title: HV-6

state: Hubei

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Raw reads were treated with Trimmomatic tools(V0.36) to remove adapters. Following reads quality control:Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15, drop reads which are less than 35% of initiation read length. Then reads quality was inspected using the FastQC software then output statistical result.
Two algorithms, CIRI2 and CIRCexplorer2 were used to detect circRNAs. Reads were mapped to human reference genome GRCh37/ hg19 (http://genome.ucsc.edu/) by BWA-MEM or Tophat, respectively.
Back-spliced junction reads identified in CIRI2 were combined and scaled to RPM (Reads Per Million mapped reads, bwa mem mapping) to quantify every circRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPM/SRPBM values and counts for each Sample

extract_protocol:
Total RNA from mock and HTNV-infected HUVECs was isolated with TRIzol reagent (Invitrogen, USA).
rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) , then RNA was treated with RNase R (Epicentre, USA) and fragmented to approximately 200bp. Subsequently, the purified RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).

value: umbilical cord

tag: htnv infection


title: HV-4

status: Public on Apr 06 2020

type: SRA

city: Wuhan

first: LI

last: LI

address: 185 Donghu Road

country: China

institute: wuhan university school of basic medical sciences

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: human umbilical vein endothelial cells

growth_protocol: HUVECs were purchased from ScienCell Research Laboratories (Cat No: 8000, Carlsbad, USA) and cultured in ECM Medium with 5% fetal bovine serum (FBS), 1% penicillin-streptomycin and endothelial cell growth supplement (ECGS) (ScienCell) at 37°C in 5% CO2.

treatment_protocol: HUVECs were mock-infected or HTNV-infected at a multiplicity of infection (MOI) of 1.

tag: tissue

tag: genotype

value: wild type

value: HTNV infected


title: HUVECs, con-3

description:
lncRNA-exp.txt
new_lncRNA-exp.txt
mRNA-exp.txt

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

extract_protocol:
Total RNA from mock and HTNV-infected HUVECs was isolated with TRIzol reagent (Invitrogen, USA).
rRNAs were removed from Total RNA using Epicentre Ribo-Zero rRNA Removal Kit (illumina, USA) and fragmented to approximately 200bp. Subsequently, the purified  RNAs were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA).

tag: cell type

value: human umbilical vein endothelial cells

tag: infection

value: mock infected


title: SCN-14yrs-F-Cell36

city: Cincinnati

first: H. Leighton

last: Grimes

state: OH

address: 3333 Burnet Ave. MLC 7038

department: Immunobiology

country: USA

institute: Cincinnati Childrens Hospital Medical Center

description:
G_D12_38Cell_36_USPD16100592-N708-AK392_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

data_processing:
RSEM version 1.3.0 was run using a GTF transcriptome referenced that contained both exon and intron regions (pre-mRNA sequences) for Ensembl version 72 (hg19). 96 single-cell libraries captured per donor or patient, with only 3 cells removed with less than 100,000 reads. Differential expression between each SCN patient and the combination of healthy donor was conducted in the software AltAnalyze, using an empirical Bayes moderated t-test p<0.05 (FDR corrected), a cell-level, to identify SCN impacted genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file of log2 (incremented by 1 before log2) TPM RSEM expression values
Supplementary_files_format_and_content: donors.Neutrophils-RSEM-TPMs: Donor annotations for individual cells

source_name: Peripheral blood neutrophils

extract_protocol:
De-identified clinical data and peripheral blood from healthy donors or neutropenic patients was obtained at Cincinnati Children’s Hospital Medical Center through informed consent under an approved institutional review board research protocol.  Human Neutrophils were enriched from whole blood using the EasySep™ Direct Human Neutrophil Isolation Kit (Stemcell Technologies) and sequenced using the Fluidigm C1 platform using the SMART-Seq v4 chemistry.
cDNA was made with the SMARTer mRNA-Seq Kit version 4 (Clontech) and libraries were constructed using the Nextera XT DNA Library Preparation Kit (Illumina).

value: Peripheral blood neutrophils

tag: cdna synthesis

value: Fluidigm C1 protocol (v4 chemistry)

tag: library prep

tag: sequencing parameters

value: 75bp Paired-End, 150 million reads/96 cell library

tag: age

value: 14 year old

tag: Sex

value: female

tag: disease

value: with Severe Congenital Neutropenia


title: con-5


title: HV-2


title: con-4


title: SCN-14yrs-F-Cell35

description:
G_D12_38Cell_35_USPD16100592-N707-AK391_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: Nextera XT DNA Library Preparation Kit (Illumina)


title: SCN-14yrs-F-Cell39

description:
G_D12_38Cell_39_USPD16100592-N711-AK402_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-14yrs-F-Cell34

description:
G_D12_38Cell_34_USPD16100592-N706-AK390_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-14yrs-F-Cell33

description:
G_D12_38Cell_33_USPD16100592-N705-AK394_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-789_YMMCHM_rep3

city: Morgantown

first: Amaury

last: Pupo

state: West Virginia

address: Life Sciences Building, PO Box 6057

department: Biology

institute: West Virginia University

data_processing:
Basecalls performed with Illumina’s FASTQ Generation (v1.0.0) available in BaseSpace.
Transcripts quantification was done with salmon (v0.9.1) vs the transcripts file BY4741_Toronto_2012_cds.fsa (available from https://downloads.yeastgenome.org/sequence/strains/BY4741/BY4741_Toronto_2012/)

organism: Saccharomyces cerevisiae

source_name: Yeast cells

growth_protocol: Yeast were grown in YPD with G418 or YM with G418 and hisitidine,uracil, and leucine, methionine until mid-log phase

extract_protocol:
Hot-phenol extraction (Short protocols in molecular biology, 1995)
PolyA extraction (KAPA stranded mRNA library prep kit , cat# KK8420)
Illumina PE50bp high output flowcell

treatment_protocol: 3.9 mM crude MCHM was added to cultures for 30 minutes before harvest, washed once with water and flash frozen

tag: strain

tag: medium

value: YM

tag: treatment

value: treated

tag: mutant


title: BYpMM-BY_YMMCHM_rep3


title: BYpMM-789_YMMCHM_rep2


title: BYpMM-BY_YMMCHM_rep2


title: BYpMM-BY_YMMCHM_rep1


title: SCN-14yrs-F-Cell31

description:
G_D12_38Cell_31_USPD16100592-N710-AK402_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-789_YMMCHM_rep1


title: BYmed15_YMCHM_rep3

value: BY4741 med15::NatR pGS35


title: Fra2_cl2-Select_2

type: RNA

city: Moscow

first: Diana

last: Maltseva

address: Myasnitskaya str. 13/4

department: Faculty of Biology and Biotechnology

country: Russia

institute: National Research University Higher School of Economics

hyb_protocol: The samples were hybridized on GeneChip® Human Transcriptome Array 2.0 (Affymetrix Inc., Santa Clara, CA, USA) at 60 rpm for 16 h at 45°C.

scan_protocol: Arrays were washed to remove nonspecifically bound nucleic acids and stained on Fluidics Station 450 (Affymetrix) and then scanned on Gene- Chip Scanner 3000 7G system (Affymetrix).

data_processing: CEL-files were jointly preprocessed in Affymetrix Expression Console (build 1.4.1.46) using RMA-sketch method.

label: biotin

source_name: tumour tissue

label_protocol: The procedures for cDNA synthesis and labelling were carried out according to the GeneChip® Hybridization Wash and Stain Kit (Affymetrix Inc., Santa Clara, CA, USA) using 500 ng total RNA as starting material.

growth_protocol: Cells were adjusted to 5 x 106 ml-1 medium. 200 µl of this suspension were injected subcutaneously between the scapulae of each mouse. When the primary tumours had reached maximum 20% of the body weight of the animal at the beginning of the experiment or ulcerated, the mice were terminally narcotized, sacrificed by cardiocentesis and cervical dislocation.

extract_protocol: The total RNA was isolated using QIAzol Lysis Reagent (Qiagen, Hilden, Germany) and the miRNeasy Mini Kit (Qiagen, Hilden, Germany), according to manufacturer`s instruction.

treatment_protocol: No further treatment was administered.

tag: origin

value: Xenograft

value: E- and P-selectin deficient scid

tag: cell transfection

tag: fra-2 overexpressing clone

value: clone 2


title: BYmed15_YMCHM_rep2


title: SCN-14yrs-F-Cell30

description:
G_D12_38Cell_30_USPD16100592-N709-AK428_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Fra2_cl2-Select_3


title: Fra2_cl2-SCID_3

value: scid


title: BY4741_YMMCHM_rep3


title: BYmed15_YMCHM_rep1


title: SCN-14yrs-F-Cell3

description:
G_D12_38Cell_3_USPD16100592-N703-AK391_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Fra2_cl2-SCID_1


title: BY4741_YMMCHM_rep2


title: con-3

tag: tissue

value: umbilical cord

value: wild type

tag: htnv infection


title: Fra2_cl1-Select_3

value: clone 1


title: Fra2_cl2-Select_1


title: SCN-14yrs-F-Cell29

description:
G_D12_38Cell_29_USPD16100592-N708-AK400_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

tag: cell type

value: Peripheral blood neutrophils


title: BY4741_YMMCHM_rep1


title: SCN-14yrs-F-Cell32

description:
G_D12_38Cell_32_USPD16100592-N711-AK403_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: Fluidigm C1 protocol (v4 chemistry)


title: SCN-14yrs-F-Cell28

description:
G_D12_38Cell_28_USPD16100592-N707-AK392_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: 75bp Paired-End, 150 million reads/96 cell library


title: BYpMM-BY_YM_rep2

value: untreated


title: Fra2_cl1-Select_2


title: BYpMM-BY_YM_rep3


title: SCN-14yrs-F-Cell27

description:
G_D12_38Cell_27_USPD16100592-N706-AK391_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: 14 year old

value: female


title: BYpMM-789_YM_rep3


title: Fra2_cl2-SCID_2


title: BYpMM-789_YM_rep2


title: BYpMM-BY_YM_rep1


title: Fra2_cl1-Select_1


title: BYmed15_YM_rep3


title: Fra2_cl1-SCID_3


title: BYpMM-789_YM_rep1


title: SCN-14yrs-F-Cell26

description:
G_D12_38Cell_26_USPD16100592-N705-AK390_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: Nextera XT DNA Library Preparation Kit (Illumina)

value: with Severe Congenital Neutropenia


title: SCN-14yrs-F-Cell25

description:
G_D12_38Cell_25_USPD16100592-N704-AK394_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYmed15_YM_rep2

value: YM


title: BYmed15_YM_rep1

value: BY4741 med15::NatR pGS35


title: BY4741_YM_rep3


title: SCN-14yrs-F-Cell24

description:
G_D12_38Cell_24_USPD16100592-N710-AK403_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BY4741_YM_rep1


