title: 9_16_c_1209

city: Cologne

first: Ludwig

last: Eichinger

state: NRW

address: Joseph-Stelzmann-Str. 52

department: Biochemistry Medical Faculty

institute: Centre for Biochemistry Medical Faculty University of Cologne

description: atg9‾ /16‾

data_processing:
Illumina Casava software used for basecalling
RNA-Seq data were processed through the QuickNGS analysis pipeline  version 1.2.7, based on Ensembl release 33
Sequenced reads mapped to Dictyostelium_discoideum
Fragment Per Kilobase of exon per Million (FPKM) were calculated using a Cufflinks
Genome_build: Dictyostelium_discoideum 33
Supplementary_files_format_and_content: Excel file include FPKM values for each Sample

organism: Dictyostelium discoideum

source_name: D. discoideum cells

growth_protocol: D. discoideum cells were grown to log phase and 1 x 107 cells were harvested (500 x g, 5 min, 4°C), followed by two washing steps with 10 ml Soerensen’s phosphate buffer

extract_protocol:
total RNA extraction was carried out using the Qiagen RNeasy® Mini Kit according to the manufacturer’s instructions
Illumina RNASeq library Protocol
Libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit

treatment_protocol: Total RNA from vegetative D. discoideum cells was isolated

value: ATG9-/16- mutant

tag: state

value: vegetative


title: 9_16_b_1197

status: Public on May 19 2021

type: SRA

country: Germany

description: atg9‾ /16‾

library_source: transcriptomic

molecule: total RNA

tag: genotype


title: 9_16_c_LE6_3668

description: atg9‾ /16‾


title: EEDmethy_23_Batch1

type: genomic

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw Illumina BeadChip data (i.e. IDAT files) were imported into R and normalized using  minfi version 1.30.0.  IDAT files were normalized using functional normalization (FunNorm). probes located on X and Y chromosomes and probes closer than 3 bp to a SNP were excluded.
Average Beta normalized using functional normalization (FunNorm)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: DNA were isolated from duodenal biopsies obtained during diagnostic esophagogastroduodenoscopy using the Qiagen AllPrep RNA/DNA Mini Kit (Qiagen, Valencia, CA)

tag: diagnosis

value: EED

tag: gender

value: Female

tag: age (month)

value: Duodenum

tag: pid


title: 9_16_a_LE6_3656

description: atg9‾ /16‾


title: flp-21 mutant, mRNA_21_29

city: Basel

first: Jadiel

last: Wasson

address: Klingelbergstrasse 50/70

department: Zell Biologie

country: Switzerland

institute: Biozentrum, University of Basel

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WBcel235 using BWA alignment tool.
featureCounts was used to count all alignments. Multi-read correction was used on all mRNA read counts. mRNA read counts from each library were normalized to the total number of mapped reads
variance stabilizing transformation was utilized and each library was analyzed for differential expression using Deseq2
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: early embryos

extract_protocol:
Early embryos were isolated from C. elegans mothers when 1-2 eggs were present, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina instrument following the manufacturer's protocols.

tag: developmental stage

value: early embryos


title: 9_16_c_LE8_4421

description: atg9‾ /16‾


title: EEDmethy_14_Batch1

value: Male


title: EEDmethy_13_Batch1


title: EEDmethy_18_Batch1


title: EEDmethy_10_Batch1


title: 16_b_LE6_3661

value: ATG16- mutant


title: 16_c_1208


title: EEDmethy_07_Batch1


title: EEDmethy_08_Batch1


title: 16_1184


title: EEDmethy_06_Batch1


title: EEDmethy_09_Batch1


title: Col (FigS5) BSPCR [P3_Col]

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

country: USA

institute: University of California - Los Angeles

library_source: genomic

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using Bismark and processed into per-position methylation data.
For BS-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using Bismark, and PCR duplicates were removed using a custom Bismark script. A bismark function was used to process alignments into per-position methylation data.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR, and only uniquely mapped reads were kept. Presumed PCR duplicates were removed using MarkDuplicates from the Picard tools suite. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 1 --normalizeUsing CPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq and BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For RNA-seq, count files are text files listing gene IDs and the number of overlapping reads (by htseq-count) in the first and second column, respectively. Coverage tracks are bigWig files and contain per-position sequencing coverage data for each RNA-seq library.

organism: Arabidopsis thaliana

source_name: Col  BSPCR

growth_protocol: Plants were grown under long-day conditions (16h light/8h dark) at 23°C in controlled growth chambers.

extract_protocol:
CTAB-based method was used to extract DNA
Qiagen EpiTect bisulfite kit was used to treat DNA per manufacturer’s instruction. Libraries were made from purified PCR products amplified by using previously described primers (Gallego-Bartolomé et al. 2019) using an Ovation Ultralow V2 kit (NuGEN).

tag: ecotype background

tag: genetic background

value: wild-type

tag: transgene present

value: no transgene

value: rosette stage

tag: tissue

value: rosette leaf


title: EEDmethy_12_Batch1


title: EEDmethy_01_Batch1


title: 9_1183

value: ATG9- mutant


title: 9_c_LE6_3665


title: 9_a_LE6_3653


title: wildtype, mRNA_N2_11

value: wildtype


title: flp-21 mutant, mRNA_21_22


title: 9_16_1185

description: atg9‾ /16‾


title: wildtype, mRNA_N2_22


title: 9_a_LE8_4416


title: AX2_c_1206

value: AX2 wild-type


title: 9_16_b_LE8_4420

description: atg9‾ /16‾


title: 9_16_a_LE8_4419

description: atg9‾ /16‾


title: 16_b_1196


title: AX2_b_LE6_3658


title: AX2_a_LE6_3652


title: AX2_c_LE8_4406


title: AX2_a_LE8_4404


title: 16_c_LE6_3667


title: 16_a_LE6_3655


title: 16_c_3388


title: 9_16_b_LE6_3662

description: atg9‾ /16‾


title: 16_b_3376


title: 16_a_3364


title: 9_c_1207


title: 9_b_1195


title: 9_b_LE6_3659


title: 9_b_LE8_4417


title: AX2_b_1194


title: CIN58

type: RNA

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from CA3 explant

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

source_name: hippocampus, CA3 region

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Brain tissue explants from GD (3-4 mm3) were homogenized with TissueRupter (Qiagen) and total RNA was extracted from the homogenates using the RNeasy Lipid Tissue Kit (Qiagen)

treatment_protocol: Fresh ex-vivo explants of patients were obtained at the surgery room and immediately preserved with 600 uL of RNAlater (Qiagen).

value: hippocampus, CA3 region

value: F

tag: age at surgery (yr)

tag: age of ipi (yr)

tag: age of epilepsy onset (yr)

tag: side

value: L


title: CIN55

description: Gene expression from CA3 explant

value: M

value: R


title: CIN36

description: Gene expression from CA3 explant


title: AX2_1218

value: vegetative


title: CIN39

description: Gene expression from CA3 explant


title: AX2_c_LE6_3664


title: CIN29

description: Gene expression from CA3 explant


title: CIN33

description: Gene expression from CA3 explant


title: CIN46

description: Gene expression from CA3 explant


title: 9_c_LE8_4418


title: AX2_b_LE8_4405


title: PFC1-A8-c94

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

country: United Kingdom

institute: Imperial College London

data_processing:
Alignment with STAR
Filtering for genes expressed in at least three cells
Filtering for cell with at least 200 genes
Genome_build: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: h5ad

organism: Mus musculus

source_name: germ cell

extract_protocol:
The illumina Nextera XT DNA preparation kit was used to prepare the library directly from the lysate of single cell.
The RNA library was prepared using the standard illumina protocol

treatment_protocol: Single cells were sorted in 96 well plates containing 4ul of lysis buffer and frozen on dry ice.

tag: cell type

value: germ cell

tag: oxygen condition

value: Hypo

tag: cell

value: positive


title: PFC1-A8-c95


title: PFC1-A8-c96


title: PFC1-A8-c91


title: CIN10

description: Gene expression from CA3 explant


title: CIN60

description: Gene expression from CA3 explant


title: CIN49

description: Gene expression from CA3 explant


title: CIN18

description: Gene expression from CA3 explant


title: CIN56

description: Gene expression from CA3 explant


title: CIN22

description: Gene expression from CA3 explant


title: PFC1-A8-c90


title: CIN17

description: Gene expression from CA3 explant


title: CIN47

description: Gene expression from CA3 explant


title: PFC1-A8-c89


title: CIN31

description: Gene expression from CA3 explant


title: CIN64

description: Gene expression from CA3 explant


title: s7999_R

city: Chicago

first: Han

last: Peng

state: IL

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

data_processing: raw counts

source_name: corneal epithelium

extract_protocol: none provided by the submitter

tag: genotype

value: wild type


title: s7976_R


title: CIN24

description: Gene expression from CA3 explant


title: CIN26

description: Gene expression from CA3 explant


title: CIN27

description: Gene expression from CA3 explant


title: s7976_N


title: s7975_N

value: EphA2 null


title: s7998_B


title: s7998_N


title: CIN19

description: Gene expression from CA3 explant


title: PFC1-A8-c93


title: PFC1-A8-c92


title: PFC1-A8-c85


title: PFC1-A8-c86


title: PFC1-A8-c83


title: PFC1-A8-c84


title: PFC1-A8-c76

value: negative


title: PFC1-A8-c72


title: PFC1-A8-c71


title: PFC1-A8-c69


title: PFC1-A8-c87


title: PFC1-A8-c82


title: PFC1-A8-c65


title: PFC1-A8-c81


title: PFC1-A8-c66


title: PFC1-A8-c63


title: PFC1-A8-c80


title: PFC1-A8-c62


title: PFC1-A8-c88


title: PFC1-A8-c60


title: PFC1-A8-c61


title: PFC1-A8-c56


title: PFC1-A8-c57


title: PFC1-A8-c78


title: PFC1-A8-c79


title: CIN05

description: Gene expression from CA3 explant


title: PFC1-A8-c77


title: PFC1-A8-c75


title: PFC1-A8-c74


title: PFC1-A8-c73


title: PFC1-A8-c68


title: PFC1-A8-c67


title: PFC1-A8-c49


title: PFC1-A8-c50


title: PFC1-A8-c48


title: PFC1-A8-c47


title: PFC1-A8-c46


title: PFC1-A8-c45


title: PFC1-A8-c44


title: PFC1-A8-c64


title: PFC1-A8-c59


title: PFC1-A8-c58


title: PFC1-A8-c55


title: PFC1-A8-c70


title: PFC1-A8-c54


title: PFC1-A8-c38


title: PFC1-A8-c34


title: PFC1-A8-c43


title: PFC1-A8-c53


title: PFC1-A8-c42


title: RX_41_NEG_3_

city: Philadelphia

first: Brian

last: Estevez

state: Pennsylvania

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

description: 10X genomics Single Cell 3’ Reagent Kits v3_

data_processing:
Demultiplexed FASTQ files were processed using the CellRanger count pipeline (10x Genomics, v.3.1.014) for alignment of sequencing reads to the GRCh38 transcriptome and creation of feature-barcode matrices. As each sample was initially split into two lanes during sequencing they are denoted below in "RAW FILES" as,  'L001' and 'L002', and were merged by CellRanger processing.
The Seurat package (v.3.0.215) within the R computing environment was used to aggregate and analyze the dataset.
To account for possible batch effects, a canonical correlation analysis was used to integrate and aggregate the individual libraries.
Gene expression matrices were log normalized and scaled, and a Wilcoxon rank sum test was used to determine differentially expressed genes between experimental groups.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cell Ranger output
Supplementary_files_format_and_content: tab-delimited text files include log2FC values for each Sample … S10 Cell cluster specific analysis corresponding to all samples, S11 bulk analysis of all cells correspond ing to all samples. S13 Merged analysis corresponding to all samples

