title: GFP_Overexpression_8_S6_R1_001.fastq.gz

description: merged

value: xenograft tumor


title: CAF1-exo

status: Public on Nov 09 2022

type: SRA

city: Nanjing

first: Hongqian

last: Guo

state: Jiangsu

address: 321 Zhongshan Road

department: Department of Urology

country: China

institute: Drum Tower Hospital, Medical School of Nanjing University

library_source: transcriptomic

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) , repeats, and sequences <18 nt or >26 nt in length. Subsequently, the unique sequences with a length of 18~26nt were mapped to miRNA sequences in miRBase 22.0 (http://www.mirbase.org/).
Assembly: hg38
Supplementary files format and content: excel including the raw counts of all expressed miRNAs for each sample

molecule: total RNA

organism: Homo sapiens

source_name: kidney

growth_protocol: CAFs and NFs were isolated from fresh RCC tissues and their paired normal kidney tissues respectively, and cultured with 10% FBS DMEM culture medium at 37℃ in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted from exosomes using TRIzol reagent (Invitrogen).
Approximately 1 µg of total RNA were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA). And then we performed the single-end sequencing (1x50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

treatment_protocol: Exosomes were isolated from the cell culture medium  using Total Exosome Isolation Kit (Invitrogen, California, United States) following the manufacturer’s instructions

tag: tissue

value: kidney

tag: cell line

value: primary cancer-associated fibroblasts derived from fresh RCC tissue of patient 1

tag: cell type

value: primary cancer-associated fibroblasts

tag: genotype

value: cancer-associated fibroblasts

tag: treatment

value: collecting exosomes from the cell culture medium


title: input_wt_21-24hr__#5

city: Martinsried

first: Jürg

last: Müller

state: Bavaria

address: Am Klopferspitz

country: Germany

institute: Max Planck Institute of Biochemistry

library_source: genomic

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of H3K36me2 enriched-regions and H3K27me3 enriched-regions.
The proportion of D. pseudoobscura reads as compared to D. melanogaster reads in input and in samples was used to normalize the ChIP-seq datasets for histone marks in embryos. Reference samples for normalization with D. pseudoobscura chromatin are indicated. Other samples were normalized based on total read number per million reads. Normalization factor for each sample is indicated.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: 21-24hr old embryos

growth_protocol: Drosophila embryos and larvae were grown on standard medium at 25˚C

extract_protocol:
Lysates were clarified from sonicated fixed nuclei (for embryos) and from sonicated fixed hand-dissected imaginal disc tissues (for 3rd instar larvae). Histone/Protein-DNA complexes were isolated with antibody. D. pseudoobscura chromatin was spiked in at a 1:5 ratio of dm / dp chromatin before the addition of the antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq kit.

value: 21-24hr old embryos

value: wt

tag: normalization factor


title: GFP_Overexpression_12_S5_R1_001.fastq.gz

city: Dallas

first: W. Lee

last: Kraus

state: TX

address: 5323 Harry Hines Blvd.

country: USA

institute: UT Southwestern Medical Center

description: merged

data_processing:
The RNA-seq reads were aligned to the hg38 human reference genome using TopHat a fast splice junction mapper for RNA-Seq reads using the ultra high-throughput short read aligner Bowtie (Langmead et al, 2009) .
Mapped reads were sorted and captured in bam files for further downstream analysis of differential gene expression and  bigwig files were generated to for presentation as browser tracks using custom R scripts.
Genome_build: hg38
Supplementary_files_format_and_content: BigWig

molecule: polyA RNA

source_name: MDA-MB-231 cell line

growth_protocol: All animal experiments were performed in compliance with the Institutional Animal Care and Use Committee (IACUC) at the UT Southwestern Medical Center.  Female NOD-scid-gamma (NSG) mice at 6-8 weeks of age were used

extract_protocol:
The frozen xenograft tumor tissues were pulverized using a tissue mill and lysed in Whole Cell Lysis Buffer (20 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% NP-40, 1% sodium deoxycholate, 0.1% SDS, 1 mM DTT, supplemented with protease and phosphatase inhibitors) for extraction of protein
Total RNA from seven xenograft tumor tissue of each group using the RNeasy Plus Kit (Qiagen, 74134) according to the manufacturer’s instructions were used to generate strand-specific RNA-seq libraries.  The RNA was then enriched for polyA+ RNA using Dynabeads Oligo(dT)25 (Invitrogen, 61002).  The polyA+ RNA was then used to generate strand-specific RNA-seq libraries as described previously (Zhong et al., 2011).  The RNA-seq libraries were subjected to QC analyses (i.e., number of PCR cycles required to amplify each library, the final library yield, and the size distribution of the final library DNA fragments) and sequenced using an Illumina HiSeq 2500 and NextSeq 500

treatment_protocol: To establish breast cancer xenografts, MDA-MB-231 cells engineered for Dox-inducible expression of GFP mRNA or lnc152 (5 x 106 in 100 uL) were injected subcutaneously into the flank of the mice in a 1:1 ratio PBS and Matrigel.  Ten days post-tumor cell injection, the mice were placed on a Dox-containing diet (625 mg/kg; Envigo)

tag: genotype/variation

value: GFP overexpression

tag: rna-seq

value: polyA-RNA


title: NF3-exo

value: primary normal fibroblasts derived from fresh  normal kidney tissue of patient 3

value: primary normal fibroblasts

value: normal fibroblasts


title: Lnc152_Overexpression_15_S12_R1_001.fastq.gz

description: merged

value: Lnc152 overexpression


title: Genomic DNA from endometrioid endometrial cancer_TY41

type: genomic

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

department: Pathology

country: Japan

institute: Keio University School of Medicine

description: Endometrioid endometrial cancer

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

scan_protocol: Hybridization fluorescence signals were read by the iScan reader using standard recommended Illumina scanner setting.

data_processing: Genome Studio methylation software

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: High-molecular-weight DNA was extracted from fresh frozen tissue samples using phenol–chloroform, followed by dialysis. Areas showing a tumor cell content of more than 80% were dissected from FFPE tissue samples using a toothpick under a microscope, avoiding contamination with non-cancerous epithelial cells, myometrial cells and infiltrating inflammatory cells. Subsequently, the genomic DNA was extracted from the microdissected specimens using a GeneRead FFPE Kit (QIAGEN GmbH, Hilden, Germany).

tag: sample type

value: FFPE


title: Genomic DNA from endometrioid endometrial cancer_TY34

description: Endometrioid endometrial cancer


title: input_wt_21-24hr__#2


title: GFP_Overexpression_10_S4_R1_001.fastq.gz

description: merged


title: Genomic DNA from endometrioid endometrial cancer_F9935

description: Endometrioid endometrial cancer


title: NF2-exo

value: primary normal fibroblasts derived from fresh  normal kidney tissue of patient 2


title: Genomic DNA from endometrioid endometrial cancer_TY50

description: Endometrioid endometrial cancer


title: GFP_Overexpression_41_S3_R1_001.fastq.gz

description: merged


title: input_wt_21-24hr__#1


title: GFP_Overexpression_9_S2_R1_001.fastq.gz

description: merged


title: input_wt_HaltereLeg_Larva__#14

source_name: haltere and 3rd leg imaginal discs from 3rd instar larvae


title: Genomic DNA from endometrioid endometrial cancer_TY18

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_TY17

description: Endometrioid endometrial cancer


title: input_wt_HaltereLeg_Larva__#13

value: haltere and 3rd leg imaginal discs from 3rd instar larvae


title: GFP_Overexpression_6_S1_R1_001.fastq.gz

description: merged

value: xenograft tumor


title: Genomic DNA from endometrioid endometrial cancer_TY39

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_16-810

description: Endometrioid endometrial cancer

value: Frozen


title: NF1-exo

value: kidney

value: primary normal fibroblasts derived from fresh  normal kidney tissue of patient 1


title: 1851030113-BC130CS5_S13 [scRNA-seq]

city: New Delhi

first: Sarita

last: Poonia

state: Delhi

address: IIITD

department: Computational Biology

country: India

institute: IIITD

data_processing:
RSEM index generated on hg19.
Read data aligned to index using RSEM/bowtie2.
Genomic mappings (GM) performed with RSEM/bowtie2.
Quantified gene expression levels in counts and TPM using RSEM-1.3.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count and TPM values for each sample.

source_name: Peripheral Blood of Cancer Patient

extract_protocol:
Circulating tumor cells enriched by ClearCell FX were captured by Polaris System (Fluidigm). PolyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System, Clontech #634936).
Amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina).
Paired-end NextSeq 74bp sequencing.

tag: subject id

tag: diagnosis

value: Breast cancer

tag: hormone receptor status

value: Circulating tumor cells (CTCs)


title: colon-derived activated Treg clone F1'

city: Nantes

first: Raluca

last: TEUSAN

address: IRS-UN - 8 quai Moncousu - BP 70721

country: France

institute: Inserm

data_processing:
Pipeline details have been published by Charpentier E et al. 2018 (10.21203/rs.3.pex-1336/v1). Pipeline are available :  https://bio.tools/3SRP
Genome_build: Hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: patient 4

growth_protocol: Clones were expanded using a polyclonal stimulation by  PHA (phyto-hemagglutinin) together with IL-2 and irradiated feeder cells.

extract_protocol:
mRNA was extracted from all samples at once (to avoid batch effects) using the NucleoSpin RNA kit (Macherey-Nagel) and quantified with a NanoDrop.
The libraries was prepared from 10 ng of total RNA in 4µl. The mRNA poly(A) tails are tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during template-switching reverse transcription. Barcoded cDNAs from multiple samples are then pooled, amplified and tagmented using a transposon-fragmentation approach which enriches for 3′ends of cDNA : 100ng of full-lentgth cDNAs are used as input to the Nextera DNA Sample Prep kit (ref FC-121-1030, Illumina) which enriches for 3′ends of cDNA. Size library is controlled on 2200 Tape Station Sytem (Agilent Technologies). A library of 350–800 bp length is run on an Illumina HiSeq 2500 using a Hiseq Rapid SBS Kit v2-50 cycles (ref FC-402-4022) and a Hiseq Rapid PE Cluster Kit v2 (ref PE-402-4002) according to manufacturer’s protocol (Denaturing and Diluting Libraries for the HiSeq® and GAIIx, Part # 15050107 v03 protocol, Illumina).
3’seq-RNA

treatment_protocol: Resting clones were used  3 to 4 weeks after a stimulation. Activated clones were resting clones stimulated for 4 hours with 0.5 mM of an agonistic anti-CD3 antibody  (OKT3)

tag: individual

value: patient 4

tag: disease state

value: colorectal cancer patient

value: colon

value: regulatory T cell

tag: t cell clone

value: activated Treg clone F1'


title: input_SceI48A_21-24hr__#6

value: 21-24hr old embryos


title: 1851030113-BC130CS4_S12 [scRNA-seq]


title: colon-derived activated Treg clone H4'

source_name: patient 5

value: patient 5

value: activated Treg clone H4'


title: Genomic DNA from endometrioid endometrial cancer_TY7

description: Endometrioid endometrial cancer

value: FFPE


title: colon-derived resting Treg clone F1'

value: resting Treg clone F1'


title: 1851030113-BC130CS3_S11 [scRNA-seq]


title: colon-derived resting Treg clone H4'

value: resting Treg clone H4'


title: input_SceI48A_13-17hr__#7

source_name: 13-17hr old embryos

value: 13-17hr old embryos


title: Genomic DNA from endometrioid endometrial cancer_TY10

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_19-121

description: Endometrioid endometrial cancer

value: Frozen


title: colon-derived activated Treg clone C3'

