title: mrc1-3A_H3K4me3_eSPAN_rep_1

first: Danesh

last: Moazed

address: 240 Longwood Avenue, LHRRB 517

institute: Harvard Medical School/HHMI

data_processing:
Reads are mapped to S. pombe reference genome by Bowtie2. Read coverage in a bin of 1bp was calculated from filtered bam files by deepTools2 and then normalized with total filtered reads number into reads per million (RPM). Origins were called by MACS2 from BrdU-IP
Assembly: S. pombe, ASM294v2
Supplementary files format and content: Supplementary files format and content: bw, bigwig format, contains the read density at each genomic position

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Strains containing the cdc25-22 temperature-sensitive mutant were first grown at permissive temperature (25°C) until the early-mid log phase (OD 0.2~0.4). Cultures were then incubated at 36°C for 4 hours to arrest cells at the G2 phase of the cell cycle. Cells were then shifted to 25°C to allow them to enter the S phase synchronously.

extract_protocol: Cells were crosslinked at 60 minutes after temperature shift with the addition of 1% formaldehyde and incubated for 20 minutes with shaking at 25°C. Immunoprecipitation was performed as described in ChIP. Crosslinking was reversed by Chelex-100. Briefly, total and ChIP DNA were incubated at 100°C for 5 minutes and then immediately cooled on ice for 5 minutes. DNA was diluted ten times with BrdU IP buffer (PBS, 0.0625% Triton X-100(v/v)), and incubated with BrdU antibody (BD Bioscience 555627) for two hours at 4°C. Next, Sepharose Protein G beads (Cytiva 17-0618-01) were added and incubated for an additional one hour at 4°C. The beads were then washed three times with BrdU IP buffer and once with TE. Finally, DNA was eluted with TES and purified with the QIAGEN MinElute PCR Purification kit (Qiagen 28004).

treatment_protocol: BrdU was added to a final concentration of 650 μM at 25 minutes after the temperature shift.

value: Schizosaccharomyces pombe

value: h+ leu1-32:hENT1-leu1+ his7-366::hsv-tk-his7+ ura4 ade6 mrc1-M755A,F758A,L774A-myc::kanMX6 cdc25-22 #1


title: PC3-Replicate 2 hypoxia (1%O2)

status: Public on Jul 29 2024

type: RNA

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation in BeadStudio 3.1.3.0. Non-normalized data are listed in SampleProbe_NonNormalized.txt.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Prostate cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: The cells were kept in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1% penicillin–streptomycin and 1% L-glutamine.

extract_protocol: RNA was extracted using miRNeasy MiniKit (Quiagen), according to the manufacturers’ instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Hypoxia treatment (0%, 0.2%, 0.5%, 1%, 2% or 5% O2) of exponentially growing cells was carried out at 60-70% cell confluence in an In Vivo2 200 chamber for 24 hours at 37°C.

tag: cell line

tag: cell type

value: Bone metastasis

tag: group

value: Hypoxia


title: mrc1-3A_H3K4me3_ChIP_rep_2

type: SRA

city: Boston

state: MA

country: USA

library_source: genomic

molecule: genomic DNA

tag: genotype

value: h+ leu1-32:hENT1-leu1+ his7-366::hsv-tk-his7+ ura4 ade6 mrc1-M755A,F758A,L774A-myc::kanMX6 cdc25-22 #2


title: PC3-Replicate 1 normoxia (control for 0.5%O2)

value: Normoxia


title: p22rv1-Replicate 1 normoxia (control for 0%O2)

value: Primary, from xenograft CWR22R subline


title: mrc1-3A_H3K4me3_ChIP_rep_1


title: PC3-Replicate 1 normoxia (control for 0.2%O2)


title: PC3-Replicate 2 normoxia (control for 0.5%O2)


title: PC3-Replicate 2 hypoxia (0%O2)


title: PC3-Replicate 2 normoxia (control for 0.2%O2)


title: PC3-Replicate 2 hypoxia (2%O2)


title: PC3-Replicate 1 hypoxia (0.5%O2)


title: PC3-Replicate 1 normoxia (control for 0%O2)


title: mrc1-3A_H3K4me3_BrdU_rep_2


title: PC3-Replicate 2 hypoxia (5%O2)


title: PC3-Replicate 1 hypoxia (1%O2)


title: PC3-Replicate 1 hypoxia (0.2%O2)


title: PC3-Replicate 1 hypoxia (5%O2)


title: PC3-Replicate 1 normoxia (control for 2%O2)


title: PC3-Replicate 1 normoxia (control for 5%O2)


title: PC3-Replicate 1 hypoxia (0%O2)


title: PC3-Replicate 1 hypoxia (2%O2)


title: mrc1-3A_H3K4me3_input_rep_2


title: mrc1-3A_H3K4me3_input_rep_1


title: Axolotl_replicate_1

first: Shamsuddin

last: Bhuiyan

address: 60 Fenwood Road

institute: Brigham and Women's Hospital

description:
PREP0077_BErdo11362_A1v1_DRG
10x Genomics

library_source: transcriptomic single cell

data_processing:
For alignment of 10X reads, we reformatted an axolotl genome using Cellranger v7. Sequencing data were then mapped to the reformatted axolotl genome using Cellranger v7.
Assembly: AmexG_v6.0DD
Supplementary files format and content: Seurat object (.rds)

organism: Ambystoma mexicanum

source_name: Dorsal root ganglia

extract_protocol:
For DRG dissociation at single-cell level, 10X Genomics “Dissociation of Mouse Embryonic Neural Tissue for Single Cell RNA Sequencing” protocol was adapted to axolotl tissue. DRGs of brachial plexus nerves located at C3, C4 and C5 were collected from both left and right sides and combined (total of 6 DRGs) in a single tube containing chilled 0.7X HBSS buffer and kept on ice. For dissociation, 400ul papain (Worthington Biochemical, Cat: #LK003178) dissolved in 0.7X PBS was pre-warmed in 37˚C water bath for 10 minutes to activate the enzyme.
scRNA-seq libraries were prepared with the Chromium™ Single Cell 3′ NextGEM, Library and Gel Bead Kit v3.1.

tag: tissue

value: Dorsal root ganglia


title: mrc1-3A_H3K4me3_eSPAN_rep_2


title: mrc1-3A_H3K4me3_BrdU_rep_1


title: ZIKV-infected

city: New Haven

first: Tse-Yu

last: Chen

state: CT

address: 300 Cedar St.

institute: Yale University

data_processing:
Cell Ranger (version 7.1.0) was used for the initial data analysis at KMSR. In summary, the analysis included demultiplexing, collapsing unique molecular identifiers (UMIs), and aligning the data to the Ae. aegypti LVP_AGWG AaegL5 chromosome and transcripts reference files, accessible on VectorBase (https://vectorbase.org/). Additionally, alignment to the Zika virus genome obtained from the National Center for Biotechnology Information (NCBI) was conducted as part of the comprehensive analysis.
Assembly: Ae. aegypti LVP_AGWG AaegL5
Supplementary files format and content: Matrix file

organism: Aedes aegypti

source_name: Midgut

extract_protocol:
Female mosquito midguts were dissected after 4 days of either blood feeding or infection. Each midgut was finely chopped into small pieces using a needle and immediately transferred into an Eppendorf tube containing 200 μl of cold Schneider’s Drosophila Medium with 0.2 mM ethylenediaminetetraacetic acid (EDTA) to minimize exposure to room temperature. A total of fifty midguts from each group were collected and incubated with 200 μl of a 2 mg/ml elastase/PBS solution on a shaker at 37°C for 30 minutes. To halt the digestion reaction and prevent cell aggregation, 400 μl of 2% bovine serum albumin (BSA) in PBS was added. The cell suspension was then passed through a 40 μm cell strainer and loaded onto the top of an Optiprep (Axis-Shield) density gradient with a density of 1.216 g/ml. Viable cells were isolated from the top layer of the sample after centrifugation at 800g for 20 minutes. Cell viability and count were determined through 0.4% trypan blue staining and cell counting using a hemocytometer.
Reverse transcription and library preparation were conducted at KMSR using the Chromium Next GEM Single Cell 5' GEM Kit v2. Both poly-dT primer and the Zika virus NS5 RT primer were employed in the generation of the cDNA library, facilitating subsequent processing with the 10x Genomics.

value: Midgut

tag: treatment

value: Zika virus infected


title: A549 cells, AlgLung, rep1

city: Istanbul

first: Nurcan

last: Tuncbag

state: Istanbul

address: Koc University, College Of Eng Sna Z28

country: Turkey

institute: Koc University

library_source: transcriptomic

data_processing:
Reads were mapped against the ENSEMBL Homo Sapiens reference genome (GRCh38/hg38) using STAR version 2.7.3a.
Counts were calculated from the aligned reads using the featureCounts function of the Rsubread R package.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: A549 cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA samples were extracted using TRIzol reagent followed by Nucleospin RNA II isolation kit.
Library construction, sequencing and initial data filtering including adaptor removal were performed by BGI Genomics.

value: AlgLung


title: A549 cells, S-AlgLung, rep2

value: S-AlgLung


title: A549 cells, AlgLung, rep3


title: HDF_RNA_shCSB_rep2

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9500 Gilman Drive

institute: University of California San Diego

description:
Human dermal fibroblasts were trans-differentiated into functional neurons by depleting the RNA-binding protein PTBP1.
HDF_RNA_counts.txt

data_processing:
The FASTQ reads underwent quality checking and adaptor trimming using Trim Galore. Subsequently, they were mapped to either the hg38 or mm10 reference genomes using STAR. The read counts per gene were then determined using featureCounts.
Assembly: hg38 or mm10
Supplementary files format and content: tab-delimited text files include read counts for each sample

molecule: polyA RNA

source_name: Human Dermal Fibroblasts

extract_protocol:
RNA was extracted by TRIzol and then constructed into library.
RNA libraries for RNA-seq were prepared using NEBNext rRNA Depletion Kit v2 (E7400L) followed by NEBNext Ultra II RNA Library Prep kit (E7775S).

value: Human Dermal Fibroblasts

value: shCSB


title: PC3-Replicate 1 normoxia (control for 1%O2)


title: A549 cells, AlgLung, rep2


title: HDF_RNA_shCSB_rep1

treatment_protocol: Human dermal fibroblasts were trans-differentiated into functional neurons by depleting the RNA-binding protein PTBP1.