source_name: hematopoietic progenitor cells

extract_protocol: Sorted cells were counted, and adjusted to a target of 5,000 cells in a 38 µL volume of 1X PBS (Gibco) and 0.04% BSA (Sigma-Aldrich). Cells, reverse transcription (RT) master mix (10X Genomics), primer-coated 10X gel beads, and partitioning oil were loaded onto a Single Cell A chip (10X Genomics) and into a 10X Genomics Chromium Controller instrument for microfluidic droplet-based encapsulation of cells, RT reagents, and gel beads. RT reaction was performed within droplets in a thermocycler (Bio-Rad) and following the 10X Genomics incubation protocol. Droplets were then broken down, and the released barcoded cDNAs were purified using magnetic beads, and amplified by PCR. cDNA concentrations were determine using a Qubit 3.0 fluorometer and Qubit HS dsDNA assay kit (both, ThermoFisher). Enzymatic digestion and size selection were performed to generate the optimal cDNA size for library construction. Sequencing primers P5, P7, R2 and sample-specific index primers were added during library construction. Quality and size of generated libraries was verified using the Bioanalyzer high-sensitivity DNA analysis kit (Agilent). Library concentrations were determined using kapa DNA library quantification kit (KAPA Biosystems). Libraries were sequenced on an Illumina HiSeq 4000

value: G-CSF mobil. PB CD34+ HSPCs

tag: lv shrna

tag: surface markers


title: PFC1-A8-c51


title: NT_41_NEG_3_

value: non-targeting control


title: PFC1-A8-c52


title: PFC1-A8-c30


title: PFC1-A8-c39


title: PFC1-A8-c29


title: NT_41_POS_3_


title: PFC1-A8-c40


title: RX_41_POS_3_


title: PFC1-A8-c36


title: PFC1-A8-c37


title: PFC1-A8-c33


title: PFC1-A8-c32


title: RX_41_POS_2_


title: PFC1-A8-c35


title: RX_41_NEG_1_


title: PFC1-A8-c26


title: PFC1-A8-c41


title: RX_41_NEG_2_


title: PFC1-A8-c27


title: PFC1-A8-c31


title: NT_41_NEG_2_


title: PFC1-A8-c28


title: NT_41_POS_1_


title: PFC1-A8-c25


title: PFC1-A8-c24


title: NT_41_POS_2_


title: PFC1-A8-c23


title: TE5_TP63_KD_Input

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Dr

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Paired end 151 bp reads were aligned to the hg19 reference genome using Bowtie2.
PCR duplicate reads were removed using Picard MarkDuplicates.
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

growth_protocol: TE5 is maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). The medium is supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Standard Illumina library preparation protocol

value: esophageal squamous cell carcinoma


title: TE5_Scramble_TP63_ChIP

tag: antibody

value: Scramble


title: RX_41_POS_1_


title: TE5_Scramble_Input


title: PFC1-A8-c22


title: PFC1-A8-c21


title: PFC1-A8-c20


title: TE5_TP63_KD_TP63_ChIP


title: PFC1-A8-c19


title: PFC1-A8-c18


title: PFC1-A8-c17


title: PFC1-A8-c16


title: PFC1-A8-c15


title: PFC1-A8-c13


title: PFC1-A8-c14


title: TT_ARV-771_H3K27ac

address: 14 Medical Drive, #12-01,

data_processing:
Single end 49 bp reads were aligned to the hg19 reference genome using Bowtie.
PCR duplicate reads were removed using Picard MarkDuplicates.
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

source_name: TT ARV-771 H3K27ac

growth_protocol: TT is maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). The medium is supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

treatment_protocol: TT cells were treated with either ARV-771, Romidepsin or DMSO, and harvested at indicated time points, with indicated concentrations.

tag: cell line

value: TT


title: TT_DMSO_H3K4Me3

source_name: TT DMSO H3K4Me3


title: TT_ARV-771_H3K4Me3

source_name: TT ARV-771 H3K4Me3


title: TT_Romidepsin_H3K27ac

source_name: TT Romidepsin H3K27ac


title: TE5_SCRAMBLE [RNA-seq]

data_processing:
Paired end fastq files were pseudoaligned to Ensembl (hg19, v82) transcripts using Kallisto.
Transcript level abundances and counts were summarized to gene level using the TxImport bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto

growth_protocol: TE5 cell line is cultured in RPMI-1640 medium, the media is supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

extract_protocol:
Total RNA from each sample was extracted according to the manufacturer’s instruction of RNeasy Mini kit (QIAGEN).
RNA library was prepared using TruSeq Library Prep Kit (Illumina) according to the manufacturer’s instructions and subjected to massive parallel sequencing using Hiseq (Illumina) at Beijing Genomics Institute.

treatment_protocol: TE5 cells were transfected with either scramble or shKLF5, and harvested after 48 hrs.

value: esophageal squamous cell carcinoma (ESCC) cell line

tag: transfected with


title: TE5_shKLF5_1 [RNA-seq]


title: TT_DMSO_H3K27ac

source_name: TT DMSO H3K27ac


title: NT_41_NEG_1_


title: PFC1-A8-c12

tag: developmental stage


title: PFC1-A8-c11


title: TT_H3K4Me1

data_processing:
Single end 49 bp reads were aligned to the hg19 reference genome using Bowtie
PCR duplicate reads were removed using Picard MarkDuplicates
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

growth_protocol: KYSE150/180/200/70 and TE5 cell lines are cultured in RPMI-1640 medium; TT is maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). All media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

tag: chip antibody

value: Rabbit Anti-Histone H3 (mono methyl K4) antibody, Abcam, Cat# ab8895


title: TE5_shKLF5_2 [RNA-seq]


title: TT_H3K4Me3

value: Rabbit Anti-Histone H3 (tri methyl K4), Abcam, Cat# ab8580


title: TE5_Pol_II

value: Rabbit Anti-Pol II (N-20) X, Santa Cruz Biotechnology, Cat# sc-899X


title: PFC1-A8-c9


title: PFC1-A8-c7


title: TT_Romidepsin_H3K4Me3

source_name: TT Romidepsin H3K4Me3


title: TE5_H3K4Me1


title: PFC1-A8-c10


title: PFC1-A8-c8


title: PFC1-A8-c6


title: KYSE70_Pol_II


title: TE5_H3K4Me3


title: PFC1-A8-c4


title: KYSE70_H3K4Me1


title: KYSE70_H3K4Me3


title: PFC1-A8-c3


title: KYSE200_INPUT

value: INPUT


title: PFC1-A8-c2


title: PFC1-A8-c1


title: KYSE200_H3K27ac

value: Rabbit Anti-Histone H3 (acetyl K27), Abcam, Cat# ab4729


title: PFC1-A7-c96

value: germ cell

value: Norm


title: KYSE180_INPUT


title: KYSE180_H3K27ac


title: KYSE150_INPUT


title: PFC1-A7-c95

value: positive


title: PFC1-A7-c94


title: KYSE150_H3K27ac


title: PFC1-A7-c93


title: PFC1-A7-c92


title: TT_shTP63

data_processing:
Single end 50 bp reads were aligned to the hg19 reference genome using Bowtie
PCR duplicate reads were removed using Picard MarkDuplicates
Reads aligning to the mitochondrial chromosome were removed.
Peaks were called subsequently using macs2 while simultaneously generating bedgraph files in Reads Per Million scale
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files representing signal normalized to per million reads

growth_protocol: KYSE140 and TE5 cell lines are cultured in RPMI-1640 medium; TT is maintained in Dulbecco’s modiﬁed Eagle medium (DMEM). All media are supplemented with 10% fetal bovine serum (Invitrogen, San Diego, CA), penicillin (100 U/mL) and streptomycin (100 mg/mL).

extract_protocol: ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

treatment_protocol: KYSE140, TE5 and TT cells were transfected with either scramble, shTP63, shSOX2 or shKLF5, and harvested after 48 hrs.


title: PFC1-A8-c5

value: Hypo


title: PFC1-A7-c91


title: TE5_shTP63

source_name: TE5 _shTP63


title: PFC1-A7-c89


title: PFC1-A7-c90


title: TT_shKLF5


title: PFC1-A7-c87


title: PFC1-A7-c88


title: TE5_Scramble

source_name: TE5 _Scramble


title: TE5_shSOX2

source_name: TE5 _shSOX2


title: PFC1-A7-c86


title: TE5_shKLF5

source_name: TE5 _shKLF5


title: PFC1-A7-c85


title: PFC1-A7-c84


title: 140_shSOX2


title: 140_shTP63


title: PFC1-A7-c82


title: PFC1-A7-c83


title: 140_Scramble


title: 140_shKLF5


title: PFC1-A7-c81


title: PFC1-A7-c80


title: TT_shSOX2


title: PFC1-A7-c79


title: TT_Scramble


title: PFC1-A7-c78


title: PFC1-A7-c77


title: PFC1-A7-c75


title: PFC1-A7-c76


title: PFC1-A7-c73


title: PFC1-A7-c74


title: PFC1-A7-c72


title: PFC1-A7-c70


title: PFC1-A7-c69


title: PFC1-A7-c68


title: PFC1-A7-c67


title: PFC1-A7-c66


title: VISUAL_60h

city: Kobe

first: Tomoyuki

last: Furuya

address: 1-1, Rokkodai-cho, Nada-ku

country: Japan

institute: Kobe University

hyb_protocol: Hybridization, washing, staining procedures were conducted with Fluidics Station 450 as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

scan_protocol: Scanning procedure ws conducted with GeneChip Scanner 3000 7G as described in the GeneChip Expression Analysis Techinical Manual (Affymetrix).

data_processing: GCOS

label: biotin

source_name: Col-0, 6-day-old seedlings, cotyledons

label_protocol: Biotinylated cRNA was prepared from total RNA with GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix).

growth_protocol: Arabidopsis seeds were sterilized with sodium hypochlorite for 5 min, and then washed with sterile water. These seeds were grown with MS liquid medium at 22ºC under the continuous light conditions for 6 days.

extract_protocol: Total RNA was extracted and purified with Rneasy Plant Mini Kit (QIAGEN).

treatment_protocol: Cotyledons were cultured with the induction medium containing 2,4-D (1.25 mg/L), kinetin (0.25 mg/L), and bikinin (10 μM). Samples were collected from 0 to 72 hours at every 6 hours after inuduction.

tag: organ

value: Col-0, 6-day-old cotyledons

tag: time

value: induction after 60h


title: VISUAL_36h

value: induction after 36h


title: PFC1-A7-c64


title: VISUAL_54h

value: induction after 54h


title: VISUAL_48h

value: induction after 48h


title: VISUAL_24h

value: induction after 24h


title: VISUAL_42h

value: induction after 42h


title: VISUAL_30h

value: induction after 30h


title: PFC1-A7-c63


title: PFC1-A7-c71

value: negative


title: VISUAL_66h

value: induction after 66h


title: VISUAL_72h

value: induction after 72h


title: PFC1-A7-c65


title: PFC1-A7-c62


title: VISUAL_18h

value: induction after 18h


title: PFC1-A7-c61


title: PFC1-A7-c60


title: VISUAL_12h

value: induction after 12h


title: PFC1-A7-c59

value: germ cell


title: VISUAL_0h

value: induction after 0h


title: VISUAL_6h

value: induction after 6h


title: PFC1-A7-c55

value: Norm

value: positive


title: PFC1-A7-c58


title: DMSO_3

city: Kyoto

first: Etsuko

middle: Yamamoto

last: Hattori

state: Kyoto

address: 54 Kawahara-Cho, Shogoin, Sakyo-Ku

institute: Kyoto University

hyb_protocol: The arrays are incubated for 16 hours in a hybridization system (GeneChipTM Hybridization Oven 640) at 45°C and 60 rpm.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data analyses were processed using Expression Console Software 1.4.1(Expression Console).

source_name: A172 (glioblastoma cell line)

label_protocol: Samples were fragmented by UDG and APE 1. Terminal deoxynucleotidyl transferase is used to label the 3' ends of the fragmented ds-cDNA with biotin.

growth_protocol: Cells were supplemented with Dulbecco’s Modified Eagle’s Medium (DMEM), 10% heat-inactivated foetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with an atmosphere of 5% CO2.

extract_protocol: RNeasy Plus Mini kit

treatment_protocol: Cells were cultured in DMEM medium containing 1% DMSO or 1% Chb-M' 1µM for 48 hours.

tag: smple type

value: glioblastoma cell line (brain, 53y.o.)

