title: G11_plate 5A_E10.5_liver

description:
BSSE-QGF-65039
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E12_plate 5A_E10.5_liver

status: Public on Jul 13 2021

type: SRA

city: London

first: Francesca

middle: M.

last: Spagnoli

address: Great Maze Pond

department: CGTRM

country: United Kingdom

institute: King's College London

description:
BSSE-QGF-65045
processed data file: E8.5-E14.5_AllCells_genes.csv

library_source: transcriptomic

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Reads were uniquely aligned to mouse reference genome (GRCm38) using STAR (v.2.5.3.a).
Comparison of expression level between samples had been conducted with cufflinks.cuffdiff (2.2.1).
The gene expression matrices were generated employing GeneCounts as quantification type in STAR.
The gtf and fasta formatted annotations for mouse were retrieved from GENCODE project (released version v26, primary assembly).
Scater Package was used for filtering. All samples with at least 2000 genes and 500000 counts (visualised in log10 scale) were retained. These thresholds were calculated based on the average of library size and number of expressed genes in each library. We also applied a gene filtering step (transcript > 2 in at least 2 cells). Scran package was used for data normalization. For data visualization, we used t-SNE plot with a perplexity value of 20% of the total number of cells. Clustering of the cells was computed using SC3 package. Pseudo-time reconstruction was performed using Tscan package.
Genome_build: UCSC mm 10 (GRCm38)
Supplementary_files_format_and_content: E8.5-E14.5_AllCells_genes.csv: Comma-separated text file including a table of genes (rows) x cells (columns) showing logcounts (normalized counts) per single cell. Processed data file includes only samples that passed the QC check.

molecule: total RNA

organism: Mus musculus

source_name: Liver Bud

extract_protocol:
GFP+ ventral foregut (E8.5), pancreatic (E10.5, E14.5), and hepatic progenitors (E10.5) were dissected from Tg(Prox1-EGFP) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to ETH Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.

tag: tissue

value: Liver

tag: developmental stage

tag: genotype


title: E11_plate 5A_E10.5_liver

description:
BSSE-QGF-65037
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D11_plate 5A_E10.5_liver

description:
BSSE-QGF-65036
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A11_plate 5A_E10.5_liver

description:
BSSE-QGF-65033
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C11_plate 5A_E10.5_liver

description:
BSSE-QGF-65035
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Organoid_0mM_Control_2

type: RNA

city: Milwaukee

first: Thiago

last: Arzua

state: WI

address: 8701 W Watertown Plank Rd

country: USA

institute: Medical College f Wisconsin

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5μl 10 × Blocking Agent and 1μlof 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using GeneSpring GX v12.1 software package (Agilent Technologies).

organism: Homo sapiens

source_name: Cerebral organoid, control (6 hours)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μgcRNA) were measured by NanoDrop ND-1000.

growth_protocol: The protocol we used for the generation of cerebral organoids was developed by Lancaster et al 2013

extract_protocol: Total RNA was extracted with the QIAzol lysis reagent kit (Qiagen Inc., Valencia, CA).Before performing the microarray assay, RNA underwent quality control analysis of RNA integrity, quantity, and purity, in addition to the detection of genomic DNA contamination and the efficacy of probe labeling

treatment_protocol: 2-month old cerebral organoids were exposed to 50 mM of ethanol for 6 hours by mixing ethanol (Sigma-Aldrich) into 15 mL of culture medium and adding it to the cell culture plate.

tag: cell type

value: 2-month old iPSC-derived cerebral organoid

tag: agent

value: normal media


title: B11_plate 5A_E10.5_liver

description:
BSSE-QGF-65034
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A12_plate 5A_E10.5_liver

description:
BSSE-QGF-65041
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G10_plate 5A_E10.5_liver

description:
BSSE-QGF-65031
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F10_plate 5A_E10.5_liver

description:
BSSE-QGF-65030
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E10_plate 5A_E10.5_liver

description:
BSSE-QGF-65029
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C10_plate 5A_E10.5_liver

description:
BSSE-QGF-65027
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A10_plate 5A_E10.5_liver

description:
BSSE-QGF-65025
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D10_plate 5A_E10.5_liver

description:
BSSE-QGF-65028
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B10_plate 5A_E10.5_liver

description:
BSSE-QGF-65026
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E9_plate 5A_E10.5_liver

description:
BSSE-QGF-65021
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B9_plate 5A_E10.5_liver

description:
BSSE-QGF-65018
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F9_plate 5A_E10.5_liver

description:
BSSE-QGF-65022
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C9_plate 5A_E10.5_liver

description:
BSSE-QGF-65019
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G9_plate 5A_E10.5_liver

description:
BSSE-QGF-65023
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A9_plate 5A_E10.5_liver

description:
BSSE-QGF-65017
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G8_plate 5A_E10.5_liver

description:
BSSE-QGF-65015
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F8_plate 5A_E10.5_liver

description:
BSSE-QGF-65014
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E8_plate 5A_E10.5_liver

description:
BSSE-QGF-65013
processed data file: E8.5-E14.5_AllCells_genes.csv


title: H7_plate 5A_E10.5_liver

description:
BSSE-QGF-65008
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C8_plate 5A_E10.5_liver

description:
BSSE-QGF-65011
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G7_plate 5A_E10.5_liver

description:
BSSE-QGF-65007
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D8_plate 5A_E10.5_liver

description:
BSSE-QGF-65012
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F7_plate 5A_E10.5_liver

description:
BSSE-QGF-65006
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C7_plate 5A_E10.5_liver

description:
BSSE-QGF-65003
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D7_plate 5A_E10.5_liver

description:
BSSE-QGF-65004
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E7_plate 5A_E10.5_liver

description:
BSSE-QGF-65005
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A7_plate 5A_E10.5_liver

description:
BSSE-QGF-65001
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G6_plate 5A_E10.5_liver

description:
BSSE-QGF-64999
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E6_plate 5A_E10.5_liver

description:
BSSE-QGF-64997
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F6_plate 5A_E10.5_liver

description:
BSSE-QGF-64998
processed data file: E8.5-E14.5_AllCells_genes.csv


title: H6_plate 5A_E10.5_liver

description:
BSSE-QGF-65000
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D6_plate 5A_E10.5_liver

description:
BSSE-QGF-64996
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C6_plate 5A_E10.5_liver

description:
BSSE-QGF-64995
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B6_plate 5A_E10.5_liver

description:
BSSE-QGF-64994
processed data file: E8.5-E14.5_AllCells_genes.csv


title: H5_plate 5A_E10.5_liver

description:
BSSE-QGF-64992
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D9_plate 5A_E10.5_liver

description:
BSSE-QGF-65020
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A6_plate 5A_E10.5_liver

description:
BSSE-QGF-64993
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G5_plate 5A_E10.5_liver

description:
BSSE-QGF-64991
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F5_plate 5A_E10.5_liver

description:
BSSE-QGF-64990
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D5_plate 5A_E10.5_liver

description:
BSSE-QGF-64988
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C5_plate 5A_E10.5_liver

description:
BSSE-QGF-64987
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B5_plate 5A_E10.5_liver

description:
BSSE-QGF-64986
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A5_plate 5A_E10.5_liver

description:
BSSE-QGF-64985
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F4_plate 5A_E10.5_liver

description:
BSSE-QGF-64982
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C4_plate 5A_E10.5_liver

description:
BSSE-QGF-64979
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D4_plate 5A_E10.5_liver

description:
BSSE-QGF-64980
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B4_plate 5A_E10.5_liver

description:
BSSE-QGF-64978
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A4_plate 5A_E10.5_liver

description:
BSSE-QGF-64977
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F3_plate 5A_E10.5_liver

description:
BSSE-QGF-64974
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E3_plate 5A_E10.5_liver

description:
BSSE-QGF-64973
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C3_plate 5A_E10.5_liver

description:
BSSE-QGF-64971
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B3_plate 5A_E10.5_liver

description:
BSSE-QGF-64970
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A3_plate 5A_E10.5_liver

description:
BSSE-QGF-64969
processed data file: E8.5-E14.5_AllCells_genes.csv


title: H2_plate 5A_E10.5_liver

description:
BSSE-QGF-64968
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D3_plate 5A_E10.5_liver

description:
BSSE-QGF-64972
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C2_plate 5A_E10.5_liver

description:
BSSE-QGF-64963
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B2_plate 5A_E10.5_liver

description:
BSSE-QGF-64962
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G2_plate 5A_E10.5_liver

description:
BSSE-QGF-64967
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A2_plate 5A_E10.5_liver

description:
BSSE-QGF-64961
processed data file: E8.5-E14.5_AllCells_genes.csv


title: F1_plate 5A_E10.5_liver

description:
BSSE-QGF-64958
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E5_plate 5A_E10.5_liver

description:
BSSE-QGF-64989
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B1_plate 5A_E10.5_liver

description:
BSSE-QGF-64954
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E12_plate 3_E10.5_VP

description:
BSSE-QGF-60236
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Ventral Pancreatic Bud

value: Ventral Pancreas


title: E1_plate 5A_E10.5_liver

description:
BSSE-QGF-64957
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E11_plate 3_E10.5_VP

description:
BSSE-QGF-60235
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C1_plate 5A_E10.5_liver

description:
BSSE-QGF-64955
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E9_plate 3_E10.5_VP

description:
BSSE-QGF-60233
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E6_plate 3_E10.5_VP

description:
BSSE-QGF-60230
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E7_plate 3_E10.5_VP

description:
BSSE-QGF-60231
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E4_plate 3_E10.5_VP

description:
BSSE-QGF-60228
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D12_plate 3_E10.5_VP

description:
BSSE-QGF-60226
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D11_plate 3_E10.5_VP

description:
BSSE-QGF-60225
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E3_plate 3_E10.5_VP

description:
BSSE-QGF-60227
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D9_plate 3_E10.5_VP

description:
BSSE-QGF-60223
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D10_plate 3_E10.5_VP

description:
BSSE-QGF-60224
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E2_plate 5A_E10.5_liver

description:
BSSE-QGF-64965
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D5_plate 3_E10.5_VP

description:
BSSE-QGF-60219
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D7_plate 3_E10.5_VP

description:
BSSE-QGF-60221
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D2_plate 3_E10.5_VP

description:
BSSE-QGF-60216
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D8_plate 3_E10.5_VP

description:
BSSE-QGF-60222
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D6_plate 3_E10.5_VP

description:
BSSE-QGF-60220
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C9_plate 3_E10.5_VP

description:
BSSE-QGF-60214
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C8_plate 3_E10.5_VP

description:
BSSE-QGF-60213
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G1_plate 5A_E10.5_liver

description:
BSSE-QGF-64959
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C5_plate 3_E10.5_VP

description:
BSSE-QGF-60210
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C4_plate 3_E10.5_VP

description:
BSSE-QGF-60209
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C2_plate 3_E10.5_VP

description:
BSSE-QGF-60207
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C1_plate 3_E10.5_VP

description:
BSSE-QGF-60206
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C3_plate 3_E10.5_VP

description:
BSSE-QGF-60208
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B12_plate 3_E10.5_VP