title: A549 cells, S-AlgLung, rep1


title: HDF_RNA_shNC_rep2

value: shNC


title: hoGCSFR-TCR-T-TIL-3

city: Stanford

first: Yang

last: Zhao

address: Beckman B169B, 279 Campus Drive

department: MCP

institute: Stanford University

description: Omni-ATAC-seq

data_processing:
ATAC-seq reads were mapped onto the reference genome (hg19) using RSubread (version 2.18.0) in the “DNA” mode
The aligned reads were then subjected to peak calling with MACS3
Assembly: hg19
Supplementary files format and content: ATACSeq_DESeq2_rsubread.rds, summarized peak count data

source_name: tumor

growth_protocol: Tumor infiltrating T cells

extract_protocol:
NSG mice were inoculated s.c. with A375 cells (1 × 106) and received i.v. adoptive cell transfer of 3 × 106 NY-ESO-1 TCR-T cells (WT NY-ESO-1 TCR-T cells, or ho22R, or hoGCSFR expressing NY-ESO-1 TCR-T cells) on day 10 post-tumor inoculation followed by i.p. administration of MSA-hoIL-2 (2.5 × 104 unit  × 3 doses, 2.5 × 104 unit  × 3 doses) or PBS control every other day until day 20. On day 21, mice were sacrificed, tumors were minced and dissociated using a human tumor dissociation kit (Miltenyi Biotec) and a gentleMACS Octo Dissociator (Miltenyi Biotec). Tumor-infiltrating lymphocytes (TILs) were first enriched by density gradient centrifugation against Percoll (GE healthcare), and then stained with surface markers and DAPI (Sigma-Aldrich). CD3+ EGFR+ or CD3+ EGFR+YFP+ T cells were sorted using an Aria II sorter (BD Biosciences) at the Stanford Share FACS Facility for ATAC sequencing
ATAC-seq library was generateded using Active Motif ATAC-Seq Kit

treatment_protocol: i.p. injection of PBS or orthogonal human IL-2

value: tumor

value: primary cells

value: TCR-engineered human T cells

value: NY-ESO-1 TCR and hoGCSFR expression

value: Orthogonal human IL2


title: ho22R-TCR-T-TIL-3

description: Omni-ATAC-seq

value: NY-ESO-1 TCR and ho22R expression


title: hoGCSFR-TCR-T-TIL-1

description: Omni-ATAC-seq


title: ho22R-TCR-T-TIL-2

description: Omni-ATAC-seq


title: HDF_RNA_shNC_rep1


title: A549 cells, S-AlgLung, rep3


title: Control

value: Blood fed


title: TCR-T-TIL-6

description: Omni-ATAC-seq

value: NY-ESO-1 TCR expression

value: PBS


title: TCR-T-TIL-5

description: Omni-ATAC-seq


title: hoGCSFR-TCR-T-TIL-2

description: Omni-ATAC-seq


title: SHSY5Y_RNA_siNC_rep2

description:
SH-SY5Ys were induced to differentiate into neurons through the addition of Retinoic acid.
SHSY5Y_RNA_counts.txt

value: siNC


title: ho22R-TCR-T-TIL-1

description: Omni-ATAC-seq


title: TCR-T-TIL-4

description: Omni-ATAC-seq


title: SHSY5Y_RNA_siCSB_rep2

value: siCSB


title: SHSY5Y_RNA_siCSB_rep1


title: SHSY5Y_RNA_siNC_rep1


title: monocyte_cite_9, GEX

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description:
mono_RNA_protein_15.mtx.gz
mono_RNA_protein_obs.txt
mono_RNA_protein_var.txt

data_processing:
Fastq files were processed by Cell Ranger 5.0.1 from 10x genomics to generate count matrices of unique molecular identifiers (UMIs). Reads were mapped to human reference genome GRCh38 and transcriptome annotated by GENCODE v32 from 10x prebuilt reference package version 2020-A. An additional feature barcode reference of 283 antibody-derived tags was included for quantification. Duplicate gene symbols were suffixed with numbers.
Genes were included if they were expressed in ≥10 cells. Cells were included if they had ≥200 RNAs expressed. The maximum number of RNAs and the maximum number of UMIs from RNA allowed varies slightly across samples. A maximum of 10% reads were allowed that were mapped to mitochondrial genes. In addition, cells were filtered if there were >50 UMIs mapped to control antibodies.
Assembly: GRCh38
Supplementary files format and content: UMI count matrix in MTX format
Supplementary files format and content: Tab-delimited text file of cell ids and sample ids
Supplementary files format and content: Text file of gene symbols
Library strategy: CITE-seq

source_name: blood monocyte

extract_protocol:
RNA was extracted using 10x Genomics Single Cell 3' v3 protocol.
Library was constructed following 10x Genomics Single Cell 3' v3 protocol. 5000 cells and 100M reads were targeted per sample. CITE-seq libraries were prepared following 10x Genomics 3’ v3 protocol according to manufacturer’s instructions for cDNA amplification using 0.2 uM of ADT additive primer (5’CCTTGGCACCCGAGAATTCC).

value: blood monocyte

tag: race

value: African American

tag: Sex

value: Female

tag: age

tag: library type

value: mRNA


title: monocyte_cite_10, ADT

library_source: other

molecule: protein

value: Male

value: ADT

tag: adt

value: TotalSeq-A panel of 274 ADTs and 9 control ADTs


title: monocyte_cite_8, GEX

value: Caucasian


title: monocyte_cite_8, ADT


title: monocyte_cite_9, ADT


title: monocyte_cite_7, ADT


title: monocyte_cite_5A, GEX


title: monocyte_cite_5B, ADT

source_name: blood monocyte and dendritic cell

value: blood monocyte and dendritic cell


title: monocyte_cite_4B, ADT


title: monocyte_cite_6, ADT


title: monocyte_cite_5A, ADT


title: monocyte_cite_3B, ADT


title: monocyte_cite_3A, ADT


title: monocyte_cite_3A, GEX


title: monocyte_cite_5B, GEX


title: monocyte_cite_4A, GEX


title: monocyte_cite_2A, GEX


title: monocyte_cite_2B, GEX


title: monocyte_cite_2B, ADT


title: monocyte_cite_3B, GEX


title: monocyte_cite_2A, ADT


title: monocyte_cite_1B, ADT


title: monocyte_cite_10, GEX


title: monocyte_cite_6, GEX


title: monocyte_cite_1A, ADT


title: monocyte_cite_7, GEX


title: monocyte_cite_1A, GEX


title: monocyte_cite_4B, GEX


title: monocyte_cite_4A, ADT


title: monocyte_116

description:
monocyte_118_cts.mtx.gz
monocyte_118_obs.txt
monocyte_var.txt

data_processing:
Fastq files were processed by Cell Ranger 5.0.1 from 10x genomics to generate count matrices of unique molecular identifiers (UMIs). Reads were mapped to human reference genome GRCh38 and transcriptome annotated by GENCODE v32 from 10x prebuilt reference package version 2020-A. Duplicate gene symbols were suffixed with numbers.
Genes were included if they were expressed in ≥10 cells. Cells were included if they had ≥200 RNAs expressed. The maximum number of RNAs and the maximum number of UMIs from RNA allowed varies slightly across samples. A maximum of 10% reads were allowed that were mapped to mitochondrial genes.
Assembly: GRCh38
Supplementary files format and content: UMI count matrix in MTX format
Supplementary files format and content: Tab-delimited text file of cell ids and sample ids
Supplementary files format and content: Text file of gene symbols

extract_protocol:
RNA was extracted using 10x Genomics Chromium Single Cell 3' v3 protocol.
Library was constructed using 10x Genomics Chromium Single Cell 3' v3 protocol. 5000 cells and 100M reads were targeted per sample.


title: monocyte_117


title: monocyte_118


title: monocyte_115


title: monocyte_104


title: monocyte_102


title: monocyte_113


title: monocyte_cite_1B, GEX


title: monocyte_108


title: monocyte_111


title: monocyte_112


title: monocyte_98


title: monocyte_99

value: Native American / Alaska Native


title: monocyte_106


title: monocyte_103


title: monocyte_105


title: monocyte_114


title: monocyte_109


title: monocyte_101


title: monocyte_97


title: monocyte_107


title: monocyte_94


title: monocyte_110


title: monocyte_92


title: monocyte_96


title: monocyte_95


title: monocyte_93


title: monocyte_89


title: monocyte_87


title: monocyte_90


title: monocyte_88


title: monocyte_100


title: monocyte_91


title: monocyte_84


title: monocyte_83


title: monocyte_82


title: monocyte_80


title: monocyte_75


title: monocyte_73


title: monocyte_72


title: monocyte_69


title: monocyte_86


title: monocyte_81


title: monocyte_68

value: Asian


title: monocyte_79


title: monocyte_77


title: monocyte_78


title: monocyte_76


title: monocyte_66


title: monocyte_70


title: monocyte_74


title: monocyte_71


title: monocyte_85


title: monocyte_61


title: monocyte_60


title: monocyte_62


title: monocyte_58


title: monocyte_57


title: monocyte_56


title: monocyte_55


title: monocyte_65


title: monocyte_63


title: monocyte_59


title: monocyte_53


title: monocyte_64


title: monocyte_67

value: Other


title: monocyte_52


title: monocyte_54


title: monocyte_51


title: monocyte_49


title: monocyte_50


title: monocyte_48


title: monocyte_45


title: monocyte_47


title: monocyte_42


title: monocyte_40


title: monocyte_39


title: monocyte_41


title: monocyte_43


title: monocyte_37


title: monocyte_38


title: monocyte_44


title: monocyte_36


title: monocyte_35


title: monocyte_34


title: monocyte_33


title: monocyte_30


title: monocyte_29


title: monocyte_25


title: monocyte_32


title: monocyte_28


title: monocyte_26


title: monocyte_31


title: monocyte_23


title: monocyte_27


title: monocyte_24


title: monocyte_20


title: monocyte_18


title: monocyte_21


title: monocyte_22


title: monocyte_19


title: monocyte_46


title: monocyte_15


title: monocyte_17


title: monocyte_14


title: monocyte_11


title: monocyte_12


title: monocyte_10


title: monocyte_9


title: monocyte_8


title: monocyte_7


title: monocyte_6


title: monocyte_5


title: monocyte_4


title: monocyte_3


title: monocyte_2


title: SINRV-TGM1-ΔTGM1_K81p7_ATAC

city: Padova

first: Oriana

last: Romano

address: Via U. Bassi 58/B

department: Molecular Medicine

country: Italy

institute: University of Padova

description: 150PE, average 213,000 reads per cell

data_processing:
The Cell Ranger ARC pipeline (v2.0.2) was used to generate FASTQ files, to align reads to the reference transcriptome (GRCh38) for the GEX library, or to the reference genome (GRCh38) plus the exogenous SINγ-RV-TGM1 sequence for ATAC library, and to calculate UMI (unique molecular identifier) counts from the mapped reads.
The feature-barcode matrix was imported in R (v 4.2.2) and analyzed using Seurat (v4.3.0; Stuart et al., 2019), Signac (v1.9.0; Stuart et al., 2021) and popsicleR (v 0.2.1; Grandi et al., 2022) R packages.
Assembly: GRCh38
Supplementary files format and content: Tab-separated data and matrix files

source_name: skin

growth_protocol: Human skin samples were obtained as anonymised surgical waste, typically from abdominoplasty or mammoplasty. Briefly, skin biopsies were minced and trypsinized (0.05% trypsin/0.01%EDTA) at 37°C for 4 hr. Cells were collected every 30 min, plated (2.5–3 × 104/cm2) on lethally irradiated 3T3-J2 cells (2.4 × 104/cm2) and cultured in 5% CO2 and humidified atmosphere in keratinocyte growth medium (KGM): DMEM and and Ham’s F12 media (3:1 mixture) containing Fetal Bovine Serum (FBS) (10%), insulin (5 μg/ml), adenine (0.18 mM), hydrocortisone (0.4 μg/ml), cholera toxin (CT, 0.1 nM), triiodothyronine (Liothyronine Sodium) (2 nM), epidermal growth factor (EGF, 10 ng/ml), glutamine (4 mM), and penicillin-streptomycin (50 lU/ml) and cultivated on a feeder-layer of lethally irradiated 3T3-J2 cells as described (DOI: 10.1089/hum.1998.9.9-1359).