tag: treatment

value: DMSO


title: PFC1-A7-c57


title: Chb-M'_3

value: Chb-M' (1uM)


title: PFC1-A7-c54


title: PFC1-A7-c53


title: DMSO_1


title: DMSO_2


title: Chb-M'_2


title: PFC1-A7-c52


title: Chb-M'_1


title: U2OS daughter cells (N+1) replication timing in APH condition - Rep1

city: Toulouse cedex 1

first: Valérie

last: Bergoglio

address: 2 avenue Hubert Curien

country: France

institute: INSERM UMR1037

hyb_protocol: The hybridization was performed according to the manufacturer instructions on 4× 180K human microarray (SurePrint G3 Human CGH Microarray Kit, 4x180K, AGILENT Technologies, genome reference Hg18) that covers the whole genome with one probe every 13 Kb (11 KB in RefSeq sequences).

scan_protocol: Microarrays were scanned with an Agilent's High-Resolution C Scanner (Agilent C-scanner) using a resolution of 3 µm and the autofocus option.

data_processing:
Feature extraction was performed with the Feature Extraction 9.1 software (Agilent technologies). For each experiment, the raw data sets were automatically normalized by the Feature extraction software. Analysis was performed with the Agilent Genomic Workbench 5.0 software.
US92003687*txt raw data file:  This file contains the raw values of log ratio for each probe (Cy3/Cy5 = E/L) - column P
*log_ratio.txt file:  LOESS SMOOTH of log ratio Early/Late values
To determine the replication domains and do the comparative analysis in different conditions, the online platform specific for replication timing data START-R (Hadjadj et al., 2020) was used, with biological duplicates for each condition. The output bed file gave the list of significantly impacted genomic regions (ADVANCED or DELAYED) and the report of number and percentage of genomic regions impacted.
genome build: hg18
Bed file:  Genomic coordinate of regions significant replication timing modifications (ADVANCED or DELAYED) between DMSO and Aphidicolin conditions.  Note: K562_DMSO_vs_APH_N+1.bed is empty because there are no significant differences between the two conditions.

source_name: Nascent DNA from early S phase

label_protocol: Microarray hybridization requires a minimum of 1000 ng of DNA and to obtain sufficient specific immunoprecipited DNA, whole genome amplification was conducted (WGA, Sigma). To be sure that this step does not introduce bias, an after WGA qPCR was performed to confirm the specific enrichment in each fractions S1 and S2. After amplification, early and late neo-synthesized DNA were labeled with Cy3 and Cy5 ULS molecules (Genomic DNA labeling Kit, Agilent) as recommended by the manufacturer.

growth_protocol: Each cells were grown in appropriate culture condition (see material and method)

extract_protocol: cells were incubated with BrdU (50µM) for one hour, then collected, washed three times in PBS, fixed in 75% ethanol, and stored at −20°C. Fixed cells were re-suspended in PBS first with RNAse (0.5 mg/ml) and then with propidium iodide (PI) (50 µg/ml) following by an incubation of 30 min at room temperature. 80,000 cells were sorted in two fractions S1 and S2 using INFLUX 500 (Cytopeia purchased by BD Biosciences) corresponding to Early and Late fractions respectively. Neo-synthesized DNA was immunoprecipited by BrdU antibodies (Anti BrdU Pure, BD Biosciences, # 347580) as described by Hiratani et al 2008. To control the quality of enrichment of early and late fractions in S1 and S2, qPCR was performed with BMP1 oligonucleotides (early control) and with Dppa2 oligonucleotides (late control).

treatment_protocol: Aphidicolin (Sigma aldrich) was used at 0.2µM during appropriate duration (see Table S2)

tag: tissue

value: Osteosarcoma

tag: condition

value: APH condition

tag: timing

value: (N+1) replication timing

tag: phase

value: early S phase

source_name: Nascent DNA from late S phase

value: late S phase


title: PFC1-A7-c50

source_name: germ cell

tag: cell type

tag: oxygen condition

tag: cell


title: U2OS daughter cells (N+1) replication timing in APH condition - Rep2


title: RPE-1 daughter cells (N+1) replication timing in APH condition - Rep2

value: Retina


title: RPE-1 daughter cells (N+1) replication timing in APH condition - Rep1


title: A549-T-shCNOT3-2 DOX

city: Bethesda

first: Yo-taro

last: Shirai

state: MD

address: Building 37, Room 3118

department: Center for Cancer Research

institute: NIH

description:
SAMPLE F
A549-T-shCNOT3-2 cultured with DOX

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

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.

source_name: A549 human NSCLC cells from RIKEN Cell Bank

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: The A549 stables were cultured in DMEM medium containing 10% fetal bovine serum (FBS), penicillin (50U/mL), and streptomycin (50U/mL).  All the cells were grown up in 5% CO2 atmosphere at 37C in the incubator.

extract_protocol: Extraction of total RNA using RNeasy Mini Kit was performed according to the manufacturer's instructions.

treatment_protocol: The A549 stables were cultured with and without DOX (1 ug/ml ) treatment for 72 hours starting from the next day of the seeding.

value: human non-small cell lung cancer (NSCLC) cell line

tag: genotype/variation

value: stably expressing tetracyclin-induible shRNA against CNOT3 targeting sequences (A549-T-shCNOT3-2)

tag: treated with

value: Doxycyclin (DOX; 1 ug/ml) for 72 hrs


title: RKO daughter cells (N+1) replication timing in APH condition - Rep2

tag: cell line

value: RKO

value: colon cancer


title: PFC1-A7-c56

value: germ cell


title: RKO daughter cells (N+1) replication timing in DMSO condition - Rep2

value: DMSO condition


title: PFC1-A7-c49

value: Norm

value: positive


title: A549-T-shCNOT3-1 DOX

description:
SAMPLE D
A549-T-shCNOT3-1 cultured with DOX

value: stably expressing tetracyclin-induible shRNA against CNOT3 targeting sequences (A549-T-shCNOT3-1)


title: H2228 cells treated with IL4

city: Tianjin

first: Yongwen

last: Li

address: No.154, Anshan Road, Heping District

country: China

institute: Tianjin Medical University General Hospital

description: Gene expression data from H2228 cells treated with IL4

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix Human Genome U133 PLUS 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Analysis of the microarray expression data was done using the R/Bioconductor through a graphical user interface, Chipster 3.12.5. Normalization was performed using custom chip description file for hgu133Aplus2. Intensity data were log2-transformed, and quantile normalized using robust multi-array average (RMA).

source_name: lung cancer

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 5% CO2 incubator at 37℃.

extract_protocol: Qiagene RNeasy mini kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Cell were transfected with EML4-ALK plasimids or EML4-ALK siRNAs or negative controls for 48 hours. Then cells were use for this experiment.

tag: agent

value: H2228 cells


title: A549-T-shCNOT3-2 (-)

description:
SAMPLE E
A549-T-shCNOT3-2 cultured without DOX


title: A549-T-shCNOT3-1 (-)

description:
SAMPLE C
A549-T-shCNOT3-1 cultured without DOX


title: A549-T-shNTC DOX

description:
SAMPLE B
A549-T-shNTC cultured with DOX

value: stably expressing tetracyclin-induible shRNA against non-targeting control (A549-T-shNTC)


title: A549-T-shNTC (-)

description:
SAMPLE A
A549-T-shNTC cultured without DOX


title: H2228 cells non-treatment

description: Gene expression data from H2228 cells

value: non-treatment


title: PFC1-A7-c48

tag: developmental stage

value: negative


title: PFC1-A7-c46


title: RKO daughter cells (N+1) replication timing in APH condition - Rep1

value: APH condition

value: (N+1) replication timing

value: early S phase


title: PFC1-A7-c45


title: PFC1-A7-c51


title: PFC1-A7-c42


title: PFC1-A7-c44


title: PFC1-A7-c41


title: MRC5N daughter cells (N+1) replication timing in APH condition - Rep1

value: Lung

value: late S phase


title: PFC1-A7-c43


title: PFC1-A7-c40


title: U2OS replication timing in APH condition - Rep2

value: Osteosarcoma

value: T0 replication timing


title: HCT116 daughter cells (N+1) replication timing in APH condition - Rep1

value: colon cancer


title: HCT116 daughter cells (N+1) replication timing in APH condition - Rep2


title: PFC1-A7-c39

value: germ cell


title: U2OS replication timing in DMSO condition - Rep2

value: DMSO condition


title: U2OS replication timing in APH condition - Rep1


title: PFC1-A7-c47

value: Norm


title: U2OS replication timing in DMSO condition - Rep1


title: PFC1-A7-c38


title: PFC1-A7-c37


title: PFC1-A7-c36


title: RPE-1 replication timing in DMSO condition - Rep1

value: Retina


title: RPE-1 replication timing in APH condition - Rep1


title: RPE-1 replication timing in DMSO condition - Rep2


title: RKO daughter cells (N+1) replication timing in DMSO condition - Rep1

value: RKO


title: K562 daughter cells (N+1) replication timing in APH condition - Rep2

value: CML


title: K562 daughter cells (N+1) replication timing in APH condition - Rep1


title: RKO replication timing in APH condition - Rep2


title: RKO replication timing in DMSO condition - Rep2


title: PFC1-A7-c30

value: positive


title: PFC1-A7-c32


title: PFC1-A7-c33


title: RKO replication timing in DMSO condition - Rep1


title: PFC1-A7-c31


title: MRC5N replication timing in APH condition - Rep2


title: PFC1-A7-c28


title: PFC1-A7-c27


title: MRC5N replication timing in DMSO condition - Rep2


title: MRC5N replication timing in APH condition - Rep1


title: PFC1-A7-c25


title: PFC1-A7-c26


title: MRC5N replication timing in DMSO condition - Rep1


title: RPE-1 replication timing in APH condition - Rep2


title: PFC1-A7-c24


title: PFC1-A7-c35


title: K562 replication timing in DMSO condition - Rep2


title: PFC1-A7-c23


title: PFC1-A7-c22


title: K562 replication timing in APH condition - Rep1


title: RKO replication timing in APH condition - Rep1


title: HCT116 replication timing in APH condition - Rep2


title: PFC1-A7-c21


title: PFC1-A7-c29


title: PFC1-A7-c20


title: HCT116 replication timing in DMSO condition - Rep2


title: PFC1-A7-c19


title: HCT116 replication timing in APH condition - Rep1


title: PFC1-A7-c17


title: sgTLE4 stimulated

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

data_processing:
Single cell RNA-sequencing files were processed using the Cell Ranger workflow.
FASTQ files were generated using the Cell Ranger ‘mkfastq’ command with default parameters
FASTQs were aligned to the hg19 genome build using the ‘count’ function and aggregated using the default Cell Ranger ‘aggr’ parameters with normalization performed by subsampling wells to equalize read depth across cells.
Downstream analyses were performed using the R/Bioconductor package Seurat
Genome_build: hg19
Supplementary_files_format_and_content: matrix

source_name: CAR T cells

growth_protocol: Cultures were maintained in X-Vivo15 with 10% FCS, 50 U/mL rhIL-2 and 0.5 ng/mL rhIL-15 (cytokines were supplied every 48 hours)

extract_protocol:
Total mRNA from GSCs or CAR T cells was isolated and purified by an RNeasy Mini Kit.
10x library construction protocol

treatment_protocol: Primary T cells were stimulated with Dynabeads Human T expander CD3/CD28 (T cells : beads = 1:2) for 24 hours and transduced with sgRNA lentivirus (1:250 v/v ratio). Cells were washed after 6 hours and then transduced with CAR lentivirus (multiplicity of infection [MOI] = 0.5).  4 days after CAR transduction, CD3/CD28 beads were removed and cells were resuspended in Lonza electroporation buffer P3 (2x108 cells/mL). Cas9 protein was then added to the cell suspension (1:10 v/v ratio) and electroporation was performed using a 4D-NucleofactorTM Core Unit. Cells were recovered in pre-warmed X-VIVO 15 media for 30 min before proceeding to ex vivo expansion. All T cell transduction and ex vivo expansion were performed in X-VIVO 15 containing 10% FCS, 50 U/ml recombinant human IL-2 (rhIL-2), and 0.5 ng/ml rhIL-15, at 6x105 cells/mL. Stimulated samples were co-cultured with glioblastoma stem cells. Unstimulated samples were monocultured.