description:
BSSE-QGF-60205
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C6_plate 3_E10.5_VP

description:
BSSE-QGF-60211
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B7_plate 3_E10.5_VP

description:
BSSE-QGF-60200
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E4_plate 2B_E10.5_DP

description:
BSSE-QGF-60180
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Dorsal Pancreatic Bud

value: Dorsal Pancreas


title: E2_plate 2B_E10.5_DP

description:
BSSE-QGF-60178
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D9_plate 2B_E10.5_DP

description:
BSSE-QGF-60173
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D10_plate 2B_E10.5_DP

description:
BSSE-QGF-60174
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D11_plate 2B_E10.5_DP

description:
BSSE-QGF-60175
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D8_plate 2B_E10.5_DP

description:
BSSE-QGF-60172
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D2_plate 2B_E10.5_DP

description:
BSSE-QGF-60166
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D7_plate 2B_E10.5_DP

description:
BSSE-QGF-60171
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D1_plate 2B_E10.5_DP

description:
BSSE-QGF-60165
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C11_plate 2B_E10.5_DP

description:
BSSE-QGF-60163
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C10_plate 2B_E10.5_DP

description:
BSSE-QGF-60162
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C8_plate 2B_E10.5_DP

description:
BSSE-QGF-60160
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C9_plate 2B_E10.5_DP

description:
BSSE-QGF-60161
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B11_plate 3_E10.5_VP

description:
BSSE-QGF-60204
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C2_plate 2B_E10.5_DP

description:
BSSE-QGF-60154
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C6_plate 2B_E10.5_DP

description:
BSSE-QGF-60158
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C5_plate 2B_E10.5_DP

description:
BSSE-QGF-60157
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E5_plate 2B_E10.5_DP

description:
BSSE-QGF-60181
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B11_plate 2B_E10.5_DP

description:
BSSE-QGF-60151
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C4_plate 2B_E10.5_DP

description:
BSSE-QGF-60156
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C1_plate 2B_E10.5_DP

description:
BSSE-QGF-60153
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B9_plate 2B_E10.5_DP

description:
BSSE-QGF-60149
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B7_plate 2B_E10.5_DP

description:
BSSE-QGF-60147
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B5_plate 2B_E10.5_DP

description:
BSSE-QGF-60145
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B4_plate 2B_E10.5_DP

description:
BSSE-QGF-60144
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B3_plate 2B_E10.5_DP

description:
BSSE-QGF-60143
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A11_plate 2B_E10.5_DP

description:
BSSE-QGF-60139
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A10_plate 2B_E10.5_DP

description:
BSSE-QGF-60138
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Dach1OE

city: Stanford

first: Kristy

last: Red-Horse

state: CA

address: 318 Campus Drive

department: Biology

institute: Stanford Univeristy

data_processing:
raw illumina reads were processed in Cell Ranger (10X Genomics)
BCL files were demultiplexed and converted to FASTQ files using the mkfastq in Cell Ranger function
reads were aligned to the mouse genome (mm10) as well as EGFP and tdTomato sequences using the count function
doublets, dead cells, and endocardial cells were removed from analysis through processing in R and Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Seurat object (.RDS)

molecule: polyA RNA

source_name: Coronary Endothelial

extract_protocol:
10x gel bead
Libraries were constructed using the Chromium Single Cell 3' Reagent Kits acording to manufacturer instructions

treatment_protocol: Hearts were digested to a single cell suspension and FACS sorted to purify coronary endothelial cells

value: ApjCreER; Dach1OE/+

value: Coronary Endothelial


title: A9_plate 2B_E10.5_DP

description:
BSSE-QGF-60137
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C7_plate 2B_E10.5_DP

description:
BSSE-QGF-60159
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Td

value: ApjCreER; Td/+


title: 3940_Tam-24h_RNAseq_R1

city: LOS ANGELES

first: Jesse

middle: R

last: Zamudio

address: 610 CHARLES E. YOUNG DRIVE EAST BOX 957239

department: MCDB

institute: University of California, Los Angeles

data_processing:
Reads mapped to the mm10 genome assembly using Tophat (ver 2.0.12).
Additional transcripts were assembled using stringtie (1.2.4).
Reads within genes counted using HTSeq (HTSeq-0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: KPRCountDataOutput.txt, merge160827.gtf

source_name: mouse sarcoma

growth_protocol: Cell lines were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, and Pen/Strep (50 U/ml).

extract_protocol:
Total RNA was extracted with Trizol and purified with the Qiagen RNAeasy kit
ribo- RNA
Strand-specific RNA sequencing libraries were prepared using Ribo Minus Eukaryote Kit for RNAseq (Invitrogen) and TruSeq Stranded mRNA Kit (Illumina)

treatment_protocol: Cells were harvested untreated or 8 or 24 hours post treatment with 500 nM 4-hydroxytamoxifen (4-OHT)

value: mouse sarcoma

tag: cell line

tag: treatment

value: 500 nM 4-hydroxytamoxifen for 24h

tag: experimental series

value: p53 reconstitution timecourse


title: C3_plate 2B_E10.5_DP

description:
BSSE-QGF-60155
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A8_plate 2B_E10.5_DP

description:
BSSE-QGF-60136
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A7_plate 2B_E10.5_DP

description:
BSSE-QGF-60135
processed data file: E8.5-E14.5_AllCells_genes.csv


title: jam2b positive cells

city: Tampa

first: Sanjeeva

middle: Sudhakar

last: Metikala

state: FL

address: 560 Channelside Dr

department: Pathology and Cell Biology

institute: University of South Florida

data_processing:
The fastq files obtained from sequencing were mapped to the Danio rerio genome (version zv11) to generate single-cell feature counts using Cell Ranger version 3.0.2.
Filtered matrix files were imported into Partek Flow analysis Suite (partek.com).
The gene count CPM (counts per million) values were normalized by adding 1.0 and calculating log2 values.
Features (genes) were filtered to exclude values of 0 in at least 99.9% of cells. Two samples were combined and graph-based clustering was performed using PCA=15. Subsequently, UMAP plots were obtained and exported from Partek.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Danio rerio

source_name: jam2b positive (mCherry) cells

growth_protocol: zebrafish embryos were raised at 28.5 deg. centigrade

extract_protocol:
Single cells suspension was achieved using cold protease tissue dissociation protocol, Potter and Potter, 2019
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 36 hours post fertilization (hpf)

tag: strain


title: etv2 positive cells

source_name: etv2 positive (venus) cells


title: A5_plate 2B_E10.5_DP

description:
BSSE-QGF-60133
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B8_plate 2B_E10.5_DP

description:
BSSE-QGF-60148
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B10_plate 2B_E10.5_DP

description:
BSSE-QGF-60150
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_Tam-24h_RNAseq_R1

source_name: mouse lymphoma

value: mouse lymphoma


title: A6_plate 2B_E10.5_DP

description:
BSSE-QGF-60134
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Kpr10_Tam-24h_RNAseq_R1

source_name: mouse lung adenocarcinoma

value: mouse lung adenocarcinoma


title: 306_Tam-24h_RNAseq_R1


title: A3_plate 2B_E10.5_DP

description:
BSSE-QGF-60131
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E8_plate 2A_E10.5_DP

description:
BSSE-QGF-60128
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3940_Tam-8h_RNAseq_R1

value: 500 nM 4-hydroxytamoxifen for 8h


title: Kpr8_Tam-24h_RNAseq_R1


title: E6_plate 2A_E10.5_DP

description:
BSSE-QGF-60126
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B2_plate 2B_E10.5_DP

description:
BSSE-QGF-60142
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_Tam-8h_RNAseq_R1


title: 3472_Tam-8h_RNAseq_R1


title: E5_plate 2A_E10.5_DP

description:
BSSE-QGF-60125
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 306_Tam-8h_RNAseq_R1


title: 3472_Tam-24h_RNAseq_R1


title: E4_plate 2A_E10.5_DP

description:
BSSE-QGF-60124
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E2_plate 2A_E10.5_DP

description:
BSSE-QGF-60122
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Kpr8_Tam-8h_RNAseq_R1


title: E3_plate 2A_E10.5_DP

description:
BSSE-QGF-60123
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3940_Tam-0h_RNAseq_R1

value: untreated


title: E1_plate 2A_E10.5_DP

description:
BSSE-QGF-60121
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D12_plate 2A_E10.5_DP

description:
BSSE-QGF-60120
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3472_Tam-0h_RNAseq_R1


title: D11_plate 2A_E10.5_DP

description:
BSSE-QGF-60119
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 306_Tam-0h_RNAseq_R1


title: D10_plate 2A_E10.5_DP

description:
BSSE-QGF-60118
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_Tam-0h_RNAseq_R1


title: Kpr8_Tam-0h_RNAseq_R1


title: E7_plate 2A_E10.5_DP

description:
BSSE-QGF-60127
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Kpr10_Tam-0h_RNAseq_R1


title: 3940_24h_IP

library_source: genomic

data_processing:
Reads were aligned to the mouse genome (genome build mm10) with Bowtie version 1.0.1 allowing up to 2 mismatches. For reads with multiple reportable alignments, one was reported at random (-M 1)
Peaks were called with Macs2 2.2.7.1
Genome_build: mm10
Supplementary_files_format_and_content: BED files for peaks were generated using MACS 2.2.7.1. Processed data is the unmodified narrow peak output.

molecule: genomic DNA

growth_protocol: Cell lines were grown  in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco), 0.1 mM nonessential amino acids, 2 mM L-glutamine, and Pen/Strep (50 U/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and bound DNA fragments were isolated with p53 antibody (NCL-L-p53-CM5p, Leica Biosystems).
Genomic DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were harvested untreated or 24 hours post treatment with 500 nM 4-hydroxytamoxifen (4-OHT)

tag: chip antibody

value: p53 reconstitution ChIP


title: 3472_24h_IP

value: p53 antibody (NCL-L-p53-CM5p, Leica Biosystems)


title: D8_plate 2A_E10.5_DP

description:
BSSE-QGF-60116
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D9_plate 2A_E10.5_DP

description:
BSSE-QGF-60117
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D6_plate 2A_E10.5_DP

description:
BSSE-QGF-60114
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_24h_IP


title: D5_plate 2A_E10.5_DP

description:
BSSE-QGF-60113
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Organoid_50mM_Alcohol_1

source_name: Cerebral organoid, ethanol (50 mM, 6 hours)

value: 2-month old iPSC-derived cerebral organoid

value: ethanol


title: 306_24h_IP


title: D4_plate 2A_E10.5_DP

description:
BSSE-QGF-60112
processed data file: E8.5-E14.5_AllCells_genes.csv


title: kpr10_24h_IP


title: Kpr10_Tam-8h_RNAseq_R1


title: D3_plate 2A_E10.5_DP

description:
BSSE-QGF-60111
processed data file: E8.5-E14.5_AllCells_genes.csv


title: kpr8_24h_IP


title: C12_plate 2A_E10.5_DP

description:
BSSE-QGF-60108
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C10_plate 2A_E10.5_DP

description:
BSSE-QGF-60106
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3472_0h_IP


title: 928_0h_IP


title: C7_plate 2A_E10.5_DP

description:
BSSE-QGF-60103
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 306_0h_IP


title: kpr8_0h_IP


title: C4_plate 2A_E10.5_DP

description:
BSSE-QGF-60100
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C8_plate 2A_E10.5_DP

description:
BSSE-QGF-60104
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3472_24h_input


title: kpr10_0h_IP


title: C5_plate 2A_E10.5_DP

description:
BSSE-QGF-60101
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D7_plate 2A_E10.5_DP

description:
BSSE-QGF-60115
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C6_plate 2A_E10.5_DP

description:
BSSE-QGF-60102
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C2_plate 2A_E10.5_DP

description:
BSSE-QGF-60098
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C3_plate 2A_E10.5_DP

description:
BSSE-QGF-60099
processed data file: E8.5-E14.5_AllCells_genes.csv


title: kpr10_24h_input


title: C1_plate 2A_E10.5_DP

description:
BSSE-QGF-60097
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_24h_input


title: 3940_24h_input


title: B12_plate 2A_E10.5_DP

description:
BSSE-QGF-60096
processed data file: E8.5-E14.5_AllCells_genes.csv


title: kpr8_24h_input


title: B11_plate 2A_E10.5_DP

description:
BSSE-QGF-60095
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 3940_0h_IP


title: 3472_0h_input


title: B9_plate 2A_E10.5_DP

description:
BSSE-QGF-60093
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D1_plate 2A_E10.5_DP

description:
BSSE-QGF-60109
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B8_plate 2A_E10.5_DP

description:
BSSE-QGF-60092
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B7_plate 2A_E10.5_DP

description:
BSSE-QGF-60091
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 928_0h_input


title: 306_0h_input


title: B6_plate 2A_E10.5_DP

description:
BSSE-QGF-60090
processed data file: E8.5-E14.5_AllCells_genes.csv


title: kpr8_0h_input


title: B4_plate 2A_E10.5_DP

description:
BSSE-QGF-60088
processed data file: E8.5-E14.5_AllCells_genes.csv


title: B3_plate 2A_E10.5_DP

description:
BSSE-QGF-60087
processed data file: E8.5-E14.5_AllCells_genes.csv


title: 306_24h_input


title: SLFN11_WT_cntrl_6h_25

city: Cambridge

first: Joshua

last: Armenia

address: 1 Francis Crick Avenue

institute: AstraZeneca

data_processing:
Data was analyzed by Rosalind (https://www.rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA).
Reads were trimmed using cutadapt. Quality scores were assessed using FastQC.
Reads were aligned using STAR.
Individual sample reads were quantified using HTseq and normalized via Relative Log Expression (RLE) using DESeq2 R library.
DEseq2 was also used to calculate fold changes and p-values and perform optional covariate correction.
Functional enrichment analysis of pathways, gene ontology, domain structure and other ontologies was performed using HOMER.
Genome_build: RCh38
Salmon (0.13.1) generated TPM data: RNA_seq_SLFN11.txt.gz
HTseq normalized counts: SLFN11_RNAseq_data_normalizedCounts.txt.

source_name: DU145 wild type

growth_protocol: DU145 cells were cultured in EMEM media (ATCC) supplemented with 10% FBS

extract_protocol:
Total RNA was isolated from cells using the RNeasy Mini kit from Qiagen
Library preparation was done using the llumina TruSeq mRNA Stranded HS kit and sequencing was performed on 4 lanes of HiSeq4000, SE50.

treatment_protocol: DU145 wild type and two different SLFN11 knockout clones were treated for 0, 6 or 24 hours with 100 nM gemcitabine (three independent experiments) before the cells were harvested for total RNA isolation

value: WT

tag: compound

value: cntrl

tag: time course


title: 3940_0h_input


title: SLFN11_WT_cntrl_6h_13


title: B2_plate 2A_E10.5_DP

description:
BSSE-QGF-60086
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Dorsal Pancreas


title: SLFN11_WT_cntrl_6h_1


title: A11_plate 2A_E10.5_DP

description:
BSSE-QGF-60083
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 64_lh 154

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

country: Italy

institute: Azienda USL- IRCCS di Reggio Emilia

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

hyb_protocol: RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol. Each reporter probe provided by the manufacturer was labeled with a propierty flourescent barcode system specific for each transcript.

scan_protocol: Scaning was conducted using the NanoString Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (POLR2A, ERCC3, DNAJC14). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

label: Molecular barcode on reporter probe

source_name: Classical Hodgkin Lymphoma

label_protocol: RNA was not labeled, but it was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: Formalin-fixed, paraffin-embedded (FFPE) tumor diagnostic biopsies of classical Hodgkin Lymphoma were reviewed by three different pathologists. For RNA purification, five 5um FFPE slides were cut for each tumor. Total RNA was extracted by Maxwell® RSC RNA FFPE kit (Promega). RNA quantity and quality were assessed by NanoDrop2000 (Thermo Fisher Scientific). For samples that reached the quality standards (A260/A280 ≥ 1.7 and A260/A230 ≥ 1.8), we evaluated the expression profile of 773 genes by NanoString using the PanCancer Immune Profiling Panel (NanoString Technologies).

treatment_protocol: Pretreatment diagnostic biopsies from ABVD-treated classical Hodgkin Lymphoma patients

tag: gender

value: M

tag: age

tag: Stage

value: I

tag: serum vitamin d <15ng/ml

value: yes


title: SLFN11_WT_cntrl_24h_31


title: SLFN11_WT_cntrl_24h_7


title: Patient 63_lh 153

value: IV


title: Patient 61_lh 149

value: F

value: no


title: A10_plate 2A_E10.5_DP

description:
BSSE-QGF-60082
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 62_lh 151

value: II


title: Patient 60_lh 147


title: Patient 57_lh 144


title: Patient 58_lh 134


title: Patient 59_lh 145


title: Patient 56_lh 143


title: kpr10_0h_input

value: mouse lung adenocarcinoma


title: A9_plate 2A_E10.5_DP

description:
BSSE-QGF-60081
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_WT_cntrl_24h_19


title: Patient 55_lh 142


title: B5_plate 2A_E10.5_DP

description:
BSSE-QGF-60089
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 54_lh 141


title: Patient 53_lh 139

value: III


title: B1_plate 2A_E10.5_DP

description:
BSSE-QGF-60085
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A6_plate 2A_E10.5_DP

description:
BSSE-QGF-60078
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_WT_100nM_Gem_6h_28

value: Gem


title: A5_plate 2A_E10.5_DP

description:
BSSE-QGF-60077
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 52_lh 137


title: SLFN11_WT_100nM_Gem_6h_16


title: Patient 50_lh 133


title: Patient 51_lh 135


title: SLFN11_WT_100nM_Gem_24h_34


title: Patient 49_lh 122


title: Patient 48_lh 130


title: SLFN11_WT_100nM_Gem_24h_22


title: A3_plate 2A_E10.5_DP

description:
BSSE-QGF-60075
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A2_plate 2A_E10.5_DP

description:
BSSE-QGF-60074
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_WT_100nM_Gem_24h_10


title: SLFN11_KO2_cntrl_6h_3

source_name: DU145 SLFN11 knockout

value: KO 2


title: F12_plate 4A_E14.5_PA

description:
BSSE-QGF-60070
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Pancreatic epithelium

value: Pancreas


title: Patient 46_lh 128


title: Patient 45_lh 127


title: D12_plate 4A_E14.5_PA

description:
BSSE-QGF-60068
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 47_lh 129


title: Patient 43_lh 125


title: SLFN11_KO2_cntrl_6h_27


title: Patient 42_lh 123


title: Patient 41_lh 121


title: SLFN11_WT_100nM_Gem_6h_4


title: Patient 40_lh 120


title: C12_plate 4A_E14.5_PA

description:
BSSE-QGF-60067
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO2_cntrl_6h_15


title: Patient 38_lh 117


title: A4_plate 2A_E10.5_DP

description:
BSSE-QGF-60076
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 37_lh 118


title: SLFN11_KO2_cntrl_24h_9


title: F11_plate 4A_E14.5_PA

description:
BSSE-QGF-60062
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 44_lh 126


title: G11_plate 4A_E14.5_PA

description:
BSSE-QGF-60063
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO2_cntrl_24h_33


title: Patient 35_lh 115


title: SLFN11_KO2_cntrl_24h_21


title: E11_plate 4A_E14.5_PA

description:
BSSE-QGF-60061
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 36_lh 116


title: Patient 32_lh 112


title: Patient 39_lh 93


title: SLFN11_KO2_100nM_Gem_6h_6


title: Patient 34_lh 114


title: C11_plate 4A_E14.5_PA

description:
BSSE-QGF-60059
processed data file: E8.5-E14.5_AllCells_genes.csv


title: D11_plate 4A_E14.5_PA

description:
BSSE-QGF-60060
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO2_100nM_Gem_6h_30


title: B11_plate 4A_E14.5_PA

description:
BSSE-QGF-60058
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO2_100nM_Gem_6h_18


title: Patient 30_lh 110

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol


title: Patient 31_lh 111


title: Patient 29_lh 109


title: Patient 27_lh 107


title: A11_plate 4A_E14.5_PA

description:
BSSE-QGF-60057
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 26_lh 106


title: Patient 25_lh 105


title: Patient 24_lh 104


title: Patient 23_lh 103


title: G10_plate 4A_E14.5_PA

description:
BSSE-QGF-60055
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 33_lh 113


title: F10_plate 4A_E14.5_PA

description:
BSSE-QGF-60054
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO2_100nM_Gem_24h_24


title: Patient 22_lh 102


title: SLFN11_KO2_100nM_Gem_24h_12


title: Patient 28_lh 108


title: Patient 21_lh 101


title: E10_plate 4A_E14.5_PA

description:
BSSE-QGF-60053
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO1_cntrl_6h_26

value: KO 1


title: Patient 20_lh 99


title: C10_plate 4A_E14.5_PA

description:
BSSE-QGF-60051
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 18_lh 97


title: SLFN11_KO1_cntrl_6h_2


title: Patient 19_lh 98


title: B10_plate 4A_E14.5_PA

description:
BSSE-QGF-60050
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 17_lh 96


title: Patient 16_lh 95


title: A10_plate 4A_E14.5_PA

description:
BSSE-QGF-60049
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO1_cntrl_6h_14


title: SLFN11_KO2_100nM_Gem_24h_36


title: Patient 15_lh 94


title: SLFN11_KO1_cntrl_24h_8


title: H9_plate 4A_E14.5_PA

description:
BSSE-QGF-60048
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 12_lh 89


title: Patient 14_lh 92


title: Patient 13_lh 90


title: Patient 10_lh 87


title: Patient 11_lh 88


title: SLFN11_KO1_cntrl_24h_32


title: G9_plate 4A_E14.5_PA

description:
BSSE-QGF-60047
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO1_cntrl_24h_20


title: Patient 9_lh 86


title: SLFN11_KO1_100nM_Gem_6h_5


title: Patient 8_lh 85


title: SLFN11_KO1_100nM_Gem_6h_29


title: Patient 7_lh 84


title: F9_plate 4A_E14.5_PA

description:
BSSE-QGF-60046
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E9_plate 4A_E14.5_PA

description:
BSSE-QGF-60045
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 6_lh 83


title: D9_plate 4A_E14.5_PA

description:
BSSE-QGF-60044
processed data file: E8.5-E14.5_AllCells_genes.csv


title: SLFN11_KO1_100nM_Gem_6h_17


title: Patient 5_lh 82


title: Patient 4_lh 81


title: Patient 1_lh 77


title: Patient 2_lh 78


title: Patient 52_dlb64

data_processing:
Data were collected as NanoString RCC files. The data were normalized using 3 HK genes (ERCC3, EIF2B4, TLK2). Raw values are the number of copies of each molecular barcode representative of a specific transcript.
Mean count of negative controls plus two standard deviations was subtracted from each gene count to eliminate negative background. Then normalization on synthetic positive controls was conducted by multiplying the count of each gene for a correction factor. This factor was calculated for each sample as the ratio between the quadratic mean of positive controls counts and the mean of quadratic means in all samples. In order to performed CodeSet Content normalization on housekeeping genes, three reference genes were selected among the forty available in the panel based on the lowest coefficients of variation (CV= ratio between mean counts and standard deviations across all samples). Finally, CodeSet Content normalization was performed by multiplying genes counts for a further correction factor calculated on reference genes as described for positive technical controls. After completion of normalization processes, counts were log2 transformed.

source_name: Diffuse Large B Cell Lymphoma

treatment_protocol: Pretreatment diagnostic biopsies from DLBCL patients

tag: vitamin d <15ng/ml


title: C9_plate 4A_E14.5_PA

description:
BSSE-QGF-60043
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: tissue


title: SLFN11_KO1_100nM_Gem_24h_35


title: SLFN11_KO1_100nM_Gem_24h_23


title: B9_plate 4A_E14.5_PA

description:
BSSE-QGF-60042
processed data file: E8.5-E14.5_AllCells_genes.csv

tag: developmental stage


title: Patient 51_dlb61


title: SLFN11_KO1_100nM_Gem_24h_11

tag: genotype


title: Patient 49_dlb57


title: Patient 48_dlb56


title: H8_plate 4A_E14.5_PA

description:
BSSE-QGF-60040
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 50_dlb58


title: Patient 47_dlb55


title: Patient 3_lh 79


title: Patient 45_dlb52


title: G8_plate 4A_E14.5_PA

description:
BSSE-QGF-60039
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 46_dlb53

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol


title: F8_plate 4A_E14.5_PA

description:
BSSE-QGF-60038
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E8_plate 4A_E14.5_PA

description:
BSSE-QGF-60037
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_IGF2BP1KO_DMS+_rep2

city: Seoul

first: Daehyun

last: Baek

address: Rm 402, Bldg 504, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul

department: School of Biological Sciences

country: South Korea

institute: Seoul National University

description: DMS-treated RNA-seq in HEK293T (IGF2BP1 KO)

data_processing:
1. Base-calling by RTA(Real Time Analaysis) software within HiSeq 2500 (mRNA-Seq) or HiSeq 2000 (sRNA-Seq)
2. Quality trimming by the highest scoring path algorithm (hsptrim-1.2.6)
3. Adapter trimming by cutadapt-1.2.1
4. Remove tRNA, rRNA-derived reads by Bowtie2 alignment
5. Remove sequencing artifacts by fastx_artifacts_filter of fastx_toolkit
6. Alignment of filtered reads to human reference genome by Tophat2 (mRNA-Seq) or Bowtie2 (sRNA-Seq)
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Tab-delimited text file (*.quants.txt) contains expression levels for individual genes. Columns: (1) id: Gene identifier (e.g. NM_000000), (2) symbol: Gene symbol (e.g. GAPDH), (3) readcount: Number of mapped reads, (4) exlev: Expression level (RPM or RPKM), (5) expct: Expression percentile rank
Supplementary_files_format_and_content: BED file (*.dmscount.{plus,minus}.txt) contains RT truncation counts by DMS treatment in single nucleotide resolution

source_name: human embryonic kidney

extract_protocol:
For DMS-seq, total RNA was extracted with Trizol reagent (Qiagen) according to the manufacturer's instructions. After total RNA extraction, mRNA was selected using Dynabead (Thermofisher). Isolated mRNA was then randomly fragmented using fragmentation reagent (Invitrogen). Size-selected RNA fragments (60-70nt) were used for library preparation.
poly(A)-selected RNA-seq
Total RNA was extracted using TRIzol (Invitrogen).
Both of the library preparations (mRNA-Seq and sRNA-Seq) were done based on the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G). DMS-seq libraries were prepared using adaptors from a previous study (PMID: 30605524) following procedures from Rouskin et al., 2014 (PMID: 24336214).
mRNA-seq, sRNA-seq, DMS-seq

tag: condition

value: IGF2BP1 KO

value: DMS treated

tag: concentration

tag: incubation


title: Patient 41_dlb48


title: Patient 40_dlb46


title: Patient 43_dlb50


title: HEK293T_WT_DMS+

description: DMS-treated RNA-seq in HEK293T (WT)

tag: cell line

value: WT

tag: treatment


title: Patient 38_dlb44


title: B8_plate 4A_E14.5_PA

description:
BSSE-QGF-60034
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_IGF2BP1KO_DMS-_rep1

description: DMS-untreated RNA-seq in HEK293T (IGF2BP1 KO)

value: DMS untreated


title: HEK293T_IGF2BP1KO_DMS-_rep2


title: HEK293T_IGF2BP1KO_DMS+_rep1


title: C8_plate 4A_E14.5_PA

description:
BSSE-QGF-60035
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_WT_DMS-_rep2

description: DMS-untreated RNA-seq in HEK293T (WT)


title: Patient 39_dlb45

value: M


title: A8_plate 4A_E14.5_PA

description:
BSSE-QGF-60033
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 35_dlb41


title: Patient 36_dlb42


title: Patient 34_dlb39

value: I


title: HEK293T_WT_DMS-_rep1

description: DMS-untreated RNA-seq in HEK293T (WT)


title: Patient 44_dlb51

value: yes


title: Patient 33_dlb40


title: HEK293T_miR-193b-3p_IGF2BP1KO

description: hsa-miR-193b-3p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

extract_protocol:
For mRNA-seq, total RNA was extracted with Trizol reagent (Qiagen) according to the manufacturer's instructions. After total RNA extraction, mRNA was selected using Dynabead (Thermofisher). Isolated mRNA was then randomly fragmented using fragmentation reagent (Invitrogen). Size-selected RNA fragments (200-400nt) were used for library preparation.
poly(A)-selected RNA-seq
Total RNA was extracted using TRIzol (Invitrogen).
Both of the library preparations (mRNA-Seq and sRNA-Seq) were done based on the Illumina Truseq small RNA library preparation protocol (TruSeq Small RNA Library Prep Guide, Part # 15004197 Rev. G). DMS-seq libraries were prepared using adaptors from a previous study (PMID: 30605524) following procedures from Rouskin et al., 2014 (PMID: 24336214).
mRNA-seq, sRNA-seq, DMS-seq

value: hsa-miR-193b-3p transfection


title: Patient 32_dlb37


title: Patient 31_dlb38

value: F


title: G7_plate 4A_E14.5_PA

description:
BSSE-QGF-60031
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-214-5p_IGF2BP1KO

description: hsa-miR-214-5p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: hsa-miR-214-5p transfection


title: Patient 37_dlb43

value: no


title: Patient 29_dlb33

value: IV


title: F7_plate 4A_E14.5_PA

description:
BSSE-QGF-60030
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-29a-3p_IGF2BP1KO

description: hsa-miR-29a-3p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: hsa-miR-29a-3p transfection


title: Patient 28_dlb32

value: II


title: Patient 27_dlb31


title: E7_plate 4A_E14.5_PA

description:
BSSE-QGF-60029
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-212-5p_IGF2BP1KO

description: hsa-miR-138-5p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: hsa-miR-138-5p transfection


title: D7_plate 4A_E14.5_PA

description:
BSSE-QGF-60028
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Pancreas


title: HEK293T_miR-455-3p_IGF2BP1KO


title: Patient 23_dlb36


title: Patient 24_dlb27


title: HEK293T_miR-122-5p_IGF2BP1KO

description: hsa-miR-212-5p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: hsa-miR-212-5p transfection


title: Patient 25_dlb28

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol


title: C7_plate 4A_E14.5_PA

description:
BSSE-QGF-60027
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 26_dlb30


title: H7_plate 4A_E14.5_PA

description:
BSSE-QGF-60032
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 21_dlb24


title: Patient 22_dlb25

value: III


title: A7_plate 4A_E14.5_PA

description:
BSSE-QGF-60025
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-199b-5p_IGF2BP1KO

value: IGF2BP1 KO


title: Patient 20_dlb23


title: Patient 30_dlb34


title: H6_plate 4A_E14.5_PA

description:
BSSE-QGF-60024
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 19_dlb22


title: Patient 18_dlb21


title: HEK293T_miR-129-2-3p_IGF2BP1KO

description: hsa-miR-129-2-3p-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: hsa-miR-129-2-3p transfection


title: G6_plate 4A_E14.5_PA

description:
BSSE-QGF-60023
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 17_dlb20


title: HEK293T_miR-193b-3p_PCBP2KO

description: hsa-miR-193b-3p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: PCBP2 KO


title: Patient 42_dlb49


title: Patient 15_dlb17

value: M


title: Patient 16_dlb18


title: Patient 14_dlb16


title: HEK293T_miR-214-5p_PCBP2KO

description: hsa-miR-214-5p-transfected mRNA-seq in HEK293T (PCBP2 KO)


title: HEK293T_miR-455-3p_PCBP2KO

description: hsa-miR-455-3p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: hsa-miR-455-3p transfection


title: Patient 12_dlb14

value: yes


title: HEK293T_miR-212-5p_PCBP2KO

description: hsa-miR-212-5p-transfected mRNA-seq in HEK293T (PCBP2 KO)


title: B6_plate 4A_E14.5_PA

description:
BSSE-QGF-60018
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-122-5p_PCBP2KO

description: hsa-miR-122-5p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: hsa-miR-122-5p transfection


title: Patient 10_dlb8

value: F


title: Patient 11_dlb9

value: I


title: Patient 9_dlb7


title: HEK293T_miR-199b-5p_PCBP2KO

description: hsa-miR-199b-5p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: hsa-miR-199b-5p transfection


title: Patient 8_dlb4

value: IV

value: no


title: Patient 6_dlb2


title: Patient 7_dlb3


title: Patient 5_dlb1


title: F6_plate 4A_E14.5_PA

description:
BSSE-QGF-60022
processed data file: E8.5-E14.5_AllCells_genes.csv


title: H5_plate 4A_E14.5_PA

description:
BSSE-QGF-60016
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 4_dlb13