extract_protocol:
Fully confluent keratinocytes were detached, and cells were accurately resuspended to obtain a single-cell suspension in PBS containing 0.04% BSA. About 8 x 104 cells of SINγ-RV-TGM1-transduced keratinocytes sample were subjected to nuclei isolation and DNA fragmentation according to manufacturer’s instructions (#CG000338 Rev F, 10X Genomics).
About 15,000 nuclei were loaded into the Chromium Next GEM Chip J using the Single Cell Multiome ATAC + Gene Expression kit (10X Genomics). The sample was pre-amplified and half-divided to generate the Illumina sequencing ATAC and GEX libraries. Sequencing was performed on the NovaSeq6000 SP platform following the 10X Genomics instruction for read generation (150PE), reaching on average 67,000 reads per cell for the GEX library and 213,000 reads per cell for the ATAC library.
Single Cell Multiome ATAC + Gene Expression (10X Genomics)

value: skin

value: keratinocytes

value: ATAC


title: monocyte_1


title: SINRV-TGM1-ΔTGM1_K81p7_GEX

description: 150PE, average 67,000 reads per cell

molecule: nuclear RNA

value: GEX


title: HEK293T ZFC3H1 shRNA PAS-seq Replicate 1

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

data_processing:
We used Cutadapt (v2.10) to produce trimmed PAS-seq reads by: 1) trimming the 6 nucleotide linker sequence, 2) trimming the poly(A) tail sequence, and 3) removing any untrimmed reads. Trimmed reads were then mapped to a concatenated hg19 and mm9 genome using STAR (v2.7.3a) with the --alignEndsType EndToEnd parameter. The mapped reads were converted from a bam file to a bed file using bedtools (v2.29.2). Reads were removed as potential internal priming events if they mapped to a genomic region where 6 consecutive A's or 7 A's out of 10 nucleotides were observed in the 10 nucleotides downstream of the read using a custom python script. The remaining reads were converted back to a bam file and were used to generate bigwig files using bedtools.
Assembly: hg19 and mm9 (concatenated)
Supplementary files format and content: bigwig
Library strategy: PAS-seq

growth_protocol: HEK293T cells were grown in DMEM supplemented with 10% FBS and grown at 37˚C with 5% CO2

extract_protocol:
Total RNA was extracted from Trizol following the manufacturer's protocol
PAS-seq libraries were prepared as previously described (PMID: 34183125),  with the following minimal modifications. Purified mRNA was fragmented at 94˚C for 3 minutes using the NEBNext Magnesium RNA fragmentation module. In addition, the final libraries were run out on a 2.5% standard agarose gel and the region between 200-300 basepairs was gel extracted and sequenced. For all samples, a small amount of mouse RNA was spiked in but was not used in data processing. For the spike-ins, an extra control or treatment well was prepared and the cells in this extra well were counted and recorded. 1 µg total RNA from each sample was used and up to 100 ng (10%) spike-in RNA purified from mouse brain tissue was added based on the original cell number. For example, if there were 1 x 10^6 control cells and 0.8 x 10^6 treated cells, then 100 ng mouse spike-in RNA would be added to 1 µg of control total RNA and 80 ng mouse spike-in RNA would be added to 1 µg of treated total RNA. As such, the level of spike-in RNA could be used to normalize sequencing reads to the original cell number.

treatment_protocol: For siRNA-treated samples: An siRNA targeting EXOSC3 (IDT) or a pool of control siRNAs (Sigma) was transfected into cells using Lipofectamine RNAiMAX at a final concentration of 20 nM. Two days following the initial transfection, the transfection was repeated. 24 hours later, cells were harvested in Trizol for RNA purification. For lentiviral shRNA treated samples: HEK293T cells were transduced at an MOI of 10 with lentivirus expressing one or two different shRNAs targeting MTR4, ZFC3H1, PABPN1 or a control scramble sequence. Polybrene (8 µg/mL) was included during transduction. Beginning 24 hours after viral transduction, transduced cells underwent puromycin selection (1.25 µg/mL) for 3 more days. 4 days after transduction, cells were harvested in Trizol for RNA purification. For AMO-treated samples: 25 µM control or U1 AMO (GeneTools, LLC) was delivered into 1x10^6 cells by nucleofection using the Lonza SF Cell Line 4D-NucleofectorTM X Kit using the DH-135 program of the 4D-NucleofectorTM X Unit. Cells were harvested 16 hours later in Trizol for RNA purification.

value: WT

value: ZFC3H1 targeting shRNA


title: HEK293T MTR4 shRNA PAS-seq Replicate 1

value: MTR4 targeting shRNA


title: HEK293T EXOSC3 siRNA PAS-seq Replicate 3

value: EXOSC3 targeting siRNA


title: HEK293T PABPN1 shRNA PAS-seq Replicate 2

value: PABPN1 targeting shRNA


title: HEK293T MTR4 shRNA PAS-seq Replicate 2


title: monocyte_16

value: blood monocyte

value: Male


title: HEK293T ZFC3H1 shRNA PAS-seq Replicate 2


title: HEK293T scramble shRNA PAS-seq Replicate 2

value: Non-targeting scramble shRNA


title: HEK293T scramble shRNA PAS-seq Replicate 1


title: HEK293T ZFC3H1 shRNA PAS-seq Replicate 3


title: HEK293T EXOSC3 siRNA PAS-seq Replicate 2


title: monocyte_13

value: Caucasian


title: HEK293T scramble shRNA PAS-seq Replicate 3


title: HEK293T Control siRNA PAS-seq Replicate 3

value: Non-targeting Control siRNA


title: HEK293T EXOSC3 siRNA PAS-seq Replicate 1


title: HEK293T Control siRNA PAS-seq Replicate 1


title: HEK293T Control siRNA PAS-seq Replicate 2


title: HEK293T PABPN1 shRNA PAS-seq Replicate 1


title: SKOV3 cells, shSAT1, H3K27ac, ChIP, bio rep 3

city: Guangzhou

first: Chaoyun

last: Pan

address: 74 Zhongshan Er Rd.

country: China

institute: Sun Yat-sen University

data_processing:
Fastp (version 0.19.7) (Chen et al 2018) was used to perform basic statistics on the quality of the raw reads and obtain clean data. (1) Discard a paired reads if either one read contains adapter contamination;(2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read.
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.5.3. Only uniquely mapping reads with at most two mismatches were retained
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150bp to represent sequenced fragments, renormalized (to reads per million, rpm), reformatted in the bigwig file format
Peaks were called using MACS v 3.0.1. with the significance cut-off q-value <=0.01
bigwig files were generated using the genomicRanges R package. Peaks files were generated using MACS v3 with default settings. Peak annotation were generated using ChIPseeker R package.
Assembly: hg38
Supplementary files format and content: bigWig, peaks&annotation (except for input samples)

growth_protocol: SKOV3 cells were cultured in complete McCoy’s 5a medium with fetal bovine serum (10%) and penicillin/streptomycin (1%)

extract_protocol:
SimpleChIP Enzymatic Chromatin IP Kit (CST, Cat#9003) was used for chromatin immunoprecipitation and DNA isolation
After the DNA samples quality control，the purified DNA was used NEBNext® Ultra™ II DNA Library Prep Kit （NEB, USA, Catalog #: E7645L）for ChIP-seq library preparation.

treatment_protocol: SKOV3 cells were cultured in the detached conditions for 12 hours

value: Ovarian cancer cell line

value: SAT1 knockdown

value: cell cultured in detached condition

tag: chip antibody


title: SKOV3 cells, shSAT1,input


title: SKOV3 cells, shControl, H3K27ac, ChIP, bio rep 3

value: pLKO control


title: SKOV3 cells, shControl, H3K27ac, ChIP, bio rep 2


title: SKOV3 cells, shSAT1, H3K27ac, ChIP, bio rep 2


title: SKOV3 cells, shControl,input


title: SKOV3 cells,shSAT1, detached condition, bio rep 3

description:
ds3_quant
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv

data_processing:
Fastp (version 0.19.7) (Chen et al 2018) was used to perform basic statistics on the quality of the raw reads and obtain clean data.
Salmon (version 1.10.2) was used for transcript quantification from RNA-seq data.
The tximport R package (version 1.32.0) was used to import salmon’s results into DESeq2.
DESeq2 package (version 1.44.0) was used for the detection and analysis of  differentially expressed genes
GSEA software and clusterProfiler were used for downstream enriched pathway analysis.
Assembly: hg19
Supplementary files format and content: csv file include fold change, p value and raw counts of genes

extract_protocol:
RNA was isolated using RNeasy Mini Kit (Qiagen), 1 μg of total RNA was used for the construction of library
RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA.

treatment_protocol: SKOV3 cells were cultured in the attached or detached conditions for 12 hours


title: SKOV3 cells,shSAT1, detached condition, bio rep 2

description:
ds2_quant
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv


title: SKOV3 cells,shSAT1, detached condition, bio rep 1

description:
ds1_quant
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv


title: SKOV3 cells, shControl,detached condition, bio rep 3

description:
dp3_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv


title: SKOV3 cells, shControl, detached condition, bio rep 2

description:
dp2_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv


title: SKOV3 cells, shControl, attached condition, bio rep 2

description:
ap2_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv

value: cell cultured in attached condition


title: Block_3_044

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

description: In-situ hybridization

data_processing:
Samples were acquired on a Nanostring GeoMx DSP instrument using standard protocols.
Barcoded UMIs from regions of interest were acquired via a photoactivatable linker, sequenced, demuliplexed, and quantified using the R software package "GeoMxWorkflows" according to the vignette (https://bioconductor.org/packages/devel/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html). Raw counts and segments were filtered according to the default quality control thresholds in the vignette, with the modification that segments from which less than 2% of genes in the genome were detected were excluded. Raw counts were normalized using the variant stabilizing transformation function from the DESeq package (https://github.com/thelovelab/DESeq2). Covariates, including donor ("Tissue_ID"), batch, aquisition area ("rounded_area"), region of interest ("Segment"), diagnosis ("Disease"), and MUC5B promoter genotype according to a dominant model (either "G" for GG homozygotes, or "T" for heerozygous or homozygous variants, "Geno"). Downstream analysis used linear mixed effects modeling including region of interest area and batch as fixed effects and donor as a random effect for specimens with multiple regions from the same donor using the "lme4" wrapper, "lmerSeq" (https://github.com/stop-pre16/lmerSeq).
Supplementary files format and content: Variance stabilizing transformed count values.
Supplementary files format and content: dcc

growth_protocol: Formalin-fixed, paraffin-embedded tissues were obtained from the Lung Tissue Research Consortum or from patients undergoing lung transplant at the University of Colorado (Colorado Multi-Institutional Review Board protocol #15-1147).

extract_protocol:
Barcoded, UMI-labelled probes targeting specific mRNA were hybridized to formalin-fixed, paraffin-embedded tissues and acquired at Nanostring (Seattle, WA) or the University of Colorado Anschutz Medical Campus (Aurora, CO).
A commercially available protocol was followed  (Nanostring, Seattle, WA).

treatment_protocol: Formalin-fixed, paraffin-embedded lung tissues from 75 age-matched donors who were either unaffected (21) or had IPF (54) were arranged into tissue macroarray blocks at National Jewish Health by our histopathologist (D.H.). 310 regions were acquired which fell into one of five categories: Airway, alveolus, transition zones characterized by fibroblastic foci, dense fibrosis, or honeycomb cysts guided by our pathologist (C.D.C.). Specimens were genotyped for the IPF risk variant in the promoter for the MUC5B gene, rs35705950 G:T, with 7 control specimens and 31 IPF specimens containing at least one copy of the variant allele.

tag: origin

value: University of Colorado

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

value: non-hispanic

value: white

tag: smoking

value: Never

tag: muc5b rs35705950_genotype

value: GT

tag: disease

value: IPF

tag: segment roi_morphology

value: HC


title: SKOV3 cells, shControl, attached condition, bio rep 3

description:
ap3_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: SKOV3 cells, shControl, attached condition, bio rep 1

description:
ap1_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv


title: Block_3_049

description: In-situ hybridization

tag: origin

value: LTRC

tag: age

tag: Sex

value: Not Hispanic or Latino

tag: race

value: former

value: control

value: alveolar


title: Block_3_042

description: In-situ hybridization

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

value: Male

value: transition


title: SKOV3 cells, shSAT1, H3K27ac, ChIP, bio rep 1

value: Ovarian cancer cell line

value: SAT1 knockdown

value: cell cultured in detached condition

tag: chip antibody


title: Block_3_040

description: In-situ hybridization

value: University of Colorado

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking

value: dense


title: Block_3_039

description: In-situ hybridization

tag: cell line

value: non-hispanic

value: white

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology


title: Block_3_030

description: In-situ hybridization

tag: origin

tag: age

value: Female

value: Former-3 pack years

value: GT


title: Block_3_041

description: In-situ hybridization

tag: Sex

tag: race

value: Never

value: IPF


title: Block_3_029

description: In-situ hybridization

tag: batch

tag: roi area


title: Block_3_032

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation


title: Block_3_031

description: In-situ hybridization

tag: limit of_quantification

value: airway


title: Block_3_028

description: In-situ hybridization

tag: genesdetected


title: SKOV3 cells, shControl, H3K27ac, ChIP, bio rep 1

tag: cell type

tag: genotype

value: pLKO control

tag: treatment

tag: chip antibody


title: Block_3_027

description: In-situ hybridization

tag: cell line

value: LTRC

tag: genedetectionrate

tag: ethnicity

value: not hispanic or latino

value: Caucasian

tag: smoking

value: former

tag: muc5b rs35705950_genotype

value: HC


title: Block_3_022

description: In-situ hybridization

tag: origin

tag: age

tag: Sex

tag: disease

tag: segment roi_morphology


title: Block_3_025

description: In-situ hybridization

tag: batch

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: race

value: alveolar


title: Block_3_023

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

value: transition


title: Block_3_026

description: In-situ hybridization

tag: cell line


title: Block_3_024

description: In-situ hybridization

tag: genedetectionrate


title: Block_3_018

description: In-situ hybridization

value: University of Colorado

value: Male

tag: ethnicity

value: dense


title: Block_3_020

description: In-situ hybridization

value: non-hispanic

value: white

tag: smoking


title: Block_3_048

description: In-situ hybridization

value: Not Hispanic or Latino

tag: muc5b rs35705950_genotype

value: GT

value: control


title: Block_3_021

description: In-situ hybridization

tag: origin

value: Never

value: IPF


title: Block_3_043

description: In-situ hybridization

tag: age


title: SKOV3 cells, shControl,detached condition, bio rep 1

description:
dp1_quant
raw counts&fold change--detach vs attach--pLKO_control_genotype.csv
raw counts&fold change--shSAT1 vs pLKO--detached_condition.csv

tag: cell type

value: Ovarian cancer cell line

tag: genotype

value: pLKO control

tag: treatment

value: cell cultured in detached condition


title: Block_3_019

description: In-situ hybridization

tag: batch

tag: Sex

tag: disease

tag: segment roi_morphology


title: Block_3_015

description: In-situ hybridization

value: LTRC

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: race

value: Caucasian

value: former

value: GG


title: Block_3_016

description: In-situ hybridization

tag: cell line

tag: limit of_quantification

tag: genesdetected

tag: genedetectionrate

value: airway


title: Block_3_014

description: In-situ hybridization

tag: origin

value: Male

tag: ethnicity

tag: smoking

tag: muc5b rs35705950_genotype


title: Block_3_011

description: In-situ hybridization

tag: age

value: transition


title: Block_3_013

description: In-situ hybridization

tag: batch

value: dense


title: Block_3_009

description: In-situ hybridization

tag: Sex


title: Block_3_010

description: In-situ hybridization

tag: disease


title: Block_3_006

description: In-situ hybridization

tag: segment roi_morphology


title: Block_3_008

description: In-situ hybridization

tag: roi area

value: alveolar


title: Block_3_003

description: In-situ hybridization

tag: negative probe_geometric_mean

value: Hispanic or Latino

value: Hispanic

value: nonsmoker


title: Block_3_001

description: In-situ hybridization

tag: negative probe_standard_deviation


title: Block_2-2_063

description: In-situ hybridization

value: Female

value: Not Hispanic or Latino

tag: race

value: Asian

value: control


title: nsRBNS input

city: Chapel Hill

first: Daniel

last: Dominguez

state: NC

address: 120 Mason farm

department: Pharmacology

institute: UNC Chapel Hill

data_processing:
Reads were trimmed using fastx_toolkit before mapping with STAR to generate counts
Counts were normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: Custom genome (see supplementary files)
Supplementary files format and content: tab-delimited text file includes enrichment values for each sample

organism:
Homo sapiens
Mus musculus

source_name: in vitro large scale binding experiment, input

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 4 mM biotin (nsRBNS) or 0.1% SDS with 0.3 mg/mL proteinase K (100vertRBNS). RNA was concentrated via phenol-chloroform extraction
RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified

tag: cell type

value: nsRBNS input


title: Block_2-2_061

description: In-situ hybridization

tag: cell line

value: LTRC

tag: limit of_quantification


title: UNK nsRBNS, 500nM, rep2

source_name: in vitro large scale binding experiment

value: UNK nsRBNS


title: Block_2-2_060

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

value: Caucasian

value: GT


title: UNK nsRBNS, 500nM, rep1


title: Block_2-2_059

description: In-situ hybridization

tag: origin

tag: ethnicity


title: Block_2-2_058

description: In-situ hybridization

tag: smoking

tag: muc5b rs35705950_genotype


title: UNK nsRBNS, 50nM, rep1


title: UNK nsRBNS, 50nM, rep2


title: Block_3_012

description: In-situ hybridization

tag: batch

tag: age

value: former

value: GG

value: IPF


title: Block_2-2_057

description: In-situ hybridization

tag: Sex

value: Male

tag: disease

value: airway


title: UNK nsRBNS, 5nM, rep2


title: Block_3_005

description: In-situ hybridization

tag: roi area

value: Hispanic or Latino

tag: segment roi_morphology

value: transition


title: Block_3_004

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

value: Hispanic

value: nonsmoker


title: Block_2-2_053

description: In-situ hybridization

value: Not Hispanic or Latino

tag: race

value: White

value: TT

value: alveolar


title: UNK nsRBNS, 5nM, rep1

tag: cell type


title: Block_2-2_052

description: In-situ hybridization

tag: cell line

value: LTRC

tag: limit of_quantification


title: Block_2-2_056

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

value: control


title: Block_3_002

description: In-situ hybridization

tag: origin

tag: ethnicity

value: HC


title: Block_2-2_051

description: In-situ hybridization

tag: smoking

tag: muc5b rs35705950_genotype


title: Block_2-2_062

description: In-situ hybridization

tag: batch

tag: age

value: Female

value: Asian


title: Primary tumor - patient P9623

city: Duarte

first: Peter

middle: P

last: Lee

address: 1500 E. Duarte Rd.

department: Immuno-Oncology

institute: Beckman Research Institute at City of Hope

description: FFPE samples were subjected to NanoString analyses.

hyb_protocol: Total RNA was hybridized overnight at 65°C for 14 to 18 hours as per manufacturers’ recommendations.

scan_protocol: Post-hybridization, probe-target mixture was purified by nCounter Prep Station and then quantified with nCounter Digital Analyzer.

data_processing: Quality control and normalization of data were performed with nSolver Analysis Software version 4.0 and nCounter Advanced Analysis Software version 2.0.115, in which the measured gene expression values were normalized to the geometric mean of 40 housekeeping genes.

source_name: Breast

extract_protocol: RNA was extracted from 10µm thick slices of unbaked formalin fixed paraffin embedded (FFPE) tissue using Qiagen miRNeasy FFPE kits. RNA transcripts related to immuno-oncology were detected using NanoString® PanCancer Immune Panel with nCounter® technology (NanoString Technologies) for both TDLN and primary tumors. The regions for RNA extraction were selected by a clinical pathologist with valid TDLN regions. RNA concentration was assessed with the Nanodrop spectrophotometer ND-1000 and Qubit 3.0 Fluorometer (Thermo Fischer Scientific). RNA fragmentation and quality control were further determined by 2100 Bioanalyzer (Agilent).

tag: cohort

value: HOT

tag: grade

tag: Stage


title: Primary tumor - patient P4169


title: Primary tumor - patient P4224


title: Primary tumor - patient P7952


title: Block_2-2_048

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

value: Caucasian

value: former

value: GT

tag: disease

value: IPF

tag: segment roi_morphology


title: Primary tumor - patient P3652


title: Primary tumor - patient P3636


title: Block_2-2_047

description: In-situ hybridization

tag: cell line

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: race


title: Primary tumor - patient P1138


title: Block_2-2_045

description: In-situ hybridization

tag: origin

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

value: transition


title: Block_2-2_044

description: In-situ hybridization

tag: batch

tag: age

tag: smoking

tag: muc5b rs35705950_genotype


title: Primary tumor - patient P9560

tag: cohort

value: COLD

tag: grade

tag: Stage


title: Primary tumor - patient P6830


title: KYSE 150 cells

city: FoShan

first: yuanyuan

last: zhou

state: GuangDong

address: 33, GuangYun Road

institute: foshan university

description: Gene expression data from KYSE 150 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. After that data were analyzed in R, using affy package to extract gene expression and identify different expression genes among the two examples.  Based on the degs,  Go & KEGG  analysis were performed.  And with the help of STRING database, we also inplemented PPI analysis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: KYSE150 cells were cultured in a 6-well plate at 37 °C with 5% CO2 overnight to let the cells adhere and grow to reach about 70~80% confluent monolayers

extract_protocol: Total RNA was extracted by RNeasy Mini Kit (Qiagen, MA, USA)

treatment_protocol: KYSE150 were treated with 91b1 at 9.5μg/ml or DMSO for 48 hours before extraction

tag: treatment


title: Primary tumor - patient P8300


title: KYSE 150 cells treated with compound 91b1

description: Gene expression data from KYSE 150 cells cells treated with compound 91b1