value: CAR T Cell

tag: genotype

value: TLE4 Knockout

value: Stimulated


title: PFC1-A7-c16

value: negative


title: sgTLE4 unstimulated

value: Unstimulated


title: HCT116 replication timing in DMSO condition - Rep1

value: early S phase


title: PFC1-A7-c15


title: K562 replication timing in APH condition - Rep2

value: APH condition

value: late S phase


title: PFC1-A7-c14


title: PFC1-A7-c13


title: sgIKZF2 unstimulated

value: IKZF2 Knockout


title: PFC1-A7-c12


title: sgCONT stimulated

value: Control


title: PFC1-A7-c11

value: germ cell


title: PFC1-A7-c10


title: K562 replication timing in DMSO condition - Rep1

value: DMSO condition

value: T0 replication timing


title: T36_sgRELA_2

data_processing:
Trim Galore was used to trim adaptors and remove low quality reads.
Reads were quantified against Gencode v29 using Salmon with correction for fragment-level GC bias, positional bias and sequence-specific bias.
Transcripts were summarized to gene level and processed to transcripts per million (TPM) using the R/Bioconductor package DESeq2
Comparisons were performed using contrasts in DESeq2 followed by Benjamini-Hochberg adjustment to correct for false discovery rate.
Genome_build: hg19
Supplementary_files_format_and_content: CSV; gene-level TPM expression values

source_name: Glioblastoma stem cells

growth_protocol: Glioblastoma stem cells

extract_protocol:
Total mRNA from GSCs or CAR T cells was isolated and purified by an RNeasy Mini Kit.
PolyA capture

treatment_protocol: For lentiviral transduction, GSC tumorspheres were dissociated into single cells using Accutase, resuspended in GSC media and lentivirus was added at a 1:50 v/v ratio. GSCs were then washed once after 12 hours, resuspended in fresh GSC media and cultured for 3 days. To ensure that only transduced cells were expanded for further assays, GSCs were selected by puromycin for 7 continuous days, with a 1:10000 v/v ratio into GSC media.

value: Glioblastoma stem cell

value: RELA Knockout


title: PFC1-A7-c9

value: Norm


title: T30_sgRELA_3


title: PFC1-A7-c7


title: PFC1-A7-c18

value: positive


title: PFC1-A7-c8


title: T36_sgNPLOC4_3

value: NPLOC4 Knockout


title: PFC1-A7-c6


title: T30_sgRELA_2


title: T36_sgNPLOC4_2


title: PFC1-A7-c3


title: sgIKZF2 stimulated

value: CAR T Cell


title: T30_sgNPLOC4_2


title: PFC1-A7-c34


title: T36_sgRELA_3


title: PFC1-A7-c4


title: PFC1-A7-c5


title: T30_sgNPLOC4_3


title: PFC1-A7-c1


title: PFC1-A7-c2


title: sgCONT unstimulated


title: PFC1-A6-c95

value: Hypo


title: PFC1-A6-c96


title: CAR T sgEIF5A-2

treatment_protocol: Primary T cells were stimulated with Dynabeads Human T expander CD3/CD28 (T cells : beads = 1:2) for 24 hours and transduced with sgRNA lentivirus (1:250 v/v ratio). Cells were washed after 6 hours and then transduced with CAR lentivirus (multiplicity of infection [MOI] = 0.5).  4 days after CAR transduction, CD3/CD28 beads were removed and cells were resuspended in Lonza electroporation buffer P3 (2x108 cells/mL). Cas9 protein was then added to the cell suspension (1:10 v/v ratio) and electroporation was performed using a 4D-NucleofactorTM Core Unit. Cells were recovered in pre-warmed X-VIVO 15 media for 30 min before proceeding to ex vivo expansion. All T cell transduction and ex vivo expansion were performed in X-VIVO 15 containing 10% FCS, 50 U/ml recombinant human IL-2 (rhIL-2), and 0.5 ng/ml rhIL-15, at 6x105 cells/mL.

value: EIF5A Knockout


title: CAR T sgTLE4-2

value: TLE4 Knockout


title: CAR T sgTLE4-1


title: CAR T sgEIF5A-1


title: CAR T sgIKZF2-2


title: PFC1-A6-c93


title: PFC1-A6-c92


title: CAR T sgIKZF2-1


title: CAR T sgTMEM184B-2

value: TMEM184B Knockout


title: PFC1-A6-c91


title: CAR T sgTMEM184B-1


title: T36 sgCONT


title: PFC1-A6-c90


title: PFC1-A6-c89


title: CAR T sgNT-2


title: CAR T sgNT-1


title: PFC1-A6-c88


title: PFC1-A6-c85


title: FL Early MOLM14 Gilteritinib Day 21 R2 [LIB191203BD_S10_FLT3earlyD2giltR2_S7_L002]

city: Portland

first: Sunil

middle: Kumar

last: Joshi

state: OR

address: 3181 SW Sam Jackson Park Rd. Mail Code: KR-HEM

department: Knight Cancer Institute

institute: Oregon Health & Science University

description: LIB191203BD_S10_FLT3earlyD2giltR2_S7_S7_L002

data_processing:
library strategy: PCR library sequencing
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Genome_build: Custom reference created from CRISPR library
Supplementary_files_format_and_content: Read counts per sgRNA for each sample

source_name: FL Early Gilteritinib Resistant MOLM14 cells infected with library

growth_protocol: Early and late gilteritinib resistant MOLM14 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone. Early cell lines were also supplemented with 10 ng/mL  or FGF2 or FL.

extract_protocol:
30 million cells were collected from gilteritinib-treated flasks on day 14 (late resistance screens) and 21 (early resistance screens). DNA was extracted by desalting method
100 micrograms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/mL concentration for 7 days. 100 nM of  gilteritinib was applied to 30 million cells in a single flask

tag: cell line/type

value: infected with CRISPR/Cas9 library

value: day 21 post puromycin selection, Gilteritinib


title: FL Early MOLM14 DMSO Day 21 R2 [LIB191203BD_S10_FLT3earlyD21DMSOR2_S9_L002]

description: LIB191203BD_S10_FLT3earlyD21DMSOR2_S9_S9_L002

value: FL Early  Gilteritinib Resistant MOLM14 cells

value: day 21 post puromycin selection, DMSO


title: FL Early MOLM14 Gilteritinib Day 21 R1 [LIB191203BD_S10_FLT3earlyD21GiltvR1_S6_L001]

description: LIB191203BD_S10_FLT3earlyD21GiltvR1_S6_S6_L001


title: FL Early MOLM14 DMSO Day 21 R1 [LIB191203BD_S10_FLT3earlyD21DMSOR1_S8_L002]

description: LIB191203BD_S10_FLT3earlyD21DMSOR1_S8_S8_L002


title: PFC1-A6-c83

value: germ cell


title: PFC1-A6-c84


title: PFC1-A6-c86


title: FL Late MOLM14 DMSO Day 14 R2 [LIB191203BD_S9_Flt3lateDMSoD14R2_S54_L002]

description: LIB191203BD_S9_Flt3lateDMSoD14R2_S54_S11_L002

source_name: FL Late Gilteritinib Resistant MOLM14 cells infected with library

value: day 14 post puromycin selection, DMSO


title: PFC1-A6-c82


title: PFC1-A6-c94


title: FL Late MOLM14 DMSO Day 14 R1 [LIB191203BD_S9_Flt3lateDMSoD14R1_S53_L002]

description: LIB191203BD_S9_Flt3lateDMSoD14R1_S53_S10_L002

value: FL Late Gilteritinib Resistant MOLM14 cells


title: PFC1-A6-c80

value: negative


title: FL Late MOLM14 Gilteritinib Day 14 R2 [LIB191203BD_S9_Flt3latGil1D14R2_S56_L003]

description: LIB191203BD_S9_Flt3latGil1D14R2_S56_S13_L003

value: day 14 post puromycin selection, Gilteritinib


title: PFC1-A6-c79


title: FL Late MOLM14 Gilteritinib Day 14 R1 [LIB191203BD_S9_Flt3latGil1D14R1_S55_L002]

description: LIB191203BD_S9_Flt3latGil1D14R1_S55_S12_L002


title: PFC1-A6-c87


title: FGF2 Late MOLM14 DMSO Day 14 R2 [LIB190430JT_S9_Molm14FGF2GR_dmso_d14dup_S32_addtl]

description: LIB190430JT_S9_Molm14FGF2GR_dmso_d14dup_S32_S7_L002

source_name: FGF2 Late Gilteritinib Resistant MOLM14 cells infected with library


title: PFC1-A6-c78


title: FGF2 Late MOLM14 DMSO Day 14 R2 [LIB190430JT_S9_Molm14FGF2GR_dmso_d14dup_S32]

description: LIB190430JT_S9_Molm14FGF2GR_dmso_d14dup_S32_S31_L006

value: FGF2 Late Gilteritinib Resistant MOLM14 cells


title: PFC1-A6-c77


title: FGF2 Late MOLM14 DMSO Day 14 R1 [LIB190430JT_S9_Molm14FGF2GR_dmso_d14_S31_addtl]

description: LIB190430JT_S9_Molm14FGF2GR_dmso_d14_S31_S6_L001


title: PFC1-A6-c76


title: PFC1-A6-c75


title: FGF2 Late MOLM14 DMSO Day 14 R1 [LIB190430JT_S9_Molm14FGF2GR_dmso_d14_S31]

description: LIB190430JT_S9_Molm14FGF2GR_dmso_d14_S31_S30_L005


title: PFC1-A6-c81

value: positive


title: PFC1-A6-c74


title: PFC1-A6-c71


title: FGF2 Late MOLM14 Gilteritinib Day 14 R1 [LIB190430JT_S9_Molm14FGF2GR_GILt_d14_S33]

description: LIB190430JT_S9_Molm14FGF2GR_GILt_d14_S33_S32_L006


title: Crenolanib day 21 replicate

first: Daniel

last: Bottomly

address: 3181 S.W. Sam Jackson Park Rd.

institute: Oregon Health and Science University

description:
PCR library sequencing
mv411_crenolanib_yusa_library.count.txt

data_processing:
Read Trimming: cutadapt -j 2 -n 2 -g ACGAAACACCG -a GTTTAAGAGC  (Version 2.3)
Alignment: bowtie2 -p 1 -x yusa_library --norc -U {file}.trimmed.fastq {file}.tmp.sam (Version 2.3.5.1)
Conversion to BAM: samtools view -bS {file}.tmp.sam > {file}.bam (Version 1.9)
Filter to unique matches allowing no mismatches using bamtools (Version 2.5.1)
Counting reads for each sgRNA using MAGeCK: mageck count --norm-method none (Version: v0.5.8)
Genome_build: Custom reference created from CRISPR library
Supplementary_files_format_and_content: Read counts per sgRNA for each sample

source_name: MV411 cells infected with library

growth_protocol: MV411 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone.

extract_protocol:
30 million cells were collected for Crenolanib day 14 and 21. DNA was extracted by desalting method
50 microgramms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 7 days. Crenolanib (20nM) was applied to 30 million cells in single flask

tag: genotype/variatioan

value: day 21 post puromycin selection, Crenolanib


title: Y.Kosuke Plasmid Library

source_name: Library plasmid sequencing

value: Library plasmid sequencing


title: FGF2 Late MOLM14 Gilteritinib Day 14 R2 [LIB190430JT_S9_Molm14FGF2GR_GILt_d714dup_S34_addtl]

description: LIB190430JT_S9_Molm14FGF2GR_GILt_d714dup_S34_S9_L002


title: PFC1-A6-c72

data_processing:
Alignment with STAR
Filtering for genes expressed in at least three cells
Filtering for cell with at least 200 genes
Genome_build: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: h5ad

value: Hypo


title: Crenolanib day 21


title: FGF2 Late MOLM14 Gilteritinib Day 14 R1 [LIB190430JT_S9_Molm14FGF2GR_GILt_d14_S33_addtl]

description: LIB190430JT_S9_Molm14FGF2GR_GILt_d14_S33_S8_L002


title: PFC1-A6-c73


title: PFC1-A6-c70


title: PFC1-A6-c67


title: PFC1-A6-c68


title: PFC1-A6-c69


title: DMSO day 21 replicate


title: DMSO day 21


title: PFC1-A6-c65


title: PFC1-A6-c64


title: Crenolanib day 14

value: day 14 post puromycin selection, Crenolanib


title: DMSO day 14 replicate


title: PFC1-A6-c63


title: FGF2 Late MOLM14 Gilteritinib Day 14 R2 [LIB190430JT_S9_Molm14FGF2GR_GILt_d714dup_S34]

description: LIB190430JT_S9_Molm14FGF2GR_GILt_d714dup_S34_S33_L006


title: PFC1-A6-c62


title: DMSO day 14


title: Sorafenib day 14 replicate

description:
PCR library sequencing
LIB171004JT_YUSASorD14dupl_S12

source_name: MOLM13 cells infected with library

growth_protocol: MOLM13 cells were grown in RPMI-1640, supplemented with 20% serum, pen/strep, fungizone.