source_name: patient 6

value: patient 6

value: activated Treg clone C3'


title: input_SceI48A_13-17hr__#6


title: 1851030113-BC130CS2_S10 [scRNA-seq]

value: Breast cancer


title: colon-derived resting Treg clone C3'

value: resting Treg clone C3'


title: input_SceI48A_0-6hr__#7

source_name: 0-6hr old embryos

value: 0-6hr old embryos


title: 1851030113-BC130CS1_S9 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: colon-derived activated Treg clone B3'

source_name: patient 2

value: patient 2

value: colorectal cancer patient

value: colon

value: activated Treg clone B3'


title: input_SceI48A_0-6hr__#6


title: 1851030001-BC297CS8_S24 [scRNA-seq]


title: colon-derived resting Treg clone B3'

value: regulatory T cell

value: resting Treg clone B3'


title: input_SceI48A_21-24hr__#7

value: 21-24hr old embryos


title: input_SceI48A_21-24hr__#8


title: colon-derived activated DP8a clone H20

value: patient 5

value: activated DP8a clone H20


title: input_calyC131S_21-24hr__#7


title: 1851030001-BC297CS6_S22 [scRNA-seq]


title: 1851030001-BC297CS7_S23 [scRNA-seq]


title: colon-derived resting DP8a clone H20

value: resting DP8a clone H20


title: Genomic DNA from endometrioid endometrial cancer_19-319

description: Endometrioid endometrial cancer

value: Frozen


title: input_calyC131S_21-24hr__#6


title: 1851030001-BC297CS5_S21 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_16-526

description: Endometrioid endometrial cancer


title: colon-derived activated DP8a clone H9

value: activated DP8a clone H9


title: 1851030001-BC297CS4_S20 [scRNA-seq]


title: input_calyC131S_13-17hr__#7

value: 13-17hr old embryos


title: colon-derived resting DP8a clone H9

value: resting DP8a clone H9


title: 1851030001-BC297CS3_S19 [scRNA-seq]

value: Breast cancer


title: input_calyC131S_13-17hr__#6


title: colon-derived activated DP8a clone F1

value: patient 4

value: activated DP8a clone F1


title: 1851030001-BC297CS2_S18 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: input_calyC131S_0-6hr__#7

value: 0-6hr old embryos


title: Genomic DNA from endometrioid endometrial cancer_TY2

description: Endometrioid endometrial cancer

value: FFPE


title: colon-derived resting DP8a clone F1

value: colorectal cancer patient

value: colon

value: resting DP8a clone F1


title: Genomic DNA from endometrioid endometrial cancer_19-083

description: Endometrioid endometrial cancer


title: input_calyC131S_0-6hr__#6


title: Genomic DNA from endometrioid endometrial cancer_19-063

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_18-115

description: Endometrioid endometrial cancer


title: 1851030001-BC297CS1_S17 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_17-102

description: Endometrioid endometrial cancer


title: colon-derived activated DP8a clone D1

source_name: patient 3

value: patient 3

value: regulatory T cell

value: activated DP8a clone D1


title: 1851013039_CS6_S70 [scRNA-seq]

value: ER+/PR+/HER-


title: colon-derived resting DP8a clone D1

value: resting DP8a clone D1


title: input_Asx0_21-24hr__#10

value: 21-24hr old embryos


title: input_Asx0_21-24hr__#9


title: 1851013039_CS47_S67 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_18-121

description: Endometrioid endometrial cancer

value: Frozen


title: colon-derived resting DP8a clone B7

value: patient 2

value: resting DP8a clone B7


title: colon-derived activated DP8a clone B7

value: activated DP8a clone B7


title: input_Asx0_21-24hr__#8


title: 1851013039_CS43_S63 [scRNA-seq]

value: Breast cancer


title: 1851013039_CS41_S61 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: Genomic DNA from endometrioid endometrial cancer_16-19

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_16-51

description: Endometrioid endometrial cancer


title: input_Asx0_21-24hr__#5


title: 1851013039_CS40_S60 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_16-32

description: Endometrioid endometrial cancer


title: colon-derived resting DP8a clone A10

source_name: patient 1

value: patient 1

value: resting DP8a clone A10


title: Genomic DNA from endometrioid endometrial cancer_16-316

description: Endometrioid endometrial cancer


title: colon-derived activated DP8a clone A10

value: colorectal cancer patient

value: activated DP8a clone A10


title: Genomic DNA from endometrioid endometrial cancer_16-87

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_15-160

description: Endometrioid endometrial cancer


title: blood-derived activated Foxp3 clone 2149-7

source_name: donor 4

value: donor 4

value: healthy volunteer

value: blood

value: activated Foxp3 clone 2149-7


title: 1851013039_CS37_S56 [scRNA-seq]

value: ER+/PR+/HER-


title: H2Aub1_wt_Wing_Larva_rep1_#13

source_name: wing imaginal discs form 3rd instar larvae

value: wt

tag: antibodies

value: H2Aub1 (cell signaling (#8240))


title: 1851013039_CS36_S55 [scRNA-seq]


title: blood-derived resting FoxP3 clone 2149-7

value: regulatory T cell

value: resting FoxP3 clone 2149-7


title: blood-derived activated Foxp3 clone 1986-19

source_name: donor 3

value: donor 3

value: activated Foxp3 clone 1986-19


title: 1851013039_CS34_S53 [scRNA-seq]

value: Breast cancer


title: Genomic DNA from endometrioid endometrial cancer_15-064

description: Endometrioid endometrial cancer

value: Frozen


title: 1851013039_CS39_S58 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: blood-derived resting FoxP3 clone 1986-19

value: resting FoxP3 clone 1986-19


title: H2Aub1_wt_13-17hr_rep2_#7

value: 13-17hr old embryos


title: Genomic DNA from endometrioid endometrial cancer_09-055

description: Endometrioid endometrial cancer


title: 1851013039_CS33_S52 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_15-040

description: Endometrioid endometrial cancer


title: H2Aub1_wt_Wing_Larva_rep2_#14

value: wing imaginal discs form 3rd instar larvae


title: blood-derived activated Foxp3 clone 62-6

source_name: donor 2

value: donor 2

value: activated Foxp3 clone 62-6


title: 1851013039_CS32_S51 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_14-159

description: Endometrioid endometrial cancer


title: H2Aub1_wt_13-17hr_rep1_#6


title: H2Aub1_wt_0-6hr_rep2_#7

value: 0-6hr old embryos


title: 1851013039_CS31_S50 [scRNA-seq]


title: blood-derived activated Foxp3 clone 60-4

source_name: donor 1

value: donor 1

value: healthy volunteer

value: blood

value: activated Foxp3 clone 60-4


title: H2Aub1_wt_0-6hr_rep1_#6

value: wt

value: H2Aub1 (cell signaling (#8240))


title: Genomic DNA from endometrioid endometrial cancer_13-191

description: Endometrioid endometrial cancer


title: blood-derived resting FoxP3 clone 62-6

value: regulatory T cell

value: resting FoxP3 clone 62-6


title: Genomic DNA from endometrioid endometrial cancer_14-083

description: Endometrioid endometrial cancer


title: blood-derived resting FoxP3 clone 60-4

value: resting FoxP3 clone 60-4


title: H2Aub1_wt_21-24hr_rep3_#10

source_name: 21-24hr old embryos

value: 21-24hr old embryos


title: Genomic DNA from endometrioid endometrial cancer_16-14

description: Endometrioid endometrial cancer

value: Frozen


title: input_Asx0_21-24hr__#11


title: Genomic DNA from endometrioid endometrial cancer_15-142

description: Endometrioid endometrial cancer


title: blood-derived activated DP8a clone 2122-26

value: donor 4

value: activated DP8a clone 2122-26


title: 1851013039_CS29_S47 [scRNA-seq]

value: Breast cancer

value: ER+/PR+/HER-

value: Circulating tumor cells (CTCs)


title: Genomic DNA from endometrioid endometrial cancer_15-012

description: Endometrioid endometrial cancer


title: blood-derived resting DP8a clone 2122-26

value: resting DP8a clone 2122-26


title: Genomic DNA from endometrioid endometrial cancer_14-082

description: Endometrioid endometrial cancer


title: 1851013039_CS3_S48 [scRNA-seq]


title: 1851013039_CS25_S43 [scRNA-seq]


title: blood-derived resting DP8a clone 1986-9

value: donor 3

value: resting DP8a clone 1986-9


title: 1851013039_CS30_S49 [scRNA-seq]


title: H2Aub1_wt_HaltereLeg_Larva_rep1_#13

value: haltere and 3rd leg imaginal discs from 3rd instar larvae


title: 1851013039_CS24_S42 [scRNA-seq]


title: blood-derived activated DP8a clone 1986-9

value: healthy volunteer

value: blood

value: activated DP8a clone 1986-9


title: blood-derived activated DP8a clone 62-6

value: donor 2

value: regulatory T cell

value: activated DP8a clone 62-6


title: Genomic DNA from endometrioid endometrial cancer_12-021

description: Endometrioid endometrial cancer


title: 1851013039_CS23_S41 [scRNA-seq]


title: 1851013039_CS22_S40 [scRNA-seq]


title: blood-derived activated DP8a clone 60-2

value: donor 1

value: activated DP8a clone 60-2


title: Genomic DNA from endometrioid endometrial cancer_13-176

description: Endometrioid endometrial cancer

value: Frozen


title: H2Aub1_SceI48A_13-17hr_rep2_#7

value: 13-17hr old embryos

value: H2Aub1 (cell signaling (#8240))


title: 1851013039_CS21_S39 [scRNA-seq]

value: Breast cancer

value: ER+/PR+/HER-


title: Genomic DNA from endometrioid endometrial cancer_13-149

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_12-100

description: Endometrioid endometrial cancer


title: 1851013039_CS26_S44 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: Genomic DNA from endometrioid endometrial cancer_12-017

description: Endometrioid endometrial cancer


title: 1851013039_CS2_S37 [scRNA-seq]


title: H2Aub1_SceI48A_13-17hr_rep1_#6


title: GDM rep12

city: Guangzhou

first: Bin

last: Liu

address: Guangzhou, 510080, PR China

department: Department of Obstetrics and Gynecology

institute: the First Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina Bcl2FastQ  software used for basecalling
Raw reads were processed to trim barcode and 3’ adaptor sequences, as well as discarded low-quality bases using FASTX ToolKit. Human genome sequence (GRCh38) obtained from the Ensembl database was used to build index by bowtie, and then the remaining reads were aligned to miRBase v21 miRNA sequences.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: plasma sEVs

extract_protocol:
Exosomal RNA was was harvested using Trizol reagent. Qualified RNA was subjected for library preparation using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: condition

value: gestational diabetes mellitus

tag: gestational age

value: 24-28 weeks of gestation

value: plasma sEVs

tag: molecule subtype

value: microRNA


title: H2Aub1_SceI48A_0-6hr_rep2_#7

tag: tissue

value: 0-6hr old embryos


title: H2Aub1_wt_HaltereLeg_Larva_rep2_#14

source_name: haltere and 3rd leg imaginal discs from 3rd instar larvae

tag: genotype

value: wt


title: Genomic DNA from endometrioid endometrial cancer_12-069

description: Endometrioid endometrial cancer


title: 1851013039_CS19_S36 [scRNA-seq]