value: treatment


title: Block_2-2_043

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

value: Not Hispanic or Latino

tag: disease

tag: segment roi_morphology

value: dense


title: Primary tumor - patient P5060


title: Primary tumor - patient P0115


title: Block_2-2_038

description: In-situ hybridization

tag: cell line

tag: origin

tag: negative probe_standard_deviation

tag: limit of_quantification

value: Male

tag: race


title: Primary tumor - patient P1934

tag: age


title: Primary tumor - patient P7268


title: Block_2-2_041

description: In-situ hybridization

tag: batch

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking

value: airway


title: Block_2-2_050

description: In-situ hybridization

value: LTRC

value: White

tag: muc5b rs35705950_genotype

value: TT


title: Primary tumor - patient P4353

tag: cohort

tag: grade

tag: Stage


title: TDLN - patient P9623

source_name: Tumor draining lymph node


title: Block_2-2_049

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

tag: disease


title: Block_2-2_042

description: In-situ hybridization

tag: cell line

tag: origin

tag: negative probe_standard_deviation

value: Female

tag: segment roi_morphology


title: Block_2-2_037

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: age

tag: race

value: HC


title: Block_2-2_034

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: TDLN - patient P7952

tag: cohort

value: HOT

tag: grade

tag: Stage


title: Block_2-2_036

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

value: Caucasian

tag: muc5b rs35705950_genotype


title: Block_2-2_035

description: In-situ hybridization

tag: cell line

tag: origin

tag: negative probe_standard_deviation

value: former

tag: disease

value: alveolar


title: TDLN - patient P7268

tag: age


title: Block_2-2_033

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: race

value: GT

value: IPF

tag: segment roi_morphology


title: TDLN - patient P4169


title: Block_2-2_032

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: TDLN - patient P4224

tag: cohort

tag: grade

tag: Stage


title: TDLN - patient P3652


title: Block_2-2_030

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype


title: Block_2-2_031

description: In-situ hybridization

tag: cell line

tag: origin

tag: negative probe_standard_deviation

tag: disease


title: TDLN - patient P3636

tag: age


title: TDLN - patient P9560

value: COLD


title: Block_2-2_029

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: race

tag: segment roi_morphology


title: Block_2-2_040

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: TDLN - patient P1138

tag: cohort

tag: grade

tag: Stage


title: Block_2-2_028

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype

value: transition


title: TDLN - patient P8300


title: TDLN - patient P6830


title: Block_2-2_027

description: In-situ hybridization

tag: cell line

tag: origin

tag: negative probe_standard_deviation

value: Not Hispanic or Latino

tag: disease


title: TDLN - patient P5060

tag: age


title: Block_2-2_024

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: race

tag: segment roi_morphology

value: dense


title: Block_2-2_026

description: In-situ hybridization

tag: genesdetected

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: Block_2-2_025

description: In-situ hybridization

tag: roi area


title: TDLN - patient P4353

tag: cohort

tag: grade

tag: Stage


title: Block_2-2_023

description: In-situ hybridization

tag: cell line

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype


title: TDLN - patient P0115

tag: age


title: TDLN - patient P1934


title: Primary tumor from patient P9623

extract_protocol: RNA was extracted from 10µm thick slices of unbaked formalin fixed paraffin embedded (FFPE) tissue using Qiagen miRNeasy FFPE kits. RNA transcripts related to immuno-oncology were detected using NanoString® PanCancer Pathway Panel with nCounter® technology (NanoString Technologies) for both TDLN and primary tumors. The regions for RNA extraction were selected by a clinical pathologist with valid TDLN regions. RNA concentration was assessed with the Nanodrop spectrophotometer ND-1000 and Qubit 3.0 Fluorometer (Thermo Fischer Scientific). RNA fragmentation and quality control were further determined by 2100 Bioanalyzer (Agilent).


title: Primary tumor from patient P7952


title: Block_2-2_021

description: In-situ hybridization

tag: origin

tag: batch

tag: negative probe_standard_deviation

tag: disease


title: Block_2-2_020

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: race

tag: segment roi_morphology


title: Block_2-2_018

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: Primary tumor from patient P7268

tag: cohort

tag: grade

tag: Stage


title: Primary tumor from patient P4169


title: Block_2-2_017

description: In-situ hybridization

tag: cell line

tag: negative probe_geometric_mean

tag: Sex

value: Male

tag: muc5b rs35705950_genotype

value: GG


title: Primary tumor from patient P4224

tag: age


title: Block_2-2_016

description: In-situ hybridization

tag: origin

value: LTRC

tag: batch

tag: negative probe_standard_deviation

tag: disease


title: Block_2-2_015

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: race

tag: segment roi_morphology


title: Primary tumor from patient P3652


title: Primary tumor from patient P1138


title: Block_2-2_014

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

tag: smoking


title: Primary tumor from patient P9560

tag: cohort

tag: grade

tag: Stage


title: Primary tumor from patient P3636


title: Block_2-2_013

description: In-situ hybridization

tag: cell line

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype


title: Primary tumor from patient P6830

tag: age


title: Block_2-2_012

description: In-situ hybridization

tag: origin

tag: batch

tag: negative probe_standard_deviation

tag: disease


title: Primary tumor from patient P8300


title: Block_2-2_022

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: race

tag: segment roi_morphology


title: Block_2-2_008

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

tag: smoking

value: nonsmoker


title: Primary tumor from patient P5060

tag: cohort

tag: grade

tag: Stage


title: Primary tumor from patient P4353


title: Primary tumor from patient P1934


title: Block_2-2_006

description: In-situ hybridization

tag: cell line

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype


title: Block_2-2_004

description: In-situ hybridization

tag: origin

tag: batch

tag: negative probe_standard_deviation

tag: age


title: Block_2-2_003

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: race

tag: disease


title: Block_2-2_019

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

tag: segment roi_morphology


title: Block_1_079

description: In-situ hybridization

tag: smoking

value: airway


title: Block_1_078

description: In-situ hybridization

tag: cell line


title: Primary tumor from patient P0115

tag: cohort

tag: grade

tag: Stage


title: LM, case 3, scRNAseq

city: Jinan

first: Detian

last: Yuan

address: Wenhuaxi 44

institute: Shandong University

description: 10x Genomics

data_processing:
The Cell Ranger software pipeline (version 2.2.0) provided by 10 × Genomics was used to demultiplex cellular barcodes, align reads and generate the featurebarcode unique molecular identifier (UMI) matrices based on the human reference genome GRCh38.
Assembly: hg38
Supplementary files format and content: Expression matrix in csv format

source_name: Gastric cancer liver metastasis

extract_protocol:
Each tissue sample was placed in a sterile Petri dish on ice. The tissue was subsequently minced to smaller pieces of less than 3 mm. Sample pieces were transferred to a gentle MACS C Tube (Miltenyi #130-093-237) containing 5 ml digestion enzyme mix. The C tube was then placed on a gentleMACS Octo Dissociator for mechanical dissociation. Upon run completion, the sample was incubated for 30 min at 37°C under continuous low shaking. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300 x 3 g and 4°C for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco).
Single-cell RNA-seq libraries were prepared with Chromium Single cell 30 Reagent v2 Kits according to the manufacturer’s protocol. The Chromium Single Cell 30 Library and Gel Bead Kit v2 (PN-120237), Chromium Single Cell 30 Chip kit v2 (PN-120236) and Chromium i7 Multiplex Kit (PN-120262) were used. Briefly, single-cell suspensions were loaded on the Chromium Single Cell Controller Instrument (10 × Genomics) to generate single cell gel beads in emulsions (GEMs). After generation of GEMs, reverse transcription reactions were engaged barcoded fulllength cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, index adaptor ligated and library amplification.

tag: tissue

value: Gastric cancer liver metastasis


title: LM, case 1, scRNAseq

description: 10x Genomics


title: LM, case 2, scRNAseq

description: 10x Genomics


title: GC, case 3, scRNAseq

description: 10x Genomics

source_name: Gastric cancer

value: Gastric cancer


title: Block_1_075

description: In-situ hybridization

tag: origin

tag: batch

tag: negative probe_geometric_mean

tag: Sex

tag: muc5b rs35705950_genotype


title: Block_1_073

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

tag: age

tag: race


title: HL, case 3, scRNAseq

description: 10x Genomics

source_name: Liver

value: Liver


title: Block_1_071

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

value: Caucasian

tag: disease

tag: segment roi_morphology


title: HL, case 2, scRNAseq

description: 10x Genomics


title: Block_1_070

description: In-situ hybridization

tag: cell line

tag: smoking

value: former


title: Block_1_069

description: In-situ hybridization

tag: origin

value: Unk

value: alveolar


title: chr_RNA_siCSB_rep2

data_processing:
STAR was used to align the sequence reads to reference genome; DESeq2 was  used to detect differentially expressed genes.
Assembly: hg38

extract_protocol:
Trizol extraction of chromatin associated RNA
RNA-seq library was prepared by NEBNext Ultra II RNA Kits.

tag: treatment

value: siCSB


title: HL, case 1, scRNAseq

description: 10x Genomics

tag: tissue


title: Block_1_068

description: In-situ hybridization

tag: batch

tag: negative probe_geometric_mean

tag: Sex

value: IPF


title: Block_1_067

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: muc5b rs35705950_genotype

value: transition


title: PRO_siCSB_rep2

description:
PRO_siCSB_fwd.bw
PRO_siCSB_rev.bw

data_processing:
FASTQ reads were quality-checked and adaptor-trimmed with trim galore, and then mapped to the human hg38 reference genomes with bwa mem.
Assembly: hg38
Library strategy: PRO-seq

extract_protocol:
Trizol extraction of RNA
PRO-seq library was prepared by Multiplex Small RNA Library Prep kit, details are described in methods.


title: Block_1_066

description: In-situ hybridization

tag: genesdetected

tag: age

tag: race

value: HC


title: chr_RNA_siNC_rep2

value: siNC


title: Block_1_065

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity


title: chr_RNA_siCSB_rep1

tag: cell line


title: chr_RNA_siNC_rep1


title: PRO_siCSB_rep1

description:
PRO_siCSB_fwd.bw
PRO_siCSB_rev.bw


title: PRO_siNC_rep2

description:
PRO_siNC_fwd.bw
PRO_siNC_rev.bw


title: Block_1_077

description: In-situ hybridization

value: Male

value: Not Hispanic or Latino

tag: smoking

tag: disease

tag: segment roi_morphology


title: Block_2-2_009

description: In-situ hybridization

tag: origin

value: LTRC

value: Female

value: GG


title: Block_1_076

description: In-situ hybridization

tag: batch

value: dense


title: Block_1_062

description: In-situ hybridization

tag: negative probe_geometric_mean


title: GC, case 2, scRNAseq

description: 10x Genomics

tag: tissue

value: Gastric cancer


title: Block_1_060

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: Sex


title: PRO_siNC_rep1

description:
PRO_siNC_fwd.bw
PRO_siNC_rev.bw

tag: treatment


title: PolII_ChIP_siCSB_input_rep1

data_processing:
FASTQ reads were quality-checked and adaptor-trimmed with trim galore, and then mapped to the human hg38 reference genomes with bwa mem. ChIP peak calling were performed with MACS2.
Assembly: hg38

extract_protocol: ChIP-seq libraries were prepared based on ChIPmentation protocols.


title: GC, case 1, scRNAseq

description: 10x Genomics


title: Block_1_074

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: muc5b rs35705950_genotype


title: PolII_ChIP_siCSB_input_rep2


title: Block_1_061

description: In-situ hybridization

tag: roi area

tag: age

tag: race


title: Block_1_059

description: In-situ hybridization

tag: cell line

tag: genedetectionrate

tag: ethnicity


title: PolII_ChIP_siCSB_rep2


title: PolII_ChIP_siNC_input_rep2


title: Block_1_058

description: In-situ hybridization

tag: smoking

tag: disease

tag: segment roi_morphology

value: airway


title: Block_1_064

description: In-situ hybridization

tag: origin

tag: batch

tag: negative probe_geometric_mean


title: Block_1_057

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: Sex

value: Caucasian


title: Block_1_056

description: In-situ hybridization

tag: limit of_quantification

value: former

value: GT


title: Block_1_063

description: In-situ hybridization

tag: genesdetected


title: PolII_ChIP_siNC_input_rep1

tag: treatment


title: Block_1_055

description: In-situ hybridization

tag: roi area

tag: muc5b rs35705950_genotype

value: alveolar


title: PolII_ChIP_siNC_rep1


title: CSB_ChIP_input

value: WT


title: RChIP_siNC_input

description:
RChIP_siNC.fwd.bed
RChIP_siNC.rev.bed

data_processing:
FASTQ reads were quality-checked and adaptor-trimmed with trim galore, and then mapped to the human hg38 reference genomes with bwa mem. ChIP peak calling were performed with MACS2 as described in methods.
Assembly: hg38
Supplementary files format and content: RChIP narrowPeak file of both forward and reverse strand.
Library strategy: R-ChIP

extract_protocol: R-ChIP library was prepared based on published R-ChIP protocols.


title: Block_1_051

description: In-situ hybridization

tag: age

tag: race

value: IPF


title: Block_1_053

description: In-situ hybridization

tag: cell line

tag: genedetectionrate


title: Block_1_054

description: In-situ hybridization

tag: ethnicity

tag: smoking

value: transition


title: RChIP_siCSB_input

description:
RChIP_siCSB.fwd.bed
RChIP_siCSB.rev.bed

value: siCSB


title: Block_1_052

description: In-situ hybridization

tag: disease

tag: segment roi_morphology


title: CSB_ChIP_rep1


title: CSB_ChIP_rep2


title: Block_1_050

description: In-situ hybridization

tag: origin

tag: batch

value: HC


title: Block_1_048

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

value: Male

value: White


title: Block_1_049

description: In-situ hybridization

value: LTRC

tag: limit of_quantification

tag: Sex

value: Not Hispanic or Latino


title: PolII_ChIP_siCSB_rep1

tag: treatment


title: Block_1_047

description: In-situ hybridization

tag: roi area

tag: genesdetected


title: Block_1_046

description: In-situ hybridization

tag: age

tag: muc5b rs35705950_genotype


title: Block_1_045

description: In-situ hybridization

tag: cell line

tag: race


title: Block_1_044

description: In-situ hybridization

tag: genedetectionrate

tag: ethnicity


title: 36 [neurons]

city: Cardiff

last: de la Fuente

address: Maindy Road

country: United Kingdom

institute: Cardiff University

description:
EA062d35.txt
36

data_processing:
trimming of sequences with trimmomatic
read quality assessed with FastQC version 0.11.2
reads mapped to reference genome with STAR 2.5.1b
gene counts obtained with Samtools
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each sample

source_name: neurons

growth_protocol: All hPSCs lines were maintained on Matrigel-coated plates in TeSR-E8 media and were passaged via manual dissociation using 0.02% EDTA. For differentiation into cortical projection neurons, hPSCs were plated directly on Growth Factor Reduced Matrigel in TeSR-E8.  When cells reached >80% confluency, neural differentiation was initiated by switching E8 to DMEM-F12/Neurobasal (2:1) supplemented with N2 and retinol free B27. For the first 10 days, cultures were supplemented with SB431542 (10µM) and LDN-193189 (100nM). During differentiation the cultures were split twice using EDTA. The first split was done en bloc onto fibronectin-coated plates at approximately day 10 and the second split to single cells (5X10^4 cells per cm^2) onto poly-D-lysine/laminin-coated coverslips at around day 18. Cells were remained in basal N2B27 until the end of the protocol. Retinol free B27 was switched to standard B27 on day 25 to aid neuronal maturation.

extract_protocol:
Total RNA was extracted from TRIzol lysates using the PureLink RNA mini kit.
mRNA Hyperprep KAPA kit was used for isolating mRNA and constructing the libraries.

tag: developmental stage

value: iPSC-derived neurons

tag: day of differentiation


title: 32 [neurons]

description:
EA062d35.txt
32


title: 33 [neurons]

description:
EA062d35.txt
33


title: PolII_ChIP_siNC_rep2

value: siNC


title: 35 [neurons]

description:
EA062d35.txt
35


title: 34 [neurons]

description:
EA062d35.txt
34


title: Block_1_041

description: In-situ hybridization

tag: origin

tag: smoking

tag: disease

tag: segment roi_morphology


title: Block_1_042

description: In-situ hybridization

tag: batch

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: limit of_quantification


title: 31 [neurons]

description:
EA062d35.txt
31


title: Block_1_040

description: In-situ hybridization

tag: roi area

tag: genesdetected

tag: Sex


title: 30 [neurons]

description:
EA008d35.txt
30

tag: cell line


title: 29 [neurons]

description:
EA008d35.txt
29


title: 28 [neurons]

description:
EA008d35.txt
28


title: 27 [neurons]

description:
EA008d35.txt
27


title: Block_1_038

description: In-situ hybridization

tag: age

tag: race

tag: muc5b rs35705950_genotype

value: dense


title: Block_1_037

description: In-situ hybridization

tag: genedetectionrate

tag: ethnicity


title: 24 [neurons]

description:
EA008d35.txt
24

tag: developmental stage

tag: day of differentiation

value: ctrl 202


title: Block_1_034

description: In-situ hybridization

tag: origin

value: Unk

value: Caucasian

tag: smoking

tag: disease


title: Block_1_039

description: In-situ hybridization

tag: batch

tag: negative probe_geometric_mean

value: former

value: GT

tag: segment roi_morphology


title: Block_1_033

description: In-situ hybridization

tag: roi area

tag: negative probe_standard_deviation

tag: limit of_quantification

value: airway


title: Block_1_035

description: In-situ hybridization

tag: cell line

tag: genesdetected

tag: Sex

value: IPF

value: alveolar


title: 25 [neurons]

description:
EA008d35.txt
25


title: 23 [neurons]

description:
EA008d35.txt
23


title: 22 [neurons]

description:
EA008d35.txt
22


title: Block_1_032

description: In-situ hybridization

tag: age

tag: race

tag: muc5b rs35705950_genotype

value: transition


title: Block_1_031

description: In-situ hybridization

tag: genedetectionrate

tag: ethnicity


title: Block_1_030

description: In-situ hybridization

tag: origin


title: Block_1_027

description: In-situ hybridization

tag: smoking


title: 17 [neural progenitor cells]

description:
EA062d15.txt
17

source_name: neural progenitor cells

tag: developmental stage

value: iPSC-derived neural progenitor cells

tag: day of differentiation


title: 15 [neural progenitor cells]

description:
EA062d15.txt
15


title: 14 [neural progenitor cells]

description:
EA062d15.txt
14


title: 21 [neurons]

description:
EA008d35.txt
21

value: ctrl 900


title: Block_1_029

description: In-situ hybridization

tag: batch

tag: negative probe_geometric_mean

value: Male

tag: disease


title: Block_1_028

description: In-situ hybridization

value: LTRC

tag: roi area

tag: negative probe_standard_deviation

tag: segment roi_morphology


title: 13 [neural progenitor cells]

description:
EA062d15.txt
13

tag: cell line


title: 16 [neural progenitor cells]

description:
EA062d15.txt
16


title: 18 [neural progenitor cells]

description:
EA062d15.txt
18


title: 20 [neurons]

description:
EA008d35.txt
20


title: 19 [neurons]

description:
EA008d35.txt
19


title: Block_1_026

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: Sex

value: Not Hispanic or Latino


title: Block_1_019

description: In-situ hybridization

tag: age

tag: race

tag: muc5b rs35705950_genotype


title: Block_1_023

description: In-situ hybridization

tag: origin

tag: genedetectionrate

tag: ethnicity


title: Block_1_018

description: In-situ hybridization

tag: smoking


title: Block_1_022

description: In-situ hybridization

tag: batch


title: Block_1_024

description: In-situ hybridization

tag: negative probe_geometric_mean


title: 12 [neural progenitor cells]

description:
EA008d15.txt
12

tag: developmental stage

tag: day of differentiation


title: 11 [neural progenitor cells]

description:
EA008d15.txt
11


title: Block_1_021

description: In-situ hybridization

tag: roi area

tag: negative probe_standard_deviation

tag: disease


title: 10 [neural progenitor cells]

description:
EA008d15.txt
10

tag: cell line


title: 9 [neural progenitor cells]

description:
EA008d15.txt
9


title: 6 [neural progenitor cells]

description:
EA008d15.txt
6


title: 8 [neural progenitor cells]

description:
EA008d15.txt
8


title: Block_1_015

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

tag: segment roi_morphology

value: HC


title: Block_1_020

description: In-situ hybridization

tag: age

tag: Sex

tag: race


title: Block_1_014

description: In-situ hybridization

tag: origin

tag: genedetectionrate

tag: muc5b rs35705950_genotype


title: Block_1_017

description: In-situ hybridization

tag: batch

tag: ethnicity

tag: smoking


title: 3 [neural progenitor cells]

description:
EA008d15.txt
3

tag: developmental stage

tag: day of differentiation


title: 7 [neural progenitor cells]

description:
EA008d15.txt
7


title: 1 [neural progenitor cells]

description:
EA008d15.txt
1


title: Block_1_016

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation


title: Block_1_011

description: In-situ hybridization

tag: cell line

tag: limit of_quantification

value: TT

tag: disease


title: 5 [neural progenitor cells]

description:
EA008d15.txt
5


title: Block_1_010

description: In-situ hybridization

tag: genesdetected

tag: age

tag: segment roi_morphology

value: dense


title: 4 [neural progenitor cells]

description:
EA008d15.txt
4

value: ctrl 202


title: Block_1_013

description: In-situ hybridization

tag: origin

tag: Sex

tag: race


title: COEd10C [neuroepithelium]

description:
coe_vs_h7_d10.txt
296

source_name: neuroepithelium

value: ES-derived neuroepithelium


title: COEd10B [neuroepithelium]

description:
coe_vs_h7_d10.txt
295


title: Block_1_008

description: In-situ hybridization

tag: batch

tag: genedetectionrate

value: Unk

tag: muc5b rs35705950_genotype


title: 2 [neural progenitor cells]

description:
EA008d15.txt
2

tag: developmental stage


title: Block_1_012

description: In-situ hybridization

tag: ethnicity

tag: smoking


title: Block_1_007

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean


title: Block_1_009

description: In-situ hybridization

tag: cell line

tag: negative probe_standard_deviation


title: H7d10A [neuroepithelium]

description:
coe_vs_h7_d10.txt
291

tag: day of differentiation


title: Block_1_003

description: In-situ hybridization

tag: limit of_quantification

tag: genesdetected

value: Caucasian

value: former

value: GG

tag: disease

value: control


title: Block_1_002

description: In-situ hybridization

tag: origin

tag: age

tag: segment roi_morphology

value: alveolar


title: H7d10B [neuroepithelium]

description:
coe_vs_h7_d10.txt
292


title: H7d10C [neuroepithelium]

description:
coe_vs_h7_d10.txt
293


title: Block_1_005

description: In-situ hybridization

tag: batch

tag: Sex

tag: race

value: IPF

value: transition


title: COEd43B [neurons]

description:
coe_vs_h7_d43.txt
267

tag: developmental stage

value: ES-derived neurons


title: H7d43B [neurons]

description:
coe_vs_h7_d43.txt
264


title: COEd43C [neurons]

description:
coe_vs_h7_d43.txt
268


title: H7d43C [neurons]

description:
coe_vs_h7_d43.txt
265


title: Block_1_001

description: In-situ hybridization

tag: genedetectionrate

value: Male

tag: ethnicity

tag: muc5b rs35705950_genotype


title: COEd43A [neurons]

description:
coe_vs_h7_d43.txt
266


title: COEd18A [neuroepithelium]

description:
coe_vs_h7_d18.txt
301

value: ES-derived neural progenitor cells


title: Block_5_024

description: In-situ hybridization

value: University of Colorado

tag: roi area

tag: negative probe_geometric_mean

value: Female

value: Non-hispanic

value: White

tag: smoking

value: Never

value: GT


title: COEd10A [neuroepithelium]

description:
coe_vs_h7_d10.txt
294

value: ES-derived neuroepithelium

tag: day of differentiation

tag: cell line


title: Block_5_025

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

tag: genesdetected

value: dense


title: Block_5_026

description: In-situ hybridization

tag: origin

tag: age

value: Former

tag: disease

value: airway


title: COEd18B [neural progenitor cells]

description:
coe_vs_h7_d18.txt
261


title: COEd18C [neural progenitor cells]

description:
coe_vs_h7_d18.txt
262


title: H7d18C [neural progenitor cells]

description:
coe_vs_h7_d18.txt
259


title: Block_1_004

description: In-situ hybridization

value: LTRC

tag: batch

value: Unk

tag: Sex

value: TT

tag: segment roi_morphology


title: H7d43A [neurons]

description:
coe_vs_h7_d43.txt
263

tag: developmental stage


title: Block_1_006

description: In-situ hybridization

tag: genedetectionrate

tag: ethnicity

tag: race

value: IPF

value: transition


title: H7d18A [neural progenitor cells]

description:
coe_vs_h7_d18.txt
257


title: Block_5_022

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

value: Male

tag: muc5b rs35705950_genotype

value: HC


title: Block_5_023

description: In-situ hybridization

tag: cell line

value: University of Colorado

tag: smoking


title: Block_5_020

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: limit of_quantification

value: alveolar


title: Block_5_021

description: In-situ hybridization

tag: origin

tag: genesdetected

value: Non-hispanic


title: Block_5_017

description: In-situ hybridization

tag: age

value: Female

value: White

value: GG

tag: disease


title: CAS930B [neurons]

description:
cko_vs_cas9_d30.txt
241101

value: ES-derived neurons

tag: day of differentiation


title: H7d18B [neural progenitor cells]

description:
coe_vs_h7_d18.txt
258

value: ES-derived neural progenitor cells


title: Block_5_019

description: In-situ hybridization

tag: batch

tag: Sex

value: Former

value: GT

tag: segment roi_morphology

value: dense


title: CKO05A [neuroepithelium]

description:
cko_vs_cas9_d05.txt
296102

tag: developmental stage

value: ES-derived neuroepithelium


title: CAS930C [neurons]

description:
cko_vs_cas9_d30.txt
242190


title: Block_5_011

description: In-situ hybridization

value: LTRC

tag: genedetectionrate

tag: ethnicity

tag: race


title: Block_5_010

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: muc5b rs35705950_genotype

value: IPF

value: airway


title: Block_5_014

description: In-situ hybridization

tag: cell line

tag: negative probe_standard_deviation

value: Male

value: Unk

tag: smoking

value: Current

value: control


title: Block_5_016

description: In-situ hybridization

tag: origin

tag: limit of_quantification

tag: genesdetected

value: Non-hispanic

value: alveolar


title: CAS930A [neurons]

description:
cko_vs_cas9_d30.txt
240185

tag: day of differentiation


title: CAS912C [neural progenitor cells]

description:
cko_vs_cas9_d12.txt
239104


title: Block_5_009

description: In-situ hybridization

tag: batch

tag: age

value: White

tag: disease


title: Block_5_013

description: In-situ hybridization

tag: Sex

value: Female

tag: segment roi_morphology


title: Block_5_008

description: In-situ hybridization

tag: genedetectionrate

tag: ethnicity

value: transition


title: 26 [neurons]

description:
EA008d35.txt
26

tag: developmental stage

value: iPSC-derived neurons


title: Block_5_007

description: In-situ hybridization

tag: roi area

tag: negative probe_geometric_mean

tag: race

value: Former


title: Block_5_012

description: In-situ hybridization

tag: cell line

tag: negative probe_standard_deviation

tag: muc5b rs35705950_genotype

value: GT

value: HC


title: CAS912B [neural progenitor cells]

description:
cko_vs_cas9_d12.txt
238186

value: ES-derived neural progenitor cells


title: CKO30B [neurons]

description:
cko_vs_cas9_d30.txt
232185

value: ES-derived neurons


title: CAS912A [neural progenitor cells]

description:
cko_vs_cas9_d12.txt
237103


title: CAS905B [neuroepithelium]

description:
cko_vs_cas9_d05.txt
235102

value: ES-derived neuroepithelium


title: CAS905A [neuroepithelium]

description:
cko_vs_cas9_d05.txt
234190


title: CKO30C [neurons]

description:
cko_vs_cas9_d30.txt
233101


title: Block_5_002

description: In-situ hybridization

tag: origin

value: University of Colorado

tag: limit of_quantification

tag: smoking

value: GG


title: CKO5B [neuroepithelium]

description:
cko_vs_cas9_d05.txt
226190

tag: day of differentiation


title: CAS905C [neuroepithelium]

description:
cko_vs_cas9_d05.txt
236189


title: Block_5_018

description: In-situ hybridization

tag: batch

tag: genesdetected

tag: age

value: Male

value: IPF


title: Block_5_015

description: In-situ hybridization

value: LTRC

tag: Sex

value: Unk

tag: disease

tag: segment roi_morphology

value: airway


title: CKO30A [neurons]

description:
cko_vs_cas9_d12.txt
231104

tag: developmental stage


title: CKO5A [neuroepithelium]

description:
cko_vs_cas9_d05.txt
225101


title: Block_5_006

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: ethnicity

value: Non-hispanic

value: White

value: alveolar


title: CKO12A [neural progenitor cells]

description:
cko_vs_cas9_d12.txt
228189

tag: cell line


title: Block_5_005

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: race


title: Block_8_020

description: In-situ hybridization

tag: origin

tag: limit of_quantification

value: Female

value: Never

tag: muc5b rs35705950_genotype


title: N_SH8h_REF6-HA/ref6-1_set2-IP

city: Shanghai

first: Qican

last: Cheng

state: Shanghai

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

data_processing:
Trimmomatic software were used to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.]
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff foldchange > 2, qvalue < 0.05.
Reads distributions (from bigwig) across peaks are presented as an average plot (average of reads signals across all peaks). The deeptools tool is used for this analysis.
Assembly: Tair10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: whole seedling

extract_protocol:
Fixation: The sample is fixed with 1% formaldehyde (Sigma, 47608).
Fragmentation: Nuclear chromatin is extracted and sonicated to fragmentize it to 100-400 base pairs (bp), 5% is taken out as input, and the rest is used for immunoprecipitation.
Immunoprecipitation: The primary antibody is incubated with beads, and then mixed with the fragmented chromatin and incubated at 4°C for 6 hours.
Elution: The antibody-magnetic bead-protein-DNA complex is sequentially washed with high salt and low salt buffers, and then the IP (Immunoprecipitated) products are eluted.
De-crosslinking: The IP products and input are de-crosslinked with RNase A (NEB, T3018L) and Proteinase K (NEB, P8107S).
Purification: The de-crosslinked input DNA and IP DNA are purified using a kit (QIAquick PCR Purification Kit, 28106).
Purified Input DNA and IP DNA are used to construct libraries with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) kit.

tag: tissue

value: whole seedling

tag: genotype

tag: treatment

value: 8 hr shade


title: N_SH8h_REF6-HA/ref6-1_set1-IP


title: N_SH8h_REF6-HA/pif7-1_set1-IP

extract_protocol:
Fixation: The sample is fixed with 1% formaldehyde (Sigma, 47608). Fragmentation: Nuclear chromatin is extracted and sonicated to fragmentize it to 100-400 base pairs (bp), 5% is taken out as input, and the rest is used for immunoprecipitation. Immunoprecipitation: The primary antibody is incubated with beads, and then mixed with the fragmented chromatin and incubated at 4°C for 6 hours. Elution: The antibody-magnetic bead-protein-DNA complex is sequentially washed with high salt and low salt buffers, and then the IP (Immunoprecipitated) products are eluted. De-crosslinking: The IP products and input are de-crosslinked with RNase A (NEB, T3018L) and Proteinase K (NEB, P8107S). Purification: The de-crosslinked input DNA and IP DNA are purified using a kit (QIAquick PCR Purification Kit, 28106).
Purified Input DNA and IP DNA are used to construct libraries with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S) kit.


title: Block_8_019

description: In-situ hybridization

tag: batch

tag: genesdetected

tag: age

tag: Sex

tag: smoking

value: transition


title: N_SH8h_REF6-HA/pif7-1_set1-input


title: Block_8_018

description: In-situ hybridization

tag: roi area

tag: genedetectionrate

tag: disease

tag: segment roi_morphology

value: dense


title: Block_8_015

description: In-situ hybridization

tag: cell line

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: ethnicity

value: Former

value: GT

value: control


title: Block_8_014

description: In-situ hybridization

tag: origin

value: University of Colorado

tag: limit of_quantification

value: Male

tag: race

tag: muc5b rs35705950_genotype


title: Block_5_003

description: In-situ hybridization

tag: batch

value: GG


title: Block_8_012

description: In-situ hybridization

tag: genesdetected

value: IPF


title: N_SH8h_REF6-HA/ref6-1_set2-input

tag: tissue

tag: genotype

tag: treatment


title: N_SH8h_REF6-HA/ref6-1_set1-input


title: Block_8_013

description: In-situ hybridization

tag: roi area

tag: age

tag: Sex

tag: smoking


title: N_WL_REF6-HA/ref6-1_set2-IP

value: white light


title: Block_5_001

description: In-situ hybridization

tag: cell line

tag: genedetectionrate

value: Unk

tag: disease

tag: segment roi_morphology

value: airway


title: Block_8_021

description: In-situ hybridization

tag: origin

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: ethnicity

value: Non-hispanic

value: White

value: HC


title: Block_8_010

description: In-situ hybridization

tag: batch

tag: limit of_quantification

value: Female

tag: race

value: Never

tag: muc5b rs35705950_genotype


title: N_WL_REF6-HA/ref6-1_set1-IP

tag: tissue

value: whole seedling

tag: genotype

tag: treatment


title: N_SH8h_REF6-HA/pif7-1_set2-IP

value: 8 hr shade


title: N_SH8h_REF6-HA/pif7-1_set2-input


title: N_WL_REF6-HA/ref6-1_set2-input


title: Block_8_007

description: In-situ hybridization

tag: roi area

tag: genesdetected

tag: age

tag: Sex

value: dense


title: Block_8_009

description: In-situ hybridization

tag: cell line

tag: genedetectionrate

tag: smoking

tag: disease


title: Block_8_008

description: In-situ hybridization

tag: origin

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: segment roi_morphology

value: transition


title: D5_PATZ1

first: Prashant

last: Rajbhandari

state: New York

address: 1468 Madison Ave, Annenberg 18-10

institute: Icahn School of Medicine at Mount Sinai

data_processing:
ChIP-Seq was performed as described (45, 76). To confirm the robustness of peaks, the same BAM files were analyzed via HOMER where 84% of the peaks (marked by genomic coordinates) overlapped.  77,599 significant peaks (P<1e-3) were detected in the D0, and 131553 significant peaks (P<1e-3) were detected in D5.  While little significant peaks overlapped between d0 and d5 (132) at the genomic coordinate level, 452 genes were observed to intersect between the two. We note that, possibly due to sequencing depth or other parameters, the most significant results were observed in D0 evident by comparing a highly stringent threshold (P<1e-10) where 696 peaks were observed in D0. Reads were aligned to the mouse genome (NCBI37/mm9) with Bowtie2. Uniquely mapped reads were used for peak calling and annotation using HOMER (80). Peaks were called if they passed a false discovery rate of 0.01 and were enriched over input. Peaks were annotated to the nearest TSS.
Assembly: mm10 (GRCm38)
Supplementary files format and content: BigWig

organism: Mus musculus

extract_protocol:
ChIP experiments were performed according to standard protocols (78, 79). Lysed cells were sonicated using a Bioruptor (Diagenode) according to the manufacturer’s protocol, and chromatin was immunoprecipitated with antibodies against PATZ1 (sc-390577, Santa Cruz Biotechnology) for D0 and D5, sequential PATZ1 and GTF2I (PA5-17642, Thermo Fisher) for ChIP-reChip seq, PATZ1 (A10053,Abclonal) for D-2, D0, D5, D8, and IgG (PP64, Millipore) overnight at 4°C in the presence of Protein A beads (GE Healthcare).
ChIP-Seq libraries were prepared using the Kapa LTP Library Preparation Kit (Kapa Biosystems). The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount. cDNA libraries were single-end sequenced (50bp) on an Illumina HiSeq  4000.

tag: cell type


title: Input


title: D0_PATZ1


title: Block_8_006

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: ethnicity

value: Hispanic

tag: race

value: Former

tag: muc5b rs35705950_genotype

value: GT


title: Block_8_005

description: In-situ hybridization

value: University of Colorado

tag: roi area

tag: genesdetected

value: Male


title: Block_8_003

description: In-situ hybridization

value: LTRC

tag: age

tag: Sex

value: IPF


title: Block_8_011

description: In-situ hybridization

tag: cell line

tag: genedetectionrate

value: alveolar


title: UNK ZnF4-6 RBNS, 500nM

description: Counts were normalized for library size prior to enrichment analysis against 20mer_input

data_processing:
Reads were trimmed to 20nt
6mer counts were generated and normalized for library size
Enrichments were calculated as the frequency of an oligo in the protein bound sample divided by the frequency in the input pool
Assembly: None
Supplementary files format and content: tab-delimited files includes 6mer enrichment values

organism: synthetic construct

source_name: UNK ZnF1-3 RBNS

extract_protocol:
Bound RNA was eluted from streptavidin magnetic beads in 4 mM biotin (nsRBNS) or 0.1% SDS with 0.3 mg/mL proteinase K (100vertRBNS). RNA was concentrated via phenol-chloroform extraction RNA libraries for sequencing were reverse transcribed with SuperScript IV following manufacturer's protocols, PCR amplified with Phusion DNA polymerase to attach Illumina TrueSeq Small RNA adapters, then agarose gel purified
Individual libraries were analyzed via Qubit then normalized for concentration match prior to pooling and sequencing

value: UNK ZnF1-3 RBNS


title: UNK ZnF4-6 RBNS, 1000nM


title: UNK ZnF4-6 RBNS, 250 nM


title: Block_8_002

description: In-situ hybridization

value: Non-hispanic

value: Unk

tag: smoking

tag: disease


title: Block_7_019

description: In-situ hybridization

tag: origin

tag: negative probe_geometric_mean

value: Female

value: GG

value: control


title: Block_8_004

description: In-situ hybridization

tag: negative probe_standard_deviation

tag: segment roi_morphology


title: Block_8_001

description: In-situ hybridization

tag: batch


title: Block_7_018

description: In-situ hybridization

tag: limit of_quantification

value: White

value: HC


title: UNK ZnF1-3 RBNS, 250nM

tag: cell type


title: UNK ZnF1-3 RBNS, 500nM


title: Block_7_021

description: In-situ hybridization

tag: ethnicity

tag: race

value: Never


title: Swr1 Swr1∆11-Bdf1

city: Ithaca

first: Justin

middle: Sungsoo

last: Cha

address: 526 Campus Rd

department: Computational Biology

institute: Cornell University

data_processing:
ChIP-exo reads were aligned using bwa-mem with the following settings: -v (1)  -T (30) -h (5)
Remove duplicate reads and generate a deduplicated BAM file using picard MarkDuplicates and samtools
Generate forward and reverse BIGWIG files from deduplicated BAM file using deeptools bamCoverage (forward: --binSize 1 --Offset 1 --samFlagInclude 64 --samFlagExclude 16, reverse: --binSize 1 --Offset 1 --samFlagInclude 80 --samFlagExclude 0)
Assembly: sacCer3
Supplementary files format and content: Bigwig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: Bigwig for reverse strand -- coverage of 5' end of Read 1 across the genome

organism: Saccharomyces cerevisiae

source_name: S. Cerevisiae cells

growth_protocol: S. cerevisiae strains containing FLAG-tagged H2A.Z or TAP-tagged Swr1 in WT or mutants were grown in YPD media to an O.D600 of 0.6-0.8 at 25˚C

extract_protocol:
50 mL cell pellets were resuspended in 750 uL FA lysis buffer (50 mM HEPES-KOH, pH7.5, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate and complete protease inhibitor (Roche) along with 1 ml of 0.5 mm acid washed zirconia beads. Lysis was performed by bead beating for 4 cycles of 3 min on and 7 min off in a Mini-Beadbeater-96 machine (Biospec). Whole cell lysates were centrifuged at 14,000 rpm for 3 min at 4 ˚C. Cytoplasmic supernatants were discarded and nuclear pellets were resuspended in 200 uL FA lysis buffer supplemented with 0.1% SDS and 75 uL 0.1 mm zirconia beads. Nuclear samples were sonicated in a Bioruptor (Diagenode) for 4 cycles of 30 sec on and 30 sec off. Samples were centrifuged at 14,000 rpm for 10 min to collect sonicated chromatin fraction which was predominantly enriched with DNA fragments in a range of 100-500 bp in size (verified on agarose gels). Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: anti-FLAG (Sigma, M8823), anti-IgG (Sigma, i5006). Chromatin obtained from 50 mL culture was used for a single ChIP experiment. Appropriate antibodies (3-5 ug per ChIP) were conjugated to protein A/G magnetic Sepharose resin (GE Healthcare Life Sciences) at 4 ˚C for 6-8 hr. Unconjugated antibody was removed, then chromatin sample were immunoprecipitated overnight (12-16 hr) at 4 ˚C. For TAP-tagged samples, 40 uL IgG-Dynabeads slurry was used per sample. Subsequent steps were performed as described previously (Rossi et al., 2018).
ChIP-exo libraries were gel purified and were sequenced in a paired-end mode with NextSeq 500 (Read_1 40 cycles, Read_2 36 cycles).

value: S. Cerevisiae cells

tag: base strain

tag: genetic modification

tag: epitope tag

tag: antibody

tag: growth media

value: YPD


title: CKO12B [neural progenitor cells]

description:
cko_vs_cas9_d12.txt
229103

tag: developmental stage

value: ES-derived neural progenitor cells

tag: day of differentiation

tag: cell line


title: UNK ZnF1-3 RBNS, 1000nM


title: N_WL_REF6-HA/ref6-1_set1-input

tag: tissue

value: whole seedling

tag: genotype

tag: treatment

value: white light


title: Block_7_015

description: In-situ hybridization

tag: origin

value: LTRC

tag: roi area

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

value: Male

tag: smoking

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology


title: Block_1_025

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: ethnicity

value: Not Hispanic or Latino

tag: race

value: Caucasian

value: former

value: GT

value: IPF

value: dense


title: Block_7_020

description: In-situ hybridization

tag: cell line

value: University of Colorado

value: Female

value: Unk

value: GG

value: control

value: airway


title: 20mer_RNA_input

tag: cell type

value: UNK ZnF1-3 RBNS


title: Block_7_017

description: In-situ hybridization

tag: origin

tag: roi area

value: Non-hispanic

value: White


title: Swr1 Yaf9-YEATS3A

value: S. Cerevisiae cells

tag: base strain

tag: genetic modification

value: Yaf9 T69A-Y70A-W89A

tag: epitope tag

tag: antibody

tag: growth media

value: YPD


title: Swr1 Swr1∆11-Bdf1 Yaf9-YEATS3A


title: Htz1 Swr1∆11-Bdf1 Yaf9-YEATS3A rep2

value: YPDad


title: Block_7_013

description: In-situ hybridization

tag: negative probe_geometric_mean

tag: negative probe_standard_deviation

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: smoking

value: Never

value: alveolar


title: Htz1 Yaf9-YEATS3A rep2


title: Block_7_012

description: In-situ hybridization

tag: batch

tag: limit of_quantification

tag: ethnicity

tag: race

tag: muc5b rs35705950_genotype

tag: disease

tag: segment roi_morphology


title: Block_7_016

description: In-situ hybridization

tag: cell line

tag: origin

value: LTRC

tag: roi area

value: GT

value: IPF


title: Block_7_010

description: In-situ hybridization

tag: negative probe_geometric_mean

value: Male


title: Htz1 Swr1∆11-Bdf1 rep2

tag: cell type

tag: base strain

tag: genetic modification

tag: epitope tag

tag: antibody

tag: growth media


title: Htz1 Swr1∆11-Bdf1 rep1


title: Swr1 WT

value: WT


title: Block_7_008

description: In-situ hybridization

tag: batch

tag: negative probe_standard_deviation

tag: genesdetected

tag: genedetectionrate

tag: age

tag: Sex

tag: smoking

value: dense


title: Htz1 WT rep1


title: Block_7_014

description: In-situ hybridization

tag: cell line

tag: limit of_quantification

tag: ethnicity

tag: race

tag: muc5b rs35705950_genotype

value: GG

tag: disease

tag: segment roi_morphology

value: transition


title: Block_7_011

description: In-situ hybridization

tag: origin

tag: roi area

tag: negative probe_geometric_mean

value: airway


title: p22rv1-Replicate 2 hypoxia (0.2%O2)

city: Oslo

first: Heidi

last: Lyng

address: Montebello

institute: Oslo University Hospital

data_processing:
Single-end sequencing of 50 bases of each cDNA
Real-time analysis, base calling, adapter clipping and filtering of low quality reads performed by Illumina software according to standard protocols.
Quality assessment was based on the reads using the FASTQC quality control
Read alignment software: miRDeep2 v.2.0.0.5 with mirBase v.21 for annotation of mature miRNAs
Assembly: Hg19
Supplementary files format and content: Cellines_miRNAcounts_unnorm_matrix: matrix with raw counts for every miRNA in every sample . In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.
Supplementary files format and content: Cellines_miRNA_TMMnorm_matrix: matrix with normalized counts (RPM) for every miRNA in every sample. In cases when mature miRNA IDs had duplicates, the duplicate with the highest mean expression was kept.

source_name: Prostate cancer cell line

extract_protocol:
Total RNA was isolated using miRNeasy MiniKit, according to the information given for each sample.
Small RNA preparation for sequencing was performed according to Illumina TruSeq Small RNA library protocols. Briefly, indexed 3’- and 5’end RNA adapters were ligated to 1 ug of isolated total RNA per sample followed by reverse transcription and library amplification. The cDNA was purified on a PAGE gel by cutting out bands corresponding to 140-160 bp (length of miRNA + adapter and index sequences), pooled and ethanol precipitated.

treatment_protocol: Hypoxia treatment (0%, 0.2%, 0.5%, 1%, 2% or 5% O2) of exponentially growing cells was carried out at 60-70% cell confluence in an In Vivo2 200 chamber for 24 hours at 37°C. All hypoxia treatments were performed in duplicate.

tag: tissue

value: Prostate cancer cell line

value: Primary, from xenograft CWR22R subline

tag: treatment

value: Hypoxia


title: Htz1 Yaf9-YEATS3A rep1

tag: cell type

value: S. Cerevisiae cells

tag: base strain

tag: genetic modification

value: Yaf9 T69A-Y70A-W89A

tag: epitope tag

tag: antibody

tag: growth media


title: Htz1 Swr1∆11-Bdf1 Yaf9-YEATS3A rep1

value: YPDad