title: pIRES-Select_1

value: Xenograft

value: pIRES


title: SCN-14yrs-F-Cell23

description:
G_D12_38Cell_23_USPD16100592-N709-AK402_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: Fra2_cl1-SCID_2


title: BY4741_YM_rep2


title: BYpMM-BY_YPDMCHM_rep3

value: treated


title: Fra2_cl1-SCID_1

value: scid


title: BYpMM-789_YPDMCHM_rep3

value: YPD


title: pIRES-SCID_3


title: SCN-14yrs-F-Cell22

description:
G_D12_38Cell_22_USPD16100592-N708-AK428_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-789_YPDMCHM_rep2


title: SCN-14yrs-F-Cell21

description:
G_D12_38Cell_21_USPD16100592-N707-AK400_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-789_YPDMCHM_rep1


title: BYpMM-BY_YPDMCHM_rep1


title: BYmed15_YPDMCHM_rep3


title: PATU8902_DCLK1IN1_24h_rep1

city: Boston

first: Behnam

last: Nabet

state: MA

address: 360 Longwood Ave, LC-2100

department: Cancer Biology

institute: Dana-Farber Cancer Institute

data_processing:
Fastq files were aligned to human genome build hg19 using HiSat with default parameters.
Transcripts were assembled and cuffquant and cuffnorm from the cufflinks pipeline were used to generate FPKM values as previously described (Trapnell et al., Nat. Biotechnol. 28, 511-515, 2010).
FPKM values were then normalized to synthetic ERCC spike-in RNAs as previously described previously (Loven et al., Cell 151, 476-482, 2012).
Genome_build: hg19
Supplementary_files_format_and_content: PDAC_cell_line_cuffnorm_all_fpkm_exprs.txt: Tab-delimited text file matix containing ERCC cell count normalized FPKM values for each transcript from the cell line experiment.

molecule: polyA RNA

growth_protocol: PATU-8988T (source: DSMZ, media: DMEM, 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin) and PATU-8902 (source: DSMZ, media: DMEM, 10% FBS, 100 U/mL penicillin, 100 μg/mL streptomycin) were cultured at 37 ºC and 5% CO2.

extract_protocol:
PATU-8988T and PATU-8902 cells were treated with DMSO or 2.5 μM DCLK1-IN-1, washed twice with PBS, lysed and homogenized using Qiashredder columns (Qiagen). RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Prior to library preparation, ERCC RNA Spike-In Mix #1 (Life Technologies) was added to cell-count-normalized RNA samples.
Illumina sequencing libraries were prepared using the KAPA mRNA HyperPrep kit (Roche). Equimolar multiplexed libraries were sequenced on a NextSeq 500 (Illumina, 75 bp single-end reads).

treatment_protocol: PATU-8988T and PATU-8902 cells were treated with DMSO or 2.5 μM DCLK1-IN-1 for the times indicated.

tag: cell line

value: PDAC

tag: culture condition

value: DMEM, 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin

value: 2.5 μM DCLK1-IN-1 for 24 h


title: PATU8902_DCLK1IN1_24h_rep3


title: PATU8902_DCLK1IN1_24h_rep2


title: pIRES-SCID_2


title: SCN-14yrs-F-Cell2

description:
G_D12_38Cell_2_USPD16100592-N702-AK390_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: Peripheral blood neutrophils

tag: cdna synthesis

value: Fluidigm C1 protocol (v4 chemistry)

tag: library prep


title: BY4741_YPDMCHM_rep3


title: BYmed15_YPDMCHM_rep2


title: pIRES-SCID_1


title: PATU8902_DCLK1IN1_6h_rep2

value: 2.5 μM DCLK1-IN-1 for 6 h


title: PATU8902_DCLK1IN1_6h_rep3


title: SCN-14yrs-F-Cell19

description:
G_D12_38Cell_19_USPD16100592-N705-AK391_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

tag: sequencing parameters

value: 75bp Paired-End, 150 million reads/96 cell library

tag: age

value: 14 year old


title: BYpMM-BY_YPDMCHM_rep2


title: BYpMM-BY_YPD_rep3

value: untreated


title: SCN-14yrs-F-Cell20

description:
G_D12_38Cell_20_USPD16100592-N706-AK392_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs

value: Nextera XT DNA Library Preparation Kit (Illumina)

tag: Sex

value: female

tag: disease

value: with Severe Congenital Neutropenia


title: SCN-14yrs-F-Cell18

description:
G_D12_38Cell_18_USPD16100592-N704-AK390_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BY4741_YPDMCHM_rep2

tag: strain

tag: medium


title: PATU8902_DMSO_rep3

tag: treatment

value: DMSO for 24 h


title: BY4741_YPDMCHM_rep1

tag: mutant


title: PATU8902_DCLK1IN1_6h_rep1


title: SCN-14yrs-F-Cell17

description:
G_D12_38Cell_17_USPD16100592-N703-AK394_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-BY_YPD_rep1


title: PATU8902_DMSO_rep2


title: BYpMM-789_YPD_rep3


title: BYpMM-789_YPD_rep2


title: BYmed15_YPDMCHM_rep1

value: BY4741 med15::NatR pGS35


title: SCN-14yrs-F-Cell16

description:
G_D12_38Cell_16_USPD16100592-N709-AK403_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-789_YPD_rep1


title: SCN-14yrs-F-Cell15

description:
G_D12_38Cell_15_USPD16100592-N708-AK402_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: PATU8988T_DCLK1IN1_24h_rep3


title: PATU8902_DMSO_rep1


title: SCN-14yrs-F-Cell14

description:
G_D12_38Cell_14_USPD16100592-N707-AK428_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYmed15_YPD_rep3


title: BYmed15_YPD_rep2


title: BYmed15_YPD_rep1


title: BY4741_YPD_rep1


title: PATU8988T_DCLK1IN1_24h_rep1


title: PATU8988T_DCLK1IN1_24h_rep2


title: BY4741_YPD_rep3


title: SCN-14yrs-F-Cell13

description:
G_D12_38Cell_13_USPD16100592-N706-AK400_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: BYpMM-BY_YPD_rep2


title: PATU8988T_DCLK1IN1_6h_rep3


title: SCN-14yrs-F-Cell12

description:
G_D12_38Cell_12_USPD16100592-N705-AK392_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: PATU8988T_DCLK1IN1_6h_rep2


title: SCN-14yrs-F-Cell10

description:
G_D12_38Cell_10_USPD16100592-N703-AK390_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: SCN-14yrs-F-Cell11

description:
G_D12_38Cell_11_USPD16100592-N704-AK391_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: PATU8988T_DCLK1IN1_6h_rep1


title: BY4741_YPD_rep2


title: cultures_invitro_chip94709

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

description:
ScRNA-seq of airway epithelial cells from differentiated ALI cultures sampled along a time course
RNA-seq from 8,722 cells sampled at days -5 (aka seed day), -2, 0, 1, 2, 4, 5, 7, 9, 11, 12, 14, 16, 18, 21, 23, 25, 28, 30, an d 32 after airlift of ALI-cultured tracheal epithelia from three human donors sequenced across 13 batches
Processed data files:
*_invitro_expression_matrix.txt
*_invitro_metadata.txt
Processed_invitro_raw.txt
Processed_invitro_norm.txt
Processed_invitro_metadata.txt

data_processing:
R1 contains the barcode (first 16 bp) and UMI (next 10 or 12 bp)
R2 contains the biological read
in vivo datasets: Initial pre-processing of the 10X in vivo scRNA-seq data, including demultiplexing, alignment to the hg38 human genome, and UMI-based gene expression quantification, was performed using Cell Ranger (version 3.0, 10X Genomics).
in vivo datasets: We carried out donor-specific filtering of cells to ensure that high quality single cells were used for downstream analysis. Although samples comprising multiple cells were removed during the cell selection stage, we safeguarded against doublets by removing all cells with either a gene count or UMI count over the 99th percentile. Furthermore, we removed cells exhibiting fewer than 1500 genes or greater than 40% of mapped reads originating from the mitochondrial genome. Prior to downstream analysis, select mitochondrial and ribosomal genes (genes beginning with MTAT, MT-, MTCO, MTCY, MTERF, MTND, MTRF, MTRN, MRPL, MRPS, RPL, or RPS), or very lowly expressed genes (expressed in < 0.1% of cells) were also removed. The final quality-controlled dataset consisted of 40,929 cells. After initial clustering and visualization, which allowed for identification of 12 major cell populations (see Supplementary Figure S1a), 2,461 cells were removed that we characterized as non-epithelial (immune, endothelial, and mesenchymal cells). We then repeated the same QC filtering above for this culled dataset (except further reducing the percent mitochondrial reads cutoff to 30%), which left us with 36,248 epithelial cells for further analysis.
in vivo datasest: To account for differences in coverage across cells, prior to downstream analysis we normalized and variance stabilized UMI counts for each donor using SCTransform, which yields Pearson residuals from a generalized linear model that includes sequence depth as a covariate. Normalization was carried out using the Seurat R package (version 3).
in vivo dataset: Prior to clustering and visualizing each of the two scRNA-seq datasets (in vitro and in vivo), we reduced the dimensionality of variation in a way that accounted for batch-based shifts in expression among donors. To do this in the in vivo dataset, we used single cell integration102 implemented in Seurat v3, which identifies mutual nearest neighbor (MNN) cells across pairwise donors to use as “anchors” by which a batch correction can be calculated and then applied in order to bring expression across datasets into a common subspace. We carried out the integration analysis using the top 30 dimensions from a canonical correlation analysis (CCA) based on SCTransform normalized expression of the top 3,000 most informative genes across donor datasets, where “informativeness” was defined by gene dispersion (i.e., the log of the ratio of expression variance to its mean) across cells, calculated after accounting for its relationship with mean expression (using the SelectIntegrationFeatures function).
in vitro datasets: We trimmed and culled raw demultiplexed cDNA reads in FASTQ files using Cutadapt, trimming poly A tails and 5’ and 3’ ends with q < 20 and removing any reads shorter than 25 base pairs. Trimmed reads were then aligned to the hg38 human genome with GSNAP, setting “max-mismatches=0.05” and accounting for both known Ensembl splice sites and SNPs. Gene expression was quantified using HTSeq with “stranded=yes”, “mode=intersection-nonempty”, and “t=gene” and then summed the number of unique molecular identifiers (UMIs) for each gene across runs for each cell to obtain a UMI count matrix used for all downstream analysis.
in vitro datasets: We carried out quality-control filtering using a similar approach to that used for the in vivo dataset, removing 100 cells for which the percentage of reads mapping to genes was <50%, 2,262 cells with > 25% of mapped reads being mitochondrial, and 384 cells with UMI counts outside the 3rd and 97th percentiles. We filtered genes using the procedure described above for the in vivo dataset. The final quality-controlled dataset consisted of 5,976 cells, and 23,825 genes.
Genome_build: hg38
Supplementary_files_format_and_content: "expression_matrix" text files contain expression count tables that include all samples in the original fastq files. All sample names include the sequencing barcode
Supplementary_files_format_and_content: "metadata" text files don't contain counts, but rather important variables associated with each sample
Supplementary_files_format_and_content: "processed" text files contain either raw counts, normalized counts, batch integrated counts, or metadata only for samples and genes that have gone through QC filtering. These are the data used for analysis in the study