source_name: Peripheral Blood of Cancer Patient

tag: cell type


title: GDM rep11


title: blood-derived resting DP8a clone 60-2

value: healthy volunteer

value: blood

value: resting DP8a clone 60-2


title: Genomic DNA from endometrioid endometrial cancer_13-034

description: Endometrioid endometrial cancer


title: GDM rep10


title: H2Aub1_SceI48A_0-6hr_rep1_#6

tag: normalization factor


title: blood-derived resting DP8a clone 62-6

value: donor 2

value: regulatory T cell

value: resting DP8a clone 62-6


title: H2Aub1_calyC131S_21-24hr_rep2_#7

value: 21-24hr old embryos


title: 1851013039_CS17_S34 [scRNA-seq]


title: GDM rep9


title: Genomic DNA from endometrioid endometrial cancer_12-007

description: Endometrioid endometrial cancer

value: Frozen


title: 1851013039_CS16_S33 [scRNA-seq]

value: Breast cancer


title: GDM rep8


title: Genomic DNA from endometrioid endometrial cancer_13-072

description: Endometrioid endometrial cancer


title: Genomic DNA from endometrioid endometrial cancer_11-200

description: Endometrioid endometrial cancer


title: 1851013039_CS18_S35 [scRNA-seq]

value: ER+/PR+/HER-


title: GDM rep7


title: H2Aub1_calyC131S_13-17hr_rep1_#6

value: 13-17hr old embryos

value: H2Aub1 (cell signaling (#8240))


title: 1851013039_CS14_S31 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: GDM rep6

value: gestational diabetes mellitus

value: 24-28 weeks of gestation

value: plasma sEVs


title: Genomic DNA from endometrioid endometrial cancer_10-123

description: Endometrioid endometrial cancer


title: H2Aub1_calyC131S_21-24hr_rep1_#6


title: Genomic DNA from endometrioid endometrial cancer_13-157

description: Endometrioid endometrial cancer


title: H2Aub1_calyC131S_13-17hr_rep2_#7


title: Genomic DNA from endometrioid endometrial cancer_10-032

description: Endometrioid endometrial cancer


title: H2Aub1_calyC131S_0-6hr_rep2_#7

value: 0-6hr old embryos


title: shSuv4-20h2_#2_3

city: Frankfurt am Main

first: Mohammed

middle: Hossameldin

last: Mosa

state: Hessen

address: Paul-Ehrlich Str. 42-44

hyb_protocol: Labeled DNA Samples were hybridized for 24 hours at 67°C and 20 rpm rotation speed according to manufacturer´s protocol (Agilent Technologies, Santa Clara, CA, USA).

scan_protocol: Microarray slides were scanned using a G2565CA microarray scanner (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The scanned images were analyzed with the Feature Extraction Software 12.0.0 (Agilent).

organism: Mus musculus

source_name: tumor organoids (small intestine)

label_protocol: 1µg of the isolated genomic DNA was digested and labeled by random primer with Cyanine 5-UTP (liver tumor) or Cyanine 3-UTP (reference: liver) using the SureTag Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) according to the manufacturer´s protocol.

growth_protocol: Organoids were grown and maintaied as reported before (Mosa et.al, 2020)

extract_protocol: Genomic DNA was isolated from tumor organoids and kidney (control) according to standard phenol-chloroform extraction protocol.

treatment_protocol: To induce the expression of the doxycycline-inducible hairpins, organoids were cultured for 4 days in the presence of 0.5 µg/ml doxycycline in the culture medium.

value: Suv4-20h2 knockdown

tag: gender

value: male

source_name: kidney

value: young healthy bl6 mouse


title: 1851013039_CS13_S30 [scRNA-seq]


title: shSuv4-20h2_#2_2


title: H2Aub1_calyC131S_0-6hr_rep1_#6


title: Genomic DNA from endometrioid endometrial cancer_11-026

description: Endometrioid endometrial cancer


title: 1851013039_CS15_S32 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_10-022

description: Endometrioid endometrial cancer


title: shCtrl APT

value: Control


title: mESC_ChIP-seq_G4_TERRA_KD_rep2

city: Taipei

first: Hsueh-Ping

last: Chu

address: No. 1 Sec. 4 Roosevelt Road

department: Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

data_processing:
For ChIP-seq and ATAC-seq paired-end reads, adapter sequence and low-quality reads were removed by Trimgalore (v0.5.0) using options: --fastq -q 30.
Paired-end reads were mapped to the Mus musculus mm10 reference genome using bowtie2 (v2.3.4.1) with default parameters.
BAM files were sorted and deduplicated by SamTools (v1.9)
Bigwig files were generated by deepTools (v3.1.1) bamCoverage with parameters: --normalizeUsing CPM, --centerReads, --extendReads 150.
Normalized bigwig files were generated by deepTools (v3.1.1) bamCompare with parameters: --scaleFactorsMethod None, --normalizeUsing CPM, --smoothLength 250, --centerReads.
For ATRX, H3K9me3, and G4, peaks were called by MACS1.4 with p value < 0.01 cutoff and default parameters, using input as control. For ATAC-seq, peak calling was performed with MACS2 with p value < 0.01 cutoff.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig and peak bed

source_name: TERRA KD mESCs

growth_protocol: Cells were cultured in regular ES medium (15% FBS) with LIF

extract_protocol:
For G4 ChIP-seq experiments, TERRA KD or scramble KD cells were fixed with 1% formaldehyde for 5 min at RT. Chromatin were sonicated to ~250 bp by Covaris S220. Immunoprecipitations were performed overnight at 4℃. Sample without antibody capture was used as input control. After incubation overnight, immunocomplexes were incubated with Dynabeads Protein G (Thermo Fisher Scientific, 10004D) for 2 hours at 4℃. Immunocomplexes were washed by RIPA buffer containing 500 mM of LiCl. Immunoprecipitated DNA were purified by using PCR DNA isolation system (Viogene, GP1001) following manufacturer' s protocol.
For ChIP-seq, DNA library were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to manufacturer' s protocol.

treatment_protocol: TERRA LNA knockdown for 12 hours

tag: strain background

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

tag: capture antibody

value: Anti-DNA/RNA G-quadruplex [BG4] (absolute antibody, Ab00174-1.1)

tag: knockdown

value: TERRA LNA knockdown for 12 hours


title: mESC_ChIP-seq_G4_scramble_KD_rep2

treatment_protocol: scramble LNA knockdown for 12 hours

value: scramble LNA knockdown for 12 hours


title: Genomic DNA from endometrioid endometrial cancer_10-116

description: Endometrioid endometrial cancer

tag: sample type

value: Frozen


title: Gli1Cre uninjured

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

description:
Mesenchymal cells
Nox

library_source: transcriptomic single cell

data_processing:
Reads were aligned against the mouse genome (mm10) and counted by StarSolo.
Count matrix from StarSolo output was processed using Seurat R package (version 4.1.0).
Low quality cells and potential doublets were discarded according to UMIs content (> 20000), number of detected genes (<1000), and percent of UMIs from mitochondrial genes among all UMIs (>15%).
Raw counts were log-normalized and scaled for computing PCA and performing kNN clustering.
Assembly: mm10
Supplementary files format and content: starsolo outputs

source_name: Lung

extract_protocol: 10x Genomics Single Cell 3′ v3.1 RNA-seq kit.

value: Lung

value: GLI1+ cells

value: Gli1Cre-ERT2; tdTomatoflox

tag: treatment

value: Uninjured


title: GDM rep2

value: gestational diabetes mellitus

value: 24-28 weeks of gestation

value: microRNA


title: 1851013039_CS1_S26 [scRNA-seq]

tag: subject id

tag: diagnosis

value: Breast cancer

tag: hormone receptor status

value: ER+/PR+/HER-

value: Circulating tumor cells (CTCs)


title: Genomic DNA from endometrioid endometrial cancer_09-073

description: Endometrioid endometrial cancer


title: wt_13-17hr_rep2

data_processing:
Reads from fastq files were aligned to the dm6 genome (and to the D. pseudoobscura dp3 genome for subsequent normalization) using STAR (Dobin et al., 2013). Only sequences that mapped uniquely to the genome with a maximum of two mismatches were considered for further analyses.
Bam files were used as inputs to run Bioconductor packages.
The STAN Bioconductor package (Zacher et al., 2014) was used to define the location of regions associated with low, intermediate and high DNA accessibility in wild-type embryos.
Datasets were normalized based on total read number per million reads.
Assembly: dm6
Supplementary files format and content: Normalized bigwig files (bin size = 1) were generated with deepTools (Ramirez et al., 2016).

source_name: 13-17hr old embryos

growth_protocol: Drosophila embryos were grown on standard medium at 25˚C

extract_protocol:
Nuclei were purified from embryos of the desired genotype and 25000 nuclei were used for the tagmentation reaction.
Libraries were prepared according to Active Motif's instructions accompanying the ATAC-seq kit (#53150).

value: 13-17hr old embryos

value: wt


title: mESC_ChIP-seq_H3K9me3_TERRA_KD_rep2

extract_protocol:
For ATRX and H3K9me3 ChIP-seq experiments, TERRA KD or scramble KD cells were fixed with 1% formaldehyde for 5 min at RT. Chromatin were sonicated to 200-300 bp by Covaris S220. Immunoprecipitations were performed overnight at 4℃. Sample without antibody capture was used as input control. After incubation overnight, immunocomplexes were incubated with Dynabeads Protein G (Thermo Fisher Scientific, 10004D) for 2 hours at 4℃. Immunocomplexes were washed by RIPA buffer containing 500 mM of NaCl. Immunoprecipitated DNA were purified by using PCR DNA isolation system (Viogene, GP1001) following manufacturer' s protocol.
For ChIP-seq, DNA library were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) according to manufacturer' s protocol.

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells

value: Rabbit polyclonal antiH3K9me3 (abcam, ab8898)


title: mESC_ChIP-seq_H3K9me3_scramble_KD_rep2

value: scramble LNA knockdown for 12 hours


title: GDM rep3

value: plasma sEVs


title: wt_13-17hr_rep1


title: Genomic DNA from endometrioid endometrial cancer_08-162

description: Endometrioid endometrial cancer

value: Frozen


title: 1851009049_CS9_S25 [scRNA-seq]


title: 1851009049_CS8_S24 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_06-111

description: Endometrioid endometrial cancer


title: NGT rep12

value: normal glucose tolerance


title: H2Aub1_Asx0_21-24hr_rep2_#10

value: 21-24hr old embryos

tag: antibodies

value: H2Aub1 (cell signaling (#8240))


title: mESC_ChIP-seq_H3K9me3_TERRA_KD_rep1

value: TERRA LNA knockdown for 12 hours


title: GDM rep1

tag: condition

value: gestational diabetes mellitus

value: 24-28 weeks of gestation


title: calyC131S_13-17hr_rep1


title: 1851009049_CS7_S23 [scRNA-seq]

value: Breast cancer


title: mESC_ChIP-seq_H3K9me3_scramble_KD_rep1


title: Genomic DNA from endometrioid endometrial cancer_08-148

description: Endometrioid endometrial cancer


title: NGT rep11

tag: gestational age

value: microRNA


title: Genomic DNA from endometrioid endometrial cancer_08-036

description: Endometrioid endometrial cancer


title: 1851009049_CS5_S22 [scRNA-seq]

value: ER+/PR+/HER-

value: Circulating tumor cells (CTCs)


title: mESC_ChIP-seq_ATRX_TERRA_KD_rep2

value: Rabbit polyclonal antiATRX (Santa Cruz, sc-15408)


title: Pre-sort

city: Houston

first: Jeffrey

middle: J.