extract_protocol:
30 million cells were collected for Sorafenib day 14. DNA was extracted by desalting method
50 microgramms of DNA were used to PCR amplify library using Herculase II enzyme following published protocols and instructions supplied by authors on Addgene  (Shalem, et al Science 2014. 343(6166): p. 84-87, Tzelepis et al, Cell Rep, 2016. 17(4): p. 1193-1205)
Shalem et al Science 2014. 343(6166): p. 84-87

treatment_protocol: Puromycin was applied at 2mg/ml concentration for 7 days. Sorafenib (50nanoMolar) was applied to 30 million cells in single flask

value: day 14 post puromycin selection, Sorafenib


title: PFC1-A6-c61


title: Sorafenib day 14

description:
PCR library sequencing
LIB171004JT_YUSASorD14_S10


title: PFC1-A6-c60


title: PFC1-A6-c58


title: PFC1-A6-c59


title: PFC1-A6-c55


title: PFC1-A6-c54


title: PFC1-A6-c53


title: PFC1-A6-c52


title: PFC1-A6-c51


title: PFC1-A6-c50


title: PFC1-A6-c57


title: PFC1-A6-c56


title: Crenolanib day 14 replicate


title: PFC1-A6-c46


title: PFC1-A6-c48


title: PFC1-A6-c47


title: PFC1-A6-c49


title: PFC1-A6-c66


title: PFC1-A6-c45


title: PFC1-A6-c44


title: PFC1-A6-c43


title: PFC1-A6-c41


title: PFC1-A6-c42


title: PFC1-A6-c40


title: PFC1-A6-c39


title: PFC1-A6-c38


title: PFC1-A6-c36


title: PFC1-A6-c35


title: Area X_knockdown

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description: 10X single-nuclei

data_processing:
The Cell Ranger pipeline from 10X Genomics was used.
"cellranger mkfastq" was used to demultiplex the raw base call files and create FASTQ files.
"celllranger count" was used to align, filter, and generate count matrices from the FASTQ files.
Genome_build: bTaeGut1_v1.p
Supplementary_files_format_and_content: gzipped tab-delimited text file with columns as cells, rows as genes. Additional columns for meta data are also added prior to genes.

organism: Taeniopygia guttata

source_name: Area X_knockdown

extract_protocol:
Each bird was rapidly decapitated and its brain was placed in ice-cold ACSF (126 mM NaCl, 3 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 10 mM D-(+)-glucose, 2 mM MgSO4, 2 mM CaCl2) bubbled with carbogen gas (95% O2, 5% CO2). The cerebellum was removed with a razor and the cerebrum was glued to a specimen tube for sectioning with a VF-200 Compresstome (Precisionary Instruments). Coronal 500 µm sections were made in ice-cold ACSF and allowed to recover in room temperature ACSF for 5 min. Area X punches were collected into a tube containing ACSF on ice until all punches were collected and pooled from 2 birds per condition. Tissue punches were dounce-homogenized in 500 µl ice-cold Lysis Buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and transferred to a clean 2 ml tube. Then 900 µl of 1.8 M Sucrose Cushion Solution (#NUC201-1KT, Sigma) was added and pipette-mixed with nuclei 10 times. To a second clean 2 ml tube, 500 µl of 1.8 M Sucrose Cushion Solution was added, and the nuclei sample was layered on top of the cushion without mixing. The sample was centrifuged at 13,000 × g for 45 min at 4°C and all but ~100 µl of supernatant was discarded to preserve the pellet. The pellet was washed in 300 µl Nuclei Suspension Buffer (NSB) (1% UltraPure BSA (#AM2618, Thermo Fisher Scientific) and 0.2% RNase inhibitors in PBS) and centrifuged at 550 × g for 5 min at 4°C. All but ~50 µl of supernatant was discarded and the pellet was resuspended in the remaining liquid and filtered through a FLOWMI 40 µm tip strainer(#H13680-0040, Bel-Art). Samples were diluted to 1000 nuclei/µl with NSB for targeting 10,000 nuclei for snRNA-seq. Libraries were prepared using the Chromium Single Cell 3’ Library & Gel Bead Kit v3 according to the manufacturer’s instructions and sequenced using an Illumina NovaSeq 6000 at the North Texas Genome Center at UT Arlington.
Followed 10X Genomics kit manufacturer guidelines.

treatment_protocol: Birds were subjected to reversed day light cycles for at least three days prior to tissue collection. Tissue was collected just prior to lights turning on.

tag: knockdown

value: FoxP2 knockdown

value: brain

tag: brain region

value: Area X

value: striatal projection neurons

tag: Sex

value: M

tag: age


title: PFC1-A6-c34

extract_protocol:
The illumina Nextera XT DNA preparation kit was used to prepare the library directly from the lysate of single cell.
The RNA library was prepared using the standard illumina protocol

value: germ cell


title: Area X_scrambled

description: 10X single-nuclei

source_name: Area X_scrambled

value: scrambled

tag: tissue


title: PFC1-A6-c33


title: PFC1-A6-c32

value: Norm


title: PFC1-A6-c29


title: PFC1-A6-c28


title: PFC1-A6-c27


title: PFC1-A6-c26


title: PFC1-A6-c25


title: PFC1-A6-c24


title: PFC1-A6-c22


title: HepG2 S1 rep2 [G2]

city: BEIJING

first: Guanghou

last: Shui

address: Bei Chen Road(west)

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Guppy (v3.2.4) was used for real-time base-calling
Adaptor sequence and barcode sequence were trimmed using Qcat for clean data, then aligned to human whole genome using minimap2 with default parameters.
The number of reads aligned to human genes was calculated using BEDtools multicov with human gene annotation file GFF (GENCODE v37)
Genome_build: GRCH38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HepG2 S1

growth_protocol: HepG2 and A549 cells were obtained from the American Type Culture Collection. HepG2 cells were maintained in DMEM (high glucose) medium (Gibco) supplemented with 10% FBS, and A549 were maintained in RPMI 1640 medium (Gibco) supplemented with 10% FBS. Cells were cultured at 37 oC in an atmosphere with 5% CO2.

extract_protocol:
Total RNAs were extracted from cells inactivated with 1 ml of TRIzol reagent. For each phase separation, 0.2 ml of chloroform was added and the aqueous phase was collected in fresh tubes and mixed with 0.5 ml of isopropyl alcohol for pelleting RNA. RNA pellets were washed with 75% ethanol and digested with DNase for 30 min to remove DNA contamination, then pelleted via addition of NaOAC and LiCl. RNA pellets were then washed with 75% ethanol and reconstituted in nuclease-free water.
RNAs were reverse transcribed into cDNAs and PromethION library preparation was performed based on the manufacturer's instructions for the barcoding cNDA (SQK-LSK109, EXP-NBD104 and EXP-NBD114).

treatment_protocol: EVs were isolated from 1 ml of pooled plasma from each of the clinical stages, which included healthy controls (HC), as well as S1, S2, S3 and S4 phases of COVID-19. Cells were incubated with culture medium containing the appropriate concentrations of EVs in 12-well plates for 12 h at 37 oC. At the end of the incubation, cell culture medium was aspirated. The cells were washed three times with ice-cold 1XPBS.

tag: treatment

value: after incubation with EVs isolated from presymptomatic(S1)

value: wild type


title: HepG2 HC rep3 [F3]

source_name: HepG2 HC

value: after incubation with EVs isolated from healthy controls(HC)


title: PFC1-A6-c21

treatment_protocol: Single cells were sorted in 96 well plates containing 4ul of lysis buffer and frozen on dry ice.

tag: cell type

value: positive


title: PFC1-A6-c30

tag: oxygen condition


title: HepG2 S4 rep2 [J2]

source_name: HepG2 S4

value: after incubation with EVs isolated from convalescent (S4)


title: HepG2 S4 rep1 [J1]


title: HepG2 S2 rep3 [H3]

source_name: HepG2 S2

value: after incubation with EVs isolated from hyperinflammatory (S2)


title: HepG2 S4 rep3 [J3]


title: HepG2 S1 rep3 [G3]


title: HepG2 S2 rep2 [H2]


title: HepG2 S2 rep1 [H1]


title: HepG2 S3 rep1 [I1]

source_name: HepG2 S3

value: after incubation with EVs isolated from resolution (S3)


title: HepG2 S3 rep2 [I2]


title: PFC1-A6-c31

source_name: germ cell

tag: cell


title: HepG2 S1 rep1 [G1]

tag: genotype/variation


title: PFC1-A6-c20


title: HepG2 S3 rep3 [I3]


title: HepG2 HC rep1 [F1]


title: PFC1-A6-c18


title: PFC1-A6-c23


title: PFC1-A6-c37

value: Hypo

value: negative


title: PFC1-A6-c19


title: A549 S4 rep3 [E3]


title: A549 S4 rep2 [E2]


title: PFC1-A6-c16


title: PFC1-A6-c17


title: A549 S4 rep1 [E1]


title: HepG2 HC rep2 [F2]


title: PFC1-A6-c15


title: A549 S3 rep3 [D3]


title: PFC1-A6-c14


title: A549 S3 rep2 [D2]


title: A549 S3 rep1 [D1]


title: T30 sgCONT

value: Glioblastoma stem cell

value: Control


title: A549 S2 rep1 [C1]


title: A549 S2 rep2 [C2]


title: PFC1-A6-c7


title: PFC1-A6-c9


title: PFC1-A6-c11


title: PFC1-A6-c10


title: PFC1-A6-c12


title: PFC1-A6-c8


title: A549 S1 rep2 [B2]

value: after incubation with EVs isolated from presymptomatic (S1)


title: A549 HC rep2 [A2]

source_name: A549 HC

value: after incubation with EVs isolated from healthy controls (HC)


title: A549 HC rep3 [A3]


title: PFC1-A6-c13


title: A549 S2 rep3 [C3]


title: A549 S1 rep3 [B3]


title: PFC1-A6-c5


title: A549 HC rep1 [A1]


title: PFC1-A6-c3


title: PFC1-A6-c2


title: GC7

city: Wuhan

last: Jiang

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Blood

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using BD RNA tube. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease

value: Vogt-Koyanagi-Harada Syndrome

value: GC

value: blood

value: post 20 years old


title: GC6


title: PFC1-A6-c4

value: germ cell

value: Norm


title: PFC1-A6-c1


title: GC5


title: PFC1-A5-c96


title: PFC1-A6-c6


title: A549 S1 rep1 [B1]

tag: cell line

value: wild type


title: PFC1-A5-c95

value: positive


title: GC4

tag: agent


title: GC3


title: PFC1-A5-c93

tag: developmental stage


title: PFC1-A5-c94


title: GC1


title: VKH6


title: GC2


title: PFC1-A5-c92


title: PFC1-A5-c89


title: PFC1-A5-c91


title: PFC1-A5-c88


title: PFC1-A5-c86


title: VKH4


title: VKH5


title: VKH7


title: VKH3


title: VKH1


title: PFC1-A5-c87


title: PFC1-A5-c90


title: VKH2


title: PFC1-A5-c83


title: HC7

value: healthy control


title: PFC1-A5-c84


title: HC3


title: PFC1-A5-c80


title: HC5


title: HC4


title: PFC1-A5-c82


title: PFC1-A5-c81


title: HC2


title: HC1


title: PFC1-A5-c85


title: PFC1-A5-c77


title: PFC1-A5-c76


title: HC6


title: PFC1-A5-c79


title: PFC1-A5-c75


title: PFC1-A5-c72


title: PFC1-A5-c78


title: PFC1-A5-c74


title: PFC1-A5-c73


title: PFC1-A5-c71


title: PFC1-A5-c70


title: PFC1-A5-c68


title: PFC1-A5-c67


title: PFC1-A5-c66


title: PFC1-A5-c65


title: PFC1-A5-c64


title: PFC1-A5-c63


title: PFC1-A5-c62


title: PFC1-A5-c61


title: JIA FLS cultured in normal media for 24 hrs [J3H24]

city: Wilmington

first: AnneMarie

last: Brescia

state: DE

address: 1601 Rockland Rd

institute: Nemours

description: FLS isolated from synovial fluid of JIA patients in IRB-approved repository

hyb_protocol: Fragmented, biotinylated cDNA was added to a hybridization cocktail, denatured, loaded on a Clariom S GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm

scan_protocol: Arrays were washed and stained using the FS450_0007 protocol. The stained arrays were scanned at 532 nm on a GeneChip Scanner 3000

data_processing:
Expression Console (Affymetrix) was used to calculate gene expression values using the SST-RMA algorithm.  The output of this software are log2 transformed values.
probe group file: Clariom_S_Human.r1.pgf
meta-probeset file: Clariom_S_Human.r1.mps

source_name: JIA FLS cultured in normal media for 24 hours

label_protocol: Fragmented cDNA was end-labeled via a terminal transferase reaction incorporating a biotinylated dideoxynucleotide

growth_protocol: All cells were incubated at 37C with 5% CO2 in DMEM+10% FBS.