source_name: Human epithelial tracheal, cultured

growth_protocol: Tracheal cells (P1) were expanded a second time on feeders in F-media/RI and harvested by differential trypsinization with FBS neutralization. After washing in 1X PBS, cells were resuspended in 1X HBSS and subjected to DNase digest for 5 min at 37°C. DNase was diluted 2-fold with HBSS, cells were centrifuged 1000 rpm, 5 min, 4°C and seeded onto bovine collagen-coated 6.5mm transwell inserts (2 x104 cells/insert) in ALI Expansion medium (50% BEBM, 50% DMEM-C, 0.5 mg/mL BSA, 80 μM ethanolamine, 10 ng/mL hEGF, 0.4 μM MgSO4, 0.3 μM MgCl2, 1 μM CaCl2, 30 ng/mL retinoic acid, 0.8X insulin*, 0.5X transferrin*, 1X hydrocortisone*, 1X epinephrine*, 1X bovine pituitary extract*, 1X gentamicin/amphotericin*, *relative to BEGM Bullet Kit aliquot) with RI (Day -5). RI was removed after 24 h, and ALI expansion medium was changed 48 hlater (Day -2). After another 48 h(Day 0), apical medium was removed and basolateral medium was replaced with PneumaCult (PC)-ALI media. Basolateral medium was exchanged for fresh PC-ALI every 48 or 72 h for the subsequent 11 days, and then daily for the following 22 days along with an apical wash of 20 μL PC-ALI.

extract_protocol:
For each timepoint, medium was removed from endpoint ALI cultures, and the apical chamber was washed with warm PBS/DTT (10mM) for 5 min at 37°C, followed by a warm PBS wash of both chambers. Cultures were dislodged from the insert with 200 μL apical dissociation solution (Accutase with 5mM EDTA and 5mM EGTA) for 30 min at 37°C with occasional manual agitation. Single cell suspensions were diluted, centrifuged, washed once with PBS/DTT and twice with PBS, before cryopreservation (F-media, 40% FBS, 10% DMSO). On the day of capture, cells were quick thawed, washed with 1X PBS (no BSA) and counted before proceeding with WaferGen capture according to the manufacturer’s instructions with the following modifications: 5 or 10 x 104 cells were stained per sample, single cell candidates were confirmed by manual visual triage.
ICELL8 single-cell poly-(A)+ transcriptome amplification hands-on workflow (with Triton X-100 for cell lysis), protocol D07-000040-003 rev4

value: Airway epithelial

tag: smoking status


title: PATU8988T_DMSO_rep3


title: Donor 4, F. alocis treated, 6h

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling
Quality control (QC) of the raw sequence data was performed using FastQC (version 0.10.1).  Quality trimming was not deemed necessary.
Raw fastq sequences were directly aligned to the Homo sapiens reference genome assembly (hg38.fa) using tophat2 (version 2.0.13) as well as STAR (version 2.6) using ENSEMBL v82 transcript annotations for hg38.
Raw counts were determined using HTSeq v 0.10.0 for the STAR mapped results.  The reverse option was used to indicate strand orientation.
Differential expression analysis between each treatment condition (1hr, 3hrs, and 6hrs) and the control condition was performed using the Tuxedo Suite program cuffdiff2 (version 2.2.1)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts and FPKM

source_name: blood

growth_protocol: Filifactor alocis: F. alocis ATCC 38596 was cultured in brain heart infusion (BHI) broth supplemented 5 mg/mL yeast extract, L-cysteine (0.05%) and arginine (0.05%) for 7 days anaerobically at 37 °C from glycerol stock. Bacteria were subcultured in BHI broth and anaerobically at 37 °C for 14 days, as previously described [1]. Bacteria were serum opsonized by incubation at 37°C for 20 min in 10% normal human serum (Complement Technology, Inc.).   Isolation and purification of human neutrophils: Human donor recruitment, blood draws, and the use of the materials were in accordance with the guidelines approved by the Institutional Review Board of the University of Louisville. Neutrophils were isolated from venous blood of healthy donors using plasma‐Percoll gradients, as described previously [2, 3]. Neutrophil populations were further enriched to obtain highly pure cells (>99%) by negative magnetic selection using the EasyEights EasySep Magnet and human neutrophil enrichment kit (Stemcell Technologies, Vancouver, BC, Canada). Cell purity was assessed by simultaneously staining with FITC‐conjugated anti‐CD66b (clone G10F5; BioLegend, San Diego, CA, USA) and APC‐conjugated anti‐CD16 (clone CB16; eBioscience, San Diego, CA, USA) antibodies and determining the percentage of CD66b+CD16+ cells using BD FACSCalibur flow cytometer (BD Biosciences, San Jose, CA, USA). Highly pure (>99%) neutrophils were cultured in complete RPMI‐1640 medium (Sigma-Aldrich) with 5% human serum (Atlanta Biologicals).

extract_protocol:
RNA was isolated from untreated and F. alocis challenged human purified neutrophils (10–20 × 106 cells) using the hybrid method of TRIzol and RNeasy minikit (Qiagen). The aqueous phase containing RNA was obtained loaded on the Qiagen column for further purification of RNA. The purified RNA quality was measured by running sample on Bioanalyzer.
Libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit-Set A (Cat # RS-122-2301) with Ribo-Zero Gold.

treatment_protocol: Human neutrophils were seeded at the density of 1 million per 12 well plate and allow to attach for 30 mins at 37 °C incubator. Neutrophils were challenged with serum opsonized F. alocis at a multiplicity of infection (MOI) of 10 bacteria per neutrophil.  Phagocytosis was synchronized by centrifugation at 14 °C for 4 min at 600 ×g. Following centrifugation, the plate was incubated at 37 °C for 1, 3 and 6h. After each time point, the cells were harvested using Trizol (Ambion) and stored at -80 °C until RNA isolation.

value: neutrophil

value: F. alocis

tag: time


title: Donor 4, F. alocis treated, 3h


title: cultures_invitro_chip94684


title: SCN-14yrs-F-Cell1

description:
G_D12_38Cell_1_USPD16100592-N701-AK394_H2W2YBBXX_L7_1
Neutrophils from a 14 year old female patient with Severe Congenital Neutropenia
exp.Neutrophils-RSEM-TPMs.txt
donors.Neutrophils-RSEM-TPMs


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 5

type: genomic

city: Amsterdam

first: Renske

middle: DM

last: Steenbergen

address: De Boelelaan 1117

department: Pathology

country: Netherlands

institute: Amsterdam UMC, location VUmc

description: US22502676_252252210500_S01_CGH_107_Sep09_1_1.txt

hyb_protocol: DNA was hybridized using the Agilent SurePrint G3 Human CGH Microarray Kit for the 4x180K Agilent platform (Agilent).

scan_protocol: Scanning was performed using a G2505B scanner (Agilent) using the protocol designed for the used platform by the manufacturer (Agilent).

data_processing: The pre-processing of CGH data comprised median normalization and segmentation using the circular binary segmentation method (Olshen et al., Biostatistics 2004).

molecule: genomic DNA

source_name: primary human foreskin keratinocytes transfected with HPV18

label_protocol: DNA was labeled using the CYTAG CGH Labeling kit (Enzo Life Sciences) according to the manufacturer's recommendations.

growth_protocol: Establishment and culture of the HPV16 (FK16A and FK16B) and HPV18 (FK18A and FK18B) transformed keratinocyte cell lines was described previously (Steenbergen et al., Oncogene 1996).

extract_protocol: Total DNA was isolated by standard proteinase K digestion followed by phenol-chloroform purification (van Zeeburg et al., Cancer Research 2005).

tag: transformation stage

value: anchorage independent

tag: time point

value: no treatment


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 8

description: US22502676_252252210500_S01_CGH_107_Sep09_1_3.txt


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 6

description: US22502676_252252210502_S01_CGH_107_Sep09_1_3.txt


title: cultures_invitro_chip94640

tag: cell type


title: Donor 4, F. alocis treated, 1h


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 7

description: US22502518_252252210499_S01_CGH_107_Sep09_1_3.txt


title: cultures_invitro_chip94633


title: cultures_invitro_chip94638


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 8

description: US22502676_252252210501_S01_CGH_107_Sep09_1_2.txt


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 7


title: PATU8988T_DMSO_rep2

tag: cell line

value: PDAC

value: DMEM, 10% FBS, 100 U/mL penicillin, 100 ug/mL streptomycin


title: cultures_invitro_chip94632


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 6

description: US22502676_252252210501_S01_CGH_107_Sep09_1_4.txt


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 3


title: Donor 4, untreated


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 1

description: US22502518_252252210499_S01_CGH_107_Sep09_1_2.txt

value: extended lifespan


title: PATU8988T_DMSO_rep1

tag: culture condition


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 4


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 4

description: US22502676_252252210501_S01_CGH_107_Sep09_1_3.txt

value: immortal


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 1

description: US22502676_252252210502_S01_CGH_107_Sep09_1_2.txt


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 3


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 2

description: US22502676_252252210501_S01_CGH_107_Sep09_1_1.txt


title: cultures_invitro_chip94618


title: HPV18-transfected human foreskin keratinocytes_line B_timepoint 2

description: US22502676_252252210500_S01_CGH_107_Sep09_1_4.txt


title: HPV18-transfected human foreskin keratinocytes_line A_timepoint 5


title: Donor 3, F. alocis treated, 6h


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 8

description: US22502676_252252210503_S01_CGH_107_Sep09_1_2.txt

source_name: primary human foreskin keratinocytes transfected with HPV16


title: cultures_invitro_chip94602


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 7

description: US22502676_252252210503_S01_CGH_107_Sep09_1_3.txt


title: cultures_invitro_chip94582


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 6


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 5


title: cultures_invitro_chip94581


title: Donor 2, F. alocis treated, 6h


title: Donor 3, untreated


title: cultures_invitro_chip94577


title: Donor 3, F. alocis treated, 3h


title: cultures_invitro_chip94575


title: Donor 2, F. alocis treated, 3h


title: Donor 3, F. alocis treated, 1h


title: Sample_881 B16_TEC_isotype

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
base calling and de-multipexing using CASAVA version 1.8
Alignment withTopHat2 version v2.0.11 and Bowtie2 version 2.2.1 using the default parameters
Quantification with Partek Genomics Suite V6.6
reads mapped to each transcript against the RefSeq mm10 annotation download on May 2015
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include DeSeq2 normalized counts for each Sample.

organism: Mus musculus

source_name: B16.F10 tumor

growth_protocol: B16.F10 melanoma cells (250.000 cells) were subcutaneously (s.c.) implanted in C57BL/6 male mice (8 weeks old, Taconic Biosciences).

extract_protocol:
The tumors were cut in small pieces and enzymatically digested by a solution containing DMEM (ThermoFisher) + 5mg/mL Collagenase II (Sigma) + 50μg/mL DNase I (Sigma) for 40 min at 37oC. Then they were passed through 70 μm cell strainers and the generated single cell suspensions undergone erythrocyte lysis on ice. The samples were blocked for unspecific binding to CD16/32 (TruStain fcX, Biolegend) and stained using the following antibodies in 2μg/mL in FACS buffer (PBS + 2% BSA + 1mM EDTA): anti-CD45-APC (clone 30-F11, Biolegend), anti-CD31-PE (clone MEC 13.3, BD Biosciences). The samples were stained for live/dead staining with DAPI. Samples were washed with FACS-buffer and sorted in a BD FACSariaIII cytometer (BD Biosciences). The sorted cells (approximately 100.000 CD45-CD31+ tumor endothelial cells) were collected in PBS and lysed in Qiazol reagent (Qiagen). Total RNA was extracted from isolated tumor endothelial cells from B16.F10 tumors treated with anti-CD40 or isotype control antibodies using the RNeasy Mini and Microkits (Qiagen).
According to the manufacturer´s instructions in the Tru-Seq RNA library preparation kit v2, 10 ng of RNA was converted into cDNA libraries

treatment_protocol: The mice were randomly divided into two groups and were treated with 2 peritumoral injections of 30µg αCD40 (FGK4.5, BioXcell) or 30µg rat IgG2a (2A3, BioXcell) isotype antibodies at day 13 and 16 after B16.F10 tumor inoculation. The mice were sacrificed one day after the last treatment and tumors were dissected out and subjected to FACS sorting of tumor endothelial cells followed by RNA-sequencing

tag: genetic background

value: isotype

tag: mouseid


title: Sample_879 B16_TEC_isotype


title: Donor 2, F. alocis treated, 1h


title: Sample_877 B16_TEC_isotype


title: Sample_875 B16_TEC_isotype


title: Donor 2, untreated


title: Donor 1, F. alocis treated, 6h


title: Sample_873 B16_TEC_anti-CD40


title: Sample_871 B16_TEC_anti-CD40


title: Donor 1, F. alocis treated, 3h


title: Sample_869 B16_TEC_anti-CD40


title: Sample_867 B16_TEC_anti-CD40


title: Gfi1 wild-type 10x scATAC-Seq replicate 3

description: Male and Female mixed gating strategy DNA

library_source: genomic

data_processing:
The fastq files for each sample generated from scATAC-Seq sequencing were processed in mm10 using the cellranger-atac count program (version 1.0.1)(10X Genomics) [https://www.ncbi.nlm.nih.gov/pubmed/28091601] (“cellranger-atac count –id – reference –fastqs”). The two replicate Gfi1+/+ mouse scATAC-Seq datasets produced 14,766 and 15,186 filtered nuclei barcodes with 11,220 and 18,402 median fragments per nuclei, respectively. The one Gfi1R412X/R412X  mouse scATAC-Seq dataset produced 15,767 filtered nuclei barcodes and 8,305 median fragments per nuclei. The resulting “filtered peak bc matrix” was used as input to downstream analysis of identifying cell clusters with Seurat (version 3.0.2), following downsampling of Gfi1+/+ capture reads to that of the Gfi1R412X/R412X (samtools) [Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck III, W. M., ... & Satija, R. (2019). Comprehensive Integration of Single-Cell Data. Cell.].  Following cicero analysis and filtering (default parameters), 18,457 Gfi1+/+ and 7,692 Gfi1R412X/R412X barcodes were retained.  To perform label transfer in Seurat, mapping scATAC-Seq to scRNA-Seq expression values, a gene activity matrix was produced from the combined Gfi1+/+ replicates, as well as the Gfi1R412X/R412X sample with the program Cicero (version 1.0.15) as previously described [Pliner, H. A., Packer, J. S., McFaline-Figueroa, J. L., Cusanovich, D. A., Daza, R. M., Aghamirzaie, D., ... & Adey, A. C. (2018). Cicero predicts cis-regulatory DNA Interactions from single-cell chromatin accessibility data. Molecular cell, 71(5), 858-871.]. The first 30 principal components were used for “FindNeighbors” and a resolution of “1.2” was used for “FindClusters”. Transfer anchors were found using the top 5,000 variable features and cell type predictions were made with the highest scoring prediction used as the cell label for downstream analysis, constituting labelled clusters from Seurat. The .bam alignment file generated by the cellranger-atac count program was then split into a separate file for each cluster based on the “CB” barcode tag associated with each read, which was used as input to IGV to display coverage for each cell state, normalized by the total number of reads. Predicted nuclei clusters from the default cellranger-atac graphclust software were also compared to the Seurat cluster predictions at the indicated resolutions (Extended Data Fig. 12b). Additionally, the SNAP-ATAC workflow was run in parallel on these data, using the default options to compare to the Seurat clusters [https://www.biorxiv.org/content/10.1101/615179v2. Both cellranger-atac graphclust as well as SNAP-ATAC provided unbiased analyses to cluster cells. These were compared to the label transfer program of Seurat by calculating the percentage of cells shared between clusters. To test for the accessibility of regions at likely Gfi1 binding locations, these files were used to compute coverage across the +/- 500 bp region for each peak found in the ChIP-Seq data analysis, which was then normalized by the total number of cells associated to each cluster in the separate .bam files.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file and HDF5
Supplementary_files_format_and_content: clusters.Gfi1-WT-rep-3531.txt: Cell Clusters: Seurat 3 assigned cluster labels for Gfi1-WT nuclei (replicate 1)
Supplementary_files_format_and_content: clusters.Gfi1-WT-rep-3534.txt: Cell Clusters: Seurat 3 assigned cluster labels for Gfi1-WT nuclei (replicate 2)
Supplementary_files_format_and_content: clusters.Gfi1-R412X-R412X.txt: Cell Clusters: Seurat 3 assigned cluster labels for Gfi1-R412X-R412X nuclei
Supplementary_files_format_and_content: Gfi1-WT-rep-3531-filtered_tf_bc_matrix.h5: DNA Accessiblility TF motifs: TF-barcode matrix for Gfi1-WT nuclei (replicate 1)
Supplementary_files_format_and_content: Gfi1-WT-rep-3534-filtered_tf_bc_matrix.h5: DNA Accessiblility TF motifs: TF-barcode matrix for Gfi1-WT nuclei (replicate 2)
Supplementary_files_format_and_content: Gfi1-R412X-R412X-filtered_tf_bc_matrix.h5: DNA Accessiblility TF motifs: TF-barcode matrix for Gfi1-R412X-R412X nuclei
Supplementary_files_format_and_content: Gfi1-WT-rep-3531-filtered_peak_bc_matrix.h5: DNA Accessiblility peaks: UMI counts for Gfi1-WT nuclei (replicate 1)
Supplementary_files_format_and_content: Gfi1-WT-rep-3534-filtered_peak_bc_matrix.h5: DNA Accessiblility peaks: UMI counts for Gfi1-WT nuclei (replicate 2)
Supplementary_files_format_and_content: Gfi1-R412X-R412X-filtered_peak_bc_matrix.h5: DNA Accessiblility peaks: UMI counts for Gfi1-R412X-R412X nuclei

source_name: Bone marrow

extract_protocol:
Bone marrow was extracted by crushing hindlimbs isolated from mice immediately following euthanasia. The following bone marrow cell populations were FACS-sorted: proNeu-2 (Live Modified Lin- CD34+ CD16/32+ CD117+ Vcam1+), preNeu-1 (Live Modified Lin- CD34+ CD16/32+ CD117+ Ly6c+ CD11b- CD115- Vcam1+), preNeu-2 & preNeu-3 (Live Modified Lin- CD34+ CD16/32+ CD117+ Ly6c+ CD11b+ CD115- Ly6g dim-mid),), immNeu (Live Modified Lin- CD34+ CD16/32+ CD117+ Ly6c+ CD11b+ CD115- Ly6g high), and Modified GMP (Live Modified Lin- CD34+ CD16/32+). See https://support.10xgenomics.com/single-cell-atac for additional details.
Cells were processed according to ‘Demonstrated Protocol – Nuclei Isolation for Single Cell ATAC Sequencing, CG000169 Rev B). Isolated nuclei (12,000-20,000) were captured with a Chromium Controller Instrument (10x Genomics) using the Chromium Next GEM Single Cell ATAC Library & Gel Bead Kit according to the manufacturer’s instructions. Nuclei from two independent Gfi1-wild-type animals were loaded onto two separate ports of the same 10x Genomics Chromium chip and sequenced to a combined target depth of ~1 billion reads. Nuclei from a single Gfi1-R412X-R412X animal was laoded onto a port on the 10x Genomics Chromium chip.

value: Bone marrow derived mixed-gating strategy

tag: genotype

value: Wild-type

tag: cdna synthesis

value: 10x Genomics single cell 3’ v2 assay protocol

tag: library prep

value: Chromium Single Cell ATAC Reagent Kits User Guide (v1 Chemistry)

tag: sequencing parameters

value: 497 million reads


title: Donor 1, F. alocis treated, 1h


title: Gfi1 wild-type 10x scATAC-Seq replicate 2

tag: strain

value: 493 million reads


title: T154_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,650 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T154_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata

source_name: Human epithelial tracheal

growth_protocol: Primary cell culture: Primary human basal airway epithelial cells from tracheal digests were expanded at 37°C on NIH 3T3 fibroblast feeders in F-media (67.5% DMEM-F, 25% Ham’s F-12, 7.5% FBS, 1.5 mM L-glutamine, 25 ng/mL hydrocortisone, 12 5ng/mL EGF, 8.6 ng/mL cholera toxin, 24 μg/mL Adenine, 0.1% insulin, 75 U/mL pen/strep) with ROCK1 Inhibitor (RI, 16 μg/mL) and antibiotics (1.25 μg/mL amphotericin B, 2 μg/mL fluconazole, 50 μg/mL gentamicin)82 and cryopreserved in freeze media upon initial passaging (P1).