last: Tabor

address: 6100 Main Street

department: Bioengineering

institute: Rice University

data_processing:
Library strategy: DNA-seq
Image analysis and base calling were conducted by the MiSeq Control Software on the Illumina MiSeq instrument (performed at GENEWIZ, Inc.).
Raw Illumina reads were checked for adapters and quality via FastQC (performed at GENEWIZ, Inc.).
Raw Illumina reads were trimmed of their adapters using Trimmomatic v. 0.36 (performed at GENEWIZ, Inc.).
Raw sequence data (.bcl files) was converted to fastq files and de-multiplexed using Illumina bcl2fastq (performed at GENEWIZ, Inc.).
Forward and reverse reads were combined using FLASH 1.2.11 as part of a custom analysis pipeline (Github: https://github.com/krbrink/PhoPQ_hAMP_sort-seq).
DNA sequences were translated in silico to amino acid sequences using BioPython. Translated sequences were counted and these counts were divided by the total number of reads to obtain frequency values using a custom analysis pipeline (Github: https://github.com/krbrink/PhoPQ_hAMP_sort-seq).
Supplementary_files_format_and_content: pre-sort_processed.csv is a comma-separated values file that lists the sequences, read counts, and frequencies of all detected peptides present in the initial library prior to sorting. Entry for which no translation is provided (empty string) represents reads for all sequences where no stop codon was encoded. Entry marked by an asterisk represents reads for all sequences where a stop codon is located in place of a peptide (no peptide control).

organism: Escherichia coli K-12

source_name: Bacterial culture

growth_protocol: A plasmid library encoding surface-displayed human AMPs and human AMP variants was transformed into KB1 (E. coli K-12 BW30007 with genomically integrated copies of S. Typhimurium phoP and phoQ) via electroporation and plated on LB agar.

extract_protocol:
Plasmid DNA was purified from the sample using a Qiagen Plasmid Plus Midiprep kit and DNA concentration was measured using a Qubit 4 Fluorometer (Invitrogen).
Phusion PCR reactions (NEB) were used to generate amplicons from purified plasmid DNA. For each sample, two 50 μL reactions were performed using 100 ng of plasmid DNA template and 0.2 μM each of forward and reverse primers. Forward and reverse primer overhangs introduced partial Illumina adapters to enable compatibility with the GENEWIZ Amplicon-EZ service.    After an initial denaturation step of 30 s at 98°C, 12 amplification cycles were performed of 10 s at 98°C, 30 s at 68°C, and 15 s at 72°C. A final elongation step was performed for 10 min at 72°C. PCR reactions were combined and purified using DNA purification spin columns (EconoSpin).    Subsequent sample preparation steps were performed at GENEWIZ, Inc. through their Amplicon-EZ service. DNA library preparation, clustering, and sequencing were performed using NEBNext Ultra DNA Library Prep kit following the manufacturer’s recommendations (Illumina). Adapter-ligated DNA was indexed and enriched by limited cycle PCR.    DNA was loaded on the Illumina MiSeq instrument according to manufacturer's instructions and sequenced using a 2x250 paired-end configuration.

treatment_protocol: The KB1 colonies were scraped into 50 mL modified M9 media (lacking CaCl2 and MgSO4) and pelleted by centrifugation at 4000 r.p.m. and 4°C for 10 min and decanting the supernatant. Pellets were washed twice by resuspending in 25 mL modified M9 media and following a similar centrifugation protocol. The final pellet was resuspended in 25 mL modified M9 media. Approximately 21 mL of this suspension was pelleted as above and stored at -30°C prior to purification.

tag: strain

tag: molecule subtype

value: plasmid DNA


title: mESC_ChIP-seq_ATRX_scramble_KD_rep2

value: CAST/Ei x 129/Sv/Jae

value: Embryonic stem cells


title: NGT rep9

tag: tissue


title: Genomic DNA from endometrioid endometrial cancer_05-091

description: Endometrioid endometrial cancer


title: Sort-seq

data_processing:
Library strategy: Sort-seq
Image analysis and base calling were conducted by the MiSeq Control Software on the Illumina MiSeq instrument (performed at GENEWIZ, Inc.).
Raw Illumina reads were checked for adapters and quality via FastQC (performed at GENEWIZ, Inc.).
Raw Illumina reads were trimmed of their adapters using Trimmomatic v. 0.36 (performed at GENEWIZ, Inc.).
Raw sequence data (.bcl files) was converted to fastq files and de-multiplexed using Illumina bcl2fastq (performed at GENEWIZ, Inc.).
Forward and reverse reads were combined using FLASH 1.2.11 as part of a custom analysis pipeline (Github: https://github.com/krbrink/PhoPQ_hAMP_sort-seq).
Each read was assigned to a fluorescence bin using custom code and translated in silico to its corresponding amino acid sequence using BioPython. For each bin, reads for each translated sequence (peptide) were counted and divided by the total number of reads in that bin to obtain a frequency value. (Github: https://github.com/krbrink/PhoPQ_hAMP_sort-seq)
Frequency values for each fluorescence bin were weighted by the percentage of the cell population in that fluorescence bin during fluorescence-activated cell sorting (Sony SH800S FACS). These weighted frequency values approximate the original fluorescence distributions of each peptide. To estimate mean fluorescence, lognormal distribution parameters mu and sigma were calculated based on the fluorescence distribution of each peptide and the fluorescence bin centers in logarithmic space. The mean fluorescence of each peptide was calculated using mu and sigma assuming a lognormal distribution. Fold change was calculated by dividing the mean fluorescence for a given peptide by the mean fluorescence of a control displaying no peptide. (Github:  https://github.com/krbrink/PhoPQ_hAMP_sort-seq)
Bootstrapping was performed to assess the robustness of our calculated fluorescence means. We performed 1,000 iterations in which each fluorescence bin was populated with peptides chosen randomly with replacement based on their frequency in the original dataset. Mean fluorescence was calculated for each peptide in each iteration as with the original dataset. We summarized the variability across 1,000 bootstrapping iterations using the width of the 5th to 95th percentile range of mean fluorescence values. We divided this range by the mean fluorescence value calculated from the original dataset to obtain a normalized 5th-95th percentile range. Peptides with a normalized 5th-95th percentile range greater than or equal to 0.4 were removed. Peptides with fewer than 100 reads across all eight fluorescence bins were also removed, as were peptides with a fold change of activation lower than that of an autofluorescence-only control. (Github: https://github.com/krbrink/PhoPQ_hAMP_sort-seq)
Supplementary_files_format_and_content: post-sort_processed.csv is a comma-separated values file that lists the sequences, read counts, and frequencies of all detected peptides present in the library after completing the sort-seq protocol. No fluorescence gating was applied to this sort sample, enabling us to analyze the effect of the sort-seq experimental protocol on library diversity. Entry for which no translation is provided (empty string) represents reads for all sequences where no stop codon was encoded. Entry marked by an asterisk represents reads for all sequences where a stop codon is located in place of a peptide (no peptide control).    sort-seq_results_processed.csv is a comma-separated values file that contains read count, frequency, weighted frequency, and fold change data for all peptides that passed quality control. Entry marked by an asterisk represents reads for all sequences where a stop codon is located in place of a peptide (no peptide control).

growth_protocol: Cells were grown in modified M9 media that lacks CaCl2 and MgSO4 and is supplemented with 1 mM MgCl2.

extract_protocol:
Minipreps were performed to isolate plasmid DNA from the cell pellets, and DNA concentrations were measured using a Qubit 4 Fluorometer (Invitrogen).
Phusion PCR reactions (NEB) were used to generate amplicons from purified plasmid DNA. For each sample, two 50 μL reactions were performed using 100 ng of plasmid DNA template and 0.2 μM each of forward and reverse primers. Forward and reverse primers were used to introduce fluorescence bin-specific 10 bp barcode sites. These barcodes enabled multiplexed sequencing of samples from all sort-seq fluorescence bins.    After an initial denaturation step of 30 s at 98°C, 12 amplification cycles were performed of 10 s at 98°C, 30 s at 68°C, and 15 s at 72°C. A final elongation step was performed for 10 min at 72°C. For each fluorescence bin sample, the two PCR reactions were combined and purified using DNA purification spin columns (EconoSpin). DNA concentrations were measured using a Qubit 4 Fluorometer (Invitrogen) and samples for each fluorescence bin were combined in equimolar concentrations to generate one sample for NGS.    Subsequent sample preparation steps were performed at GENEWIZ, Inc. through their custom short-read amplicon service. DNA library preparation was performed using NEBNext Ultra DNA Library Prep kit following the manufacturer's recommendations (Illulmina). The DNA library was validated using TapeStation (Agilent Technologies) and quantified using Qubit 2.0 Fluorometer and qPCR.    DNA was loaded on the Illumina MiSeq instrument according to manufacturer's instructions and sequenced using a 2x250 paired-end configuration.

treatment_protocol: One 50 μL frozen aliquot of the KB1 human AMP library was used to inoculate a 14 mL culture tube containing 3 mL of modified M9 media supplemented with 1 mM MgCl2, which was grown at 37°C and 250 r.p.m for 2 h. The optical density (OD600) of these cultures was measured using a Cary50 ultraviolet-visible spectrophotometer (Agilent, Inc.). The library was diluted to an initial OD600 = 0.001 in a 14 mL culture tube containing 3 mL fresh modified M9 media supplemented with 1 mM MgCl2 and 500 μM isopropyl-ß-D-1-thiogalactoside (IPTG). Cultures were grown at 37°C and 250 r.p.m for 3 h and then placed on ice to arrest growth.    Cells were sorted into 8 logarithmically-spaced fluorescence bins using a Sony SH800S cell sorter. 100,000 cells were collected for each fluorescence bin and for a control bin in which no fluorescence gating was applied. Cells were sorted into 3 mL cold LB media, which was then added to 47 mL room-temperature LB for a total culture volume of 50 mL. Each culture was grown for approximately 6 hours at 37°C and 250 r.p.m. until reaching an OD600 = 0.3 – 0.4. Cells were pelleted and pellets were stored at -30°C overnight prior to purification.


title: 1851009049_CS17_S20 [scRNA-seq]

tag: cell type


title: NGT rep8


title: 1851009049_CS4_S21 [scRNA-seq]


title: mESC_ChIP-seq_ATRX_TERRA_KD_rep1


title: GDM rep4


title: NGT rep10


title: NGT rep7


title: 1851009049_CS15_S18 [scRNA-seq]


title: mESC_ChIP-seq_ATRX_scramble_KD_rep1

value: scramble LNA knockdown for 12 hours


title: 1851009049_CS16_S19 [scRNA-seq]


title: NGT rep6

value: plasma sEVs


title: mESC_ChIP-seq_input_TERRA_KD_rep2

description: TERRA KD input rep2 specific to TERRA KD ATRX and H3Kme3 ChIP-seq rep2


title: Genomic DNA from endometrioid endometrial cancer_09-030

description: Endometrioid endometrial cancer

value: Frozen


title: mESC_ChIP-seq_input_scramble_KD_rep2

description: scramble KD input rep2 specific to scramble KD ATRX and H3Kme3 ChIP-seq rep2


title: NGT rep5

value: normal glucose tolerance


title: mESC_ChIP-seq_input_TERRA_KD_rep1

description: TERRA KD input rep1 specific to TERRA KD ATRX and H3K9me3 ChIP-seq rep1


title: 1851009049_CS12_S16 [scRNA-seq]


title: NGT rep4


title: 1851009049_CS11_S15 [scRNA-seq]


title: NGT rep3


title: 1851009049_CS14_S17 [scRNA-seq]


title: NGT rep2


title: P2-4

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description: Paired End

data_processing:
SOAPnuke v.1.5.2 was used to filter reads with adapters, reads with unknown bases more than 10%, low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read)
HiSat2 used for allignment using hg38 build and Homo Sapien GRCh38 NCBI GTF file. FeatureCounts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-deliniated files containing either raw counts from FeatureCounts or normalized counts from DESeq2

source_name: HAP1 - Human Cell Line

growth_protocol: These cell lines were maintained in IMDM media (Lonza Walkersville, 12-722F) supplemented with 10% FBS and 100ug/ml penicillin and streptomycin. The cell cultures were grown at 37°C in a 10% CO2 incubator.