extract_protocol: RNA was extracted from cell lysates using RNeasy Mini Kit from Qiagen following manufacturer's protocol.

treatment_protocol: Conditioned media was pooled from 3 chondrocyte cell lines after 48h. FLS were cultured in conditioned media from chondrocytes. Timepoints were taken after 6, 12, and 24 hours in culture.

tag: cell source

value: synovial fluid

value: Fibroblast-like Synoviocytes (FLS)

value: normal media for 24 hours


title: JIA FLS cultured in Ch-conditioned media for 6 hrs [J3ChH06]

source_name: JIA FLS cultured in Ch-conditioned media for 6 hours

value: Ch-conditioned media for 6 hours


title: JIA FLS cultured in Ch-conditioned media for 12 hrs [J3ChH12]

source_name: JIA FLS cultured in Ch-conditioned media for 12 hours

value: Ch-conditioned media for 12 hours


title: total RNA from TOsk-Gal4 > Aos1 KD with rRNA depletion replicate1

city: Vienna

first: Mostafa

last: ElMaghraby

address: Fasangasse 39-41/1/24

country: Austria

institute: IMBA

data_processing:
reads were trimmed by removal of the adaptor sequences and to a length of 6-50 bases
reads mapping to the Drosophila melanogaster rRNA precursor and the mitochondrial genome using Bowtie (release 1.2.2) with 0 mismatches were excluded
reads were mapped to the Drosophila melanogaster genome using STAR (v.2.5.2b)
reads mapping to rRNA, tRNA, mitoRNA were excluded
Genome_build: dm6
Supplementary_files_format_and_content: all mapping and unique mapping bigwig files for sense and antisense

organism: Drosophila melanogaster

source_name: Ovary RNA

extract_protocol:
RNA was extracted using Trizol
Libraries were prepared using a NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB)
rRNA depletion, RNA-seq library prep

value: Aos1 knockdown

tag: growth protocol

value: 5-7 days old flies grown at 25degree C


title: total RNA from TOsk-Gal4 > Uba2 KD with rRNA depletion replicate2

value: Uba2 knockdown


title: PFC1-A5-c59

last: Klimm

address: Exhibition Rd, South Kensington

institute: Imperial College London

value: Hypo


title: PFC1-A5-c69

value: negative


title: total RNA from TOsk-Gal4 > Uba2 KD with rRNA depletion replicate1


title: JIA FLS cultured in normal media for 6 hrs [J3H06]

source_name: JIA FLS cultured in normal media for 6 hours

value: normal media for 6 hours


title: JIA FLS cultured in Ch-conditioned media for 24 hrs [J3ChH24]

source_name: JIA FLS cultured in Ch-conditioned media for 24 hours

value: Ch-conditioned media for 24 hours


title: JIA FLS cultured in normal media for 12 hrs [J3H12]

source_name: JIA FLS cultured in normal media for 12 hours

value: normal media for 12 hours


title: JIA FLS cultured in normal media for 12 hrs [J2H12]


title: JIA FLS cultured in normal media for 6 hrs [J2H06]


title: JIA FLS cultured in normal media for 24 hrs [J2H24]


title: total RNA from TOsk-Gal4 > Aos1 KD with rRNA depletion replicate2


title: JIA FLS cultured in Ch-conditioned media for 6 hrs [J2ChH06]


title: JIA FLS cultured in normal media for 6 hrs [J1H06]


title: JIA FLS cultured in normal media for 12 hrs [J1H12]


title: JIA FLS cultured in Ch-conditioned media for 12 hrs [J2ChH12]


title: JIA FLS cultured in Ch-conditioned media for 24 hrs [J2ChH24]


title: JIA FLS cultured in normal media for 24 hrs [J1H24]


title: total RNA from TOsk-Gal4 > Su(var)2-10 KD with rRNA depletion replicate2

value: Su(var)2-10 knockdown


title: PFC1-A5-c58

value: germ cell


title: PFC1-A5-c57

value: positive


title: PFC1-A5-c60


title: PFC1-A5-c56


title: PFC1-A5-c55


title: total RNA from TOsk-Gal4 > Su(var)2-10 KD with rRNA depletion replicate1


title: PFC1-A5-c54


title: JIA FLS cultured in Ch-conditioned media for 24 hrs [J1ChH24]


title: PFC1-A5-c53


title: PFC1-A5-c52


title: PFC1-A5-c51


title: PFC1-A5-c49


title: total RNA from TOsk-Gal4 > UAP56 KD with rRNA depletion replicate1

value: UAP56 knockdown


title: total RNA from TOsk-Gal4 > Piwi KD with rRNA depletion replicate2

value: Piwi knockdown


title: PFC1-A5-c48


title: PFC1-A5-c47


title: total RNA from TOsk-Gal4 > Piwi KD with rRNA depletion replicate1


title: PFC1-A5-c45


title: total RNA from TOsk-Gal4 > control KD with rRNA depletion replicate2

value: control knockdown


title: PFC1-A5-c44


title: JIA FLS cultured in Ch-conditioned media for 6 hrs [J1ChH06]

value: synovial fluid

value: Fibroblast-like Synoviocytes (FLS)


title: normal FLS cultured in normal media for 12 hrs [C3H12]

description: normal FLS isolated from synovium of individual donors from Cell Applications, Inc.

source_name: normal FLS cultured in normal media for 12 hours

value: synovium


title: total RNA from TOsk-Gal4 > control KD with rRNA depletion replicate1


title: PFC1-A5-c43


title: total RNA from TOsk-Gal4 > UAP56 KD with rRNA depletion replicate2


title: PFC1-A5-c41


title: PFC1-A5-c40


title: PFC1-A5-c50


title: PFC1-A5-c42


title: normal FLS cultured in normal media for 24 hrs [C3H24]

source_name: normal FLS cultured in normal media for 24 hours

value: normal media for 24 hours


title: normal FLS cultured in normal media for 6 hrs [C3H06]

source_name: normal FLS cultured in normal media for 6 hours


title: PFC1-A5-c39


title: PFC1-A5-c37


title: PFC1-A5-c46


title: PFC1-A5-c38


title: total RNA from MTD-Gal4 > control KD with rRNA depletion replicate2

value: 5-7 days old flies grown at 25degree C


title: JIA FLS cultured in Ch-conditioned media for 12 hrs [J1ChH12]

value: Ch-conditioned media for 12 hours


title: normal FLS cultured in Ch-conditioned media for 24 hrs [C3ChH24]

source_name: normal FLS cultured in Ch-conditioned media for 24 hours


title: total RNA from MTD-Gal4 > control KD with rRNA depletion replicate1


title: PFC1-A5-c36

value: Hypo


title: PFC1-A5-c35

value: negative


title: total RNA from MTD-Gal4 > Piwi KD with rRNA depletion replicate1


title: PFC1-A5-c34


title: normal FLS cultured in Ch-conditioned media for 12 hrs [C3ChH12]

source_name: normal FLS cultured in Ch-conditioned media for 12 hours


title: total RNA from MTD-Gal4 > Piwi KD with rRNA depletion replicate2


title: NT5

city: changsha

first: cong

last: xu

state: China

address: No. 138 tongzipo Road, Yuelu District, Changsha

institute: the third xiangya hospital

data_processing:
library strategy: tRF-Seq
Illumina NextSeq 500 raw sequencing read data that passed the Illumina chastity filter were used for the following analysis. Sequencing quality was examined by FastQC software.
After that, the sequencing reads were 5’, 3’-adaptor trimmed, filtered for more than 15 nt by Cutadapt software, and for exactly aligned to mature-tRNA and pre-tRNA sequences from GtRNAdb (http://gtrnadb.ucsc.edu/) using NovoAlign software (v2.07.11).
The tsRNA expression levels were measured and normalized as tag counts per million of total aligned tRNA reads (TPM). For each tRNA sequence-based profile, the number of tRNA sequence reads could be used to estimate expression level of each tsRNA.
Genome_build: hg19
Supplementary_files_format_and_content: excel files include tag count and RPM values for each Sample

source_name: CD138 enrich plasma cells from bone marrow_NT

extract_protocol:
Firstly, anti-CD138 MicroBeads (Miltenyi, Germany) were used to enrich plasma cells from bone marrow samples by magnetic activated cell sorting (MACS). The purity of separated plasma cells was identified by flow cytometry and was all above 90%. Total RNA was then extracted from enriched plasma cells and myeloma cells using TRIzol (Invitrogen, USA) according to the instruction manual. Prepared RNA was stored at -80 °C. RNA samples were qualified by agarose gel electrophoresis and quantified by NanoDrop ND-1000 (NanoDrop, USA). RNA integrity number (RIN) was evaluated by Agilent BioAnalyzer 2100 and was all above 7. RNA concentration and purity were also assessed (supplementary table 1). qRT-PCR was performed using ViiA 7 Real-time PCR System (Applied Biosystems) and 2 × PCR Master Mix. The expression levels of each tRFs/tiRNAs were calculated and normalized by U6 small nuclear RNA (snRNA).
Total RNA samples were sequentially ligated to 3’ and 5’ small RNA adapters using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, USA). cDNA was then synthesized and amplified using Illumina’s proprietary reverse transcription primers and amplification primers. Subsequently, 135-170 bp PCR amplified fragments (corresponding to 15-50 nt small RNA size range) were extracted and purified from the PAGE gel. The completed libraries were quantified by Agilent 2100 Bioanalyzer. Libraries were mixed in equal amounts according to the quantification results and used for sequencing on the instrument. And then, the DNA fragments in well-mixed libraries were denatured to generate single-stranded DNA molecules and loaded onto the reagent cartridge. Finally, the sequencing run was performed on Illumina NextSeq 500 system using NextSeq 500/550 V2 kit (Illumina) according to the manufacturer’s instructions. Sequencing was carried out by running 50 cycles.