extract_protocol:
Human tracheas were wet in Stock solution (DMEM-F + 1X PSA) and fat and connective tissue were removed, before cutting into small sections. Sections were rinsed in Stock solution to remove mucus before proteolytic digest (0.2% Protease in Stock solution) overnight at 4°C, with rocking. Protease was neutralized with FBS, the supernatant was saved (tube 1), and tracheal sections washed (5 mM HEPES, 5 mM EDTA, 150 mM NaCl) for 20 min at 37°C. The supernatant was also saved (tube 2) and the loosened epithelium was then manually scraped off into stock solution with 10% FBS (tube 3), and all cells were collected by centrifugation for 10 min at 1000 rpm, 4°C (tubes 1, 2, and 3). Cell pellets resuspended in BEGM+0.5X PSA were filtered using a 70um cell strainer, collected by centrifugation (5 min, 1000 rpm, 4°C) and cryopreserved in freeze media (F-media, 30% FBS, 10% DMSO). On the day of capture, cells were quick thawed, washed twice in 1X PBS/BSA (0.04%) and resuspended at 1200 cells/μL for capture on the 10X Genomics platform.
10X single cell (version 3 chemistry)

value: heavy smoker


title: Gfi1 wild-type 10x scATAC-Seq replicate 1

description: Male mixed gating strategy DNA

value: 545 million reads


title: Donor 1, untreated

value: neutrophil


title: T165_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 2,118 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T165_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata

value: Airway epithelial

value: nonsmoker


title: T164_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 3,247 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T164_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: T167_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 2,867 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T167_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: NT3

city: Ultimo

first: Liz

last: Harry

state: NSW

address: 15 Broadway

country: Australia

institute: ithree institute

data_processing:
Base calling was undertaken using Illumina's HCS (HiSeq Control Software v3.3) software
Sequences reads were trimmed for adaptor sequence (TruSeq3 paired-ended), and masked for low-complexity / low-quality sequence using Trimmomatic (v0.36) with the default parameters
Reads were mapped to Pseudomonas aeruginosa UCBPP-PA14 genome sequence using RSubread (v 1.30.7)
Batch effects were corrected by RUVSeq (version 1.13.0) and the RUV correction method with k = 1, using replicate samples to estimate the factors of unwanted variation
Differential expression analysis was carried out using strand-specific gene-wise quantification using the DESeq2 package (version 1.18.0)
Genome_build: Pseudomonas aeruginosa UCBPP-PA14 genome accession number CP000438.1
Supplementary_files_format_and_content: featureCounts output files

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: P. aeruginosa PA14 overnight cultures were diluted to OD600 0.05 in CAMHB and grown to mid-exponential phase (OD600 0.4) in vented T250 flasks (Corning, Falcon) at 37°C and 200rpm

extract_protocol:
Cell pellets were recovered (5000 g, 15 min) and lysed in QIAzol reagent (Qiagen). Total RNA was isolated using the RNeasy mini kit (Qiagen) following manufacturer instructions and DNA removed with DNase I (TURBO DNA-free kit; Invitrogen) following manufacturer instructions. Ribosomal RNA was depleted using the Ribo-Zer rRNA Removal kit (Illumina) following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols and the TruSeq stranded mRNA kit (Illumina) and barcoding was then undertaken on RNA for HiSeq analysis. Samples were run on the Illumina HiSeq4000 platform (1X100 base pair paired-end reads).

treatment_protocol: Mid-exponential culture was split into flasks containing treatments at a final concentration of 0.5xMIC and an additional untreated flask containing an equivalent volume of media only. Cultures were incubated for a futher 30 minutes at 37°C and 200rpm

value: wild type


title: cultures_invitro_chip94572

description:
ScRNA-seq of airway epithelial cells from differentiated ALI cultures sampled along a time course
RNA-seq from 8,722 cells sampled at days -5 (aka seed day), -2, 0, 1, 2, 4, 5, 7, 9, 11, 12, 14, 16, 18, 21, 23, 25, 28, 30, an d 32 after airlift of ALI-cultured tracheal epithelia from three human donors sequenced across 13 batches
Processed data files:
*_invitro_expression_matrix.txt
*_invitro_metadata.txt
Processed_invitro_raw.txt
Processed_invitro_norm.txt
Processed_invitro_metadata.txt


title: T166_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 2,627 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T166_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: NT2_og


title: ChIP-seq of ZNF398 in BG01V human embryonic stem cells

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

institute: University of Groningen

data_processing:
Reads were mapped to the Homo sapiens hg19 reference assembly using Bowtie v1.2.2 (Langmead et al., 2009), keeping only uniquely mapped reads. Reads (75 bp) were bioinformatically extended to the average insert size (150 bp), and identical reads (reads starting and ending at the same positions) were collapsed. Peak calling was performed using MACS v2.1.1 (Zhang et al., 2008), selecting only peaks with q-value < 0.05. A non-redundant set of common peaks between the two ZNF398 ChIP-seq replicates was generated using the intersectBed utility from BEDTools (Quinlan and Hall, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files generated from BAM alignments using MACS

source_name: BG01V hESCs

growth_protocol: hESCs (HES2, H9 and BG01) and hiPSCs (KiPS) were cultured in Feeder-free on pre-coated plates with 0.5% growth factor-reduced Matrigel (CORNING Cat. 356231) (vol/vol in PBS with MgCl2/CaCl2_Sigma-Aldrich D8662) in E8 medium (made in-house according to Chen et al., 2011) or in mTeSR (StemCell Technologies 05850) at 37°C, 5% CO2, 5% O2. Cells were passaged every 3-4 days at a split ratio of 1:8 following dissociation with EDTA solution (0,5 mM in PBS without MgCl2/CaCl2_Sigma-Aldrich D8662, pH 8.0, ThermoFisher). The human foreskin fibroblasts BJ (passage 12, ATCC, CRL-2522) were cultured in DMEM/F12 (Sigma-Aldrich D6421) with 10% fetal bovine serum (FBS; Sigma-Aldrich F7524) at 37°C, 5% CO2, 21% O2. H9 line (WA09) and HES2 were obtained from and used under authorisation from WiCell Research Institute. KiPS were kindly provided by Austin Smith's laboratory (Takashima et al., 2014). All cell lines were mycoplasma-negative (Mycoalert, Lonza).

extract_protocol:
After decrosslinking, DNA was purified using QIAQuick PCR Purification Kit (Qiagen) according to the manufacturer's instructions.
ChIP-seq library was prepared with approximately 5 ng of immunoprecipitated DNA were used as input for the NEBNext® ChIP-Seq Library Prep kit, following manufacturer's instructions.

treatment_protocol: Approximately 2×107 cells were cross-linked by addition of formaldehyde to 1% for 10 min at RT, quenched with 0.125 M glycine for 5 min at RT, and then washed twice in 1× PBS. The cells were resuspended in Isotonic buffer supplemented with 1% NP-40 to isolate nuclei. The isolated nuclei were then resuspended in ChIP Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA and protease inhibitors) supplemented with different concentration of detergents: 0% SDS, 1% Triton X-100; 0.15% SDS, 1% Triton X-100; 0.5% SDS, 0.5% Triton X-100; and 1% SDS, 0% Triton X-100. Extracts were sonicated using the Bioruptor® Twin (Diagenode) for 2 runs of 10 cycles [30 sec “ON”, 30 sec “OFF”] at high power setting. Cell lysate was centrifuged at 12,000 g for 10 min at 4°C. The supernatant performed in the conditions 3 and 4 was diluted with ChIP Dilution Buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton) before immunoprecipitation step. Bio-ChIP. Streptavidin beads (Dynabeads® MyOneTM Streptavidin T1) were saturated with PBS/1% BSA at RT for 1 hour, and then incubated with sample at 4°C for 4 hours on a rotator. Immunoprecipitated complexes were successively washed with Washing Buffer I (2% SDS), Washing Buffer II (50 mM HEPES pH 7.5, 500 mM NaCl, 0.1% Deoxycholate, 1% Triton X-100, 1 mM EDTA), Washing Buffer III (10 mM Tris-Cl pH 8.1, 250 mM LiCl, 0.5% NP-40, 0.5% Deoxycholate, 1 mM EDTA,) and TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA). All washes were performed at RT for 8 min on a rotator. SDS Elution Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) was added and incubated at 65°C overnight to reverse crosslink protein-DNA complexes.

tag: antibody


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 2

description: US22502676_252252210502_S01_CGH_107_Sep09_1_4.txt

tag: treatment

value: no treatment


title: NT2


title: T153_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 3,434 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T153_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 1

description: US22502676_252252210502_S01_CGH_107_Sep09_1_1.txt


title: NT_og


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 3

description: US22502676_252252210503_S01_CGH_107_Sep09_1_4.txt

value: anchorage independent


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 3

description: US22502676_252252210498_S01_CGH_107_Sep09_1_3.txt


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 6

description: US22502676_252252210498_S01_CGH_107_Sep09_1_2.txt


title: T101_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 3,295 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T101_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 1


title: ChIP-seq of ZNF398 in H9 human embryonic stem cells

source_name: H9 hESCs


title: NT1


title: T90_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 2,230 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T90_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 2

description: US22502518_252252210499_S01_CGH_107_Sep09_1_1.txt


title: HPV16-transfected human foreskin keratinocytes_line B_timepoint 4

description: US22502676_252252210503_S01_CGH_107_Sep09_1_1.txt


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 4

description: US22502676_252252210502_S01_CGH_107_Sep09_1_2.txt


title: ZNF398 SB43 #2

description: KiPS stably overexpressing ZNF398, treated with SB43 (replicate #2)

data_processing:
Reads were mapped to the Homo sapiens hg19 reference assembly using TopHat v2.1.1, and gene counts were computed using htseq-count (Anders et al., 2015). Differential expression analysis was performed using DESeq v2 (Anders and Huber, 2010). Genes with abs(log2(FC)) ≥ 1 and p-value < 0.01 were considered significant and defined as differentially expressed (Differentially Expressed Genes = DEG).
Genome_build: hg19
Supplementary_files_format_and_content: Bedgraph files generated from BAM alignments

source_name: Keratinocyte-derived iPS (KiPS)

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), following manufacturer instructions. RNA quality was assessed on the Agilent Bioanalyzer 2100.
For overexpression experiments, approximately 2 μg of total RNA were subjected to poly(A) selection, and libraries were prepared using the TruSeq RNA Sample Prep Kit (Illumina) following manufacturer’s instructions. Sequencing was performed on the Illumina NextSeq 500 platform.
Single-read RNA-seq

treatment_protocol: Stable transgenic hPSCs expressing candidates were generated by transfecting cells with PiggyBac (PB) transposon plasmids with piggyBac transposase expression vector pBase. In order to generate the PB plasmids, the candidates (NANOG, ZNF398, KLF7, MYC, ETS2, OTX2, ID1, BCOR and PRDM14) were amplified from cDNA and cloned into a pENTR2B donor vector. Then, the transgenes were gateway cloned into the same destination vector containing PB-CAG-DEST-bghpA and pGK-Hygro selection cassette. For DNA transfection, 250,000 hPSCs were dissociated as single cells with TrypLE (ThermoFisher) and were cotransfected with PB constructs (550 ng) and pBase plasmid (550 ng) using FuGENE HD Transfection (Promega, Cat. E2311), following the protocol for reverse transfection. For one well of a 12-well plate, we used 3,9 μl of transfection reagent, 1 μg of plasmid DNA, and 250,000 cells in 1 ml of E8 medium with 10µM Y27632 (ROCKi, Rho-associated kinase (ROCK) inhibitor_Axon 1683). The medium was changed after overnight incubation and Hygromycin B (200 μg/ml; Invitrogen Cat. 10687010) was added after 48 hours. For the overexpression experiments, hPSCs stably expressing an empty vector or the candidates were plated. The next day, cells were treated with DMSO or 10µM SB43 for 5 days and then analysed.

value: Keratinocyte-derived iPS (KiPS)


title: T137_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,351 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T137_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 8

description: US22502518_252252210499_S01_CGH_107_Sep09_1_2.txt


title: ZNF398 SB43 #1

description: KiPS stably overexpressing ZNF398, treated with SB43 (replicate #1)


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 7


title: MGO3


title: MGO2


title: ZNF398 DMSO #2

description: KiPS stably overexpressing ZNF398, treated with DMSO (replicate #2)

value: DMSO


title: HPV16-transfected human foreskin keratinocytes_line A_timepoint 5

description: US22502676_252252210498_S01_CGH_107_Sep09_1_4.txt


title: MH3


title: MH1


title: MGO1


title: AHMGO2


title: ZNF398 DMSO #1

description: KiPS stably overexpressing ZNF398, treated with DMSO (replicate #1)


title: MH2


title: AH2


title: AHMGO1


title: NANOG SB43 #1

description: KiPS stably overexpressing NANOG, treated with SB43 (replicate #1)


title: NANOG SB43 #2

description: KiPS stably overexpressing NANOG, treated with SB43 (replicate #2)


title: T121_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,433 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T121_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata

value: light smoker


title: T126_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,798 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T126_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: T120_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,846 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T120_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: T89_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 2,694 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T89_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata

value: pediatric


title: MB231cells R_DES_18 h-rep3

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression data from MB231 R mutation cells after 18 hours DES tretament

hyb_protocol: Five and one-half micrograms (5.5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 16 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0001.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using the GeneChip® Command Console software.

label: Biotin

label_protocol: Three hundred nanograms (300 ng) of total RNA were amplified and labeled as directed using the Affymetrix WT Plus Reagent Kit (WT Plus Kit).

growth_protocol: MB231 cells were seeded in 60 x 15 mm dishes with 5% sFBS medium and starved for 2 days.

extract_protocol: Total RNA samples were extracted from frozen tissues of individual mice using Trizol or from cells using RNeasy Mini Kit (Qiagen).

treatment_protocol: After changing to fresh 5% sFBS medium, cells were treated with vehicle control (DMSO, final concentration < 0.01%), 100 nM E2 or DES for 18 hours.

tag: tissue

value: breast

tag: mutation

value: 18 hours DES


title: AHMGO3


title: T85_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 3,775 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T85_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata

tag: smoking status


title: MB231cells R_DES_18 h-rep2

source_name: MB231 R mutation cells after 18 hours DES


title: T84_invivo

description:
ScRNA-seq of airway epithelial tracheal samples
RNA-seq from 1,883 QCed treacheal epithelial cells sampled in vivo
Processed data files:
T84_invivo_expression_matrix.txt
Processed_invivo_raw.txt
Processed_invivo_norm.txt
Processed_invivo_metadata.txt
processed_invivo_integrated.txt
Processed_invitro_seurat.Rdata


title: MB231cells R_DES_18 h-rep1


title: MB231cells R_E2_18 h-rep3

description: gene expression data from MB231 R mutation cells after 18 hours E2 tretament

value: 18 hours E2


title: NANOG DMSO #2

description: KiPS stably overexpressing NANOG, treated with DMSO (replicate #2)


title: MB231cells R_E2_18 h-rep1

source_name: MB231 R mutation cells after 18 hours E2


title: MB231cells R_veh_18 h-rep3

description: gene expression data from MB231 R mutation cells after veh tretament

source_name: MB231 R mutation cells after veh

value: vehicle


title: MB231cells R_veh_18 h-rep2


title: MB231cells R_veh_18 h-rep1


title: MYC SB43 #2

description: KiPS stably overexpressing MYC, treated with SB43 (replicate #2)


title: MB231cells R_E2_18 h-rep2


title: MYC SB43 #1

description: KiPS stably overexpressing MYC, treated with SB43 (replicate #1)


title: AH3


title: Ramos dCas9-krab MCP-sid1

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

state: CA

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

data_processing:
Library strategy: Amplicon-seq
Cassava 1.8
FASTX_TOOLKIT 0.0.13 cat $infastq | fastx_barcode_splitter.pl --bcfile $barcodes --prefix sg_ --bol --suffix .fastq
count_spacers.py -f $infastq -o $outcounts -i guide.sequences.csv
edgeR 3.28.0
Genome_build: table_s3.xlsx

source_name: Ramos Cells

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% FBS and 1x Penicillin-Streptomycin, tetracycline-free FBS was used for P493-6 cells.

extract_protocol:
Genomic DNA was isolated using the DNaesy Blood & Tissue kit (Qiagen).
Guide sequences were PCR-amplified from genomic DNA using target specific primers with Illumina compatible adapters.

treatment_protocol: Cells were transduced with lentiviral constructs for expression of dCas9 fusion proteins (KRAB, kPOGO, SID) and/or MCP-SID. Both, control cells and dCas9-fusion protein and/or MCP-SID expresing cells were transduced with a pooled CRISPR single-guide RNA library (MYCncLibrary) and subjected to phenotypic selection.

value: Ramos

tag: mcp

value: MCP-SID


title: NANOG DMSO #1

description: KiPS stably overexpressing NANOG, treated with DMSO (replicate #1)


title: MYC DMSO #2

description: KiPS stably overexpressing MYC, treated with DMSO (replicate #2)


title: MB231cells Q_DES_18 h-rep3

description: gene expression data from MB231 Q mutation cells after 18 hours DES tretament


title: MB231cells Q_DES_18 h-rep2

source_name: MB231 Q mutation cells after 18 hours DES


title: Ramos Control rksrm 3

description:
ramoskrabmcpsid_none_3
supplementary file identical GSM4204687 since used same control


title: MB231cells Q_DES_18 h-rep1


title: MYC DMSO #1

description: KiPS stably overexpressing MYC, treated with DMSO (replicate #1)


title: AH1


title: Ramos Control rksrm 2

description:
ramoskrabmcpsid_none_2
supplementary file identical GSM4204686 since used same control


title: MB231cells Q_E2_18 h-rep2

description: gene expression data from MB231 Q mutation cells after 18 hours E2 tretament


title: MB231cells Q_E2_18 h-rep1

source_name: MB231 Q mutation cells after 18 hours E2


title: Ramos Control rksrm 1

description:
ramoskrabmcpsid_none_1
supplementary file identical GSM4204685 since used same control


title: Ramos dCas9-krab MCP-sid2


title: MB231cells Q_veh_18 h-rep2

description: gene expression data from MB231 Q mutation cells after veh tretament

source_name: MB231 Q mutation cells after veh


title: MB231cells Q_veh_18 h-rep3


title: P493-6 dCas9-sid 3

source_name: P493-6 Cells


title: MB231cells Q_veh_18 h-rep1


title: KLF7 DMSO #2

description: KiPS stably overexpressing KLF7, treated with DMSO (replicate #2)


title: MB231cells WT_DES_18 h-rep3

description: gene expression data from MB231 WT cells after 18 hours DES tretament

source_name: MB231 WT cells after 18 hours DES


title: MB231cells WT_DES_18 h-rep1


title: MB231cells WT_DES_18 h-rep2


title: KLF7 DMSO #1

description: KiPS stably overexpressing KLF7, treated with DMSO (replicate #1)


title: P493-6 dCas9-sid 2


title: P493-6 Control sid 3


title: Ramos dCas9-krab MCP-sid3


title: MB231cells WT_E2_18 h-rep3

description: gene expression data from MB231 WT cells after 18 hours E2 tretament

source_name: MB231 WT cells after 18 hours E2


title: P493-6 Control sid 2


title: Empty vector SB43 #4

description: KiPS stably overexpressing empty vector, treated with SB43 (replicate #4)


title: KLF7 SB43 #2

description: KiPS stably overexpressing KLF7, treated with SB43 (replicate #2)


title: Empty vector SB43 #3

description: KiPS stably overexpressing empty vector, treated with SB43 (replicate #3)


title: MB231cells WT_E2_18 h-rep1


title: MB231cells WT_E2_18 h-rep2


title: MB231cells Q_E2_18 h-rep3


title: MB231cells WT_veh_18 h-rep3

description: gene expression data from MB231 WT cells after veh tretament

source_name: MB231 WT cells after veh


title: P493-6 Control sid 1


title: MB231cells WT_veh_18 h-rep2


title: KLF7 SB43 #1

description: KiPS stably overexpressing KLF7, treated with SB43 (replicate #1)


title: MB231cells WT_veh_18 h-rep1


title: 15_tumor

city: Zurich

first: Enni

last: Markkanen

address: Winterthurerstr. 260

department: Institute of Veterinary Pharmacology and Toxicology

country: Switzerland

institute: University of Zurich

data_processing:
RNAseq quantification was performed with kallisto 0.44.0 with sequence-based bias correction using transcript sequences obtained from ENSEMBLE (CanFam3.1). All other parameters were set to default when running kallisto.
Kallisto's transcript-level estimates were further summarized at the gene-level using tximport 1.8.0 from Bioconductor.
Genome_build: CanFam3.1
Supplementary_files_format_and_content: CSV table of raw estimated counts as obtained from tximport. Rows represent genes and columns represent samples.