extract_protocol:
The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

tag: genotype

tag: cell line


title: 1850061049-CS8_S47 [scRNA-seq]


title: P2-3

description: Paired End


title: shSuv4-20h2_#2_1

value: Suv4-20h2 knockdown

tag: gender

value: male

value: young healthy bl6 mouse


title: NGT rep1


title: 1850061049-CS6_S45 [scRNA-seq]


title: P2-2

description: Paired End


title: MCF7-UBE2T-A9 replicate 3

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

description:
UBE2T A9 (shRNA#2)
F12

data_processing:
The base calling was performed using RTA 1.18.64.0
Reads were aligned to mm10 genome index and GRCH38 annotations using tophat version 2.1.0  with parameters -T -G mm10.gtf
Aligned read counts are estimated from alignment file and GRCH38 gtf using Htseq-count  version 0.6.0.
Genome_build: GRCH38
Supplementary_files_format_and_content: Raw read counts in .txt format

source_name: MCF7 cell line

growth_protocol: T47D and MCF7 cells stably expressing two individual shRNAs against UBE2T were grown in RPMI medium and DMEM medium respectively with 10% Fetal bovine serum and Penicilline and Streptomycin at  37 C under 5% CO2 condition.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instructions.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX or Agilent Bioanalyzer. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

treatment_protocol: T47D and MCF7 cells stably expressing two individual shRNAs against UBE2T were used for preparing the total RNA and to perfrom RNA Seq.


title: 1850061049-CS2_S12 [scRNA-seq]


title: GDM rep5

value: gestational diabetes mellitus


title: mESC_ChIP-seq_input_scramble_KD_rep1

description: scramble KD input rep1 specific to scramble KD ATRX and H3K9me3 ChIP-seq rep1

tag: strain background

tag: capture antibody


title: P2-1

description: Paired End


title: 1851009049_CS10_S14 [scRNA-seq]


title: MCF7-UBE2T-A9 replicate 2

description:
UBE2T A9 (shRNA#2)
F11


title: 1851013039_CS12_S29 [scRNA-seq]


title: Genomic DNA from endometrioid endometrial cancer_08-069

description: Endometrioid endometrial cancer

tag: sample type


title: 1850061049_CS46_S12 [scRNA-seq]


title: 1851013039_CS11_S28 [scRNA-seq]


title: MCF7-UBE2T-A9 replicate 1

description:
UBE2T A9 (shRNA#2)
F10

tag: treatment


title: C2-4

description: Paired End


title: 1850061049_CS31_S11 [scRNA-seq]

tag: subject id


title: MCF7-UBE2T-A6 replicate 3

description:
UBE2T A6 (shRNA#1)
F6


title: 1850061049_CS29_S9 [scRNA-seq]

tag: diagnosis


title: C2-3

description: Paired End


title: C2-2

description: Paired End


title: MCF7-UBE2T-A6 replicate 2

description:
UBE2T A6 (shRNA#1)
F5


title: 1850061049_CS28_S8 [scRNA-seq]

tag: hormone receptor status


title: Genomic DNA from cancer tissues [450KNS14]

city: Kolkata

first: Nilabja

last: Sikdar

state: West Bengal

address: Plot No, 203, Barrackpore Trunk Rd, Dunlop, Bonhooghly Government Colony, Baranagar, Kolkata, West Bengal 700108

department: Human Genetics Unit

institute: Indian Statistical Institute

description:
450KNS14
pancreatic cancer samples

hyb_protocol: Bisulphite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 450K BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Iscan (Illumina) BeadArray Reader using standard recommended Illumina scanner setting.

data_processing: Iscan

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from tissue samples using Qiagen DNeasy Kit according to standard instructions.

value: Pancreatic ductal adenocarcinoma

value: Female

value: Cancer tissue

tag: patient id


title: 1850061049_CS26_S7 [scRNA-seq]

value: Breast cancer

value: ER+/PR+/HER-


title: MCF7-UBE2T-A6 replicate 1

description:
UBE2T A6 (shRNA#1)
F4


title: C10-4

description: Paired End


title: 18wk MINO 75

city: Charleston

first: Matthew

last: Carson

state: South Carolina

address: 171 Ashley Avenue, basic science building room 241

institute: Medical University of South Carolina

data_processing:
Partek Flow Software Version 10.0.22.1023
Trimmed sequence reads were mapped to GrCM38/mm10 genome using Partek Flow Software benchwork utilizing STAR 2.7.8a alignment
Aligned sequences quality assurance / quality control values were determined to determine sequence alignment percentages and gene / transcript counts
CPM values were used for normalization of read counts in the Partek Flow Software Suite
Assembly: mm10
Supplementary files format and content: tab-delimited text files with normalized counts for each sample

source_name: Liver

growth_protocol: look up partek pipeline management

extract_protocol:
Total RNA was isolated from livers using the TRIzol method. 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library preparation kit coupled with polyA purification following manufacturer's protocols.

value: Liver

value: whole liver

value: SPF - Wild-type

value: Minocycline


title: C2-1

description: Paired End


title: Genomic DNA from normal tissues [450KNS13]

description:
450KNS13
pancreatic cancer samples

value: Normal tissue


title: MCF7-NS replicate 3

description:
non silcencing shRNA  (TRC)
F3

value: NS


title: 1850061049_CS24_S6 [scRNA-seq]

value: Circulating tumor cells (CTCs)


title: 18wk MINO 74


title: Genomic DNA from normal tissues [450KNS11]

description:
450KNS11
pancreatic cancer samples

value: Male


title: C10-3

description: Paired End


title: MCF7-NS replicate 2

description:
non silcencing shRNA  (TRC)
F2


title: 18wk MINO 72


title: C10-2

description: Paired End


title: MCF7-NS replicate 1

description:
non silcencing shRNA  (TRC)
F1


title: 1850061049_CS23_S5 [scRNA-seq]


title: 18wk MINO 71


title: Genomic DNA from cancer tissues [450KNS8]

description:
450KNS8
pancreatic cancer samples


title: 1850061049_CS17_S3 [scRNA-seq]


title: C10-1

description: Paired End


title: Genomic DNA from normal tissues [450KNS9]

description:
450KNS9
pancreatic cancer samples


title: Genomic DNA from cancer tissues [450KNS12]

description:
450KNS12
pancreatic cancer samples


title: T47D-UBE2T-A9 replicate 2

description:
UBE2T A9 (shRNA#2)
C11

source_name: T47D cell line


title: 1850061049_CS12_S2 [scRNA-seq]


title: T47D-UBE2T-A9 replicate 1

description:
UBE2T A9 (shRNA#2)
C10


title: 18wk MINO 70


title: A10-4

description: Paired End


title: 1850061049_CS11_S1 [scRNA-seq]


title: T47D-UBE2T-A6 replicate 2

description:
UBE2T A6 (shRNA#1)
C5


title: 18wk VEH 69

value: Vehicle-Control


title: A10-3

description: Paired End


title: 18wk VEH 67


title: 1850055018_CS41_S15 [scRNA-seq]


title: A10-2

description: Paired End


title: Genomic DNA from cancer tissues [450KNS6]

description:
450KNS6
pancreatic cancer samples


title: Genomic DNA from cancer tissues [450KNS10]

description:
450KNS10
pancreatic cancer samples


title: 18wk VEH 66


title: A10-1

description: Paired End


title: Genomic DNA from normal tissues [450KNS7]

description:
450KNS7
pancreatic cancer samples


title: Genomic DNA from normal tissues [450KNS5]

description:
450KNS5
pancreatic cancer samples


title: T47D-NS replicate 2

description:
non silcencing shRNA  (TRC)
C2


title: 1850055018_CS32_S12 [scRNA-seq]


title: 18wk VEH 65


title: 18wk VEH 64


title: 1850055018_CS31_S11 [scRNA-seq]


title: 1850055018_CS38_S14 [scRNA-seq]


title: WT input replicate 2

city: Solna

first: Vicent

last: Pelechano

address: Nobels väg 16

department: MTC

country: Sweden

institute: ScilifeLab - Karolinska Institutet

description: Input for the wildtype strain replicate 2

data_processing:
Base calling and demultiplexing was performed using bcl2fastq and a sample sheet, with default settings
Fastq reads were mapped to combined sacCer3 and S. pombe genomes using bowtie2 with default settings
Mapped files were deduplicated using Picard MarkDuplicates
Mapped reads with mapping quality less than 2 were removed using samtools
Quality-filtered mapped .bam files were converted to bigwig using deepTools bamCoverage, bin size 1
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig files with coverage across the genome

organism: Saccharomyces cerevisiae

growth_protocol: 100 ml per sample of each S. cerevisiae strain was grown in YPD medium at 30 degrees C to OD600 ~ 0.7. SNF21-TAP-natR S. pombe strain (spike-in control) was grown in YES medium to OD600 ~ 0.7.

extract_protocol:
The pellets were thawed on ice, resuspended in 500 µl zymolyase solution (1.2 M sorbitol, 10 mM Tris-HCl pH 8, 10 mM CaCl2, 1% v/v beta-mercaptoethanol, 0.1 U/µl zymolyase (Zymo Research)) per pellet and incubated at 37 °C for 30 minutes with shaking at 500 rpm to digest the cell walls. The resulting spheroplasts were isolated by centrifugation for 5 min at 3500xg. Spheroplasts were resuspended in 540 µl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% v/v Triton X-100, 0.1% w/v sodium deoxycholate, 1 mM PMSF, 1 mM benzamidine, 1:100 yeast protease inhibitor cocktail (Sigma Aldrich, P8215)). The lysates were sonicated using the Covaris ME220 instrument in 130 µl screw-cap microtubes for 3 minutes (PIP = 75, DF = 15%, 1000 cycles per burst, 9 °C). Sonicated lysates were centrifuged at 17000xg for 10 minutes to pellet insoluble material. 5 µl aliquots from each sample were decrosslinked to check the size of chromatin fragments, which was between 100-500 bp. The amount of chromatin in each sonicated sample was estimated from the DNA concentration in the decrosslinked aliquot. For the IP, equal amount of chromatin from each sample was taken based on this estimate, and S. pombe sonicated chromatin was spiked in to at approximately 1% relative to that amount (S. pombe chromatin was obtained in the same way as above, except with two times larger volume of zymolyase solution and twice as long incubation time). Volumes were adjusted with lysis buffer to be equal between samples. 250 µl of Dynabeads Pan Mouse IgG (Thermo Fisher) per sample were washed 3 times with PBS/BSA (PBS with 5 mg/ml bovine serum albumin (Sigma Aldrich)), resuspended in the sonicated chromatin solution, and rotated overnight at +4 °C. They were washed three times each with lysis buffer, lysis buffer containing 500 mM NaCl, and LiCl wash buffer (10 mM Tris-HCl pH 8, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and once with elution buffer (50 mM Tris-HCl pH 8, 1% SDS, 10 mM EDTA). Chromatin was eluted from beads in elution buffer at 65 °C with shaking for 20 minutes. Eluted material was diluted five-fold to reduce the concentration of SDS to 0.2%, then 1:100 RNase cocktail (Thermo Fisher, AM2286) was added and the samples were incubated at 37 °C for 45 minutes to digest RNA. SDS was added to a total of 0.5% and Proteinase K to 0.5 mg/ml (Thermo Fisher, AM2546), and the samples were shaken overnight at 65 °C to reverse crosslinked DNA. In parallel, input control samples (10 µl sonicated chromatin) were subjected to RNA digestion and reversion of crosslinking in the same way. Next day, the DNA was purified with the QIAquick Gel Extraction kit (QIAGEN) and eluted into 50 µl water.
Sequencing libraries were prepared using the NEBNext Ultra™ II DNA Library Prep Kit (NEB). 4 PCR cycles were used for the input samples and 17 cycles for the IP samples. The resulting libraries were pooled and dual size-selected with 0.6X and 1.2X AMPure XP (Beckman Coulter) bead ratios. The pool was sequenced on NextSeq 550, High Output kit (Illumina), paired-end with a read length of 38 bases.

treatment_protocol: Cells were crosslinked by adding 1% formaldehyde (Thermo Fisher) directly to the culture and agitating for 15 minutes. Formaldehyde was quenched by adding 0.125 M glycine and agitating for another 5 minutes. The cells were pelleted at 3500xg for 2 min, +4 °C. They were washed four times with cold TBS. Finally, pellets were flash-frozen and stored at -80 °C.

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

tag: parental strain

value: BY4741 (MATa his3-Δ1 leu2-Δ0 met15-Δ0 ura3-Δ0)

tag: chip antibody


title: 1850055018_CS26_S9 [scRNA-seq]


title: WT input replicate 1

description: Input for the wildtype strain replicate 1


title: 12wk MINO50


title: Genomic DNA from normal tissues [450KNS3]

description:
450KNS3
pancreatic cancer samples


title: 12wk MINO48


title: PUF3-TAP Δrpb4 input replicate 3

description: Input for the Puf3-TAP Δrpb4 strain replicate 3

value: MATa ade2 arg4 leu2-3,112 trp1-289 ura3-52 puf3::TAP::URA rpb4::kanMX4


title: 12wk MINO51


title: Genomic DNA from cancer tissues [450KNS4]

description:
450KNS4
pancreatic cancer samples

value: Pancreatic ductal adenocarcinoma


title: T47D-NS replicate 1

description:
non silcencing shRNA  (TRC)
C1


title: Genomic DNA from normal tissues [450KNS1]

description:
450KNS1
pancreatic cancer samples

value: Female


title: 1850055018_CS25_S8 [scRNA-seq]


title: 12wk MINO47


title: 12wk MINO 46


title: PUF3-TAP Δrpb4 input replicate 1

description: Input for the Puf3-TAP Δrpb4 strain replicate 1


title: PUF3-TAP Δrpb4 input replicate 2

description: Input for the Puf3-TAP Δrpb4 strain replicate 2


title: 1850055018_CS17_S4 [scRNA-seq]


title: 1850055018_CS24_S7 [scRNA-seq]


title: PUF3-TAP WT input replicate 3

description: Input for the Puf3-TAP strain replicate 3

value: MATa ade2 arg4 leu2-3,112 trp1-289 ura3-52 puf3::TAP::URA


title: PUF3-TAP WT input replicate 2

description: Input for the Puf3-TAP strain replicate 2


title: 12wk VEH 45


title: 1850055018_CS13_S2 [scRNA-seq]

value: Breast cancer


title: Genomic DNA from cancer tissues [450KNS2]

description:
450KNS2
pancreatic cancer samples

value: Cancer tissue


title: 1850055018_CS12_S1 [scRNA-seq]


title: 12wk VEH 44

value: Liver


title: PUF3-TAP WT input replicate 1

description: Input for the Puf3-TAP strain replicate 1


title: WT ChIP replicate 2

description: ChIP-seq in the wildtype strain replicate 2

value: Dynabeads Pan Mouse IgG (Thermo Fisher)


title: 12wk VEH 42

value: whole liver

value: SPF - Wild-type


title: 12wk VEH 41


title: Drone Replicate 2

city: London

first: Paul

last: Hurd

address: Mile End Road

department: School of Biological and Behavioural Sciences

country: United Kingdom

institute: Queen Mary University of London

data_processing:
Transcripts were quantitated using Kallisto tool (https://pachterlab.github.io/kallisto/). Default parameters were used except for bootstrapping which was set to 100 and reads set to stranded
Assembly: Amel HAv3.1
Supplementary files format and content: Transcript ID, Transcript Length, Effective Length, Estimated Read Counts, Transcripts Per Million

organism: Apis mellifera

source_name: Brain

extract_protocol:
RNA was isolated using TRIzol (ThermoFisher, 15596018), followed by RNA Clean & Concentrator kit (Zymo Reasearch, R1015). Polyadenylated mRNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490). Libraries were constructed with NEBNext Ultra
Directional RNA Library Prep Kit for Illumina (NEB, E7420). Library quality was verified by running an Agilent High Sensitivity DNA chip (Agilent, 5067-4626) on a 2100 Bioanalyzer (Agilent Genomics).

value: Brain

tag: caste

value: Drone


title: 12wk VEH 40


title: WT ChIP replicate 1

description: ChIP-seq in the wildtype strain replicate 1


title: Queen Replicate 2

value: Queen


title: Drone Replicate 1


title: PUF3-TAP Δrpb4 ChIP replicate 2

description: ChIP-seq in the Puf3-TAP Δrpb4 strain replicate 2


title: PUF3-TAP Δrpb4 ChIP replicate 1

description: ChIP-seq in the Puf3-TAP Δrpb4 strain replicate 1


title: PUF3-TAP Δrpb4 ChIP replicate 3

description: ChIP-seq in the Puf3-TAP Δrpb4 strain replicate 3


title: Worker Replicate 2

value: Worker


title: Queen Replicate 1


title: PUF3-TAP WT ChIP replicate 3

description: ChIP-seq in the Puf3-TAP strain replicate 3


title: Worker input

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were aligned to the Amel HAv3.1 genome using BWA mem version 0.7.17.
Peaks were called uing MACS 2 v2.2.7.1 with the significance cut-off q-value <=0.01
Assembly: Amel HAv3.1
Supplementary files format and content: narrowPeak

extract_protocol:
Extracts from sonicated nuclei were cleared by centrifugation (20000×g; 10 min), histone-DNA complexes were concentrated using an Amicon centrifugal filter (Millipore) and split into 50 μl aliquots. Each aliquot was diluted ten-fold with ChIP dilution buffer (0.01% SDS; 1.1% Triton X-100; 1.2 mM EDTA; 16.7 mM Tris-HCl pH 8.0; 167 mM NaCl; protease inhibitors cocktail) and histone-DNA complexes were immunoprecipitated with antibodies overnight.
Libraries were prepared with the NEBNext Ultra II Library Prep Kit for Illumina (NEB, E7645S) according to the manufacturer’s protocol. Insert sizes were selected for 250 bp with NEBNext Sample Purification Beads (NEB, E7104S). Libraries were PCR amplified using NEBNext Multiplex Oligos for Illumina (Index Primers Set 1) (NEB, E7335S). The number of PCR cycles was selected based on the amount of input DNA. Library quality was verified by running an Agilent High Sensitivity DNA chip (Agilent, 5067-4626) on a 2100 Bioanalyzer (Agilent Genomics).


title: mEGFR L860R.1 DMSO 6Day

city: Aurora

first: Lynn

last: Heasley

state: CO

department: Craniofacial Biology

institute: University of Colorado, Anschutz Medical Campus

data_processing:
Fastq files were quality checked with FastQC
illumina adapters trimmed with bbduk, and mapped to the mouse mm10 genome with STAR aligner
Counts were generated by STAR’s internal counter and reads were normalized to counts per million (CPM) using the edgeR R package
Assembly: Mus musculus mm10
Supplementary files format and content: excel files include CPM values for each sample.
Supplementary files format and content: matrix table excel file (.xlsx) includes CPM values for all samples

source_name: mEGFR L860R.1

growth_protocol: Cells were cultured and maintained at 37oC in RPMI-1640 media (Corning) with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (Corning) in a humidified incubator with 5% CO2

extract_protocol:
Total RNA was isolated using Quick-RNA MiniPrep Kit (Zymo Research), including the Dnase I treatment step
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction.

treatment_protocol: Murine EGFR mutant cell lines cultured in 10 cm dishes were treated for 1,2,4,6 days with 0.1% DMSO or 100 nM osimertinib

value: mEGFR L860R.1

value: lung adenocarcinoma

value: EGFR mutant L860R missense mutation

value: DMSO

tag: time


title: mEGFR L860R.1 100nM Osimertinib 6Day

value: 100nM Osimertinib


title: mEGFR L860R.1 100nM Osimertinib 4Day


title: mEGFR L860R.1 DMSO 4Day


title: Worker Replicate 1

tag: tissue


title: Worker H3K4me3 replicate 2

value: H3K4me3 [Active Motif, 39159]


title: PUF3-TAP WT ChIP replicate 1

description: ChIP-seq in the Puf3-TAP strain replicate 1

value: MATa ade2 arg4 leu2-3,112 trp1-289 ura3-52 puf3::TAP::URA

value: BY4741 (MATa his3-Δ1 leu2-Δ0 met15-Δ0 ura3-Δ0)


title: mEGFR L860R.1 100nM Osimertinib 2Day

tag: cell type


title: Worker H3K4me3 replicate 1


title: swap1sfpsrrc1_R_3_1.fq.gz

city: Austin

first: Enamul

last: Huq

address: 100 East 24th St., NHB 2.616, Stop A5000 Department of Molecular Biosciences University of Texas at Austin

department: Molecular Biosciences

institute: University of Texas at Austin

description: Read Length: 150bp

data_processing:
FastQC to analyze the sequencing quality.
STAR is used to map the reads to the TAIR10 genome.
Htseq is used for read count and DESeq2 are used to analyze the differential gene expression.
ASPli 2.0 is used to determine the differentially spliced events
GeneCodis 4 is used for the GO-term analysis
Assembly: TAIR10
Supplementary files format and content: Excel sheet containing multiple tabs which have differential expressed genes, differential spliced genes, and GO terms are included.
Supplementary files format and content: Dataset S1 contain differential gene expression and its coresponding GO-term analysis across all combination
Supplementary files format and content: Dataset S2 contain differential alternative splicing and its coresponding GO-term analysis across all combination

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Wild type Col-0 and swap1-1 mutant seeds in the Col-0 background were used.Wild type and mutant seeds were surface-sterilized and plated on Murashige and Skoog (MS) growth medium containing 0.9% agar without sucrose. After 4 d of chilling at 4°C in the dark for stratification, seeds were exposed to 3 hrs of white light at room temperature to induce germination before placing them in the dark for four days.

extract_protocol:
0.1g seedling materials are harvested. RNA were extracted using the Sigma plant RNA isolation kit(Catalog # STRN50-1KT). ). 5 µg total RNA was used to generate the RNA library for sequencing.
The RNA library generation process followed the manufacturer’s protocol

treatment_protocol: 4-day-old dark grown seedlings transfer to dark for 3hrs or continous red light(7μmolm-2s-1) condition for 3hrs.