title: HEK293T_miR-129-2-3p_PCBP2KO

description: hsa-miR-129-2-3p-transfected mRNA-seq in HEK293T (PCBP2 KO)


title: Patient 13_dlb15

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol


title: E6_plate 4A_E14.5_PA

description:
BSSE-QGF-60021
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G5_plate 4A_E14.5_PA

description:
BSSE-QGF-60015
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C6_plate 4A_E14.5_PA

description:
BSSE-QGF-60019
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 3_dlb12


title: HEK293T_miR-31-5p_PCBP2KO

description: hsa-miR-31-5p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: hsa-miR-31-5p transfection


title: Gill AGD fish 6 (T8_GAGD6)

city: Galway

first: Anita

middle: Mary

last: Talbot

state: Galway

address: Dublin Road Campus

department: Marine and Freshwater Research Centre

country: Ireland

institute: Galway-Mayo Institute of Technology

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD6

data_processing:
Index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using HiSeq PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.
After cluster generation, library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated.
Illumina CASAVA v1.8 software was used for base calling.
FastqQc (Version 0.11.8) (www.bioinformatics.babraham.ac.uk/projects/fastqc/) was utilised for quality assessment of reads from each sample and Multiqc (Version 1.7) was used to visualise all FastQc results
Trimmomatic (v0.36) was used to trim paired reads in FASTQ files, using default parameters for paired-end mode and a minimum read length of 50bp.
Mapping was implemented using HiSat2 (version 2.1.0), counts were generated using featureCounts (v1.6.0) using the default parameters for paired-end reads. RNA-seq specific QC, sample correlation and visualisation were implemented using Seqmonk (Version 1.45.1)
Differential expression analysis was performed on biological replicates (n=6) from 4, 7, 14 and 16 dpi using the DESeq2 (Version 1.24.0) where each time point was compared to time 0, pre-AGD control samples.
Genome_build: Salmo salar ICSASG_v2  (GenBank:GCF_000233375.1)
Supplementary_files_format_and_content: tab-delimited text files
Supplementary_files_format_and_content: Excel table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Excel table with a list of differentially regulated genes from each time point  (T4: 4dpi, T5:7 dpi, T8: 14 dpi, T9: 16 dpi)

organism: Salmo salar

source_name: Gill

growth_protocol:
Salmo salar: Post-smolt Atlantic salmon (78.8 ± 20.6g) were distributed into 4 circular black 1000 L tanks connected to recirculating aquaculture systems at a stocking density of  3.6 kg per 1000 L , water temperature 12 degrees C, artificial seawater (30 PSU), and 14h/8h light/dark cycle. Fish were fed a commercial salmon diet (Le Gouessant)at 1% body weight per day.
Neoparamoeba peruruans: N. perurans trophozoites were collected by gill swabbing from AGD affected Atlantic salmon on a commercial Irish farm. Amoebae were cultured on marine yeast agar plates (MYA; 0.01% malt, 0.01% yeast, 2% Bacto Agar), 16°C overlaid with 7 ml sterile seawater, and sub-cultured weekly by transferring free-floating cells to fresh MYA plates N. perurans were in culture for 12 weeks prior to the challenge.

extract_protocol:
For histological analyses gill arch 1 was collected into 10% neutral buffered formalin. For RNA-seq analysis and qPCR the 2nd and 4th left gill arch respectively were  collected, the arch cartilage removed prior to the individual gill tissue being immersed in RNAlater® (Ambion Inc, Austin, Texas), stored at 4 °C overnight, followed by final storage at -80°C.
Total RNA as extracted using the RNeasy® Mini Plus Kit (Qiagen, Germany) according to the manufacturer’s instructions. Total RNA from 6 individual fish from 0, 4, 7, 14  and 16 dpi was used for the construction of 30 sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

treatment_protocol: After an acclimatisation period of 6 days, 90 fish were challenged with N. perurans (2750 amoebae/L) in 300 L for 4 h with oxygen saturation, fish behaviour and welfare closely monitored.  Controls fish (90) were also held at 300 L for 4 h. Following holding in challenge or control tanks, fish were placed into new tanks containing 1000 L seawater.

tag: days post infection (dpi)


title: F5_plate 4A_E14.5_PA

description:
BSSE-QGF-60014
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Patient 1_dlb10


title: Gill AGD fish 4 (T8_GAGD4)

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD4


title: A6_plate 4A_E14.5_PA

description:
BSSE-QGF-60017
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill AGD fish 5 (T8_GAGD5)

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD5


title: E5_plate 4A_E14.5_PA

description:
BSSE-QGF-60013
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-193b-3p_Parental

description: hsa-miR-193b-3p-transfected mRNA-seq in HEK293T (Parental)

value: Parental

value: hsa-miR-193b-3p transfection


title: Gill AGD fish 3 (T8_GAGD3)

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD3


title: Gill AGD fish 1 (T8_GAGD1)

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD1


title: C5_plate 4A_E14.5_PA

description:
BSSE-QGF-60011
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Pancreas


title: Gill AGD fish 2 (T8_GAGD2)

description:
Comparison 16 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_9_annotated
T9_GAGD2


title: HEK293T_miR-214-5p_Parental

description: hsa-miR-214-5p-transfected mRNA-seq in HEK293T (Parental)

value: hsa-miR-214-5p transfection


title: Gill AGD fish 5 (T7_GAGD5)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD5


title: Gill AGD fish 4 (T7_GAGD4)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD4


title: Gill AGD fish 3 (T7_GAGD3)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD3


title: HEK293T_miR-29a-3p_Parental

description: hsa-miR-29a-3p-transfected mRNA-seq in HEK293T (Parental)

value: hsa-miR-29a-3p transfection


title: Gill AGD fish 6 (T7_GAGD6)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD6


title: HEK293T_miR-455-3p_Parental

description: hsa-miR-455-3p-transfected mRNA-seq in HEK293T (Parental)


title: Gill AGD fish 2 (T7_GAGD2)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD2


title: Patient 2_dlb11

description: Total RNA was hybridized to capture probes and reporter probes using the NanoString nCounter system according to the manufacturer's protocol

value: II


title: HEK293T_miR-24-3p_PCBP2KO

description: hsa-miR-24-3p-transfected mRNA-seq in HEK293T (PCBP2 KO)

value: PCBP2 KO

value: hsa-miR-24-3p transfection


title: F4_plate 4A_E14.5_PA

description:
BSSE-QGF-60006
processed data file: E8.5-E14.5_AllCells_genes.csv


title: A5_plate 4A_E14.5_PA

description:
BSSE-QGF-60009
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-212-5p_Parental

description: hsa-miR-212-5p-transfected mRNA-seq in HEK293T (Parental)

value: hsa-miR-212-5p transfection


title: HEK293T_miR-122-5p_Parental

description: hsa-miR-122-5p-transfected mRNA-seq in HEK293T (Parental)


title: HEK293T_miR-199b-5p_Parental

description: hsa-miR-199b-5p-transfected mRNA-seq in HEK293T (Parental)


title: G4_plate 4A_E14.5_PA

description:
BSSE-QGF-60007
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill AGD fish 6 (T5_GAGD6)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD6


title: Gill AGD fish 4 (T5_GAGD4)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD4


title: Gill AGD fish 1 (T7_GAGD1)

description:
Comparison 14 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_8_annotated
T8_GAGD1


title: Gill AGD fish 3 (T5_GAGD3)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD3


title: Gill AGD fish 5 (T5_GAGD5)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD5


title: D4_plate 4A_E14.5_PA

description:
BSSE-QGF-60004
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill AGD fish 1 (T5_GAGD1)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD1


title: Gill AGD fish 6 (T4_GAGD6)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD6


title: Gill AGD fish 5 (T4_GAGD5)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD5


title: H4_plate 4A_E14.5_PA

description:
BSSE-QGF-60008
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill AGD fish 4 (T4_GAGD4)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD4


title: HEK293T_miR-31-5p_Parental

description: hsa-miR-31-5p-transfected mRNA-seq in HEK293T (Parental)


title: Gill AGD fish 3 (T4_GAGD3)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD3


title: B4_plate 4A_E14.5_PA

description:
BSSE-QGF-60002
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_miR-24-3p_Parental

description: hsa-miR-24-3p-transfected mRNA-seq in HEK293T (Parental)


title: A4_plate 4A_E14.5_PA

description:
BSSE-QGF-60001
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill AGD fish 1 (T4_GAGD1)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD1


title: H3_plate 4A_E14.5_PA

description:
BSSE-QGF-60000
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E4_plate 4A_E14.5_PA

description:
BSSE-QGF-60005
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill control fish 5 (T0_GCRL5)


title: Gill control fish 6 (T0_GCRL6)


title: Gill AGD fish 2 (T4_GAGD2)

description:
Comparison 4 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_4_annotated
T4_GAGD2


title: HEK293T_mock_IGF2BP1KO_rep7

description: mock-transfected mRNA-seq in HEK293T (IGF2BP1 KO)

value: IGF2BP1 KO

value: mock transfection


title: Gill control fish 4 (T0_GCRL4)


title: Gill AGD fish 2 (T5_GAGD2)

description:
Comparison 7 dpi vs 0 dpi (n=6)
DESeq2_gill_0_vs_5_annotated
T5_GAGD2


title: Gill control fish 3 (T0_GCRL3)


title: HEK293T_miR-129-2-3p_Parental

description: hsa-miR-129-2-3p-transfected mRNA-seq in HEK293T (Parental)

value: hsa-miR-129-2-3p transfection


title: HEK293T_mock_IGF2BP1KO_rep5


title: C4_plate 4A_E14.5_PA

description:
BSSE-QGF-60003
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_IGF2BP1KO_rep4


title: E3_plate 4A_E14.5_PA

description:
BSSE-QGF-59997
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill control fish 2 (T0_GCRL2)


title: F3_plate 4A_E14.5_PA

description:
BSSE-QGF-59998
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Gill control fish 1 (T0_GCRL1)


title: D3_plate 4A_E14.5_PA

description:
BSSE-QGF-59996
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_IGF2BP1KO_rep3


title: BATF CAR TILs_rep2 RNAseq

city: La Jolla

first: Anjana

last: Rao

address: 9420 Athena Circle

department: Signaling and Gene Epression

institute: La Jolla institute

data_processing:
Paired raw reads were aligned to the Mus Musculus genome (version mm10) using STAR (version STAR_2.5.3a_modified).
Counts per gene were obtained using subread's fucntion featureCounts (version subread-2.0.0-source)'.
These raw counts were TPM-normalized.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized Transcripts per Million for InVitro or InVivo samples.