tag: subject status

value: multiple myeloma

value: bone marrow

value: CD138 enrich plasma cells

tag: molecule subtype

value: tiRNA and tRF


title: PFC1-A5-c32

city: London

first: Florian

value: germ cell


title: NT4


title: normal FLS cultured in Ch-conditioned media for 6 hrs [C3ChH06]

source_name: normal FLS cultured in Ch-conditioned media for 6 hours

value: Ch-conditioned media for 6 hours


title: normal FLS cultured in normal media for 12 hrs [C2H12]

value: normal media for 12 hours


title: normal FLS cultured in normal media for 24 hrs [C2H24]


title: normal FLS cultured in normal media for 6 hrs [C2H06]

value: normal media for 6 hours


title: normal FLS cultured in Ch-conditioned media for 24 hrs [C2ChH24]

value: Ch-conditioned media for 24 hours


title: PFC1-A5-c31

source_name: germ cell

value: positive


title: PFC1-A5-c30


title: NT3


title: PFC1-A5-c29


title: PFC1-A5-c28


title: NT2


title: normal FLS cultured in Ch-conditioned media for 12 hrs [C2ChH12]

value: Fibroblast-like Synoviocytes (FLS)


title: PFC1-A5-c26


title: PFC1-A5-c27


title: NT1


title: PFC1-A5-c23


title: PFC1-A5-c33


title: PFC1-A5-c22


title: T4

source_name: CD138 enrich plasma cells from bone marrow_T

value: relapsed/refractory multiple myeloma


title: PFC1-A5-c24


title: T5


title: normal FLS cultured in Ch-conditioned media for 6 hrs [C2ChH06]

value: synovium


title: PFC1-A5-c21


title: PFC1-A5-c20


title: PFC1-A5-c19


title: normal FLS cultured in normal media for 6 hrs [C1H06]


title: normal FLS cultured in normal media 24 hrs [C1H24]

source_name: normal FLS cultured in normal media 24 hours

value: normal media 24 hours


title: PFC1-A5-c18


title: T3


title: PFC1-A5-c17


title: normal FLS cultured in Ch-conditioned media for 24 hrs [C1ChH24]


title: PFC1-A5-c16


title: T1


title: PFC1-A5-c15


title: PFC1-A5-c14


title: PFC1-A5-c25


title: PFC1-A5-c13


title: normal FLS cultured in Ch-conditioned media for 12 hrs [C1ChH12]

value: Ch-conditioned media for 12 hours


title: lung adenocarcinoma  adjacent tissue-15-B

city: Kunming

first: Wanpu

last: Wang

address: No.157  Jinbi  Road

institute: he First People’s Hospital of Y unnan Province

data_processing:
The sequencing was performed on an Illumina NextSeq 500 system using a NextSeq 500/550 V2 kit.
Image analysis and base calling were performed using Solexa Pipeline v1.8 software
Reads that did not map were aligned to allow for only one mismatch to precursor tRNA sequences using bowtie software
The remaining reads were aligned to allow for only one mismatch to miRNA reference sequences with miRDeep2
Differentially expressed tRFs, tiRNAs and miRNAs were screened based on the count value using the R package edgeR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include the counts of per million mapped reads for each Sample

source_name: lung adenocarcinoma adjacent tissue

growth_protocol: The tissues were preserved in RNAlater (Invitrogen; Thermo Fisher Scientific, Inc.) at -80˚C.

extract_protocol: The library preparation processes included 3'-adapter ligation, 5'-adapter ligation, cDNA synthesis, PCR amplification and size selection of PCR amplified fragments of 134-160 base pairs in length (corresponding to ~14-40 nucleotide small RNAs). The sequencing library was quantified on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.) using an Agilent DNA 1000 chip kit (Agilent Technologies, Inc.). Libraries were mixed in equal amounts and used for sequencing.

value: upper right lobe of the lung

tag: tumor stage

value: T1N0M0 IA


title: PFC1-A5-c12

value: Hypo

value: negative


title: PFC1-A5-c11


title: lung adenocarcinoma adjacent tissue-5-B

value: T3N0M0 ⅡB


title: normal FLS cultured in normal media for 12 hrs [C1H12]


title: lung adenocarcinoma adjacent tissue-2-B

value: T2N0M0 IB


title: PFC1-A5-c10

value: germ cell


title: PFC1-A5-c8


title: T2

value: bone marrow

value: CD138 enrich plasma cells

value: tiRNA and tRF


title: RKO Aphidicolin treated for 16h and released for 13h, rep2

hyb_protocol: According to the Genechip WT PLUS Reagent kit (Affymetrix – ThermoFisher). Following fragmentation, 5,5 ug of cDNA were hybridized for 16 hr at 45C and 60 rpm on Human Clarion S arrays in GeneChip Hybridization Oven 645 for 16h at 45°C. The arrays were washed and stained in the Affymetrics Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChiP Scanner GC3000 7G and images analyzed using Command Console software to obtain the raw data (values of fluorescent intensity).

data_processing: The data were analyzed with TAC (Transcriptome Analysis Console, version 4.0.2.15) from Thermofisher. Microarrays qere normalized using the Robust Multichip Analysis (SST-RMA) method.

label_protocol: 100ng of total RNA was labeled according to the Genechip WT PLUS Reagent kit (Affymetrix – ThermoFisher)

growth_protocol: RKO cells from ATCC passage 3 were cultivate at, 37°C, 5% O2 and 5% CO2 in DMEM, 10%SVF.

extract_protocol: Rneasy kit from QIAGEN

treatment_protocol: Aphidicolin (Sigma aldrich) was used at 0,2µM. For N+1 condition RKO cells were washed with culture medium and relased for 13h in fresh medium.

tag: phenotype

value: colon cancer Mismatch repair deficient


title: RKO Aphidicolin treated for 16h and released for 13h, rep1


title: RKO Aphidicolin treated for 16h and released for 13h, rep3


title: lung adenocarcinoma tissue-15-A

source_name: lung adenocarcinoma tissue

tag: age


title: PFC1-A5-c7


title: PFC1-A5-c6


title: lung adenocarcinoma tissue-5-A

tag: tissue


title: PFC1-A5-c5


title: RKO DMSO treated and released for 13h, rep2

description: RKO DMSO treated and released for 13h

source_name: RKO DMSO treated and released for 13h


title: PFC1-A5-c4


title: PFC1-A5-c3


title: normal FLS cultured in Ch-conditioned media for 6 hrs [C1ChH06]

tag: treatment

value: Ch-conditioned media for 6 hours


title: lung adenocarcinoma tissue-2-A


title: PFC1-A5-c2

tag: cell type


title: PFC1-A5-c1

tag: oxygen condition


title: PFC1-A5-c9

tag: cell


title: PFC1-A4-c96

value: Norm

value: positive


title: RKO DMSO treated and released for 13h, rep3

description: RKO DMSO treated and released for 13h


title: PFC1-A4-c95


title: HIV_1137_RPMI

city: Nijmegen

first: Hendrik

middle: G.

last: Stunnenberg

address: Geert Grooteplein 30

country: Netherlands

institute: Radboud University Nijmegen

description:
rRNA depleted total RNA
Normalized_Annotated_Batch_Corrected_expr_rpmi_health_hiv.xlsx

data_processing:
To infer gene expression levels, RNA-seq reads were aligned to the hg38 human reference transcriptome using STAR alignment tool. Genes with fewer than 50 reads on average in all samples (Control and HIV) were excluded from downstream analysis.
Utilizing DESeq2 libraries normalized and differentially expressed genes determined. Genes with more than two-fold change between at least two time points and less that 0.05 padj value were designated as significant differentially expressed genes.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Normalized_Annotated_Batch_Corrected_expr_rpmi_health_hiv.xlsx: Normalized count table of gene expression from all samples.

source_name: Adult Human Peripheral Blood

growth_protocol:
Monocytes from HIV positive donor PBMC isolated by CD14 negative selection and cultured in RPMI medium.
After isolation from PBMC using CD14 negative selection, monocytes were cultured in RPMI medium for 24hours.

extract_protocol:
Total RNA was extracted from monocytes using the QIAGEN RNeasy RNA extraction kit (QIAGEN, Netherlands), using on-column DNaseI treatment. Thereafter, total RNA-seq analysis performed on total RNA.
Ribosomal RNA removal and library preparation for next-generation RNA-sequencing was achieved utilizing KAPA RNA HyperPrep Kit with RiboErase (Roche), following the manufacturer’s protocol. The integrity and quality of prepared libraries were assessed using Agilent 2100 Bioanalyzer. Sequencing was performed using Illumina NextSeq 500 machine in a paired end sequencing fashion.

treatment_protocol: No Treatment

tag: diagnosis

value: HIV positive

value: Monocyte


title: HIV_1218_RPMI


title: RKO DMSO treated and released for 13h, rep1

description: RKO DMSO treated and released for 13h


title: PFC1-A4-c94


title: RKO Aphidicolin treated for 16h, rep3

description: RKO Aphidicolin treated for 16h

source_name: RKO Aphidicolin treated for 16h


title: PFC1-A4-c93


title: PFC1-A4-c90


title: PFC1-A4-c91


title: PFC1-A4-c89


title: HIV_1014_RPMI


title: CFA_10_BisulfiteSeq

city: Suzhou

first: Lei

last: Wei

state: Jiangsu

address: Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu

data_processing:
RNA-seq analysis: After running fastQC (0.11.8) for quality control, Cutadapt (2.1.0) was used for trimming adapters and low-quality sequence from the raw fastq files. The cleaned fastq files were then mapped to rn4 rat genome refence by STAR (2.7.0) with suggested setting. Differential expression analysis was then performed by DEseq2 (1.29.0).
smallRNA-seq analysis: Small RNA-seq data was analyzed by using sRNAnalyzer pipeline. Adapter sequences was provided as input to the pipeline for removing adapter contamination. The cleaned reads were then mapped to rat miRNA database to generate count matrix, which was further analyzed by DEseq2 to identify differentially expressed miRNA.
Bisulfite-seq analysis: TrimGalore (0.6.4) was used for sequencing data quality control, adapter removing and trimming low-quality sequence. The cleaned data was then mapped to the rn4 rat genome reference by using Bismark (0.22.0). The generated CpG methylation ratios were then used as input for metilene to call differentially methylated regions (DMRs).
Genome_build: rn4
Supplementary_files_format_and_content: rawcount file of each sample for RNA-seq and smallRNA-seq data in txt file
Supplementary_files_format_and_content: mean methylation of DMR of each sample for target Bisulfite-seq in bed file

organism: Rattus norvegicus

source_name: dorsal root ganglion

extract_protocol:
DRG tissues from 10 randomly selected pairs of CFA-treated and untreated rats were extracted.
NEBNext Ultra RNA with Poly-A selection
NEBNext Multiplex Small RNA Library Prep Kit for Illumina

treatment_protocol: The SD rats were maintained in a standardized feeding environment under a 12-hour light-dark cycle at an ambient temperature of 24 ± 1°C. The CFA-induced chronic inflammatory pain model was established through unilateral subcutaneous injections of 0.1 mL CFA into the sterile foot skin, as described in our previous research

value: CFA injected


title: HIV_1203_RPMI


title: RKO Aphidicolin treated for 16h, rep1

description: RKO Aphidicolin treated for 16h


title: PFC1-A4-c88


title: HIV_1194_RPMI


title: PFC1-A4-c87


title: RKO DMSO treated, rep3

description: RKO DMSO treated

source_name: RKO DMSO treated


title: CFA_9_BisulfiteSeq

institute: Suzhou Municipal Hospital Affiliated to Nanjing Medical University


title: RKO Aphidicolin treated for 16h, rep2

description: RKO Aphidicolin treated for 16h


title: HIV_1188_RPMI


title: RKO DMSO treated, rep2

description: RKO DMSO treated


title: HIV_1023_RPMI


title: PFC1-A4-c85


title: HIV_1046_RPMI


title: PFC1-A4-c83


title: RKO DMSO treated, rep1

description: RKO DMSO treated


title: CFA_8_BisulfiteSeq


title: CFA_7_BisulfiteSeq


title: PFC1-A4-c82


title: PFC1-A4-c92


title: PFC1-A4-c81


title: CFA_6_BisulfiteSeq


title: PFC1-A4-c80


title: Control_1006_RPMI

growth_protocol:
Monocytes from healthy volunteer PBMC isolated by CD14 negative selection and cultured in RPMI medium.
After isolation from PBMC using CD14 negative selection, monocytes were cultured in RPMI medium for 24hours.