value: Seedlings

tag: genotype

value: Red light treated


title: mEGFR L860R.1 DMSO 2Day

tag: cell line


title: mEGFR L860R.1 100nM Osimertinib 1Day


title: Worker H3K4me1 replicate 2

value: H3K4me1 [Abcam, ab8895]


title: Worker H3K4me1 replicate 1


title: swap1sfpsrrc1_R_1_1.fq.gz

description: Read Length: 150bp


title: mEGFR del19.2 100nM Osimertinib 6Day

source_name: mEGFR del19.2

value: mEGFR del19.2

value: EGFR mutant exon deletion 19


title: swap1sfpsrrc1_R_2_1.fq.gz

description: Read Length: 150bp


title: Worker H3K27me3 replicate 2

value: Brain

value: H3K27me3 [Millipore, 07449]


title: swap1sfpsrrc1_D_3_1.fq.gz

description: Read Length: 150bp

value: Dark


title: U88 cells, GNE987-2

city: Suzhou

first: Gen

last: Li

address: No. 92 Zhongnan Street

institute: Children's Hospital of Soochow University

data_processing:
Illumina Casava v 1.8
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes count for each Sample

growth_protocol: U87 cells were cultured in DMEM with 10% FBS, 1% penicillin and streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 400 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra™ Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Glioblastoma

value: WT


title: swap1sfpsrrc1_D_2_1.fq.gz

description: Read Length: 150bp


title: U88 cells, GNE987-1


title: mEGFR del19.2 100nM Osimertinib 4Day

value: lung adenocarcinoma


title: mEGFR del19.2 DMSO 6Day


title: Worker H3K27me3 replicate 1

value: Worker


title: PUF3-TAP WT ChIP replicate 2

description: ChIP-seq in the Puf3-TAP strain replicate 2

value: Dynabeads Pan Mouse IgG (Thermo Fisher)


title: Worker H3K27ac replicate 2

value: H3K27ac [Active Motif, 39133]


title: mEGFR del19.2 DMSO 4Day

value: DMSO


title: Worker H3K27ac replicate 1


title: mEGFR L860R.1 DMSO 1Day

value: mEGFR L860R.1

value: EGFR mutant L860R missense mutation


title: 1850055018_CS18_S5 [scRNA-seq]

data_processing:
RSEM index generated on hg19.
Read data aligned to index using RSEM/bowtie2.
Genomic mappings (GM) performed with RSEM/bowtie2.
Quantified gene expression levels in counts and TPM using RSEM-1.3.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Count and TPM values for each sample.

extract_protocol:
Circulating tumor cells enriched by ClearCell FX were captured by Polaris System (Fluidigm). PolyA RNA from each single cell was reverse transcribed and cDNA amplified using SMARTer kit (SMARTer Ultra Low RNA Kit for the Fluidigm C1 System, Clontech #634936).
Amplified cDNA was used as input to prepare sequencing libraries with the NexteraXT DNA Kit (Illumina #fc-131-1096) and with dual indices (PN FC-131-1002; Illumina).
Paired-end NextSeq 74bp sequencing.

value: Breast cancer

value: Circulating tumor cells (CTCs)


title: U87 cells, DMSO-1


title: sfpsrrc1_R_3_1.fq.gz

description: Read Length: 150bp

value: Seedlings

value: Red light treated


title: mEGFR del19.2 100nM Osimertinib 2Day

value: mEGFR del19.2

value: EGFR mutant exon deletion 19

value: 100nM Osimertinib


title: Queen input

value: Brain

value: Queen


title: sfpsrrc1_R_2_1.fq.gz

description: Read Length: 150bp


title: mEGFR del19.2 DMSO 2Day


title: K562-MAT-24h replicate 3, RNA-seq

city: Huizhou City

first: Wangjing

last: Zhong

state: Guangdong Province

address: No. 1, Xuebo Street, Huicheng District

institute: Huizhou Third People's Hospital

data_processing:
Pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data
Hisat2 (v2.0.1) was used to index reference genome sequence and then clean data were aligned to reference genome
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Assembly: ENSEMBL Homo_sapiens.GRCh37
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

growth_protocol: HL-60, U937 and K562 cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS mRNA-seq V3 Library Prep Kit following manufacturer's protocols.

treatment_protocol: HL-60, U937 and K562 cells were treated with 0.8mg/mL matrine for 30min and 24h, respectively

value: myeloid leukemia cells


title: sfpsrrc1_R_1_1.fq.gz

description: Read Length: 150bp


title: sfpsrrc1_D_3_1.fq.gz

description: Read Length: 150bp

value: Dark


title: Queen H3K4me3 replicate 1

value: H3K4me3 [Active Motif, 39159]


title: K562-MAT-24h replicate 1, RNA-seq


title: mEGFR del19.2 100nM Osimertinib 1Day

value: lung adenocarcinoma


title: mEGFR del19.2 DMSO 1Day


title: K562-MAT-24h replicate 2, RNA-seq


title: Queen H3K4me3 replicate 2


title: Queen H3K4me1 replicate 2

value: H3K4me1 [Abcam, ab8895]


title: sfpsrrc1_D_2_1.fq.gz

description: Read Length: 150bp


title: swap1sfpsrrc1_D_1_1.fq.gz

description: Read Length: 150bp


title: mEGFR del19.1 100nM Osimertinib 6Day

source_name: mEGFR del19.1

value: mEGFR del19.1


title: sfpsrrc1_D_1_1.fq.gz

description: Read Length: 150bp


title: K562-MAT-30min replicate 2, RNA-seq


title: K562-MAT-30min replicate 3, RNA-seq


title: mEGFR del19.1 DMSO 6Day

value: DMSO


title: Queen H3K27me3 replicate 2

value: H3K27me3 [Millipore, 07449]


title: K562-CT replicate 3, RNA-seq

value: Control


title: K562-MAT-30min replicate 1, RNA-seq


title: mEGFR del19.1 DMSO 4Day


title: Queen H3K27me3 replicate 1


title: swap1rrc1_R_2_1.fq.gz

description: Read Length: 150bp


title: Queen H3K27ac replicate 2

value: H3K27ac [Active Motif, 39133]


title: swap1rrc1_R_3_1.fq.gz

description: Read Length: 150bp

value: Seedlings


title: K562-CT replicate 2, RNA-seq


title: mEGFR del19.1 100nM Osimertinib 2Day


title: K562-CT replicate 1, RNA-seq


title: Queen H3K27ac replicate 1


title: swap1rrc1_D_3_1.fq.gz

description: Read Length: 150bp


title: Drone input

value: Drone


title: HL-60-MAT-24h replicate 3, RNA-seq


title: mEGFR del19.1 DMSO 2Day


title: swap1rrc1_D_2_1.fq.gz

description: Read Length: 150bp


title: Drone H3K4me3 replicate 2


title: mEGFR del19.1 DMSO 1Day


title: swap1rrc1_D_1_1.fq.gz

description: Read Length: 150bp


title: mEGFR del19.1 100nM Osimertinib 1Day


title: HL-60-MAT-24h replicate 2, RNA-seq


title: Drone H3K4me3 replicate 1


title: HL-60-MAT-24h replicate 1, RNA-seq


title: Queen H3K4me1 replicate 1


title: Drone H3K4me1 replicate 2


title: HL-60-MAT-30min replicate 3, RNA-seq


title: mEGFR del19.1 100nM Osimertinib 4Day


title: swap1sfps_R_3_1.fq.gz

description: Read Length: 150bp

value: Red light treated


title: HL-60-MAT-30min replicate 2, RNA-seq


title: Fasting 1

city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

institute: China Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
FastQC and MultiQC were used to check fastq files for quality.The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
Read pairs from each sample were aligned to the reference genome by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1).
Assembly: GRCm38

source_name: inguinal WAT

extract_protocol:
RNA was harvested using TRIzol™ Reagent method (Invitrogen MAN0001271).
RNA libraries were prepared for sequencing using KAPA mRNA HyperPrep Kit Illumina® Platforms protocol

value: inguinal WAT

value: WT

tag: Sex

value: male

tag: age

value: > 2 month

value: Fasting treated


title: Fasting 2


title: Drone H3K27me3 replicate 2

value: Brain


title: T47D-UBE2T-A6 replicate 1

description:
UBE2T A6 (shRNA#1)
C4


title: Drone H3K4me1 replicate 1


title: Cold 3

value: Cold treated


title: Fasting 3


title: swap1sfps_R_1_1.fq.gz

description: Read Length: 150bp


title: swap1sfps_D_2_1.fq.gz

description: Read Length: 150bp

value: Dark


title: Drone H3K27me3 replicate 1


title: Drone H3K27ac replicate 2


title: swap1sfps_D_1_1.fq.gz

description: Read Length: 150bp


title: Cold 1


title: HL-60-CT replicate 2, RNA-seq

value: myeloid leukemia cells


title: swap1rrc1_R_1_1.fq.gz

description: Read Length: 150bp


title: Drone H3K27ac replicate 1


title: Control 3

value: non treated


title: swap1sfps_R_2_1.fq.gz

description: Read Length: 150bp


title: Drone replicate 2 brain ATAC

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ATAC-seq reads were aligned to the Amel HAv3.1 genome using BWA mem version 0.7.17.
BAM files were processed to define nucleosome free regions as fragments <100bp in size
Peaks were called uing MACS 2 v2.2.7.1 with the significance cut-off q-value <=0.01
Assembly: Amel HAv3.1
Supplementary files format and content: narrowPeak

extract_protocol:
Dissected brains were placed in 200 µl of PBS containing EDTA-free Complete protease inhibitors cocktail (Roche). Dissected brains were then gently homogenised by hand with a plastic pestle and centrifuged (900 × g / 5 min). Supernatants were removed and pellets resuspended in 1 ml of lysis buffer (10 mM Tris-HCl pH 7.5 / 10 mM NaCl / 3 mM MgCl2 / 0.2 % (v/v) IGEPAL CA-630 / EDTA-free Complete protease inhibitors cocktail) by pipetting for 30 seconds. 50 µl aliquots were removed, centrifuged (900 × g / 5 min) and pellets resuspended in 50 µl of tagmentation buffer (40 mM Tris-HCl pH 7.5 / 10 mM MgCl2 / 20 % (v/v) dimethylformamide)
0.75 µl of Tn5 transposase was added and tagmentation proceeded for 30 minutes at 37 ˚C. All transposed samples were purified using a DNA Clean & Concentrator-5 kit, using the binding buffer ratio for small PCR products (Zymo Research). Following purification, ATAC-seq library amplification was carried out with 2 × Q5 Polymerase Master Mix and 25 µM of Nextera primers. The optimal cycle number was determined using quantitative polymerase chain reaction (qPCR) as originally described.


title: U88 cells, DMSO-2

value: Glioblastoma

value: DMSO


title: U937-MAT-24h replicate 3, RNA-seq


title: swap1_R_2_1.fq.gz

description: Read Length: 150bp


title: Drone replicate 1 brain ATAC


title: Control 2


title: swap1sfps_D_3_1.fq.gz

description: Read Length: 150bp


title: U937-MAT-24h replicate 2, RNA-seq


title: HL-60-MAT-30min replicate 1, RNA-seq


title: swap1_R_3_1.fq.gz

description: Read Length: 150bp


title: swap1_R_1_1.fq.gz

description: Read Length: 150bp


title: Control 1


title: HL-60-CT replicate 3, RNA-seq

value: Control


title: Cold 2


title: U937-MAT-24h replicate 1, RNA-seq


title: swap1_D_3_1.fq.gz

description: Read Length: 150bp


title: Worker replicate 1 brain ATAC

value: Worker


title: HL-60-CT replicate 1, RNA-seq


title: swap1_D_2_1.fq.gz

description: Read Length: 150bp

value: Seedlings


title: U937-MAT-30min replicate 2, RNA-seq


title: Queen replicate 2 brain ATAC

value: Queen


title: swap1_D_1_1.fq.gz

description: Read Length: 150bp


title: Worker replicate 2 brain ATAC


title: U937-MAT-30min replicate 1, RNA-seq


title: Col-0_R_3_1.fq.gz

description: Read Length: 150bp

value: Col-0 Wild-type

value: Red light treated


title: Queen replicate 1 brain ATAC


title: 2yr Mouse Liver, CgA KO, Replicate 3

city: La Jolla

first: Shandy

last: Shahabi

state: CA

address: 9500 Gilman Dr

department: Chemistry

institute: UCSD

data_processing:
Illumina NovaSeq S2 reads were quantified at the transcript level and aligned to the GRCm38 mouse transcriptome using Salmon v1.4.0.
Raw count files were imported into R program using DESeq2 and annotated to genes based on RefSeq annotation. Read counts less than 1 were excluded in analysis.
Assembly: mm10

growth_protocol: Male WT and CgA-KO C57BL/6 mice were kept in a 12 hr dark/light cycle and fed a normal chow diet (NCD: 13.5% calorie from fat; LabDiet 5001, TX).

extract_protocol:
Total RNA was isolated from approximately 30 mg of liver tissue from 3 wild type and 3 CgA knockout mice using RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was quantified by nanodrop and was quality checked by Tapestation (Agilent).
Poly(A) selected mRNA libraries were prepared from 500 ng of total RNA using KAPA mRNA HyperPrep kit (KAPA Biosystems) and dsDNA libraries were quantified using Qubit 2.0 fluorometer (Invitrogen).

value: Liver

value: CgA KO


title: 2yr Mouse Liver, CgA KO, Replicate 1


title: Col-0_R_2_1.fq.gz

description: Read Length: 150bp


title: C77c [High-risk prostate cancer]

city: Fuzhou

first: Yu

middle: hua

last: Wang

address: 1 Keji Road, Shangjie Town, Minhou County, Fujian Province, China

institute: Fujian Normal University

description: High-risk prostate cancer

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data. Raw reads were filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Using String Tie for readcount and TPM calculation.
Differential expression analyses were performed using the DEGseq package.
Assembly: GRCh38
Supplementary files format and content: tab_delimited text files include TPM values for each Sample

source_name: homo  prostate glands

extract_protocol:
The puncture biopsies samples were collected and  stored with TRIzol® Reagent (Invitrogen,USA) and stored in liquid nitrogen.  Total RNA was extracted with Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina®(Yeasen ,China) .  RNA integrity was assessed with a 1.0% agarose gel.  RNA concentration was measured by a Qubit® 2.0 Flurometer (Life, USA).
A total amount of 1 μg RNA per sample was used.    The V AHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (vazyme, China)for Illumina was used to construct the libraries for sequencing following the manufacturer’s instructions.

value: Prostate cancer

tag: gleason score

tag: isup grade_group

value: Ⅴ

tag: proportion of_tumor


title: U937-CT replicate 3, RNA-seq

tag: treatment


title: 2yr Mouse Liver, WT, Replicate 2

value: WT


title: 2yr Mouse Liver, WT, Replicate 1


title: U937-CT replicate 2, RNA-seq


title: Col-0_D_3_1.fq.gz

description: Read Length: 150bp


title: C77a [High-risk prostate cancer]

description: High-risk prostate cancer


title: U937-MAT-30min replicate 3, RNA-seq


title: C75c [High-risk prostate cancer]

description: High-risk prostate cancer

value: Ⅳ


title: U937-CT replicate 1, RNA-seq


title: Col-0_D_2_1.fq.gz

description: Read Length: 150bp

value: Dark


title: C75b [High-risk prostate cancer]

description: High-risk prostate cancer


title: PDK1KO(GAN)

city: Kobe

first: Yusei

last: Hosokawa

address: 7-5-2 Kusunoki-cho, Chuo-ku

department: Division of Diabetes and Endocrinology, Department of internal medicine

institute: Kobe University graduate school of medicine

data_processing:
Using DRAGEN Bio-IT Platform v3.6.3 software.
Read sequences obtained by sequence analysis were mapped to the genome sequence.
Gene expression levels were calculated based on the information obtained by mapping and the gene annotation file (gencode.vM25.primary_assembly.annotation.gtf).
Assembly: GRCm38
Supplementary files format and content: Text files include TPM values for each Sample

growth_protocol: Mice were housed at 21°C-25°C on a 12-hr light/dark cycle in the animal facility at Kobe University Graduate School of Medicine.

extract_protocol:
Total RNA was extracted from tissues with RNeasy minikit (QIAGEN). 6.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Nextera XT DNA Library Prep kits following manufacturer's protocols.

treatment_protocol: After weaning at 4 weeks old, control mice and A-PDK1KO mice were fed normal chow or GAN diet for 16 weeks.

value: fed GAN diet


title: Col-0_R_1_1.fq.gz

description: Read Length: 150bp


title: Col-0_D_1_1.fq.gz

description: Read Length: 150bp


title: iSLK cells, BAC16 shLAMP3-1

city: Guangzhou

first: Ersheng

last: Kuang

state: Guangdong

address: 74 Zhongshan 2nd Rd

department: Zhongshan School of Medicine

institute: Sun Yat-Sen University

data_processing:
The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina platform and 150 bp paired-end reads were generated
The reference genomes and the annotation file were downloaded from ENSEMBL database (http://www.ensembl.org/index.html). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Under the assumption that the number of reads derived from a gene (or transcript isoform) follows abinomial distribution, DEGseq is proposed based on MA-plot and widely used for differential gene expression analysis. The P-value could be assigned to each gene and adjusted by the Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with q≤0.05 and |log2_ratio|≥1 are identified as differentially expressed genes (DEGs)
The KEGG enrichment of DEGs was implemented by the hypergeometric test, in which p-value was adjusted by multiple comparisons as q-value. KEGG terms with q<0.05 were considered to be significantly enriched.
Genome_build: Homo_sapiens.GRCh38.94.chr
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: iSLK

extract_protocol:
Discard the supernatant, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（Cat #E7530L，NEB)was used with 3 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: iSLK

value: knockdown LAMP3

tag: infection

value: Kaposi's sarcoma associated herpesvirus (KSHV)

value: under lytic induction for 72h


title: 2yr Mouse Liver, WT, Replicate 3


title: iSLK cells, STOP45-2

value: knockout ORF45


title: C75a [High-risk prostate cancer]

description: High-risk prostate cancer


title: iSLK cells, STOP45-1


title: C58c [High-risk prostate cancer]

description: High-risk prostate cancer


title: 31-MB002-2-AAVS1-t8_S31

city: Hamilton

first: Sheila

last: Singh

state: ON

address: 1280 Main Street West

department: Biochemistry and Biomedical Sciences

country: Canada

institute: McMaster University

description:
AAVS1-KO day 8 post-transduction (replicate 2)
WG_S31

data_processing:
RNA sequencing reads were trimmed and filtered using BBDukfrom the BBTools package (REF: Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2012))
Sequencing reads were aligned using STAR aligner version 2.6.0 and Ensembl reference genome GRC38.
Expression levels were quantified as TMM based usingedgeR 3.26.4 using the ‘calcNormFactors’ and ‘cpm’ functions. The pre-processing pipeline is published and freely available on GitHub for reproducibility.
Differential gene expression analysis was performed using Limma with Benjamini and Hochberg correction for multiple comparisons.
Read counts less than 10 were filtered prior to analysis. Gene set enrichment analysis was carried out using the GSEAv4.2.1(Broad Institute) (REF:Subramanian, A. et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. 102, 15545–15550 (2005)). Gene sets enriched with FDR <0.05 and p<0.05 were considered statistically significant.
Assembly: GRC38
Supplementary files format and content: counts (WG_count_matrix.txt)

extract_protocol:
Total RNA was isolated from 200,000-300,000 viable tumor cells (RNeasy Midi Kit, Qiagen) and then sequenced using Illumina HiSeq.
NEBNext® Ultra™ II Directional RNA Library kit

value: brain cancer

value: medulloblastoma

tag: karyotype

value: XX

value: day 8 post-transduction


title: 32-MB002-3-AAVS1-t8_S32

description:
AAVS1-KO day 8 post-transduction (replicate 3)
WG_S32


title: Control(NC)

value: Liver

value: Control

value: fed normal chow


title: C77b [High-risk prostate cancer]

description: High-risk prostate cancer

value: Prostate cancer


title: Treg cells, KD-rep1

city: Chengdu

first: Yanzhuo

last: Liu

address: Address of University of Electronic Science and Technology of China (Shahe)

institute: UESTC

data_processing:
lllumina bcl2fastq 2.0 software used for basecalling
Use default STAR to compare to reference genome
To study the expression of mRNA, stringTie quantitative
By using DESEQ2 to do differential analysis of differentially expressed mRNAs between paired groups
Assembly: mm10
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: spleen

extract_protocol:
Treg cells were isolated from Foxp3-Mettl14f/+ cKO mice and littermate controls on day 7 post-transplantation. Total RNA was extracted with TRIzol and mRNA was then separated by using a Dynabeads mRNA Purification Kit (Invitrogen). Standard Illumina sequencing was applied for sequencing. Raw RNA-sequencing reads were aligned to the mouse genome (mm10) with TopHat. Genes were considered significantly differentially expressed   if the fold change was greater than 1.5-fold and less than 0.1. A GO enrichment analysis and KEGG pathways enrichment analysis were performed using online bioinformatics tools.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: Treg

value: after transplantation on day 7

value: Foxp3 knockdown


title: C58a [High-risk prostate cancer]

description: High-risk prostate cancer

value: Ⅴ


title: Treg cells, Ctrl-rep1

value: wild type


title: iSLK cells, BAC16 shLAMP3-2

value: iSLK

value: knockdown LAMP3

value: Kaposi's sarcoma associated herpesvirus (KSHV)


title: 29-MB002-3-DHODH-3-t8_S29

description:
DHODH-KO day 8 post-transduction (replicate 3)
WG_S29

value: brain cancer

value: DHODH-KO


title: C58b [High-risk prostate cancer]

description: High-risk prostate cancer


title: iSLK cells, BAC16-1

value: under lytic induction for 72h


title: PDK1KO(NC)


title: Control(GAN)

value: fed GAN diet


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 6 [Tumor_10]

city: Odense

first: Lars

last: Grøntved

address: Campusvej 55

department: Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

data_processing:
Reads were aligned to mm10 using STAR
Reads at genes were quantified by featureCount

source_name: Subcutaneous whole tumor, C57BL/6, female

growth_protocol:
Pan02 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin in humidified atmosphere with 5% CO2 at 37C.
Mice were injected subcutaneously (s.c.) on the right flank with 0.5 million  Pan02 cancer cells.

extract_protocol:
Tumor fragments (≤ 20 mg) in RNAlater (Invitrogen) were transferred to RLT buffer (Qiagen) and mechanically homogenized with a Tissue Lyser (Qiagen). RNA was extracted with the RNEasy Plus Mini Kit (Qiagen),
500ng purified RNA (RIN score > 7) was enriched for polyadenylated mRNA followed by fragmentation. Random primmed cDNA synthesis was performed using NEBNext kits. This was followed by hairpin adaptor ligation and PCR mediated indexing (NEBNext). The library was size selected using AMPure beads and quantified by KAPA (Roche).

treatment_protocol: Mice were vaccinated on day 11 and 17 post-inoculation with a control vaccine (sterile water emulsified 1:1 with Montanide) or an Arg2-derived peptide solution adjuvanted  1:1 with Montanide.

tag: strain

value: pancreatic ductal adenocarcinoma

value: WT

value: Arg2-derived peptide vaccine


title: C50b [High-risk prostate cancer]

description: High-risk prostate cancer

value: Prostate cancer


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 5 [Tumor_9]


title: Pan02 whole tumor, Arg2-derived peptide vaccine, mouse 4 [Tumor_8]