source_name: CAR-expressing CD8 T cells in tumor

growth_protocol: 5 days after in vitro culture or 8 days after Transfer

extract_protocol:
GFP+CD8+Thy1.1+ CAR T cells were sorted from B16-huCD19 tumors. And  total RNA were extracted using Qiagen RNeasy plus micro kit
Libraries were constructed by Smart2seq protocol
50x50bp pair end sequencing

treatment_protocol: BATF-transduction or IRF4-transduction

tag: strain

value: Tumor

value: 8 days after Transfer

value: pMIG transduced


title: B3_plate 4A_E14.5_PA

description:
BSSE-QGF-59994
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF CAR TILS_rep1 RNAseq


title: pMIG CD8 T cells_rep2 RNAseq

source_name: in vitro cultured CD8 T cells

value: Spleen

value: 5 days after in vitro culture

value: Batf transduced


title: A3_plate 4A_E14.5_PA

description:
BSSE-QGF-59993
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_IGF2BP1KO_rep6


title: G2_plate 4A_E14.5_PA

description:
BSSE-QGF-59991
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_IGF2BP1KO_rep1


title: pMIG CD8 T cells_rep1 RNAseq


title: HEK293T_mock_PCBP2KO_rep6

description: mock-transfected mRNA-seq in HEK293T (PCBP2 KO)


title: BATF CD8 T cells_rep2 RNAseq


title: pMIG CAR TILs_rep2 RNAseq


title: pMIG CAR TILs_rep1 RNAseq


title: HEK293T_mock_PCBP2KO_rep5


title: HEK293T_mock_PCBP2KO_rep3


title: HEK293T_mock_PCBP2KO_rep4


title: BATF CD8 T cells_rep1 RNAseq


title: D2_plate 4A_E14.5_PA

description:
BSSE-QGF-59988
processed data file: E8.5-E14.5_AllCells_genes.csv


title: E2_plate 4A_E14.5_PA

description:
BSSE-QGF-59989
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG input_rep2 ChIPseq

data_processing:
Paired raw reads were aligned to the Mus Musculus genome (version mm10) using bwa mem (version 0.7.15-r1144-dirty).
Unmapped reads were cleaned for adapter sequence and clipped 1 base pair with Trim_galore (version 0.4.3) before being aligned again.
Sorted alignments from the first and second alignments were merged together with samtools (version 1.8) followed by removal of reads aligned to the mitochondrial genome using a custom perl script (version v5.18.1).
Duplicated reads were removed with Picard tools' Mark Duplicates (version 1.94).
Reads aligning to the blacklisted regions (generated by Alan Boyle and Anshul Kundaje as part of the ENCODE and modENCODE's projects) were removed by using bedtools intersect (version v2.27.1).
Final mapping results were processed using HOMER's makeTagDirectory followed by makeMultiWigHub.pl programs (version v4.10.4) to produce normalized bigwig genome browser tracks.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig. Normalized tracks.

growth_protocol: In vitro culture.

extract_protocol:
ChiP was performed as described below. pMIG-, BATF- transduced CD8+ T cells (1x106 cells/ml in culture media) were fixed with 1% formaldehyde at room temperature for 10 minutes with nutation. To quench the fixation, 0.5 ml 2.5M glycine was added per 10 ml, the cells were incubated on ice for 5 minutes, and washed twice with cold PBS. Fixed cells were transferred to low-binding tubes with 1 ml cold PBS and spun down at 2000rpm at 4℃ for 10 min. Cells were pelleted, snap-frozen with liquid nitrogen, and stored at -80℃ until further processing. To isolate nuclei, cell pellets were thawed on ice and the pellets were resuspended in 1 ml Bioruptor lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X-100), and incubated for 10 min at 4℃ with nutation. After centrifugation at 1700g at 4℃ for 5min, the resulting nuclear pellets were washed twice with washing buffer (10 mM Tris-HCl pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). The pellets were resuspended in 100 l shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA. 1% SDS), and sonicated using a Bioruptor in 1.5 ml bioruptor tubes (10 cycles, 30 seconds on, 30 seconds off). After sonication, the supernatants were transferred to 1.5 ml lo-binding tubes, and insoluble debris was removed by centrifugation at 20,000g. Pellets were resuspended in 100 µl shearing buffer, and 9 volumes of conversion buffer (10 mM Tris-HCl pH 7.5, 255 mM NaCl, 1 mM EDTA, 0.55 mM EGTA. 0.11% Na Deoxycholate, 0.11 % Triton X-100) was added. Chromatin was precleared with washed protein A and protein G Dynabeads for 1 hour, and the chromatin concentration was measured by qubit. 5% of chromatin was saved as input, and chromatin was incubated with anti-BATF (Brookwood Biomedical, USA) or anti-IRF4 (clone D9P5H, Cell Signaling Technology, USA) antibodies and protein A and protein G Dynabeads overnight at 4℃ with rotation. The following day, bead-bound chromatin was washed twice with RIPA buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS, 0.5% Na Deoxycholate), and then with high salt buffer (50 mM Tris-HCl pH8.0, 500 mM NaCl, 1 mM EDTA, 1% NP40, 0.1% SDS), LiCl buffer (50 mM Tris-HCl pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% NP40, 1% Na Deoxycholate), and TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). Chromatin was eluted with 100 l elution buffer (100 mM NaHCO3, 1% SDS, 1 mg/ml RNase A) twice for 30 minutes at 37℃ using a 1000 rpm shaking heat block. 5 l proteinase K (20 mg/ml, Ambion, USA) and 8 l of 5 M NaCl were added to the eluted DNA, and samples were incubated at 65℃ with shaking (1,200 rpm) for de-crosslinking. DNA was purified with Zymo ChIP DNA Clean & Concentrator (Zymo Research, USA).
Libraries were prepared using NEB Ultra II library Prep kits (NEB) following the manufacturer’s instructions
ChiP-seq, 2x50- cycle paired-end sequencing (illumina)

tag: chip antibody


title: C2_plate 4A_E14.5_PA

description:
BSSE-QGF-59987
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_IGF2BP1KO_rep2


title: HEK293T_mock_PCBP2KO_rep2


title: B2_plate 4A_E14.5_PA

description:
BSSE-QGF-59986
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG-aBATF_rep2 ChIPseq

value: anti-BATF (Brookwood Biomedical, USA)


title: HEK293T_mock_PCBP2KO_rep1


title: F2_plate 4A_E14.5_PA

description:
BSSE-QGF-59990
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Pancreas


title: HEK293T_mock_Parental_rep7

description: mock-transfected mRNA-seq in HEK293T (Parental)

value: Parental


title: D1_plate 4A_E14.5_PA

description:
BSSE-QGF-59980
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG input_rep1 ChIPseq


title: C1_plate 4A_E14.5_PA

description:
BSSE-QGF-59979
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG-aIRF4_rep1 ChIPseq

value: anti-IRF4 (clone D9P5H, Cell Signaling Technology, USA)


title: pMIG-aIRF4_rep2 ChIPseq


title: HEK293T_mock_Parental_rep5


title: F12_plate 1A_E8.5_foregut

description:
BSSE-QGF-59974
processed data file: E8.5-E14.5_AllCells_genes.csv

source_name: Foregut endoderm

value: Foregut


title: E12_plate 1A_E8.5_foregut

description:
BSSE-QGF-59973
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF input_rep2 ChIPseq


title: milnacipran-administered defeated group 2

city: Tsukuba

first: Kazunori

last: Sasaki

address: 1-1-1 Tennodai

country: Japan

institute: AIST

description: Milnacipran treatment

hyb_protocol: Following fragmentation, 100 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing: Data analysis was performed using the expression console and Visualization and Integrated Discovery (DAVID) v6.8 (National Institute of Allergy and Infectious Diseases (NIAID).

label: biotin

source_name: Mice hippocampus administered with milnacipran defeated group 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: BALB/c mice were housed for 4 mice per cage during acclimation under a constant condition (temperature, 23 ± 2 °C; humidity, 55% ± 10%; 12-h light/dark cycle with lights on at 8:00) with food (CE-2, CLEA Japan, Inc., Tokyo, Japan) and water ad libitum.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The kososan extract or milnacipran was suspended in distilled water. Kososan extract (1.0 g/kg), milnacipran (60 mg/kg) or distilled water was administered orally once daily for 26 days.

value: BALB/c

value: Brain (hippocampus)

tag: social condition

value: defeated

value: milnacipran


title: pMIG-aBATF_rep1 ChIPseq


title: milnacipran-administered defeated group 1

description: Milnacipran treatment

source_name: Mice hippocampus administered with milnacipran defeated group 1


title: HEK293T_mock_Parental_rep6

value: mock transfection


title: water-administered defeated group 2

description: Negative control

source_name: Mice hippocampus administered with water defeated group 2

value: water


title: kososan-administered defeated group 2

description: kososan treatment

source_name: Mice hippocampus administered with kososan defeated group 2

value: undefeated

value: kososan


title: kososan-administered defeated group 1

description: kososan treatment

source_name: Mice hippocampus administered with kososan defeated group 1


title: water-administered undefeated group 1

description: Positive Control

source_name: Mice hippocampus administered with water undefeated group 1


title: water-administered undefeated group 2

description: Positive Control

source_name: Mice hippocampus administered with water undefeated group 2


title: HEK293T_mock_Parental_rep4


title: water-administered defeated group 1

description: Negative control

source_name: Mice hippocampus administered with water defeated group 1


title: D12_plate 1A_E8.5_foregut

description:
BSSE-QGF-59972
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_Parental_rep3


title: HEK293T_mock_Parental_rep2


title: B12_plate 1A_E8.5_foregut

description:
BSSE-QGF-59970
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF-aBATF_rep2 ChIPseq


title: BATF input_rep1 ChIPseq


title: BATF-aIRF4_rep2 ChIPseq


title: H11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59968
processed data file: E8.5-E14.5_AllCells_genes.csv


title: HEK293T_mock_Parental_rep1


title: BATF-aIRF4_rep1 ChIPseq


title: BATF-aBATF_rep1 ChIPseq


title: F11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59966
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-184_rep2

description: hsa-miR-184-transfected mRNA-seq in HepG2

source_name: liver hepatocellular carcinoma

value: hsa-miR-184 transfection


title: miR-184_rep1


title: G11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59967
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG CAR TILs_rep2 ATACseq

data_processing:
Paired raw reads were aligned to the Mus Musculus genome (version mm10) using bowtie (version 1.0.0 and -X 2000 -m 1 --best --strata -tryhard -S –fr).
Unmapped reads were cleaned for adapter sequence and clipped 1 base pair with Trim_galore (version 0.4.3) before being aligned again (-X 2500 -m 1 --best --strata -tryhard -S --fr -v 3 -e 100).
Sorted alignments from the first and second alignments were merged together with samtools (version 1.8), followed by removal of reads aligned to the mitochondrial genome using a custom perl script (version v5.18.1).
Duplicated reads were removed with Picard tools' Mark Duplicates (version 1.94).
Reads aligning to the blacklisted regions (generated by Alan Boyle and Anshul Kundaje as part of the ENCODE and modENCODE's projects) were removed by using bedtools intersect (version v2.27.1).
Tn5 footprint was obtained using Jiang Li's Tn5_bed9bp_full.pl perl script: basically takes the strand orientation or a given read to take the first or last 9 base pairs for forward and reverse reads respectively.
For quality control purposes, we used Xi Chen's Fragment_length_density_plot.py python script: this program plots the histogram of the distances among the mapped usable reads.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated files of Voom-normalized Tn5 insertions on the log2 scale