value: Healthy


title: PFC1-A4-c77


title: PFC1-A4-c86


title: PFC1-A4-c78


title: Control_1004_RPMI


title: CFA_5_BisulfiteSeq


title: PFC1-A4-c79


title: PFC1-A4-c74


title: CFA_3_BisulfiteSeq


title: PFC1-A4-c76


title: PFC1-A4-c73


title: RKO-APH-3

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied
Sequences (42 nt reads, paired end) were aligned to the human genome (hg38) using the BWA algorithm (v0.7.12, mem mode, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS2 algorithm (v2.1.0) with a cutoff of pvalue = 1e-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Genome_build: hg38
Supplementary_files_format_and_content: Bed = processed ATAC-seq peaks coordinate and average value and BIGWIG = show the fragment density for 32-nt bins along the genome (“signal map”).

source_name: Colon cancer

extract_protocol:
Cells were suspended in lysis buffer, pelleted, and washed with cold PBS.
Illumina sequencing libraries were prepared using the Nextera Library Prep Kit (Illumina), purified with the MinElute PCR purification kit (Qiagen), and amplified by PCR. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: Aphidicolin (Sigma aldrich) was used at 0.2µM for 16h.

value: RKO

value: Colon cancer cells

value: APH


title: CFA_2_BisulfiteSeq


title: PFC1-A4-c72

value: negative


title: Control_1007_RPMI


title: CFA_4_BisulfiteSeq


title: PFC1-A4-c71


title: PFC1-A4-c70


title: RKO-APH-1


title: CFA_1_BisulfiteSeq


title: PFC1-A4-c69


title: Control_10_BisulfiteSeq

value: no treatment


title: PFC1-A4-c67

value: germ cell


title: PFC1-A4-c68


title: RKO-DMSO-3

value: DMSO


title: Control_1005_RPMI


title: Control_9_BisulfiteSeq


title: PFC1-A4-c66


title: PFC1-A4-c75


title: PFC1-A4-c65


title: Control_8_BisulfiteSeq


title: PFC1-A4-c64


title: PFC1-A4-c63


title: RKO-DMSO-1


title: Control_7_BisulfiteSeq


title: PFC1-A4-c62


title: RKO-APH-2


title: 17-0128_S13_COMB

city: Pittsburgh

first: Uma

last: Chandran

state: PA

address: 5607 Baum Blvd

department: Biomedical Informatics

institute: University of Pittsburgh School of Medicine

data_processing:
Samples were aligned to the GRCh38 genome with HISAT2 (v2.1.0)
Genes were quantified from the aligned samples with HTSeq (v0.9.0)
Differential expression between groups was performed with the edgeR (v3.1.8) R package
Genome_build: GRCh38.p11
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: gastric carcinoma

extract_protocol:
Total RNA was extraced using the Qiagen miRNeasy mini kit and protocol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA ACCESS library prep kit (#15049525 Revision B, Illumina, San Diego, CA).

treatment_protocol: For each tumor included in transcriptomic analysis, a representative formalin-fixed paraffin-embedded tumor tissue block was selected and the tumor area desired for transcriptomic analysis was manually circled on the hematoxylin and eosin stained tissue section. Manual macro-dissection of the desired tumor area was then performed on 6-to-10 unstained tumor tissue sections at 10 µm thickness for each tumor.

value: gastric carcinoma

tag: atl16l1 t300a genotype

tag: subjects

value: gastric cancer patients

value: surgery only


title: PFC1-A4-c60


title: PFC1-A4-c61


title: 17-0127_S12_COMB


title: Control_6_BisulfiteSeq


title: PFC1-A4-c58


title: PFC1-A4-c59


title: PFC1-A4-c57


title: 17-0125_S10_COMB


title: PFC1-A4-c56


title: Control_4_BisulfiteSeq


title: PFC1-A4-c54


title: PFC1-A4-c55


title: PFC1-A4-c53


title: Control_5_BisulfiteSeq


title: Control_2_BisulfiteSeq


title: PFC1-A4-c51


title: PFC1-A4-c52


title: Control_1_BisulfiteSeq


title: PFC1-A4-c50


title: 17-0124_S9_COMB


title: 17-0122_S7_COMB

value: WT/WT


title: 17-0123_S8_COMB


title: Control_3_BisulfiteSeq


title: RKO-DMSO-2

last: Bergoglio

address: 2 avenue Hubert Curien

institute: INSERM UMR1037

tag: cell line


title: PFC1-A4-c49

tag: developmental stage

value: Norm


title: CFA_10_smallRNAseq

description: small RNA


title: PFC1-A4-c48


title: 17-0126_S11_COMB


title: PFC1-A4-c46


title: CFA_9_smallRNAseq

description: small RNA


title: PFC1-A4-c47


title: 17-0120_S6_COMB


title: PFC1-A4-c44


title: PFC1-A4-c45


title: CFA_8_smallRNAseq

description: small RNA


title: PFC1-A4-c43


title: PFC1-A4-c42


title: CFA_7_smallRNAseq

description: small RNA


title: 17-0119_S5_COMB


title: PFC1-A4-c41


title: CFA_6_smallRNAseq

description: small RNA


title: PFC1-A4-c40


title: 17-0117_S2_COMB


title: PFC1-A4-c38


title: PFC1-A4-c37


title: 17-0116_S1_COMB


title: PFC1-A4-c39


title: PFC1-A4-c36


title: CFA_4_smallRNAseq

description: small RNA


title: CFA_3_smallRNAseq

description: small RNA


title: 17-0115_S6_COMB


title: PFC1-A4-c34


title: 17-0121_S3_COMB


title: 17-0114_S5_COMB

value: post surgical chemotherapy


title: PFC1-A4-c35


title: PFC1-A4-c33


title: PFC1-A4-c32

value: positive


title: CFA_2_smallRNAseq

description: small RNA


title: PFC1-A4-c31


title: 17-0118_S4_COMB


title: CFA_1_smallRNAseq

description: small RNA


title: PFC1-A4-c30


title: PFC1-A4-c29


title: 17-0112_S15_COMB


title: PFC1-A4-c28


title: Control_10_smallRNAseq

description: small RNA


title: CFA_5_smallRNAseq

description: small RNA


title: 17-0111_S14_COMB


title: PFC1-A4-c27


title: Control_9_smallRNAseq

description: small RNA


title: PFC1-A4-c26


title: PFC1-A4-c25


title: Control_8_smallRNAseq

description: small RNA


title: PFC1-A4-c23


title: 17-0109_S10_COMB


title: PFC1-A4-c24


title: 17-0110_S11_COMB


title: PFC1-A4-c22


title: 17-0108_S9_COMB


title: 17-0113_S16_COMB


title: PFC1-A4-c21


title: PFC1-A4-c20


title: Control_6_smallRNAseq

description: small RNA


title: 17-0107_S9_COMB


title: Control_5_smallRNAseq

description: small RNA


title: Control_7_smallRNAseq

description: small RNA


title: PFC1-A4-c17


title: Control_4_smallRNAseq

description: small RNA


title: PFC1-A4-c18


title: 17-0106_S8_COMB


title: PFC1-A4-c19


title: PFC1-A4-c14


title: 17-0104_S3_COMB


title: PFC1-A4-c15


title: Control_3_smallRNAseq

description: small RNA


title: PFC1-A4-c11


title: PFC1-A4-c10


title: Control_1_smallRNAseq

description: small RNA


title: 17-0102_S2_COMB


title: 17-0103_S4_COMB


title: PFC1-A4-c9


title: CFA_10_RNAseq

description: mRNA


title: CFA_9_RNAseq

description: mRNA


title: PFC1-A4-c84


title: PFC1-A4-c8


title: 17-0101_S7_COMB


title: 17-0100_S6_COMB


title: 17-0105_S4_COMB


title: PFC1-A4-c16


title: CFA_8_RNAseq

description: mRNA


title: PFC1-A4-c6


title: PFC1-A4-c5


title: 17-0099_S5_COMB


title: PFC1-A4-c13


title: CFA_7_RNAseq

description: mRNA


title: PFC1-A4-c2


title: PFC1-A4-c3


title: 17-0098_S16_COMB


title: 17-0097_S15_COMB


title: CFA_5_RNAseq

description: mRNA


title: CFA_6_RNAseq

description: mRNA


title: PFC1-A3-c95

value: Hypo


title: PFC1-A3-c94


title: PFC1-A3-c96


title: PFC1-A3-c93


title: PFC1-A4-c12


title: PFC1-A3-c92


title: Control_2_smallRNAseq

description: small RNA


title: CFA_3_RNAseq

description: mRNA

value: CFA injected


title: 17-0094_S14_COMB


title: PFC1-A3-c87


title: PFC1-A3-c88


title: 17-0092_S7_COMB


title: CFA_2_RNAseq

description: mRNA


title: PFC1-A3-c91


title: PFC1-A3-c90


title: CFA_4_RNAseq

description: mRNA


title: PFC1-A3-c86


title: PFC1-A3-c89


title: PFC1-A3-c85


title: PFC1-A4-c1


title: 17-0091_S3_COMB


title: 17-0096_S2_COMB


title: Control_10_RNAseq

description: mRNA


title: PFC1-A3-c84


title: 17-0095_S1_COMB


title: 17-0090_S5_COMB


title: Control_9_RNAseq

description: mRNA


title: 17-0089_S4_COMB


title: 17-0088_S3_COMB


title: PFC1-A3-c82


title: PFC1-A3-c80


title: CFA_1_RNAseq

description: mRNA


title: Control_8_RNAseq

description: mRNA


title: PFC1-A3-c79


title: PFC1-A3-c78


title: Control_6_RNAseq

description: mRNA


title: PFC1-A3-c76


title: 17-0087_S1_COMB


title: 17-0086_S2_COMB


title: PFC1-A3-c77


title: Control_7_RNAseq

description: mRNA


title: Control_5_RNAseq

description: mRNA


title: 17-0084_S8_COMB


title: PFC1-A3-c75


title: PFC1-A3-c74


title: Control_4_RNAseq

description: mRNA


title: PFC1-A3-c72


title: PFC1-A3-c73


title: PFC1-A3-c83


title: PFC1-A3-c81


title: 17-0083_S13_COMB


title: PFC1-A3-c71


title: PFC1-A3-c70


title: 17-0082_S7_COMB


title: Control_3_RNAseq

description: mRNA


title: PFC1-A3-c68


title: 17-0081_S1_COMB


title: Control_2_RNAseq

description: mRNA


title: PFC1-A3-c67


title: PFC1-A3-c66


title: PFC1-A3-c65


title: PFC1-A3-c64


title: PFC1-A3-c62


title: PFC1-A3-c61


title: VM CORT 2

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
23_S11
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv

data_processing:
Illumina NextSeq 500
Quality control was performed on the reads obtained from the core and reads with a score of less than 15 were discarded.
The reads were then aligned to the GRCm genome using the STAR aligner with Ensembl annotation and quantified to the gene-level using featureCounts.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the Limma-Voom package.
Genome_build: mm10
Supplementary_files_format_and_content: limmaVoom files contain logFC between VEH vs CORT animals and WT vs BDNF animals

source_name: BDNF Val66Met_CORT_Ventral Hippocampus

extract_protocol:
After rapid decapitation, brains were immediately dissected to separate the ventral hippocampus, which was rapidly flash frozen and stored at -80 °C. RNA was extracted from the ventral hippocampal tissue using Qiagen Lipid Tissue Mini Kit.
A total of  at least 200ng of RNA per replicate was prepared for sequencing by The Rockefeller University Genomics Core Facility using the Tru-Seq Stranded RNA-Seq library preparation kit (Illumina, USA). Three biological replicates were used per experimental group, comprising of RNA pooled from 2 animals each. cDNA libraries were sequenced on an Illumina NextSeq 500 in a single lane to obtain 75-bp single-end reads at an approximate sequencing depth of 35-40 million reads per sample.

treatment_protocol: At two months of age mice were randomly assigned to either vehicle- (1% ethanol) or CORT- (25mg/l, 1% ethanol) treated groups for 6 weeks of treatment.

tag: strain background

tag: Sex

value: Male

tag: genotype

value: BDNF Val66Met

value: CORT

value: Ventral Hippocampus


title: VM CORT 3

description:
24_S12
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv


title: 17-0080_S12_COMB


title: PFC1-A3-c60


title: PFC1-A3-c59


title: VM CORT 1

description:
22_S10
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv