigmoid junction


title: iPSC, WT.10, 975_3_S13 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_3_S3_nodups

value: WT

tag: cell line


title: healthy tumor-surrounding mucosa of sample CRC.75


title: colorectal mucosa of sample CRC.75

value: T4b N0

value: II

value: Trasverse colon


title: colorectal mucosa of sample CRC.73

value: T3 N0

value: Sigmoid colon

value: F


title: healthy tumor-surrounding mucosa of sample CRC.71


title: healthy tumor-surrounding mucosa of sample CRC.73


title: Rat Spg Chip-Seq_Sample 3

description:
USg_1 Anti-Foxa2 antibody_Rep
0 Hr in SD Medium

value: Undifferentiated Spermatogonia

value: Brown Norway

value: Cell Line

value: SG Medium

value: Primary Rat Germline


title: LNB_Sample 1

description:
Spc_1 Rep
2.5d in 10% FBS in DMEM:Ham's F12 Medium (1:1)

value: Primary Spermatocytes Enriched

value: Primary Culture

value: Negative selection in culture on plastic, collogen-I and laminin matrices


title: iPSC, WT.5, 975_1_S11 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_1_S1_nodups

value: undifferentiated

value: iPSC

value: rRNA-depleted RNA


title: iPSC, A2J2mut1 - polyclonal, Cech-991-1051_4_S4 (ChIP-seq)

description:
Flag_SUZ12_count.csv
column header in *count.csv: 4_S4_R1_001_trimmed_nodups

value: A2J2mut1 - polyclonal

tag: chip antibody

value: DNA input


title: smallRNA_TBSx2-72h-rep2

description:
snpc-1.3(2xtbs) gravid adult (72h) replicate 2
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

value: whole worm

tag: age

value: gravid adult (72h)

tag: replicate


title: iPSC, WT.8, 975_2_S12 (RNA-seq)

description:
WT_PEmut_rep2_count.csv
column header in *count.csv: 975_2_S2_nodups

value: WT

tag: cell type


title: colorectal mucosa of sample CRC.71

value: Colorectal adenocarcinoma tissue

value: pT2 N

value: I

value: Ascending colon

value: M


title: iPSC, PEmut.2, Cech-736-8_S8 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 8_S8_nodups

value: PEmut


title: healthy tumor-surrounding mucosa of sample CRC.65

value: Surrounding healthy tissue

value: F


title: healthy tumor-surrounding mucosa of sample CRC.59


title: colorectal mucosa of sample CRC.59

value: pT3 N1b

value: IIIB

value: Rectosigmoid junction


title: iPSC, PEmut.2, Cech-736-7_S7 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 7_S7_nodups

value: undifferentiated

value: iPSC

value: rRNA-depleted RNA


title: healthy tumor-surrounding mucosa of sample CRC.56


title: healthy tumor-surrounding mucosa of sample CRC.54


title: iPSC, PEmut.1, Cech-736-6_S6 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 6_S6_nodups


title: A3: brain_STRG patients_rep3

description: lncRNA, mRNA and circRNAs expression in secondary temozolomide-resistant glioblastom

tag: tissue

value: brain

tag: gender

value: male

tag: disease state

value: Glioblastoma multiforme (GBM)

tag: molecule subtypes

value: lncRNA, mRNA and circRNAs


title: colorectal mucosa of sample CRC.54

value: Colorectal adenocarcinoma tissue

value: pT2 N0

value: Hepatic flexure


title: iPSC, PEmut.1, Cech-736-5_S5 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 5_S5_nodups

tag: differentiation state

tag: clone

tag: genotype


title: colorectal mucosa of sample CRC.52

tag: diagnosis

value: pT3 N0

value: II


title: healthy tumor-surrounding mucosa of sample CRC.50

value: Surrounding healthy tissue

tag: Sex

value: M


title: colorectal mucosa of sample CRC.51

tag: tnm classification

value: Descending colon


title: iPSC, WT.2, Cech-736-4_S4 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 4_S4_nodups

value: WT

tag: fraction

tag: biological replicate


title: colorectal mucosa of sample CRC.56

tag: colorectal cancer stadium

tag: tumor localization

value: Ascending colon


title: iPSC, WT.2, Cech-736-3_S3 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 3_S3_nodups

value: undifferentiated

tag: cell line


title: colorectal mucosa of sample CRC.50

value: Rectosigmoid junction


title: healthy tumor-surrounding mucosa of sample CRC.52

value: F


title: healthy tumor-surrounding mucosa of sample CRC.51


title: GFP+UV- cells

city: Los Angeles

first: Hidekazu

last: Tsukamoto

address: 1333 San Pablo Street MMR414

department: Pathology

institute: University of Southern California

data_processing:
The sequencing libraries were clustered on 8 single lanes of a flowcell.  After clustering, the flowcell was loaded on the Illumina HiSeq instrument according to manufacturer’s instructions.  The samples were sequenced using a 2x150 Paired End (PE) configuration.  8578 cells were sequenced.  Quality and quantification of single cell preparation was assessed under 10x Cell Ranger analysis platform using reference genome mm10.  After normalization, 38901 mean reads per cell and 2776 median genes per cell were detected.  Data analysis was performed with 10X Genomics’ Loupe Browser software.
Genome_build: The sequencing reads were mapped to mouse genome build mm10 using Cell Ranger software.
Supplementary_files_format_and_content: bam file

source_name: liver cancer

extract_protocol:
A non-parenchymal liver cell fraction from liver of DEN-WAD Col1a1-Cre;Rosa26mTmG mice was collected by pronase-collagenase perfusion and gradient ultracentrifugation.  UV-/GFP+ cells were collected as p5 fraction in tubes containing the medium with DNase.  Gating for UV and GFP positivity were set by primary hepatic stellate cells isolated from wild type mouse and Col1a1Cre;Rosa26mTmG mouse, respectively, with wild type liver myofibroblasts as a UV and GFP negative cells.
Single cell was prepared using the 10X Single Gene Expression v3 with the 10x Chromium technology following manufacturer protocol (cat# 1000154 and 1000074, 10x Genomics).  The library was validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).

treatment_protocol: Two-week old male mice were injected with 25 mg/kg of diethyl nitrosamine (DEN) intraperitoneally (Sigma Aldrich, St Louis).  At three weeks after DEN injection, the mice were injected with two doses of 75mg/kg tamoxifen (Tam) (Sigma Aldrich, St Louis) intraperitoneally at the three-day interval.  On the day of the second dose, the Western Alcohol Diet (WAD) was introduced by gradually changing alcohol percent and reaching steady state 3.5% alcohol.  WAD was prepared by blending the modified high cholesterol fat liquid diet powder (#710362; Dyets Inc.) in water with appropriate amount ethyl alcohol.  The mice were fed for the diet containing no alcohol for two days.  The mice were then fed with 1% alcohol for 2 days, 2% alcohol for 3 days and 3.5% alcohol for 5-6 months.

tag: treatment

value: DEN-Western Alcoholic Diet

tag: strain


title: iPSC, WT.1, Cech-736-2_S2 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 2_S2_nodups

tag: cell type

value: iPSC

value: rRNA-depleted RNA


title: colorectal mucosa of sample CRC.65

value: pT2 N1c

value: IIIA

value: Rectum


title: smallRNA_N2_72h_rep2

description:
N2 gravid adult (72h) replicate 2
smallRNAseq_method01_RawCounts.txt
smallRNAseq_method01_NormalizedCounts.txt

tag: tissue

value: whole worm

tag: age

value: gravid adult (72h)

tag: replicate


title: healthy tumor-surrounding mucosa of sample CRC.48


title: colorectal mucosa of sample CRC.48

value: Colorectal adenocarcinoma tissue

value: pT3 N0

value: II

value: Cecum


title: 6-5-WT: wild type sample 2

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Pre-processing of raw reads was carried out using Trimmomatic (version 0.35, options: LEADING:3 TRAILING:3 MAXINFO:80:0.4 MINLEN:36)
The trimmed reads were mapped to the Mus musculus genome (GRCm38) using TopHat2 (version 2.1.0, default options).
The gene-level read counts were created from the aligned reads by HTSeq and differential gene expression analysis was carried out using R/Bioconductor DEseq2 package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count matrix calculated by using DESeq2.

source_name: Brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: brain

tag: genotype/variation

value: PTEN wild type


title: 8-2-WT: wild type sample 3


title: colorectal mucosa of sample CRC.46

value: pT3 N1c

value: IIIB

value: M


title: iPSC, WT.1, Cech-736-1_S1 (RNA-seq)

description:
WT_PEmut_rep1_count.csv
column header in *count.csv: 1_S1_nodups

tag: differentiation state

value: undifferentiated

tag: clone

value: WT


title: healthy tumor-surrounding mucosa of sample CRC.46

tag: diagnosis

value: Surrounding healthy tissue


title: colorectal mucosa of sample CRC.47

value: pT2 N0

value: I

tag: Sex


title: healthy tumor-surrounding mucosa of sample CRC.39


title: 5-4-WT: wild type sample 1


title: H3K27ac

city: Manchester

first: Michela

last: Garofalo

address: Alderley Park

country: United Kingdom

institute: CRUK Manchester Institute

data_processing:
bowtie2
macs2
homer
Genome_build: Hg19
Supplementary_files_format_and_content: bw files and peak files (bed)

source_name: H1299 cells

growth_protocol: H1299 cells were cultured in RPMI 1640 medium containing 10% FBS.

extract_protocol:
Genomic DNA was purified with QIAquick PCR purification Kit (Qiagen).
Libraries were prepared for sequencing using standard Illumina protocols.

tag: chip antibody


title: colorectal mucosa of sample CRC.39

tag: tnm classification

value: Rectum


title: 6-6-KI: Pten mutant sample 2

value: PTEN C-terminus mutant


title: healthy tumor-surrounding mucosa of sample CRC.38

value: F


title: healthy tumor-surrounding mucosa of sample CRC.37


title: GapmeR-HIF1A-As2 rep3

data_processing:
RSubRead
FeatureCount
DESeq2
Genome_build: Hg19
Supplementary_files_format_and_content: DESeq2 output

extract_protocol:
Total RNA was isolated from cells using TRIzol according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: gapmer target


title: colorectal mucosa of sample CRC.38

value: Colorectal adenocarcinoma tissue

value: T0 N0

tag: colorectal cancer stadium


title: 5-1-KI: Pten mutant sample 1


title: colorectal mucosa of sample CRC.37

value: pT3 N1b

tag: tumor localization

value: Sigmoid colon


title: GapmeR-HIF1A-As2 rep2

tag: cell line


title: colorectal mucosa of sample CRC.36

value: pT3 N0

value: II


title: healthy tumor-surrounding mucosa of sample CRC.36


title: healthy tumor-surrounding mucosa of sample CRC.47