organism: Canis lupus familiaris

source_name: canine simple mammary adenoma

growth_protocol: spontaneous tumours from canine patients removed in the context of curative surgery

extract_protocol:
RNA was extracted using the optimised Covaris-FFPE RNA isolation procedure described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7
SMARTer Stranded Total RNA-seq Kit—Pico Input Mammalian from Clontech/ Takara Bio USA, using 4 ng total RNA per sample; details described in: Amini P, Ettlin J, Opitz L, Clementi E, Malbon A, and Markkanen, E (2017) An optimised protocol for isolation of RNA from small sections of laser-capture microdissected FFPE tissue amenable for next-generation sequencing. BMC Mol Biol 18:22. doi: 10.1186/s12867-017-0099-7

tag: disease state

value: canine simple mammary adenoma

value: Cancer-associated stroma

tag: Sex

value: female

tag: age of patient (years)

tag: age of sample at analysis (months)

tag: breed

value: West Highland White Terrier


title: Ramos dCas9-sid 3


title: Empty vector SB43 #1

description: KiPS stably overexpressing empty vector, treated with SB43 (replicate #1)

tag: cell type


title: Ramos dCas9-sid 2


title: 15_normal

value: Normal stroma


title: Empty vector DMSO #4

description: KiPS stably overexpressing empty vector, treated with DMSO (replicate #4)


title: 14_tumor

value: Mittelpudel


title: Ramos dCas9-sid 1


title: 14_normal


title: Empty vector DMSO #3

description: KiPS stably overexpressing empty vector, treated with DMSO (replicate #3)


title: Empty vector DMSO #2

description: KiPS stably overexpressing empty vector, treated with DMSO (replicate #2)


title: 12_tumor

value: Chihuahua


title: Ramos Control rsid 2


title: 12_normal


title: 13_normal

value: Yorkshire Terrier


title: Empty vector SB43 #2

description: KiPS stably overexpressing empty vector, treated with SB43 (replicate #2)

value: Keratinocyte-derived iPS (KiPS)


title: 13_tumor


title: Ramos Control rsid 3


title: 11_normal

value: Bassett


title: Ramos Control rsid 1


title: Empty vector DMSO #1

description: KiPS stably overexpressing empty vector, treated with DMSO (replicate #1)

value: DMSO


title: P493-6 dCas9-pogo 2


title: peritoneal macrophages, KO3

city: Birmingham

first: Adrie

middle: JC

last: Steyn

state: AL

address: 845 19th Street South

institute: UAB

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.5.3b was used to align the FASTQ files to the reference genome with parameters --outReadsUnmapped Fastx, --outSAMtype BAM SortedByCoordinate, --outSAMattributes All
HTSeq-count version 0.9.1 was used to estimate transcript abundances with paramters -r pos, -t exon, -I gene_id, -a 10, -s no, -f bam
DESeq2 was used to normalize and calculate differentially expressed genes following their default protocol
Genome_build: Gencode GRCm38 p4 Release M11
Supplementary_files_format_and_content: tab-delimited Excel file containing raw counts for each gene in each sample

source_name: mouse peritoneal macrophages

growth_protocol: CSE-/- and WT mice were injected intraperitoneally with 2 mL of 4% thioglycollate (Brewer modified, BBL, BD Biosciences). Five days later, peritoneal exudate cells were collected from the peritoneal cavity by injecting ice-cold DMEM medium into the peritoneal cavity. Cells were cultured overnight at 37°C, 5% CO2 in DMEM medium supplemented with 10% fetal bovine serum

extract_protocol: RNA was extracted from uninfected and Mtb infected macrophages isolated from CSE-/- and WT mice using Aurum Total RNA mini kit (Bio-Rad) as per manufacturer’s instructions.

treatment_protocol: Peritoneal macrophages were either uninfected or infected with Mtb at a MOI of 4 for 24 hours

value: peritoneal macrophages

tag: infection

value: M. tuberculosis infected

tag: genotype

value: CSE-/-


title: 10_normal

value: Pinscher


title: peritoneal macrophages, KO2


title: 11_tumor


title: 9_tumor

value: Galgo Espanol


title: 10_tumor


title: P493-6 dCas9-pogo 1


title: 8_normal

value: Epagneul Breton


title: peritoneal macrophages, KO1


title: peritoneal macrophages, WT3

value: CSE+/+


title: 7_normal

value: canine simple mammary adenoma

value: Coton de Tulear


title: 6_tumor

value: Cancer-associated stroma

value: female

value: Cocker Spaniel


title: P493-6 Control I2 2


title: peritoneal macrophages, WT2


title: Ramos dCas9-pogo 3

value: Ramos


title: 5_normal

value: Normal stroma

value: Golden Retriever


title: peritoneal macrophages, KU3

value: Uninfected


title: 5_tumor


title: Ramos dCas9-pogo 2


title: 9_normal


title: 6_normal


title: peritoneal macrophages, KU2


title: Ramos dCas9-pogo 1


title: Ramos Control rpogo 2


title: 8_tumor


title: peritoneal macrophages, KU1


title: 3_tumor

value: Rhodesian Ridgeback


title: 4_normal

value: Deutscher Wachtelhund


title: P493-6 Control I2 3


title: IPEC-J2_ ETEC F4ab_3

city: Tai'an

first: Wenwen

last: Wang

address: NO. 61 Daizong street

institute: Shandong Agricultural University

description: MeDIP-chip_IPEC-J2_ ETEC F4ab_3

hyb_protocol: The labeled ChIP DNA was hybridized in 42.5 ul of hybridization solution containing 29.5ul 2×Hybridization Buffer, 1.2ul Alignment Oligo, 11.8ul Hybridization Component A. Arrays were hybridized in Hybridization System (NimbleGen, Cat. # 00895/00896) for 16 - 20 hours at 42°C and then washed in 42°C 10×Wash bufferⅠ,Ⅱ, Ⅲ and 1M DTT. Hybridization buffers and washes were completed using manufacturer's protocols (Hybridization Kit 40, NimbleGen, Cat. # KIT002-2).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol.

data_processing:
Raw data was extracted as pair files by NimbleScan software. We perform Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample. From the normalized log2-ratio data, a sliding-window peak-finding algorithm provided by NimbleScan v2.6 (Roche-NimbleGen) was applied to find the enriched peaks with specified parameters (sliding window width: 750bp; mini probes per peak: 2; P-value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp).
log2 (ChIP/Input) ratio

organism: Sus scrofa

source_name: MeDIP-chip  DNA from ETEC F4ab infected cells

label_protocol: 1. Dilute Cy3 and Cy5 dye-labeled 9mers to 1 O.D./42μl Random 9mer Buffer. Aliquot to 40μl individual reaction volumes in 0.2ml thin-walled PCR tubes and store at -20°C, protected from light.  2. Assemble “MeDIP” and “Input” samples in separate 0.2ml thin-walled PCR tubes (1ug DNA, 40ul Cy3/Cy5-9mer Primers, X ul water, total 80ul).  3. Heat-denature samples in a thermocycler at 98°C for 10 minutes. Quick-chill in an ice-water bath for 10 minutes.  4. Prepare 20μl of the following dNTP/Klenow master mix for each sample (10ul  50×dNTP mix, 8ul water, 2ul klenow(50U/ul)).  5. Add 20μl of the dNTP/Klenow master mix to each of the denatured samples. Keep on ice.  6. Mix well by pipetting up and down 10 times.  7. Quick-spin to force contents to bottom of the tube.  8. Incubate for 2 hours at 37°C in a thermocycler protected from light.  9. Stop the reaction by addition of 0.5M EDTA (10ul).  10. Add 5M NaCl (11.5ul )to each tube.  11. Vortex briefly, spin, and transfer the entire contents to a 1.5ml tube containing isopropanol (110ul).  12. Vortex well. Incubate for 10 minutes at room temperature, protected from light.  13. Centrifuge at 12,000 x g for 10 minutes. Remove supernatant with a pipette.  14. Rinse pellet with 500μl 80% ice-cold ethanol. Dislodge pellet from tube wall.  15. Centrifuge at 12,000 x g for 2 minutes. Remove supernatant with a pipette.  16. Dry contents in a SpeedVac on low heat until dry for 5 minutes, protected from light.  17. Spin tubes briefly prior to opening. Rehydrate pellets in 25μl water.  18. Vortex for 30 seconds and quick-spin to collect contents in bottom of the tube. Continue to vortex or let sit at room temperature, protected from light, until the pellet is completely rehydrated, then vortex again and quick-spin.  19. Measure the labeled DNA using Nanodrop ND1000. Use 6ug labeled MeDIP/Input DNA per hybridization reaction.  20. Dry 6ug labeled DNA in a SpeedVac on low heat until dry for 5 minutes, protected from light.

extract_protocol: Cells were cultured in the 6-hole plate, with 5 × 10E6 cell per hole, remove supernatant and add 180 μl Buffer ATL. Add 20 μl proteinase K. Mix thoroughly by vortexing, and incubate at 56°C until the cells is completely lysed. Add 4 μl RNase A (100 mg/ml), mix by vortexing, and incubate for 2 min at room temperature. Vortex for 15 s. Add 200 μl Buffer AL to the sample, and mix thoroughly by vortexing. Then add 200μl ethanol (96–100%), and mix again thoroughly by vortexing. Pipet the mixture (including any precipitate) into the DNeasy Mini spin column placed in a 2 ml collection tube. Centrifuge at 6000 x g for 1 min. Discard flow-through and collection tube. Place the DNeasy Mini spin column in a new 2 ml collection tube, add 500 μl Buffer AW1, and centrifuge for 1 min at 6000 x g. Discard flow-through and collection tube. Place the DNeasy Mini spin column in a new 2 ml collection tube, add 500 μl Buffer AW2, and centrifuge for 3 min at 20,000 x g to dry the DNeasy membrane, Remove the DNeasy Mini spin column carefully so that the column does not come into contact with the flow-through, Discard flow-through and collection tube. Place the DNeasy Mini spin column in a clean 1.5 ml microcentrifuge tube, and pipet 200 μl Buffer AE directly onto the DNeasy membrane. Incubate at room temperature for 1 min, and then centrifuge for 1 min at 6000 x g to elute.

tag: bacterial strain infection

value: ETEC F4ab

source_name: Input DNA from ETEC F4ab infected cells


title: Ramos Control rpogo 1


title: 4_tumor


title: peritoneal macrophages, WU3

value: peritoneal macrophages


title: 7_tumor


title: IPEC-J2_ ETEC F4ab_2

description: MeDIP-chip_IPEC-J2_ ETEC F4ab_2


title: IPEC-J2_ ETEC F4ab_1

description: MeDIP-chip_IPEC-J2_ ETEC F4ab_1


title: peritoneal macrophages, WT1

value: M. tuberculosis infected


title: IPEC-J2_ ETEC F4ac_3

description: MeDIP-chip_IPEC-J2_ ETEC F4ac_3

source_name: MeDIP-chip  DNA from ETEC F4ac infected cells

value: ETEC F4ac

source_name: Input DNA from ETEC F4ac infected cells


title: peritoneal macrophages, WU1


title: 3_normal


title: IPEC-J2_ ETEC F4ac_2

description: MeDIP-chip_IPEC-J2_ ETEC F4ac_2


title: Ramos Control rpogo 3


title: Ramos dCas9-KRAB 2


title: IPEC-J2_ ETEC F4ac_1

description: MeDIP-chip_IPEC-J2_ ETEC F4ac_1


title: IPEC-J2_control_3

source_name: MeDIP-chip  DNA from IPEC-J2 cells

source_name: Input DNA from IPEC-J2 cells


title: IPEC-J2_control_2


title: Ramos Control rkrab 3

description:
rkrab_none_3
supplementary file identical GSM4204714 since used same control


title: Ramos dCas9-KRAB 1


title: Ramos Control rkrab 1

description:
rkrab_none_1
supplementary file identical GSM4204712 since used same control


title: peritoneal macrophages, WU2


title: IPEC-J2_control_1


title: Ramos Control rkrab 2

description:
rkrab_none_2
supplementary file identical GSM4204713 since used same control


title: Ramos dCas9-KRAB 3


title: Ramos 2

data_processing:
Cassava 1.8
STAR 2.6.0b STAR --genomeDir ${genome} --readFilesIn $fq1 \      --readFilesCommand zcat --runThreadN 12 --genomeLoad NoSharedMemory \      --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \      --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 \      --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \      --outSAMunmapped Within --outFilterType BySJout \      --outSAMattributes NH HI AS NM MD \      --outSAMtype BAM Unsorted \      --quantMode TranscriptomeSAM GeneCounts \      --outFileNamePrefix $prefix --outTmpDir $scratch/star
sambamba sort v0.5.4 sambamba sort $inbam $outbam
htseq_count htseq-count -f bam -r pos --max-reads-in-buffer 100000000 -s reverse $inbam $ingtf $outcounts > $last
Genome_build: GRCh38.d1.vd1

growth_protocol: Cells were grown in RPMI1640 supplemented with 10% FBS and 1x Penicillin-Streptomycin.

extract_protocol:
Total RNA was isolated from cells using the "Maxwell RSC simply RNA Cells" kit (Promega) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transduced with lentiviral constructs encoding for a dCas9-SID fusion protein and a non-targeting CRISPR single-guide RNA.


title: DEV

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..

source_name: Hodgkin lymphoma cell line (Nodular lymphocyte predominant Hodgkin)

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

growth_protocol: standard cell cultures: 1x RPMI 1640 complete with 10 or 20% FCS apart from U-HO1:80% IMDM + RPMI 1640 (at 4:1) + 20% h.i. FCS, 2 mM L-glutamine

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen.RNA was amplified using the Ovation Pico WTA System V2 from NUGEN applied for 50ng total RNA

treatment_protocol: cell lines were culture and harvested without treatment

tag: cell line

value: DEV


title: Ramos 1

source_name: Ramos Cells


title: L1236

source_name: Classical Hodgkin lymphoma cell line


title: CxSCC32

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_CxSCC32

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17h in a 65°C hybridization oven (G2545A, Agilent) set to 10rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software. Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. If intensity of a probe was <50 in both channels, it was considered missing. If a probe intensity was <50 in one of the channels, it was set to 50. Probes missing in >50% of samples probe were removed from the dataset.

source_name: cervical squamous cell carcinoma

label_protocol: 500 ng of total RNA was reverse transcripted to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA using T7 RNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).

extract_protocol: 10 micrometer frozen sections of all tissue samples were first subjected to laser capture microdissection using a Leica ASLMD microscope (Leica) to enrich for neoplastic, dysplastic or normal epithelial cells as described previously (Wilting et al., Genes, Chromosomes Cancer 2008). Total RNA was isolated from microdissected tissue samples using TRIzol Reagent according to the manufacturers’ instructions. To ensure comparable RNA integrity between specimens analysed by array, RNA pico chips were performed on an Agilent 2100 Bioanalyzer (Agilent).

value: cervical squamous cell carcinoma

tag: hpv

value: high-risk HPV-positive


title: CxSCC39

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_CxSCC39


title: KMH2


title: CxSCC28

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_CxSCC28


title: CxSCC38

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_CxSCC38


title: L428


title: CxSCC36

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_CxSCC36


title: CxSCC27

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_CxSCC27


title: Patient44_Tamoxifen [FFP13.004090]

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

hyb_protocol: 200 ng fluorescent labeled RNA was hybridized to custom Agilent arrays (4x44k arrays).

scan_protocol: Agilent Technologies Scanner G2505B, Agilent Scan Control Version A.7.0.3.

data_processing: Feature Extraction software v11.5.1.1 was used to quantify fluorescent intensities, custom script were used for raw data extraction and those values were normalized by 75th percentile normalisation using DataPrint software v1.15, all by Agendia Inc. Downstream data processing was subsequently done at the Netherlands Cancer Institute, by missing data impution with knn=10 and batch correction for date of RNA extraction using ComBat from the R package sva, using all available patient material from the trial (ClinicalTrials.gov Identifier: NCT00738777). Here we deposited samples used for the Tamoxifen focused analysis described in the cited paper.

label_protocol: RNA was amplified and labeled using the lQuickAmp Labeling kit (Agilent).

extract_protocol: RNA was isolated using Qiagen RNeasy microkit according to manufacturer's specifications.

treatment_protocol:
Gene expression of primary breast cancers from patients before and after neo-adjuvant Tamoxifen treatment
FFPE sections of patient tumor material (10 x CF 5u gelcoat per sample) were sent to Agendia Inc.

tag: subject status

value: breast cancer patient

tag: subject id

value: Tamoxifen

tag: tissue/sample type

value: FFPE tumor

tag: batch

value: Batch TS


title: UHO1


title: HBMEC stimulated with VEGF-B167 [28a]

city: Huddinge

first: Lars

last: Muhl

address: Blickagången 6

department: MedH

country: Sweden

institute: Karolinska Institutet

data_processing: plier normalization performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)

source_name: VEGF-B167 stimulation for 6h

growth_protocol: commercial human primary cell line; brain microvascular endothelial cells (HBMEC)

extract_protocol: total RNA was extracted from cultured human brain microvascular endothelial cells (HBMEC) using RNAeasy kit (Qiagen)

treatment_protocol: cultered human brain microvascular endothelial cells (HBMEC) were stimulated with growth factors (VEGF-A165, PlGF, VEGF-B186, VEGF-B167) for 6h prior to RNA extraction

value: HBMEC

value: human brain microvascular endothelial cell line (HBMEC)

tag: treatment

value: VEGF-B167 stimulation for 6h


title: CxSCC15

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_4.txt
none
VUMC_CxSCC15


title: CxSCC12

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_CxSCC12


title: HBMEC stimulated with VEGF-B167 [26a]

hyb_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)


title: 31CBS-KO-K562-H3K4me2-CHIP-seq

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end RNA-seq reads from mice were aligned to the hg19 genome assembly using Tophat, and ATAC-seq, ChIP-seq, HiC-seq  reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Chromatin structure HiC-seq was calculate and display with HOMER, Juicer and Juicebox software
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for RNA-seq Samples, and peaks annotation for ATAC-seq and ChIP-seq.

growth_protocol: Human Jurkat leukemia cells and K562 cells were culture at RMPI1640 and 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K4me3, H3K4me2, H3K9/14ac and H3K27ac antibody (H3K4me3 (Millipore, #04-745), H3K4me2 (Millipore, 07-030), H3K27Ac (Abcam, #ab4729), and H3K9/14ac (Diagenode, #C15410005)).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits.  HiC-DNA was prepared with Arima-HiC kit (Arima, #A410030).
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). 4C-seq libraries were prepared according to  TruSeq ChIP Library Preparation Kit (#IP-202-1012). HiC library was prepared according to Arima-HiC Kit (Catlog: A410030). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from Jurkat T-ALL and K562 cells without any treatment

value: chronic myelogenous leukemia

tag: tissue

value: peripheral blood

tag: chip antibody


title: 31CBS-WT-K562-H3K9-14ac-CHIP-seq


title: 31CBS-KO-K562-H3K9-14ac-CHIP-seq


title: Patient50_Tamoxifen [FFP13.004096]


title: Patient43_Tamoxifen [FFP13.004089]


title: HBMEC stimulated with VEGF-B167 [27a]

scan_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)


title: Patient40_Tamoxifen [FFP13.004087]


title: 31CBS-WT-K562-H3K4me2-CHIP-seq


title: Patient45_Tamoxifen [FFP13.004091]


title: CxSCC4

description:
raw data file: US22502676_251485063646_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_CxSCC4


title: 31CBS-KO-K562-H3K4me3-CHIP-seq


title: Patient37_Tamoxifen [FFP13.004084]


title: 31CBS-WT-K562-H3K4me3-CHIP-seq


title: CxSCC2

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_CxSCC2


title: 31CBS-WT-inv-H3K27ac-CHIP-seq

source_name: Jurkat

value: Jurkat

value: T cell leukemia


title: 31CBS-WT-Jurkat-H3K27ac-CHIP-seq


title: HBMEC stimulated with VEGF-B186 [22a]

source_name: VEGF-B186 stimulation for 6h

label_protocol: performed at the Karolinska Institutet core facility BEA (Karolinska Institutet - NOVUM, Huddinge, Sweden)

value: VEGF-B186 stimulation for 6h


title: 31CBS-WT-inv-H3K4me3-CHIP-seq


title: HGCIN39

description:
raw data file: US22502676_251485063643_S01_GE2-v5_95_Feb07_1_1.txt
none
VUMC_HGCIN39

source_name: cervical intraepithelial neoplasia, grade 2-3


title: HBMEC stimulated with VEGF-B186 [21a]


title: HGCIN33

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_HGCIN33

value: cervical intraepithelial neoplasia, grade 2-3


title: Patient35_Tamoxifen [FFP13.004082]


title: HBMEC stimulated with PlGF [17a]

source_name: PlGF stimulation for 6h

value: PlGF stimulation for 6h


title: HBMEC stimulated with PlGF [19a]


title: HGCIN32

description:
raw data file: US22502676_251485063642_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_HGCIN32


title: Patient47_Pretreatment [FFP13.004073]

value: Pretreatment


title: Patient36_Tamoxifen [FFP13.004083]


title: Patient45_Pretreatment [FFP13.004071]


title: HBMEC stimulated with PlGF [16a]


title: HBMEC stimulated with VEGF-A165 [13a]

source_name: VEGF-A165 stimulation for 6h

value: VEGF-A165 stimulation for 6h


title: 31CBS-WT-Jurkat-H3K4me3-CHIP-seq


title: Patient41_Pretreatment [FFP13.004067]


title: 31CBS-KO-K562-ATAC-seq


title: 31CBS-WT-K562-ATAC-seq


title: Patient40_Pretreatment [FFP13.004066]


title: 31CBS-inv-Jurkat-ATAC-seq


title: Patient43_Pretreatment [FFP13.004069]


title: HGCIN19

description:
raw data file: US22502676_251485063644_S01_GE2-v5_95_Feb07_1_2.txt
none
VUMC_HGCIN19

value: high-risk HPV-positive


title: HGCIN25

description:
raw data file: US22502676_251485063645_S01_GE2-v5_95_Feb07_1_3.txt
none
VUMC_HGCIN25


title: Patient39_Pretreatment [FFP13.004065]

value: breast cancer patient


title: HBMEC stimulated with VEGF-A165 [11a]


title: HBMEC stimulated with VEGF-A165 [12a]


title: HBMEC control treated [3a]

source_name: control treated

value: control treated


title: 31CBS-WT-Jurkat-ATAC-seq