extract_protocol:
50,000 GFP+CD8+Thy1.1+ CAR T cells  were sorted from B16-huCD19 tumors or or 50,000 CD8+ T cells were sorted from in vitro cultured CD8 T cells.
ATAC-seq libraries were prepared following the omni-ATAC protocol with minor modification6. 50,000 cells were collected by sorting and washed twice with cold-PBS at 600g for 5 minutes. Cell pellets were resuspended in 50 µl ATAC-lysis buffer (10 mM 1 M Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin ), and incubated on ice for 3 minutes, after which 1 ml washing buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1%Tween 20) was added, and the cells were spun down at 1000g for 10 minutes at 4℃ . The supernatant was removed carefully, and the nuclei were resuspended in 50 µl of transposition mix (25l of TD buffer [20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide], 2.5 l of 2 µM transposase 16.5 l PBS, 0.5l 1% digitonin, 0.5l 10% Tween-20, 5l water) and incubated at 37℃ for 30 minutes. DNA was purified with a Qiagen MinElute Kit (Qiagen).
ATAC-seq, 2x50- cycle paired-end sequencing (illumina)

value: Tumor

value: 8 days after Transfer


title: miR-31-5p_rep2

description: hsa-miR-31-5p-transfected mRNA-seq in HepG2

value: hsa-miR-31-5p transfection


title: E11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59965
processed data file: E8.5-E14.5_AllCells_genes.csv


title: C12_plate 1A_E8.5_foregut

description:
BSSE-QGF-59971
processed data file: E8.5-E14.5_AllCells_genes.csv


title: pMIG CAR TILs_rep1 ATACseq

value: Batf transduced


title: miR-31-5p_rep1


title: D11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59964
processed data file: E8.5-E14.5_AllCells_genes.csv


title: BATF CAR TILS_rep1 ATACseq

value: pMIG transduced


title: BATF CAR TILs_rep2 ATACseq


title: C11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59963
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-147b_rep2

description: hsa-miR-147b-transfected mRNA-seq in HepG2

value: hsa-miR-147b transfection


title: miR-147b_rep1


title: pMIG CD8 T cells_rep2 ATACseq

value: Spleen

value: 5 days after in vitro culture


title: B11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59962
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: miR-187-3p_rep2

description: hsa-miR-187-3p-transfected mRNA-seq in HepG2

value: hsa-miR-187-3p transfection


title: A11_plate 1A_E8.5_foregut

description:
BSSE-QGF-59961
processed data file: E8.5-E14.5_AllCells_genes.csv


title: RD-15-132 Eplilepsy treated patient

type: genomic

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

description: FCD I

hyb_protocol: The DNA is bisulfite-converted using the EZ-96 DNA Methylation Kit from Zymo Research.  After bisulfite conversion, the DNA then undergoes restoration using the Illumina Infinium HD FFPE DNA Restore Kit. The DNA then undergoes a whole-genome overnight amplification.  The amplified DNA is then enzymatically fragmented using end-point fragmentation.  The DNA is then isolated and precipitated in isopropanol and re-suspended in Illumina RA1 buffer.  The re-suspended DNA is then denatured at 95⁰C, and the resulting single-stranded DNA is dispensed directly onto the Illumina Array for hybridization.  The DNA hybridizes with the array overnight in an oven at 48⁰C.  After hybridization, the BeadChips are then washed with Illumina PB1 buffer to remove any unhybridized and non-specifically hybridized DNA.

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: minfi- R package was used to analyze the data. Arrays were combined to 450K probes using minfi combineArray() function. Data was preprocessed, quantile normalized and poor probes were removed based on mean detection Pvalues per sample.

label: Cy5 and Cy3

source_name: Brain

label_protocol: Standard Illumina Protocol

extract_protocol: Using a Promega Maxwell 16 instrument, DNA was extracted from formalin-fixed paraffin-embedded (FFPE) specimens with the Maxwell® 16 FFPE Plus LEV DNA Purification Kit

value: Brain


title: RD-15-131 Eplilepsy treated patient

description: FCD I


title: RD-15-625 Eplilepsy treated patient

description: FCD I


title: miR-187-3p_rep1


title: BATF CD8 T cells_rep2 ATACseq


title: RD-15-130 Eplilepsy treated patient

description: FCD I


title: H10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59960
processed data file: E8.5-E14.5_AllCells_genes.csv


title: G10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59959
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-7-5p_rep2

description: hsa-miR-7-5p-transfected mRNA-seq in HepG2

value: hsa-miR-7-5p transfection


title: BATF CD8 T cells_rep1 ATACseq


title: RD-15-129 Eplilepsy treated patient

description: FCD I


title: s_GV_Mov10l1_KO_So821_r1.PE [Bisulfite-Seq]

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Raw bisulfite sequencing reads were trimmed with following parameters:   bbduk.sh -Xmx20G threads=12 in1=$ {FILE}_1.txt.gz in2=$ {FILE}_2.txt.gz out1=$ {BASE}_1.trim.txt.gz out2=$ {BASE}_2.trim.txt.gz outs=$ {BASE}_s.trim.txt.gz stats=$ {BASE}.stats literal=AGATCGGAAGAGC overwrite=t ktrim=r k=12 rcomp=t mink=8 hdist=1 minoverlap=8 minlength=25 minlength=50 tbo
Trimmed reads were mapped to the genome using Bismark:  bismark --non_directional --parallel 4 --unmapped --output_dir . --temp_dir .--genome_folder $ {BISMARK_INDEX } -1 $ {FILE}_1.trim.txt.gz -2 $ {FILE}_2.trim.txt.gz $ {FILE}_s.trim.txt.gz
In order to remove alignments arising from excessive PCR amplification, alignments were deduplicated using deduplicate_bismark script. Methylation information for individual cytosines were then extracted with bismark_methylation_extractor.
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: Coverage genome browser tracks files: bigWig format generated in a non-stranded mode
Supplementary_files_format_and_content: CpG methylation calls genome browser tracks files: bigWig format, each peak marks percentage of methylation on individual CpG position

organism: Mesocricetus auratus

source_name: GV oocyte_Mov10l1 KO

growth_protocol: Fully-grown germinal vesicle-intact oocytes were collected from ovaries by puncturing antral follicles with a syringe needle in M2 medium (Sigma) containing 0.2 mM 3-isobutyl-1-methyl-xanthine (Sigma) to prevent resumption of meiosis.

extract_protocol:
10 fully grown GV oocytes (equivalent of 40 haploid genomes, 80 single-stranded DNAs after bisulfite conversion) were directly subjected to EZ DNA Methylation-Direct kit (Zymo Research) for bisulfite conversion with the following modifications: samples were digested with proteinase K at 50°C for 35 min and bisulfite conversion was performed as follows: 98°C 6 min, 64℃ 30 min, 95°C 1 min, 64°C 90 min, 95°C 1 min, 64°C 90 min.
Bisulfite sequencing DNA libraries were prepared using EpiNext Post-Bisulfite DNA library Preparation kit according to the manufacturer´s protocol with 22 PCR cycles used for amplification. Final DNA libraries were sequenced by 250 nt pair-end sequenced on the Illumina NovaSeq6000 platform.

treatment_protocol: Production of knock-out hamsters was carried out using an in vivo electroporation CRISPR/Cas9 system. Pairs of sgRNAs were designed to cleave Mov10l1 genomic sequence in intron 19 (sequence of DNA targets: 5´- gggtatcacatgacttgggg – 3´; 5´- ggtgttgggatcatagtgggg – 3´) and intron 20 (sequence of DNA targets: 5´-tctccactcttccatgtgggg - 3´; 5´- taccattacatttgtcagggg - 3´) in order to delete exon 20. Five animals were born of which one did not exhibit any deletion, two appeared homozygous for the deletion and were not used for breeding, and one male and one female showed modification of one allele. The male was fertile but did not transmit the allele (# of progeny = 13; 8 males + 5 females) while the female (#4) transmitted the allele into progeny (# of progeny = 10; 3 males + 4 females carried the mutant allele) when bred to a wild type animal. Subsequent breeding of heterozygotes for two generations with wild type outbred animals was performed in order to minimize possible off-targeting and inbreeding effects when heterozygotes were mated to produce homozygotes.

value: Mov10l1 KO

value: GV oocyte

value: 11 weeks


title: F10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59958
processed data file: E8.5-E14.5_AllCells_genes.csv

data_processing:
Libraries were sequenced SR75 on an Illumina NextSeq 500 system (75 cycles High Output v2.5 kit).
Reads were uniquely aligned to mouse reference genome (GRCm38) using STAR (v.2.5.3.a).
Comparison of expression level between samples had been conducted with cufflinks.cuffdiff (2.2.1).
The gene expression matrices were generated employing GeneCounts as quantification type in STAR.
The gtf and fasta formatted annotations for mouse were retrieved from GENCODE project (released version v26, primary assembly).
Scater Package was used for filtering. All samples with at least 2000 genes and 500000 counts (visualised in log10 scale) were retained. These thresholds were calculated based on the average of library size and number of expressed genes in each library. We also applied a gene filtering step (transcript > 2 in at least 2 cells). Scran package was used for data normalization. For data visualization, we used t-SNE plot with a perplexity value of 20% of the total number of cells. Clustering of the cells was computed using SC3 package. Pseudo-time reconstruction was performed using Tscan package.
Genome_build: UCSC mm 10 (GRCm38)
Supplementary_files_format_and_content: E8.5-E14.5_AllCells_genes.csv: Comma-separated text file including a table of genes (rows) x cells (columns) showing logcounts (normalized counts) per single cell. Processed data file includes only samples that passed the QC check.

extract_protocol:
GFP+ ventral foregut (E8.5), pancreatic (E10.5, E14.5), and hepatic progenitors (E10.5) were dissected from Tg(Prox1-EGFP) transgenic mice and dissociated into single-cell suspensions. GFP+ cells were FACS sorted at 4°C using an Aria II or Aria III flow cytometer (BD) into 96-well plates containing cell lysis buffer. Plates containing FACS-sorted cells were then frozen and kept at -80°C until shipment to ETH Genomic Facility for library preparation and sequencing.
Libraries were prepared for sequencing using Nextera XT DNA library preparation kit (Illumina) protocols.


title: Input_2

first: Louise

last: Matheson

address: Babraham Research Campus

department: Laboratory of Lymphocyte Signalling and Development

institute: The Babraham Institute

description:
CLIPper_peaks_m6A_eCLIP_2.bed
Pureclip_xl_sites_m6A_eCLIP_2.bed

data_processing:
Library strategy: m6A-eCLIP
Data were analysed by Eclipse Bioinnovations according to their standard m6A-eCLIP analysis pipeline (https://eclipsebio.com/wp-content/uploads/2021/06/eclipsebio_data_analysis_review_m6A-eCLIP.pdf)
Briefly: The first 10 bases of each read (which comprise a UMI) were trimmed using umi_tools, followed by trimming of poor quality and adaptor sequences from the 3' end of the reads using cutadapt
Reads mapping to repetitive elements were filtered out, and the remaining reads mapped to the mouse GRCm38 genome build using STAR. PCR duplicates were removed using umi_tools
Clusters of reads (peaks of m6A modification) were identified using CLIPper, and log2 fold change relative to the corresponding input sample calculated
Single nucleotide resolution crosslink sites with enrichment relative to input were also indentified using PureCLIP
Genome_build: GRCm38
Supplementary_files_format_and_content: CLIPper_peaks_m6A_eCLIP_1/2.bed: BED file for each replicate containing locations of all m6A clusters identified by CLIPper. The 'name' column (4) contains -log10(p value), and the 'score' column (5) contains the log2-fold enrichment relative to the corresponding input sample.
Supplementary_files_format_and_content: Pureclip_xl_sites_m6A_eCLIP_1/2.bed: BED file for each replicate containing locations of all m6A crosslink sites identified by PureCLIP. The 'name' column (4) contains score calculated by the PureCLIP algorithm, and the 'score' column (5) contains the fold enrichment at the read start coordinate relative to the corresponding input sample.
Supplementary_files_format_and_content: sgRNA_library_counts.txt: tab-delimited text file containing counts for each guide RNA across all samples. Names of guide RNAs comprise the target gene and sequence.

source_name: Naïve B cells cultured in iGB conditions

extract_protocol:
On day 8 total B cell and plasma cells were separated from 40LB cells by negative selection with H-2Kd-biotin antibody and anti-biotin microbeads (Miltenyi 130-090-485) following the manufacturer’s instructions. Total RNA was prepared with a kit (Zymo R2050) following the manufacturer’s instructions.
Total RNA samples were sent to Eclipse Bioinnovations, where they performed polyA RNA isolation, fragmentation, crosslinking of an m6A antibody, immunoprecipitation and library preparation according to their standard m6A-eCLIP protocol (https://eclipsebio.com/product/m6a-eclip-kit/ ; based on doi: 10.1007/978-1-4939-7204-3_14).

treatment_protocol: In vitro induced germinal centre B cell cultures (iGB) involve a 3T3 feeder layer expressing mouse CD40L and human BAFF (40LB cells). The 40LB feeder cell line was maintained in supplemented Roswell Park Memorial Institute 1640 (RPMI-1640) media with 10% FBS and 1x GlutaMAX™ (Gibco: 35050061). Irradiated (~120Gγ) 40LB cells were seeded at 80x10^3 cells per well in a 12-well plate in supplemented RPMI-1640 media. The next day, naïve B cells were isolated with a B cell isolation kit (Miltenyi Biotec: 130-090-862) and 30x10^3 were cultured on the irradiated 40LB cells with IL-4 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol Thermo Scientific™: 31350-010, 100 units/ml penicillin, and 100μg/ml streptomycin Thermo Scientific™: 15140, 10ng/ml mIL-4 PeproTech 214-14). On day4 B cells were reseeded on freshly irradiated 40LB cells with IL-21 in supplemented RPMI-1640 media (final: 10% FBS, 1x GlutaMAX™, 50µM 2-mercaptoethanol, 100 units/ml penicillin, and 100μg/ml streptomycin, 10ng/ml mIL-21 PeproTech 210-21).

value: WT

tag: days in culture

tag: flow cytometry marker

value: Unsorted


title: pMIG CD8 T cells_rep1 ATACseq

tag: age


title: RD-15-128 Eplilepsy treated patient

description: FCD I


title: miR-499a-5p_rep2

description: hsa-miR-499a-5p-transfected mRNA-seq in HepG2

value: hsa-miR-499a-5p transfection


title: RD-14-16 Eplilepsy treated patient

description: FCD I


title: s_GV_Mov10l1_HET_So811_r1.PE [Bisulfite-Seq]

source_name: GV oocyte_Mov10l1 HET

value: Mov10l1 HET

value: 29 weeks


title: E10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59957
processed data file: E8.5-E14.5_AllCells_genes.csv


title: m6A_eCLIP_2


title: miR-499a-5p_rep1


title: s_GV_Mov10l1_WT_So812_r1.PE [Bisulfite-Seq]

source_name: GV oocyte_WT


title: D10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59956
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Input_1

description:
CLIPper_peaks_m6A_eCLIP_1.bed
Pureclip_xl_sites_m6A_eCLIP_1.bed


title: RD-15-126 Eplilepsy treated patient

description: FCD I


title: RD-15-127 Eplilepsy treated patient

description: FCD I


title: miR-216b-5p_rep2

description: hsa-miR-216b-5p-transfected mRNA-seq in HepG2

value: hsa-miR-216b-5p transfection


title: C10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59955
processed data file: E8.5-E14.5_AllCells_genes.csv


title: s_GV_Mov10l_KO_F77_r3.SE

data_processing:
Raw RNA-seq reads were mapped to golden hamster (mesAur1) and the newest golden hamster (PRJDB10770) genomes using STAR 2.7.3a with following parameters:  STAR --readFilesIn $ {FILE}.fastq.gz --genomeDir $ {GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix $ {FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 5000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --outFilterMultimapScoreRange 0 --outFilterMismatchNoverLmax 0.05 --sjdbScore 2  For analysis of expression of protein coding genes, reads were mapped with maximum of 20 multimapping alignments allowed.
Reads mapped to mesAur1 were counted over exon features annotated by Ensembl (release 99) using featureCounts v2.0.0:  featureCounts -a $ {FILE}.gtf -o $ {FILE}.counts.txt $ {FILE}.bam -T 12 -F GTF -M -O –fraction
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE}.bam -bg -split -g chrNameLength.txt > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: MesAur1.0
Supplementary_files_format_and_content: ensembl.99.MesAur1.0.Piwil3_Tex101.from_RefSeq.raw_counts.oocyte.txt: tab delimited table with counts of reads over exon coordinats from Ensembl Release 99 .gtf file with added Piwil3 and Tex101 annotated by RefSeq; samples are in columns, genes in rows
Supplementary_files_format_and_content: Coverage genome browser tracks files: bigWig format generated in a non-stranded mode, not normalized for library size

extract_protocol:
Total RNA was extracted from 6 – 12 fully-grown oocytes using Arcturus Picopure RNA isolation kit (Thermo Fisher) according to the manufacturer’s protocol.
RNA-seq libraries were generated using the Ovation RNA-Seq system V2 (NuGEN) followed by Ovation Ultralow Library system (DR Multiplex System, NuGEN) according to the manufacturer’s protocol. cDNA fragmentation was performed on Bioruptor sonication device (Diagenode) with 30 s ON, 30 s OFF for 18 cycles on low intensity. Libraries were amplified by 9 cycles of PCR and sequenced by 100 nt single-end reading using the Illumina NovaSeq6000 platform.

value: 36 weeks


title: m6A_eCLIP_1

extract_protocol:
On day 8 total B cells and plasma cells were separated from 40LB cells by negative selection with H-2Kd-biotin antibody and anti-biotin microbeads (Miltenyi 130-090-485) following the manufacturer’s instructions. Total RNA was prepared with a kit (Zymo R2050) following the manufacturer’s instructions.
Total RNA samples were sent to Eclipse Bioinnovations, where they performed polyA RNA isolation, fragmentation, crosslinking of an m6A antibody, immunoprecipitation and library preparation according to their standard m6A-eCLIP protocol (https://eclipsebio.com/product/m6a-eclip-kit/ ; based on doi: 10.1007/978-1-4939-7204-3_14).


title: RD-14-13 Eplilepsy treated patient

description: FCD I


title: RD-14-07 Eplilepsy treated patient

description: FCD I


title: B10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59954
processed data file: E8.5-E14.5_AllCells_genes.csv


title: miR-223-3p_rep2

description: hsa-miR-223-3p-transfected mRNA-seq in HepG2

value: hsa-miR-223-3p transfection


title: s_GV_Mov10l_KO_F52_r1.SE

value: 45 weeks


title: RD-14-09 Eplilepsy treated patient

description: FCD I


title: miR-216b-5p_rep1


title: s_GV_Mov10l_KO_F59_r2.SE

value: 40 weeks


title: miR-223-3p_rep1


title: Homozygous Scn2agt/gt sample2

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

description:
countMatrix.txt
HOM_2

data_processing:
FastQC v.0.11.3 was used to observe read quality
Fastp was used to remove adapter sequences
STAR was used to map reads to the genome of mus_musculus
FeatureCounts on stranded mode was used to count reads mapping to genes
edgeR was used to identify differentially expressed genes
biomaRt was used to annotate genes using Ensembl annotations
Genome_build: GRCm38
Supplementary_files_format_and_content: count matrix of raw counts in tab delimited format

source_name: neuron

growth_protocol: Mice were same-sex housed in mixed-genotype groups groups (3-5 mice per cage) on vented cage racks with 1/8" Bed-o-cobb bedding.  and > 8 g of nesting material as enrichment (shredded paper, crinkle-cut paper, and/or cotton nestles) on a 12hr light cycle. Food (2018S Teklad from Envigo) and reverse osmosis water were given ad-lib. Heterozygous (HET, Scn2aWT/gt) mice were used as breeding pairs to obtain homozygous (HOM, Scn2agt/gt) mice and WT littermates for study.

extract_protocol:
RNA isolated using Rnasy Qiagen kit
Tru-Seq stranded Illumina protocol, per manufacturer instructions
paired-end

treatment_protocol: To understand how a severe NaV1.2 deficiency affects the function of neurons, we utilized a NaV1.2-deficient mouse model generated using a gene-trap (gt) approach.

value: Homozygous Scn2agt/gt (Scn2a-deficient)

tag: cell type

value: neuron


title: H9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59952
processed data file: E8.5-E14.5_AllCells_genes.csv

value: Foregut


title: Homozygous Scn2agt/gt sample3

description:
countMatrix.txt
HOM_3


title: A10_plate 1A_E8.5_foregut

description:
BSSE-QGF-59953
processed data file: E8.5-E14.5_AllCells_genes.csv


title: Homozygous Scn2agt/gt sample4

description:
countMatrix.txt
HOM_4


title: s_GV_Mov10l_HET_F63_r3.SE


title: RD-14-05 Eplilepsy treated patient

description: FCD I

value: Brain


title: s_GV_Mov10l_HET_F58_r2.SE


title: RD-14-11 Eplilepsy treated patient

description: FCD I


title: miR-196a-5p_rep2

description: hsa-miR-196a-5p-transfected mRNA-seq in HepG2

value: hsa-miR-196a-5p transfection


title: Homozygous Scn2agt/gt sample1

description:
countMatrix.txt
HOM_1


title: RD-14-03 Eplilepsy treated patient

description: FCD I


title: miR-145-5p_rep2

description: hsa-miR-145-5p-transfected mRNA-seq in HepG2

value: hsa-miR-145-5p transfection


title: RD-14-01 Eplilepsy treated patient

description: FCD I


title: miR-196a-5p_rep1


title: s_GV_Mov10l_WT_So777_r2.SE

value: GV oocyte

value: 17 weeks


title: G9_plate 1A_E8.5_foregut

description:
BSSE-QGF-59951
processed data file: E8.5-E14.5_AllCells_genes.csv