title: wt_2_up

data_processing:
Guides were then quantified with the published ScreenProcessing (https://github.com/mhorlbeck/ScreenProcessing) method and phenotypes generated with an in-house processing pipeline, iAnalyzer (https://github.com/goodarzilab/iAnalyzer). iAnalyzer relies on fitting a generalized linear model to each gene. Coefficients from this GLM were z-score normalized to the negative control guides and finally the largest coefficients were analyzed as potential hits. For the comparison of gene phenotypes between the two cell lines, the DESeq2 ratio of ratios test was used.
Assembly: The analysis does not involve a standard genome build but utilizes a custom reference composed of synthesized oligonucleotide sequences tailored to the experimental design.
Supplementary files format and content: Tab-separated files with raw read counts for each sgRNA.
Library strategy: CRISPR screen

source_name: Reference, High expression

growth_protocol: The Jurkat cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco).

extract_protocol:
On Day 11, cells were collected and sorted using the BD FACSAria™ Fusion cell sorter. Sorting criteria included the top and bottom 25% of cells based on the ratio of GFP to mCherry fluorescence intensity. The CRISPRi screen was conducted under two conditions using cells with either a reference RORC element - GFP reporter or a mutated 77-AG RORC element - GFP reporter, with each condition tested in duplicate.
After sorting, genomic DNA was harvested (Macherey-Nagel Midi Prep kit) and amplified using NEB Next Ultra II Q5 master mix and primers containing TruSeq Indexes for NGS analysis. Sample libraries were prepared and sequenced on a HiSeq 4000.
The library preparation for CRISPRi/a-v2 involves amplifying sgRNA sequences, which are then sequenced on an Illumina HiSeq 4000 system. The library includes TruSeq indices for demultiplexing post-sequencing. The PCR amplification incorporates Illumina adapters and a unique sample index, facilitating the sequencing of pooled samples in a single sequencing run with a phiX spike-in of 10% to enhance sequence diversity and read accuracy.

treatment_protocol: The sgRNA library was transduced into Jurkat cells with a multiplicity of infection (MOI) of less than 0.3, resulting in approximately 30% BFP+ cells. After transduction, the cells were transplanted at an average coverage of 500x (Day 0). Selection with 1 µg/mL puromycin was conducted at 48 and 72 hours post-transduction to enrich for positively transduced cells.

value: Jurkat

tag: egfp reporter

value: native RORC switch

tag: gfp level

value: high


title: 4T1, Day4, single cell 469

status: Public on Jul 01 2024

type: SRA

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

country: China

institute: Tsinghua university

library_source: transcriptomic single cell

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

tag: host

value: Female BALB/c mice

tag: cell line

tag: cell type

value: metastatic tumor cells


title: H59

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: 1 Shields Ave.

department: Plant Sciences

country: USA

institute: University of California, Davis

library_source: transcriptomic

data_processing:
Quality and adapter trimming was done with Trimmomatic v0.39 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 v2.3.4.1 was used to map the reads to a combined transcriptome of tomato and the pathogen of interest with the following settings: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py  v0.913
Assembly: Pistacia vera c.v. Kerman (BioProject PRJNA1049825)
Supplementary files format and content: Read_counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

molecule: total RNA

organism: Pistacia vera

source_name: pistachio hull (pericarp)

extract_protocol:
At each time point pistachio fruit hull (exocarp) and shell (endocarp), and kernel (seed) tissue were separated, and flash frozen with liquid nitrogen. Frozen tissue was lysed using a Retsch® Mixer Mill MM 400. A total of 1 gram of ground material was used during for RNA extraction as described in Blanco-Ulate et al., 2013. Purity and concentration of the extracted RNA were determined with the use of the NanoDrop One Spectrophotometer (Thermo Scientific), followed by a more precise concentration measurement with the Qubit 3 (Invitrogen). The integrity of the RNA was confirmed via agarose gel electrophoresis.
cDNA libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v.2 (Illumina, CA) from isolated RNA. Each library was barcoded and analyzed with the High Sensitivity DNA Analysis Kit for the Agilent 2100 Bioanalyzer (Agilent Technologies, CA). Libraries were sequenced as paired-end 150-bp reads on an Illumina Hiseq X Ten platform by IDseq

tag: tissue

value: pistachio hull (pericarp)

tag: sampling (growing_degree_days,_c)

tag: cultivar

value: Kerman


title: wt_2_down

city: San Francisco

first: Hani

last: Goodarzi

department: Biochemistry and Biophysics

institute: UCSF

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: Reference, Low expression

value: low


title: H58


title: EC_UP_13258_0_GC

type: RNA

city: Stirling

first: James

last: Timmons

address: Bridge of Allan

country: United Kingdom

institute: Augur Precision Medicine LTD

description: Human Enterohinal Cortex

hyb_protocol: Standard

scan_protocol: Standard

data_processing:
CEL files were GC correct and then processed using IRON (default settings) using custom CDFs. The full length transcript probe-set based data are provided along with the custom CDF. A 2SD filter was utilised to distinguish protein coding gene expression above background
GC_Miami_CD_Brain_CDF_cv_0.3_i_8_Grch38_gencode43_transcript,binary.cdf
CDF probes were aligned to genome reference Grch38 and transcriptome reference gencode43
Log 2 values generated using IRON from GC corrected CEL files. No filter has been applied for detected above background. Critically, a filter of 2SD should be applied to remove non expressed protein coding genes, if this data is to be used for any global analysis

label: biotin

source_name: Human Enterohinal Cortex

label_protocol: Affymetrix WT kit

extract_protocol: Trizol

treatment_protocol: Confirmation of lack of histopathology evidence for dementia at the source NIH funded brain banks (Harvard, Los Angeles, University of Miami, Mount Sinai, University of Pittsburgh and Minnesota University)

tag: treatment group and time

value: Free of Dementia Histopathology

tag: age

tag: Sex

value: M

tag: biobank

value: UP


title: EC_UP_13237_0_GC

description: Human Enterohinal Cortex


title: Functional_screen_bin4_r1_DNA

data_processing:
Adaptor Removal: Used cutadapt to trim adapter sequences specific to vector-based primers.
Reference Preparation: Created and indexed a reference sequence database of oligonucleotides. Generated a GTF annotation from oligonucleotide sequences.
Mapping: Aligned reads to the reference using bwa mem, ensuring at least 80% of reads aligned exactly once. Sorted and indexed aligned reads using samtools.
Read Counting, Normalization and Analysis: Counted reads aligning to genes with featureCounts, followed by replication correlation assessment. Normalized read counts using median of ratios method to correct for library size variations. Calculated correlations between read counts across sorting bins to rank candidate RNA switches.
Assembly: The analysis does not involve a standard genome build but utilizes a custom reference composed of synthesized oligonucleotide sequences tailored to the experimental design.
Supplementary files format and content: Tab-separated files with raw read counts for each oligonucleotide.
Library strategy: MPRA

source_name: Replicate 1, Bin 4, Functional screen

growth_protocol: The HEK293 cells (ATCC CRL-3216) were cultured in DMEM high-glucose medium supplemented with 10% FBS, L-glutamine (4 mM), sodium pyruvate (1 mM), penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco).

extract_protocol:
Following FACS sorting of cells based on eGFP/mCherry expression, genomic DNA was extracted from pelleted cells using the NucleoSpin Blood kit from Macherey Nagel, chosen based on cell quantity.
Libraries were constructed using Illumina-compatible primers designed for Addgene #213963 plasmid, incorporating staggered regions to ensure cluster diversity. PCR amplification was performed using NEBNext Ultra II Q5 Master Mix, followed by product purification with the Select-a-Size DNA Clean & Concentrator MagBead Kit (Zymo Research). Quality was verified using Agilent TapeStation or BioAnalyzer.
The libraries were sequenced to achieve a depth of >20 million reads per sample, with each sample uniquely barcoded using a combination of i5 and i7 indexes. This setup ensures sufficient coverage and identification of each library component in the pooled sample.

treatment_protocol: Cells were infected with lentivirus containing a plasmid library. Post-infection, cells underwent puromycin selection until recovery with >90% viability. The infection rate was kept below 30% as estimated by the fraction of mCherry-positive cells.


title: wt_1_up


title: EC_UP_13298_0_GC

description: Human Enterohinal Cortex


title: K3

source_name: pistachio kernel (seed)

value: pistachio kernel (seed)


title: EC_UP_13232_1_GC

description: Human Enterohinal Cortex


title: H57


title: wt_1_down


title: 4T1, Day4, single cell 466


title: 4T1, Day4, single cell 472


title: 4T1, Day4, single cell 467


title: EC_UP_13231_0_GC

description: Human Enterohinal Cortex


title: H54


title: Functional_screen_bin1_r1_DNA

source_name: Replicate 1, Bin 1, Functional screen


title: 121_2_up

source_name: 77-GA, High expression

value: 77-GA mutation


title: 4T1, Day4, single cell 465


title: H53.2


title: EC_UP_13221_0_GC

description: Human Enterohinal Cortex


title: 121_2_down

source_name: 77-GA, Low expression


title: 4T1, Day4, single cell 468


title: 4T1, Day4, single cell 464


title: EC_UP_13170_0_GC

description: Human Enterohinal Cortex


title: H52


title: EC_UP_13152_0_GC

description: Human Enterohinal Cortex


title: H51


title: 121_1_down


title: 121_1_up


title: H55


title: 4T1, Day4, single cell 463


title: 4T1, Day4, single cell 462


title: EC_UP_13140_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 461


title: 293T-oMK122_2

description: RORC RNA switch DMS reactivity

data_processing:
something
Library strategy: DMS-MaPseq

growth_protocol: All the cell lines were maintained in DMEM with 10% FBS and antibiotics under humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Trizol and 10 ug total RNA was used for downstream Dnase treatment and reverse transcription
Targeted PCR was perforem with Phusion to add illumina sequencing adaptors

value: human embryonic kidney cells

tag: genotype

value: RORC mutant reporter 122 expression

tag: treatment


title: 293T-oMK122_1

description: RORC RNA switch DMS reactivity


title: 4T1, Day4, single cell 460


title: EC_UP_13122_0_GC

description: Human Enterohinal Cortex

value: F


title: H48


title: 293T-oMK118_2

description: RORC RNA switch DMS reactivity

value: RORC mutant reporter 118 expression


title: H47


title: 4T1, Day4, single cell 459


title: EC_UP_13114_0_GC

description: Human Enterohinal Cortex


title: H46


title: K31


title: EC_UP_13112_0_GC

description: Human Enterohinal Cortex


title: 293T-oMK118_1

description: RORC RNA switch DMS reactivity


title: EC_UP_13108_0_GC

description: Human Enterohinal Cortex


title: H44


title: ZR-75-1_RORCWT_DMSO_r2

description:
RORC RNA switch DMS reactivity
DMS-MaPseq_RORC_reporter_cell_lines.csv

treatment_protocol: Cells were treated with NMDI14 (50 uM), NSC95397 (10 uM) and G749 (2 uM) for 24 hours.

value: breast cancer

value: RORCWT reproter expression

value: DMSO


title: EC_UP_13138_0_GC

description: Human Enterohinal Cortex


title: ZR-75-1_RORCWT_DMSO_r1


title: 4T1, Day4, single cell 456

value: Female BALB/c mice


title: H42


title: LS174T-RORCWT_r2

value: colorectal cancer


title: 4T1, Day4, single cell 455

value: metastatic tumor cells


title: EC_UP_13107_0_GC

description: Human Enterohinal Cortex


title: H43

value: pistachio hull (pericarp)

value: Kerman


title: EC_UP_13087_0_GC

description: Human Enterohinal Cortex

value: Free of Dementia Histopathology


title: H39


title: EC_UP_13085_0_GC

description: Human Enterohinal Cortex

value: M


title: LS174T-RORCWT_r1


title: 4T1, Day4, single cell 454


title: EC_UP_13082_0_GC

description: Human Enterohinal Cortex

value: UP


title: 293T-RORCWT_r2


title: 4T1, Day4, single cell 453


title: H37


title: 4T1, Day4, single cell 452


title: 293T-RORCWT_r1


title: EC_UP_13069_0_GC

description: Human Enterohinal Cortex


title: H36


title: 4T1, Day4, single cell 457


title: MCF7_RORCWT_NMDI14_r2


title: EC_UP_13068_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 451


title: MCF7_RORCWT_NMDI14_r1


title: H35


title: EC_UP_13062_0_GC

description: Human Enterohinal Cortex


title: H33


title: MCF7_RORCWT_DMSO_r1


title: 4T1, Day4, single cell 449


title: H38


title: 4T1, Day4, single cell 448


title: EC_UP_13058_1_GC

description: Human Enterohinal Cortex


title: MCF7_RORCWT_G749_r2


title: H32


title: 4T1, Day4, single cell 447


title: 4T1, Day4, single cell 446


title: H31


title: EC_UP_13048_0_GC

description: Human Enterohinal Cortex


title: EC_UP_13054_1_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 450


title: H29


title: H50


title: 4T1, Day4, single cell 445


title: H30


title: MCF7_RORCWT_NSC_r2


title: 4T1, Day4, single cell 444


title: EC_UP_13064_0_GC

description: Human Enterohinal Cortex


title: EC_UP_13032_0_GC

description: Human Enterohinal Cortex


title: MCF7_RORCWT_NSC_r1


title: EC_UP_13019_0_GC

description: Human Enterohinal Cortex


title: MCF7_RORCWT_DMSO_r2


title: H34


title: 4T1, Day4, single cell 443


title: H26.2


title: LNCaP _RORCWT_r1

source_name: LNCaP _RORCWT

value: LNCaP

value: prostate cancer


title: EC_UM_HctZZH_0_GC

description: Human Enterohinal Cortex

value: UM


title: MCF7_RORCWT_G749_r1


title: H25


title: HEPG2_RORCWT_r2

value: liver cancer


title: 4T1, Day4, single cell 441


title: EC_UM_HctZZC_0_GC

description: Human Enterohinal Cortex

value: F


title: H23


title: HEPG2_RORCWT_r1


title: EC_UM_HctZZA_1_GC

description: Human Enterohinal Cortex


title: H22


title: 4T1, Day4, single cell 439


title: 4T1, Day4, single cell 440


title: H27


title: HEPG2_ctrl_r2

description: RORC RNA switch DMS reactivity

data_processing:
Reads from multiple lanes were merged and collapsed using fastq2collapse.pl (CTK package)
UMIs were then extracted using `umi_tools extract` with --extract-method string --bc-pattern=NNNNNNNNNNN flags
cutadapt (v3.5) was used to remove the constant sequences
bwa (v0.7.17-r1188) was used to align the reads to the reference.
Aligned reads were then sorted and deduplicated using UMICollapse (with -k 1 --algo adj --merge avgqua flags)
Mutations were then counted at each position for As and Cs (common SNPs were filtered)
Assembly: hg38
Supplementary files format and content: DMS signal at each position
Library strategy: DMS-MaPseq

value: WT


title: H21


title: 4T1, Day4, single cell 438


title: HEPG2_ctrl_r1

description: RORC RNA switch DMS reactivity


title: EC_UM_HctZR_3_GC

description: Human Enterohinal Cortex


title: LNCaP _RORCWT_r2


title: LNCaP _Ctrl_r2

description: RORC RNA switch DMS reactivity

source_name: LNCaP


title: EC_UM_HctYZA_0_GC

description: Human Enterohinal Cortex


title: H19


title: EC_UP_13387_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 436


title: 4T1, Day4, single cell 442


title: 4T1, Day4, single cell 437


title: H18


title: H17


title: LNCaP _Ctrl_r1

description: RORC RNA switch DMS reactivity


title: EC_UM_HctYRA_1_GC

description: Human Enterohinal Cortex


title: LS174T_Ctrl_r2

description: RORC RNA switch DMS reactivity


title: EC_UM_HctYOA_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 435


title: H15


title: EC_UM_HctZT_0_GC

description: Human Enterohinal Cortex


title: LS174T_Ctrl_r1

description: RORC RNA switch DMS reactivity


title: EC_UM_HctYFA_0_GC

description: Human Enterohinal Cortex


title: MCF7_Ctrl_r2

description: RORC RNA switch DMS reactivity

value: breast cancer


title: 4T1, Day4, single cell 433


title: 4T1, Day4, single cell 434


title: H14


title: EC_UM_HctYDA_0_GC

description: Human Enterohinal Cortex


title: EC_UM_HctYCA_1_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 432


title: EC_UM_HctYGA_0_GC

description: Human Enterohinal Cortex


title: H12


title: 4T1, Day4, single cell 431


title: MCF7_Ctrl_r1

description: RORC RNA switch DMS reactivity


title: ZR-75-1_Ctrl_r2

description: RORC RNA switch DMS reactivity


title: H11


title: EC_UM_HctYAA_0_GC

description: Human Enterohinal Cortex


title: ZR-75-1_Ctrl_r1

description: RORC RNA switch DMS reactivity


title: H9


title: 4T1, Day4, single cell 430


title: EC_UM_Hct15HEC_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 429


title: H8


title: 4T1, Day4, single cell 428


title: EC_UM_Hct15HBJ_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 427


title: H7


title: H5


title: H13


title: 4T1, Day4, single cell 426


title: EC_UM_Hct15HBF_0_GC

description: Human Enterohinal Cortex


title: EC_UM_Hct15HBD_0_GC

description: Human Enterohinal Cortex


title: H3


title: H2


title: 4T1, Day4, single cell 425


title: EC_UM_Hct15HBA_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 424


title: EC_UM_Hct15HAU_0_GC

description: Human Enterohinal Cortex


title: H1


title: 4T1, Day4, single cell 423


title: T003BK, treatment, CD3+ cells, blood and kidney, GEX, ADT, HTO

city: Hamburg

first: Darius

last: Schaub

state: Hamburg

address: Billhorner Kanalstraße 22

department: Center for Biomedical AI

country: Germany

institute: University Medical Center Hamburg

description: polyA RNA, Antibody-derived oligonucleotide (ADT), Hashtag-derived oligonucleotide (HTO)

library_source: other

data_processing:
The Cell Ranger software (v5.0.1 and v7.1.0, 10x Genomics) was used to demultiplex cellular barcodes and map reads to the reference genome GRCh38-3.0.0 and GRCh38-2020-A. All quality control and preprocessing steps were performed in Seurat (v4.0.4) and R (v4.1.1). The Seurat demultiplexing function HTODemux was used to demultiplex the hash-tag samples.
Assembly: refdata-cellranger-GRCh38-3.0.0 and refdata-gex-GRCh38-2020-A
Supplementary files format and content: barcodes.tsv.gz:  list of cell barcodes
Supplementary files format and content: features.tsv.gz:  list of gene IDs
Supplementary files format and content: matrix.mtx.gz:  gene expression count data (and protein count data) in Matrix Market Exchange Format
Library strategy: CITE-seq

molecule: other

source_name: Blood and Kidney

extract_protocol:
Single cell suspensions were obtained from human kidney biopsies by enzymatic digestion in RPMI 1640 medium with collagenase D at 0.4 mg/ml (Roche, 11088858001) and deoxyribonuclease I (DNase I; 10 μg/ml; Sigma-Aldrich, 10104159001) at 37°C for 30 min followed by dissociation with gentle MACS (Miltenyi Biotec). Leukocytes from blood samples were separated using Leucosep tubes (Greiner Bio-One, 10349081). Cells were stained with fluorochrome-conjugated antibodies from BioLegend and BD Biosciences, CD45 BV510 (HI30), CD3 BV785 (OKT3), CD4 BV650 (RPA-T4), CD8 APC-R700 (RPA-T8), CXCR3 Pe/Dazzle (G025H7), CCR6 PerCP-Cy5-5 (G034E3). Cells were also stained with a dead cell stain (Molecular Probes, L10119) to exclude dead cells from analysis. FACS was performed on a FACSAria Fusion cell sorter (BD Biosciences). ScRNA-seq of human samples from the kidney and peripheral blood was performed from FACS-sorted CD3 positive T cells using the Chromium Next GEM Single Cell 5' Kit v2 (10x Genomics) according to manufacturer's instructions. Libraries were sequenced aiming at 50,000 reads per cell on an Illumina NovaSeq™ (P150).
libaries were constructed according to manufacturer specifications

treatment_protocol: Ustekinumab (90 mg) in in combination with low-dose cyclophosphamide and steroids, following the RITUXVAS trial approach

value: Blood and Kidney

value: FACS-sorted CD3+ cells

tag: library type

value: mRNA+ADT+HTO

tag: cellranger version

tag: reference genome

tag: feature reference


title: 4T1, Day4, single cell 422

value: Female BALB/c mice


title: EC_UM_Hct15HAW_0_GC

description: Human Enterohinal Cortex


title: EC_UM_Hct15HAT_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 421

value: metastatic tumor cells


title: E008B, exploratory, CD3+ cells, blood, GEX

description: polyA RNA

source_name: Blood

value: Blood

value: mRNA


title: EC_UM_Hct15HAN_0_GC

description: Human Enterohinal Cortex

value: Free of Dementia Histopathology


title: E008K, exploratory, CD3+ cells, kidney, GEX

description: polyA RNA

source_name: Kidney

value: Kidney


title: 4T1, Day4, single cell 420


title: EC_UM_Hct15HBH_0_GC

description: Human Enterohinal Cortex

value: M


title: 4T1, Day4, single cell 419


title: ATAC MA32

city: South San Francisco

first: Xin

last: Luo

address: 750 Gateway Blvd

department: Research and Development

institute: Amgen Inc

description: paired single nucleus RNA + assay for transposable accessible chromatin, ATAC

data_processing:
Raw fastq files were aligned to the human GRCh38 reference genome (v) using CellRanger ARC (10x Genomics, v6.1).
ArchR (https://www.archrproject.com) was used to process the ATAC fragments and Seurat was used to process RNA.
Assembly: GRCh38
Supplementary files format and content: metadata.csv contains metainformation of all samples with cells in rows and labels in columns. For each sample, the CellRanger ARC output filtered matrix files including  barcodes.tsv, features.tsv and matrix.mtx were included as processed data files as well.

molecule: nuclear RNA

source_name: Heart

extract_protocol:
Nuclei were isolated according to 10x Genomics protocol (CG00375; Nuclei Isolation Complex Sample for ATAC GEX Sequencing RevB) and flow cytometry for 7-AAD positive nuclei was used for sorting.
Protocol CG000338 from 10x Genomics was used for Chromium Next GEM Single Cell Multiome ATAC + Gene Expression. Briefly, following nuclei isolation, permeabilization was performed, followed by transposition, GEM generation and barcoding using ChipJ (10x Genomics; PN1000234), post-GEM clean up, pre-amplification PCR, cDNA amplification, library construction, and sequencing. Gene expression and ATAC libraires were sequenced to a read depth of 50,000 and 25,000 respectively.
snRNA-Seq; snATAC-Seq

value: Heart

tag: disease state

value: ICM


title: EC_UM_Hct15HAL_0_GC

description: Human Enterohinal Cortex

value: UM


title: 4T1, Day4, single cell 418

tag: host


title: EC_UM_Hct15HAM_0_GC

description: Human Enterohinal Cortex


title: EC_UM_Hct15HAH_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 417

tag: cell line


title: ATAC MA31

value: AMI


title: EC_UM_Hct15HAG_0_GC

description: Human Enterohinal Cortex

value: F


title: ATAC MA30


title: 4T1, Day4, single cell 416

tag: cell type


title: 4T1, Day4, single cell 415


title: EC_UM_Hct15HAF_0_GC

description: Human Enterohinal Cortex


title: ATAC MA27

tag: tissue


title: ATAC MA28

value: NICM


title: EC_MS_167692_1_GC

description: Human Enterohinal Cortex

value: MS


title: EC_MS_167691_1_GC

description: Human Enterohinal Cortex


title: ATAC MA26

value: Donor


title: 4T1, Day4, single cell 413


title: ATAC MA33


title: 4T1, Day4, single cell 458


title: ATAC MA25


title: EC_LA_5694_0_GC

description: Human Enterohinal Cortex

value: LA


title: EC_LA_5165_0_GC

description: Human Enterohinal Cortex


title: EC_LA_5302_0_GC

description: Human Enterohinal Cortex


title: ATAC MA23


title: 4T1, Day4, single cell 410


title: 4T1, Day4, single cell 409


title: 4T1, Day4, single cell 412


title: EC_LA_4770_0_GC

description: Human Enterohinal Cortex


title: ATAC MA24


title: 4T1, Day4, single cell 411


title: EC_LA_4543_0_GC

description: Human Enterohinal Cortex


title: EC_LA_4528_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 407


title: ATAC MA19


title: ATAC MA20


title: 4T1, Day4, single cell 408


title: DIV4-GDNF4_S17_R5

city: Chicago

first: Oscar

last: Carballo-Molina

state: Illinois

address: 303 East Superior Street, Lurie 11-231

department: Simpson Querrey Institute for Bionanotechnology

institute: Northwestern University

data_processing:
The quality of reads, in FASTQ format, was evaluated using FastQC.  Reads were trimmed to remove Illumina adapters from the 3’ ends using cutadapt.  Trimmed reads were aligned to the homo sapiens genome (GRCh38) using STAR. Read counts for each gene were calculated using htseq-count in conjunction with a gene annotation file for GRCh38 obtained from Ensembl (http://useast.ensembl.org/index.html).  Normalization and differential expression were calculated using DESeq2 that employs the Wald test.  The cutoff for determining significantly differentially expressed genes was an FDR-adjusted p-value less than 0.05 using the Benjamini-Hochberg method.
Assembly: GRCh38 (human)
Supplementary files format and content: Excell file contains raw counts for each sample.

source_name: IPSCs

growth_protocol: Cells were cultured according to manufacter (Cellular Dynamics)  instructions.

extract_protocol:
Total RNA Purification was performed using TRIzol-extracted samples using the Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010).
Illumina TruSeq mRNA Sample Preparation Kits

treatment_protocol: human induced pluripotent stem cells-derived dopaminergic neurons were seeded on coverslips coated with GDNF mimetic nanostructures for 4 days. Media was changed one time 24 hours post-seeding.

value: IPSCs

value: iCell DopaNeurons (Cellular Dynamics)

value: dopaminergic neurons


title: 4T1, Day4, single cell 406

value: Female BALB/c mice

value: metastatic tumor cells


title: ATAC MA22


title: 4T1, Day4, single cell 414


title: EC_LA_4448_0_GC

description: Human Enterohinal Cortex

value: Free of Dementia Histopathology


title: 4T1, Day4, single cell 405


title: EC_LA_3839_0_GC

description: Human Enterohinal Cortex


title: EC_LA_3637_0_GC

description: Human Enterohinal Cortex


title: ATAC MA14


title: ATAC MA13


title: DIV4-GDNF1_S14_R2


title: EC_LA_3629_0_GC

description: Human Enterohinal Cortex


title: ATAC MA11


title: 4T1, Day4, single cell 404


title: DIV4-GDNF3_S16_R4


title: ATAC MA10


title: 4T1, Day4, single cell 403


title: DIV4-GDNF2_S15_R3


title: EC_LA_3548_0_GC

description: Human Enterohinal Cortex


title: DIV4-CT3_S12_R2


title: 4T1, Day4, single cell 402


title: 4T1, Day4, single cell 401


title: DIV4-CT4_S13_R2


title: ATAC MA9


title: EC_LA_3545_0_GC

description: Human Enterohinal Cortex


title: ATAC MA8


title: EC_LA_3529_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 400


title: ATAC MA7


title: DIV4-CT2_S11_R2


title: DIV4-CT1_S10_R2


title: ATAC MA6


title: 4T1, Day4, single cell 398


title: EC_HA_S16953_0_GC

description: Human Enterohinal Cortex

value: HA


title: ATAC MA5


title: 4T1, Day4, single cell 397


title: H7 bottom quartile

city: Portland

first: Braden

last: Lobingier

state: Oregon

address: 3181 SW Sam Jackson Park Road, Mail Code L-334

department: Chemical Physiology and Biochemistry

institute: Oregon Health and Sciences University

data_processing:
Using open-source custom software (CRISPR_FACS_v1.6 Kampmann et al., Nat Protoc, 2014), raw sequencing reads from next-generation sequencing were cropped and aligned to reference files (containing guide sequences of the sublibrary transduced in the respective sample) using Bowtie to ascertain sgRNA counts in each sample.
Assembly: hCRISPRi-v2-top5 (Horlbeck t al., eLife, 2016)
Supplementary files format and content: XCOUNTS files are lists of counts of sgRNAs found within each library, only searching the sgRNA sublibrary transfected in that sample.
Library strategy: CRISPRi screen

source_name: cell line

growth_protocol: HEK293 FLP-In and HEK293T-LentiX cells were obtained from ThermoFisher and Takara Bio, respectively and grown at 37C, 5% CO2 in Dulbecco's Modified Eagle Medium (4.5 g/L glucose and L-glutamine, no pyruvate), with 10% fetal bovine serum supplemented. Stable expression of pUBC-SSF-DOR-APEX2 was acheived with FRT mediated recombination into HEK293 FLP-In cells and hygromycin selection. This stable cell line was then lentivirally transduced with dCas-KRAB-BFP. Fluorescence activated cell sorting on a BD FACS Aria II was utilized to sort for cells expressing dCas using BFP expression and clonal populations were expanded and tested for efficacious dCas9 dependent knockdown.

extract_protocol: Sorted cells were pellet and frozen. Once all samples were collected, the QIAamp DNA Blood Maxi kit was used to extract genomic DNA from samples. PCR amplification of integraded guide sequences was performed with Q5 high-fidelity polymerase and barcoding primers for 27 cycles, purified on QIAquick PCR purification columns, and loaded onto 20% polyacrylamide/TBE gels for excision and extraction of an ~270 bp band. Extracted DNA was quantified, pooled, then sequenced on an Illumina HiSeq-4000 with custom primers.

treatment_protocol: Libraries of single guide RNAs (hCRISPRi-v2-top5, Horlbeck t al., eLife, 2016) targetting the entire human genome split across seven sublibraries (H1-H7) were separately transfected into HEK293T-LentiX cells for production of libraries of virus. Virus was used to transduce cells stably expressing pUBC-SSF-DOR-APEX2 & dCas9-KRAB-BFP at a low MOI (~0.2) such that each cell did not recieve more than one guide. Two days after transduction, cells were selected for integration of virus with 0.75 ug/ml puromycin for 3 days and grown for a total of 8 days before assaying. Day of assay, cells were stimulated with 10 uM DADLE for 90 minutes before lifting with TrypLE and performing the APEX/AUR intact cell assay (cells were resuspended in PBS, 100 uM Amplex UltraRed added and cells incubated for 15 minutes. PBS/4% (final) BSA/50 uM (final) H2O2 was added to initiate reaction and after one minute 1 mM sodium azide added to quench. Cells were washed twice with PBS/2% BSA before resuspending in PBS/1% BSA). Reacted cells were then subject to fluorescence activated cell sorting on a BD FACS Aria II, where they were binned based on fluorescence in the APC channel, and top (T) and bottom (B) quartiles were sorted into separate tubes.

value: cell line

value: HEK293 FLP In


title: EC_HA_S13278_0_GC

description: Human Enterohinal Cortex

value: M


title: GEX MA33

value: Heart


title: EC_HA_S13581_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 396


title: H6 top quartile


title: H6 bottom quartile


title: 4T1, Day4, single cell 395


title: EC_HA_S12202_0_GC

description: Human Enterohinal Cortex


title: GEX MA32

value: ICM


title: H5 top quartile


title: EC_HA_S10886_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 394


title: 4T1, Day4, single cell 399


title: H5 bottom quartile


title: EC_HA_S10626_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 393


title: EC_HA_S08106_1_GC

description: Human Enterohinal Cortex


title: EC_HA_S17689_0_GC

description: Human Enterohinal Cortex


title: H4 top quartile


title: GEX MA30


title: GEX MA28


title: 4T1, Day4, single cell 392


title: H7 top quartile


title: EC_HA_S05716_0_GC

description: Human Enterohinal Cortex


title: H4 bottom quartile


title: 4T1, Day4, single cell 391


title: GEX MA31

value: AMI


title: 4T1, Day4, single cell 390


title: EC_HA_S04166_0_GC

description: Human Enterohinal Cortex


title: H3 bottom quartile


title: 4T1, Day4, single cell 389


title: EC_HA_S03831_0_GC

description: Human Enterohinal Cortex


title: GEX MA26


title: GEX MA25

value: NICM


title: H2 top quartile


title: 4T1, Day4, single cell 388


title: EC_HA_S01868_0_GC

description: Human Enterohinal Cortex


title: EC_HA_S03377_0_GC

description: Human Enterohinal Cortex


title: EC_HA_S01069_0_GC

description: Human Enterohinal Cortex


title: 4T1, Day4, single cell 386


title: H1 top quartile


title: H1 bottom quartile


title: GEX MA22


title: KO Clone #69, 4-OHT positive (RNA)

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
For each sample, fastq files from two runs were combined
Fastq files were mapped to GRCh38 using STAR
Read counts were generated using featureCounts
Read count normalization was performed using edgeR
Assembly: GRCh38
Supplementary files format and content: Table of normalized featurecounts of RNA-seq data

source_name: BJ

growth_protocol: BJ cells were cultured in DMEM (Invitrogen) supplemented with 20% Medium 199 (Gibco), 10% fetal bovine serum (Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco).

extract_protocol:
RNA was isolated using the miRNeasy Mini kit (Qiagen) and gDNA contamination was removed with on-column DNase digestion.
Sequencing libraries were generated with the Stranded Total RNA Library Prep Kit (Illumina).

treatment_protocol: Cells were treated with 100 nM (Z)-4-Hydroxytamoxifen (sigma).

value: BJ

value: skin fibroblast

value: BJ-HRAS SNORA13 KO

value: (Z)-4-Hydroxytamoxifen treatment for 7 days


title: H3 top quartile


title: GEX MA27


title: GEX MA19


title: 4T1, Day4, single cell 387


title: Skin Neutral_3 rep3

city: Zhengzhou

first: Yongzhou

last: Li

address: No. 28, Gangwan Road, Guancheng District

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

data_processing:
sequence reads were obtained by filtering out reads containing adapters, poly-N sequences, and low-quality reads. Transcriptome analysis involved mapping the clean reads to a reference genome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030704535.1/)
Gene expression levels were calculated by fragments per kilobase of transcript per million mapped reads (FPKM) values
Assembly: GCF_030704535.1
Supplementary files format and content: Tab-delimites text files include raw counts for each sample

organism: Vitis vinifera

source_name: grape skin

extract_protocol:
Store to -80 °C with skin retained.RNA extraction and subsequent sequencing were done by igenebook Biology (Wuhan, China).
RNA library were prepared for sequence using stabdard  DNBSEQ-T7 protocol

value: grape skin

value: Neutral grape

tag: Stage


title: H2 bottom quartile


title: GEX MA14


title: KO Clone #66, 4-OHT positive (RNA)


title: 4T1, Day4, single cell 383

value: Female BALB/c mice


title: Skin Neutral_3 rep1


title: Skin Neutral_3 rep2


title: GEX MA13

value: Donor


title: GEX MA23


title: WT Clone #54, 4-OHT positive (RNA)

value: BJ-HRAS WT


title: EC_HA_S07239_0_GC

description: Human Enterohinal Cortex

value: Free of Dementia Histopathology

value: HA


title: KO Clone #69, 4-OHT negative (RNA)


title: 4T1, Day4, single cell 382

value: metastatic tumor cells


title: GEX MA24


title: 4T1, Day4, single cell 385


title: 4T1, Day4, single cell 381


title: GEX MA10


title: GEX MA20


title: WT Clone #15, 4-OHT positive (RNA)


title: Skin Neutral_2 rep2


title: KO Clone #66, 4-OHT negative (RNA)


title: 4T1, Day4, single cell 384


title: 4T1, Day4, single cell 379


title: 4T1, Day4, single cell 378


title: Skin Neutral_2 rep1


title: Skin Neutral_1 rep3


title: GEX MA9


title: Skin Neutral_2 rep3


title: WT Clone #54, 4-OHT negative (RNA)


title: GEX MA8


title: GEX MA11


title: 4T1, Day4, single cell 380


title: GEX MA7


title: WT Clone #15, 4-OHT negative (RNA)


title: Skin Neutral_1 rep1


title: Skin Muscat_3 rep3

value: Muscat grape


title: B13 OI-COL1A1

city: Shenzhen

first: Peikai

last: Chen

state: GD

address: 1 Haiyuan 1st Rd, Futian District

department: Pediatric Orthopedics

institute: The University of Hong Kong - Shenzhen Hospital

description:
control group 2
B13

data_processing:
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample for all genes

source_name: OI

growth_protocol: The skeletal samples were collected from patients after operations, with approval from IRB in HKU-Shenzhen Hospital and consents from the patients and their proxy.

extract_protocol:
Cells were lysised using Trizol (Invitrogen) and RNA was extracted according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment is applied.

tag: gender

value: Male

value: Left tibia


title: GEX MA6

value: Heart


title: 4T1, Day4, single cell 376


title: 4T1, Day4, single cell 375


title: GEX MA5


title: Skin Muscat_3 rep2


title: B10 OI-FKBP10

description:
FKBP10 group
B10

value: Right femur


title: B11 OI-FKBP10

description:
FKBP10 group
B11

value: Female

value: Right proximal femur


title: Skin Neutral_1 rep2


title: B2 control-2

description:
control group 1
B2

source_name: Polydactyly

value: Right thumb


title: Normal cells patient 5

city: Crawley

first: Andrew

middle: William

last: Stevenson

state: Western Australia

address: Room 112b, Curnow Building, Hackett Drive Carpark Entrance 2, UWA

department: School of Biomedical Sciences

country: Australia

institute: University of Western Australia

description:
primary skin cells
SAM2

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.7.5 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. The Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline was used to generate the sequence data. The data generated here meet the AGRF quality standards. 2.20.0.422 pipeline was used to generate the sequence data.
QC of raw reads was performed using FastQC (Version 0.11.3) and reads of poor quality trimmed using fastp software
Raw RNA sequences were aligned to the Human GRCh38.p102 reference genome13 using STAR read aligner (Version 2.7)
BAM files representing the aligned sequences were generated using SAMtools (Version 1.9)
Principal Component Analysis (PCA) and hierarchical clustering methods were performed to explore sample similarity using the rlog transformed raw read counts. Differential gene expression analysis was performed using DESeq2 (Version 1.24.0) on R (Version 3.6.1).
Assembly: Human GRCh38.p102
Supplementary files format and content: csv files with raw abundance counts

source_name: skin

growth_protocol: 3mm punch biopsies were taken from the forearm scar site the attendant physician. Tissue was transported to the lab where it was placed in a petri dish and sliced into three equal sized potions. Pieces of the biopsy were then placed dermis side down in a T-25 (25 cm2) (Greiner Bio-One, Germany) culture flask without any media, and a drop of 100% foetal bovine serum (FBS) added to the surface of each piece. They were then cultured in DMEM with 10% FBS and 5% pen/strep until ready for transfection.

extract_protocol:
RNA was prepared using the RNeasy mini kit (Cat. No. 74104, QIAGEN, Netherlands), as per manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Knockdown of WNT4 using siRNA was carried out using the FlexiTube GeneSolution siRNA system (QIAGEN, Netherlands) for WNT4 (Cat. No. 1027416)

value: skin

value: fibroblasts

value: WT

value: normal skin culture


title: Normal cells patient 6

description:
primary skin cells
SUM2


title: 4T1, Day4, single cell 372

value: Female BALB/c mice


title: 4T1, Day4, single cell 373


title: Skin Muscat_2 rep3

value: grape skin


title: Normal cells patient 4

description:
primary skin cells
JD2


title: 4T1, Day4, single cell 377


title: B1 control-1

description:
control group 1
B1


title: 4T1, Day4, single cell 371


title: Skin Muscat_2 rep2


title: Normal cells patient 3

description:
primary skin cells
JC2


title: 4T1, Day4, single cell 370


title: Skin Muscat_2 rep1


title: Unaffected wrist fibroblasts from dupuytren patient 4

description:
primary skin cells
D9


title: HPSC,Input1

city: Guangzhou

first: Feifei

state: Guangdong

address: Guangzhou Higher Education Mega Center, Panyu District

institute: South China University of Technology

data_processing:
ChIP-Seq reads were mapped to GRCz10 zebrafish genome by Bowtie2 (v.2.5.0) with very-sensitive configuration. The uniquely aligned fragments with MAPQ ≥ 30 were extracted using SAMtools (v.1.9). Duplicates were removed by Picard tools MarkDuplicates (https://broadinstitute.github.io/picard/, v.2.27.4). ChIP-seq peaks were called using MACS2 with parameters “-f BMAPE -q 0.01”.
Peaks were first called in individual replicates. Then reads from different replicates were merged, and peak calling was performed with merged reads. Repeated peaks were then taken as those called from the merged reads that overlapped with those called in all replicates. Signal tracks were built using the bdgcmp sub-command of MACS2 with the fold enrichment over control (FE) mode. Enhancers were defined as H3K4me3 ChIP-seq peaks that not overlap with 6kb region centered on transcriptional startsites.
Assembly: GRCz10
Supplementary files format and content: bigWig,narrowPeak(except for Input sample)

organism: Danio rerio

source_name: hematopoietic stem cell

extract_protocol:
The cells were cross-linked with a final concentration of 1% formaldehyde followed by quenching with glycine.
The cells were cross-linked with a final concentration of 1% formaldehyde and lysed with lysis buffer. Nuclei was sonicated to fragments about 300 - 500 bp. Dynabeads Protein A was incubated with antibody for 2-3 hours. The fragmented chromatin was transferred to the bead-antibody complex tubes and rotated at 4°C overnight. The beads were washed once with low salt buffer (10mM Tris-HCl pH7.5, 250mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, Cocktail proteinase inhibitor) and twice with high salt buffer (10mM Tris-HCl pH7.5, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, Cocktail proteinase inhibitor).After crosslink reversal, library was constructed using NEBNext Ultra II DNA Library Prep Kit and sequenced using an Illumina sequencing platform.

value: hematopoietic stem cell

tag: chip antibody


title: 4T1, Day4, single cell 369


title: HPSC,H3K4me3,ChIP,rep2,3m


title: Dupuytrens fibroblasts patient 4

description:
primary skin cells
D8


title: 4T1, Day4, single cell 368


title: HPSC,H3K4me3,ChIP,rep1,3m


title: Skin Muscat_1 rep1


title: Skin Muscat_1 rep2


title: Skin Muscat_1 rep3


title: Dupuytrens fibroblasts patient 3

description:
primary skin cells
D6


title: 4T1, Day4, single cell 367


title: 4T1, Day4, single cell 366


title: Unaffected wrist fibroblasts from dupuytren patient 3

description:
primary skin cells
D7


title: HPSC,rep3,RNA-seq,3month

data_processing:
The library is evaluated by FastQC. Readswith mean quality score less than orequal to 30 are removed. Raw reads were trimmed and removed for adapter sequences by fatsp(v.0.23.2) withpaired-end default parameters. Extremely short fragment with length less than or equal to 30bp were also removed.
After filtering, high-quality reads were aligned to GRCz10 zebrafish genome using HISAT2 with default parameters.
FeatureCounts wasused to quantify gene expression and obtain reads count. Fold changes in gene transcription levels were estimated using DESeq2.Enrichment analysis of gene function was performed in the Metascape platform.
Assembly: GRCz10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
Briefly, ∼10 ng of total RNA for each sample was utilized for first-strand cDNA reverse transcription in a 30 μl RT buffer containing SuperScript II RTase (100 U), RNase inhibitor (10 U), dNTP mix (10 mM each), SS III first-strand buffer (1×), DTT (5 mM), betaine (1 M), MgCl2 (6 mM) and TSO (1 μM).
The RNA library was prepared using TruePrep DNA Library Prep Kit V2 for Illumina

tag: time

value: flow cytometry


title: Unaffected wrist fibroblasts from dupuytren patient 2

description:
primary skin cells
D4


title: Japanese quail, Liver, 16v, Sample 4

city: Glasgow

first: Sayantan

last: Sur

address: University of Glasgow, Vet School, Garscube Campus, Bearsden Road

department: School of Biodiversity, One Health & Veterinary Medicine

institute: University of Glasgow

description:
Liv 108
LivExpressedGenesTranscripts.csv

data_processing:
Raw reads were demultiplexed and basealled using guppy basecaller
Porechop was used to trim adapters
Filtlong used to select long reads (>25 reads)
Minimap2 used to align reads to Mus musculus genome (GCRm39)
Transcript expression levels generated using Salmon
Assembly: GCF_016699485.2
Supplementary files format and content: Comma Separated Values Files with expressed gene transcripts for each sample

organism: Coturnix japonica

source_name: Liver tissue

extract_protocol:
RNA was extracted using the Qiagen RNEasy plus mini-kit
RNA Libraries were constructed using the PCR_cDNA sequencing barcoding kit (SQK-PCB109, Oxford Nanopore) as per manufacturers instructions

value: Liver tissue

value: Long 16v photoperiod


title: HPSC,rep2,RNA-seq,3month


title: 4T1, Day4, single cell 365

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: metastatic tumor cells


title: Japanese quail, Liver, 16v, Sample 3

description:
Liv 100
LivExpressedGenesTranscripts.csv


title: Dupuytrens fibroblasts patient 2

description:
primary skin cells
D3


title: HPSC,rep1,RNA-seq,3month


title: 4T1, Day4, single cell 364


title: Unaffected wrist fibroblasts from dupuytren patient 1

description:
primary skin cells
D2


title: 4T1, Day4, single cell 363


title: Japanese quail, Liver, 16v, Sample 1

description:
Liv 97
LivExpressedGenesTranscripts.csv


title: Dupuytrens fibroblasts patient 1

description:
primary skin cells
D1


title: Japanese quail, Liver, 12v, Sample 4

description:
Liv 78
LivExpressedGenesTranscripts.csv

value: Long 12v photoperiod


title: 4T1, Day4, single cell 362


title: HPSC,H3K27ac,ChIP,rep2,3m

data_processing:
ChIP-Seq reads were mapped to GRCz10 zebrafish genome by Bowtie2 (v.2.5.0) with very-sensitive configuration. The uniquely aligned fragments with MAPQ ≥ 30 were extracted using SAMtools (v.1.9). Duplicates were removed by Picard tools MarkDuplicates (https://broadinstitute.github.io/picard/, v.2.27.4). ChIP-seq peaks were called using MACS2 with parameters “-f BMAPE -p 0.005”.
Peaks were first called in individual replicates. Then reads from different replicates were merged, and peak calling was performed with merged reads. Repeated peaks were then taken as those called from the merged reads that overlapped with those called in all replicates. Signal tracks were built using the bdgcmp sub-command of MACS2 with the fold enrichment over control (FE) mode. Enhancers were defined as H3K27ac ChIP-seq peaks that not overlap with 6kb region centered on transcriptional startsites.
Assembly: GRCz10
Supplementary files format and content: bigWig,narrowPeak(except for Input sample)

extract_protocol:
The cells were cross-linked with a final concentration of 1% formaldehyde followed by quenching with glycine.
The cells were cross-linked with a final concentration of 1% formaldehyde and lysed with lysis buffer. Nuclei was sonicated to fragments about 300 - 500 bp. Dynabeads Protein A was incubated with antibody for 2-3 hours. The fragmented chromatin was transferred to the bead-antibody complex tubes and rotated at 4 °C overnight. The beads were washed once with low salt buffer (10mM Tris-HCl pH7.5, 250mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, Cocktail proteinase inhibitor) and twice with high salt buffer (10mM Tris-HCl pH7.5, 500mM NaCl, 1mM EDTA, 0.5mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, Cocktail proteinase inhibitor).After crosslink reversal, library was constructed using NEBNext Ultra II DNA Library Prep Kit and sequenced using an Illumina sequencing platform.


title: 4T1, Day4, single cell 361

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)


title: Normal cells patient 2

description:
primary skin cells
CRS2


title: WNT4_KO_P2 cells

description:
primary skin cells
3

value: WNT4 siRNA Knockdown


title: Normal cells patient 1

description:
primary skin cells
CK2


title: 4T1, Day4, single cell 360


title: WNT4_KO_P1 cells

description:
primary skin cells
1


title: Japanese quail, Liver, 12v, Sample 1

description:
Liv 75
LivExpressedGenesTranscripts.csv


title: CP_CYM_5

city: Singapore

first: wan Shing Brenda

last: Lam

address: MD3 #04-01 16 Medical Drive

department: Pharmacology

country: Singapore

institute: National University of Singapore Yong Loo Lin School of Medicine

description: Cisplatin with CYM5478 3

data_processing:
The RNA-sequencing library was prepared with rRNA-depleted RNA by NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, USA).
Clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina). Raw base call files from Bowtie v2.0.6 were demultiplexed with bcl2fastq v2.20, and FastQC was used for quality control.
Alignment to Rnor_6.0 (Rattus norvegicus, Norway rat, genome) was done with STAR-2.7.8a and read counts were quantified with -quantMode GeneCounts enabled. Gene read count tab-delimited files (TSV) were consolidated into a comma-delimited file (CSV) with Modern CSV v1.3.23. t iDep0.91  and DESeq2 were used for differential expression analysis, considering genes with a fold change of ± 1.5 (q-value < 0.05) as differentially expressed genes (DEGs).
Functional analysis of DEGs utilized Gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) terms through ShinyGO v0.61 (q-value < 0.05).
Gene Set Enrichment Analysis (GSEA) was performed with the GSEA software (Broad Institute), and gene symbols were converted from rat to human using the ‘’Rat_Gene_Symbol_Remapping_Human_Orthologs_MSigDB.v7.2.chip’’. Gene set permutations were performed 100,000 times to determine p-values.
Assembly: Rnor_6.0 (Rattus norvegicus, Norway rat, genome)
Supplementary files format and content: tab-delimited text files include the statistics of expression(FPKM) level of transcripts

organism: Rattus norvegicus

source_name: dorsal root ganglia

extract_protocol:
RNA was isolated from rat DRG using RNeasy Micro Kit (QIAGEN) and analyzed with NanoDrop (ThermoScientific).
libraries were generated using the rRNA-depleted RNA by NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations

treatment_protocol: Cisplatin (C2210000, Sigma) was freshly prepared before each use by dissolving in sterile saline. 3 mg/kg was administered i.p. at 2 ml/kg to the rats once a week (days 0, 7, and 14). CYM-5478 (MolPort-004-121-217, MolPort, Latvia) was prepared weekly by dissolving in 100% dimethyl sulfoxide (DMSO) at 10 mg/ml. Before each use, the DMSO stock was diluted in saline containing 0.1% Tween 20. Then 0.1 mg/ml was administered i.p. at 1 mg/kg every day.

tag: background strain

value: Sprague Dawley

value: Wild

value: Cisplatin 3 mg/kg intraperitoneally (2 mL/kg) weekly, , Day 0, 7 and 14; CYM-5478 0.1mg/kg intraperitoneally (0.1 mg/mL) daily, Day -1 to 20


title: CP_CYM_6

description: Cisplatin with CYM5478 4


title: Japanese quail, Liver, 16v, Sample 2

description:
Liv 99
LivExpressedGenesTranscripts.csv


title: CP_CYM_4

description: Cisplatin with CYM5478 2


title: Japanese quail, Liver, 8L, Sample 4

description:
Liv52
LivExpressedGenesTranscripts.csv

value: Short 8L photoperiod


title: 4T1, Day4, single cell 358


title: HPSC,Input


title: 4T1, Day4, single cell 357


title: HPSC,H3K27ac,ChIP,rep1,3m


title: CP_6

description: Cisplatin 4

value: Cisplatin 3 mg/kg intraperitoneally (2 mL/kg) weekly, Day 0, 7 and 14


title: Japanese quail, Liver, 12v, Sample 3

description:
Liv 77
LivExpressedGenesTranscripts.csv


title: 4T1, Day4, single cell 355


title: CP_4

description: Cisplatin 3


title: Japanese quail, Liver, 12v, Sample 2

description:
Liv 76
LivExpressedGenesTranscripts.csv


title: 4T1, Day4, single cell 359


title: CP_3

description: Cisplatin 2


title: Japanese quail, Liver, 8L, Sample 1

description:
Liv49
LivExpressedGenesTranscripts.csv


title: 4T1, Day4, single cell 354


title: 4T1, Day4, single cell 353


title: Japanese quail, Adipose, 16v, Sample 4

description:
Adi 104
AdiExpressedGenesTranscripts.csv

source_name: White adipose tissue

value: White adipose tissue


title: 02-07T

city: San Diego

first: Diane

middle: M

last: Simeone

address: 3855 Health Sciences Drive

institute: UCSD Health

description: 10x Genomics

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Genomics Cell Ranger software, version 5.0.1.
Assembly: hg38/GRCh38
Supplementary files format and content: raw barcodes
Supplementary files format and content: raw genes
Supplementary files format and content: raw gene-barcode matrix

source_name: Primary PDAC

extract_protocol:
Within 4-6 h of tissue acquisition, the specimen was placed in ice-cold RPMI 1640 medium (Gibco, Cat. No. 11875101). Tissue samples were washed in ice-cold phosphate-buffered saline (PBS; Corning, Cat. No. 21- 040-CM) and grossly assessed for adequacy (solid tissue component, free of large hemorrhagic or necrotic areas). Next, the tissue was manually minced with a scalpel blade and filtered through a 40 μm mesh filter (Falcon; Cat. No. 352340) to remove any excess debris or blood. The tissue was then transferred to a sterile gentleMACS C tube (Miltenyi Biotec, Cat. No. 130096334), resuspended in 3-5 mL of Miltenyi Tumor Dissociation Kit buffer (Cat. No. 130-095-929), and mechanically minced to submillimeter particles. The suspension was then digested utilizing the gentleMACS Octo Dissociator (Miltenyi Biotec, Cat. No. 130-095-937) for 25-30 min using the “37C_h_TDK_3'' program for tumor tissue. Dissociated cells were then quenched with ice-cold RPMI 1640 containing 10% fetal bovine serum (FBS; Gibco, Cat. No. 10082147) and filtered through a 40 μm mesh filter. Red blood cells were removed by treatment with 3-5 mL of ACK lysis buffer (Gibco, Cat. No. A1049201) and a subsequent washing step in RPMI 1640 with 10% FBS. Final cell counts were established with 0.4% trypan blue solution and a Countess II Automated Cell Counter (Applied Biosystems, Cat. No. A27977). The final concentration was titrated to 300-500 viable cells/μL for further analysis.
Chromium Single Cell 3′ Reagent Kits (v3)—the Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075) [for patients with prefix 02-] or the 5' kit v2 (PN-1000263) [for patients with prefix 01-], the Chromium Next GEM Chip G Single Cell Kit (PN-100120), and the i7 Multiplex Kit (PN-120262) (10x Genomics)

value: Primary PDAC

value: Treated

tag: procedure

value: EUS-Biopsy

tag: response

value: Responder

tag: Sex

value: M

tag: age


title: CP_CYM_1

description: Cisplatin with CYM5478 1

tag: genotype

tag: treatment


title: Japanese quail, Adipose, 16v, Sample 3

description:
Adi 100
AdiExpressedGenesTranscripts.csv


title: CP_1

description: Cisplatin 1


title: 02-07B

description: 10x Genomics

value: Untreated


title: V_5

description: Vehicle 4

value: Vehicle:saline containing 0.1 Tween 20 and 1% DMSO


title: Japanese quail, Adipose, 16v, Sample 2

description:
Adi 99
AdiExpressedGenesTranscripts.csv

value: Long 16v photoperiod


title: 02-06B

description: 10x Genomics

source_name: PDAC liver met

value: PDAC liver met

value: Liver-Biopsy

value: Nonresponder


title: Japanese quail, Liver, 8L, Sample 3

description:
Liv51
LivExpressedGenesTranscripts.csv

value: Liver tissue


title: 4T1, Day4, single cell 351

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 352


title: V_3

description: Vehicle 3

value: Sprague Dawley

value: Wild


title: 4T1, Day4, single cell 356


title: Japanese quail, Liver, 8L, Sample 2

description:
Liv50
LivExpressedGenesTranscripts.csv

value: Short 8L photoperiod


title: V_2

description: Vehicle 2


title: 02-02T

description: 10x Genomics

value: Primary PDAC


title: Japanese quail, Adipose, 16v, Sample 1

description:
Adi 97
AdiExpressedGenesTranscripts.csv

value: White adipose tissue


title: Japanese quail, Adipose, 12v, Sample 4

description:
Adi 78
AdiExpressedGenesTranscripts.csv

value: Long 12v photoperiod


title: 4T1, Day4, single cell 350


title: 02-02B

description: 10x Genomics

value: EUS-Biopsy


title: 4T1, Day4, single cell 349


title: Japanese quail, Adipose, 12v, Sample 3

description:
Adi 77
AdiExpressedGenesTranscripts.csv


title: 02-01TP

description: 10x Genomics

value: Treated

value: Resection

value: Responder

value: F


title: 02-01TL

description: 10x Genomics

value: PDAC liver met


title: 4T1, Day4, single cell 348


title: Severe_2

city: xi'an

first: Erliang

address: xin si street

institute: tangdu hospital

data_processing:
Cellranger standard processing
**Cell filter**  Seurat allows to easily explore QC metrics and filter cells, we can visualize gene and molecule counts, plot their relationship, and exclude cells with a clear outlier number of genes detected as potential multiplets. Followed criteria were used to filter cells:  1.gene counts 500-Inf per cell.  2.UMI counts  3. the percentage of mitochondrial genes < 25% %(customized).  4.DoubletFinder for detecting doublets.
**Cell clustering**  Cell clustering contains the following steps:  1)Normalizing the data  After removing unwanted cells from the dataset, the next step is to normalize the data. By default, we employ a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurements for each cell by the total expression.
PCA(Principal component analysis): To overcome the extensive technical noise in any single gene for scRNA-seq data, Seurat clusters cells based on their PCA scores, with each PC essentially representing a ‘metagene’ that combines information across a correlated gene set.
t-SNE (t-distributed Stochastic Neighbor Embedding) visualization: Seurat continues to use t-SNE as a powerful tool to visualize and explore these datasets. The tSNE aims to place cells with similar local neighborhoods in high-dimensional space together in low-dimensional space.
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: matrix

source_name: Severe

growth_protocol: Samples were obtained from fresh rat spinal cord tissue

extract_protocol:
The spinal cord tissue was dissected into seveal segments and the single cell suspension was obtained by enzymatic digestion. The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion , which needed to be above 85%, single cell suspensions were counted using a haemocytometer/ Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture  single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3) .The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run,150bp)

treatment_protocol: Samples were obtained from the spinal cord of rats with varying degrees of injury

value: spinal cord

tag: degree of injury

value: severe


title: Japanese quail, Adipose, 12v, Sample 1

description:
Adi 75
AdiExpressedGenesTranscripts.csv


title: Moderate _2

source_name: Moderate

value: moderate


title: V_1

description: Vehicle 1

value: Vehicle:saline containing 0.1 Tween 20 and 1% DMSO


title: 4T1, Day4, single cell 346

city: Beijing

first: Hanqiu

institute: Tsinghua university

value: Female BALB/c mice

value: metastatic tumor cells


title: Japanese quail, Adipose, 8L, Sample 4

description:
Adi52
AdiExpressedGenesTranscripts.csv


title: 02-01B

description: 10x Genomics

value: Untreated

value: Liver-Biopsy


title: 4T1, Day4, single cell 347


title: 01-06T

description: 10x Genomics

value: Nonresponder


title: Japanese quail, Adipose, 8L, Sample 3

description:
Adi51
AdiExpressedGenesTranscripts.csv

value: White adipose tissue

value: Short 8L photoperiod


title: Moderate_1


title: 4T1, Day4, single cell 345


title: 01-05B

description: 10x Genomics


title: Japanese quail, Adipose, 12v, Sample 2

description:
Adi 76
AdiExpressedGenesTranscripts.csv

value: Long 12v photoperiod


title: Mild_2

source_name: Mild

value: mild


title: 4T1, Day4, single cell 344


title: Japanese quail, Adipose, 8L, Sample 2

description:
Adi50
AdiExpressedGenesTranscripts.csv


title: 01-04B

description: 10x Genomics

source_name: PDAC peritoneal node met

value: PDAC peritoneal node met

value: PN-Biopsy

value: M


title: 4T1, Day4, single cell 343


title: Japanese quail, Adipose, 8L, Sample 1

description:
Adi49
AdiExpressedGenesTranscripts.csv


title: Severe_1


title: 01-01T

description: 10x Genomics

value: PDAC liver met

value: Treated


title: Sham_2

source_name: Sham

value: spinal cord

value: sham


title: 01-01B

description: 10x Genomics


title: Sham_1


title: 4T1, Day4, single cell 341


title: 4T1, Day4, single cell 342


title: HS360-Day0-scRNA-seq

city: Oslo

first: Mari

last: Spildrejorde

state: OSLO

address: Sognsvannsveien 9

department: Research and Innovation, Neuroscience research unit

country: Norway

institute: Oslo University Hospital

description:
Day 0", "male", "hESCs", "control
16-D0-CTRL

data_processing:
mkfastq was perfomed using standard settings. cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
cellranger-4.0.0 -count was used to generate single cell feature counts for a single library,  cellranger count  run was performed with the following arguments --expect-cells for each timepoint
cellRanger-count was used to remove and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
run cellranger aggr to aggregate multiple GEM wells from a single experiment that were analyzed by cellranger count and down stream analysis was perfomed using  R programming languages and its package  Seurat version 4
Assembly: refdata-cellranger-GRCh38 2020-A
Supplementary files format and content: Cell ranger count output: filtered count matrix, barcodes and features.

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol:
Cells were harvested using Accutase, counted and processed on the 10x Chromium controller (10x Genomics). Approximately 4200 cells were loaded per channel on the Chromium Next GEM Chip G (10x Genomics) to give an estimated recovery of 2000 cells.
The Chromium Next GEM Single Cell 3´ Library & Gel Bead Kit v3.1 (10x Genomics) and Dual Index Kit TT Set A (10x Genomics) were used to generate scRNA-seq libraries.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. Cells treated with 50-400 nM were treated from day 1 and throughout to collection day.

value: day 0, hESCs undifferentiated

value: Day 0 control


title: 9h_HS3

city: Guiyang

first: Lei

last: Gan

address: Guizhou University, Guiyang, Guizhou, People’s Republic of China

department: college of animal science

institute: Guizhou university

data_processing:
Clean reads from each sample were firstly aligned to the largemouth bass reference genome (https://www.ncbi.nlm.nih.gov/genome/?term=Largemouth+BASS) using HISAT2 (v2.1.0), and then assembled de novo into transcripts using StringTie (v1.3.3)
After removing the redundant sequences, the longest isoforms in the assembled transcripts were reserved as unigenes.
In order to identify novel lncRNAs, these reference transcripts were aligned to the largemouth bass reference genome using gffcompare (v0.10.1), and then followed by the four-steps screening process.
1) Selecting transcripts with exon number ≥ 2; 2) Selecting transcript length > 200 bp; 3) Screening LncRNAs with four computational approaches: CPC2, CNCI, Pfam and PLEK; 4) According to class code (j, i, u, o, y, x), the transcripts overlapping the exon region of the database annotation were removed.
The DE-lncRNAs were identified by comparing the TPM values between 9h_HS group and control group, and estimated by using DESeq package with a significance threshold of absolute log2 fold change > 2 and p-value < 0.05.
Assembly: HISAT2 (v2.1.0)
Supplementary files format and content: TPM value for each sample

organism: Micropterus salmoides

source_name: Intestine

growth_protocol: Largemouth bass (25.2±3.6g) was purchased from a local fish farm (Guizhou, China) and acclimated in an indoor aquaculture system of Guizhou University (Guizhou, China) for two weeks at 26.0 ± 0.5°C. During this period, this fish species was fed with commercial feed (Tongwei Feed Co., Ltd., Sichuan, China) twice daily.

extract_protocol:
Equal amounts of 3 fish intestine samples from one parallel were pooled to prepare the RNA samples for RNA-seq. Trizol reagent (Sangon Biotech, Shanghai, China) was used to isolate total RNA from fish intestine as recommended by its manufacturers’ instruction.
Sequencing libraries of total RNA were constructed using VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Vazyme Biotech, Nanjing, China).

treatment_protocol: 120 healthy fish were randomly divided into two groups, and respectively maintained at two temperatures, 26℃ and 34℃, with three parallels in each group. After 9h (determined by our pre-experiment), 9 fish samples were taken from the 26℃ group (control group) and 34°C group (9h_HS group) with 3 fish per parallel, respectively.

value: Intestine


title: 9h_HS2


title: YZ11

city: Houston

first: Xiaoping

last: Su

state: Texas

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

data_processing:
Illumina Casava1.7 software used for basecalling.
FASTQ files were analyzed for read and base quality using FastQC (Version: 0.11.9). Files that passed QC were analyzed for gene expression
Briefly, reads were aligned using STAR (Version: 2.7.10b) with default parameters to themm39 (GRCm39)reference genomeand gene expression was determined from mapped reads counted using RSEM (Version: 1.3.3)using the GENCODE (vM34) annotation ofMus musculusgenes.
Assembly: mm39 (GRCm39)
Supplementary files format and content: tab-delimited text file includes raw counts for each annotated gene for each sample

source_name: Mouse mammary tumor

growth_protocol: Trp53R172H/-, Trp53R245W/-, and Trp53-/- mice were generated via mammary gland injection of adenovirus containing Cre-recombinase (Ad-Cre). Recombination in the mammary gland results in excision of WT Trp53 cDNA sequences from the endogenous locus, resulting in mammary ductal epithelial cell-specific mutant p53 expression of Trp53R172H or Trp53R245W and biallelic loss of Trp53 (referred to as MaPR172H, MaPR245W, or MaP- from hereon)

extract_protocol:
A portion of mouse mammary tumor was homogenized using Trizol and Qiagen RNeasy Kits to isolate total RNA using a modified extraction protocol.
Bulk RNA libraries were generated and  constructed following standard Illumina protocols for RNA sequencing  on an Illumina HiSeq4000 (MaPR172H/- tumors) or Illumina NovaSeq 6000 (MaPR245W/- and MaP-/- tumors) by the the MD Anderson Cancer Center ATGC  Indexed cDNA libraries were minimally PCR amplified, pooled and sequenced.
Stranded mRNA-Seq

treatment_protocol: MaPR172H/-, MaPR245W/-, and MaP-/- mice were sacrificed upon mammary tumor burden. Portions of mammary tumors and matched metastases were flash frozen for downstream genomic analysis.

value: Mouse mammary tumor


title: 9h_HS1


title: HS360-Day13-CIT400-scRNA-seq

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
15-D13-CIT400

value: day 13, end of self-pattering stage, exposed to 400 nM citalopram

value: Day 13 400 nM citalopram


title: 4T1, Day4, single cell 339

last: Zheng

address: Haidian District

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 340


title: HS360-Day13-CIT200-scRNA-seq

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
14-D13-CIT200

value: day 13, end of self-pattering stage, exposed to 200 nM citalopram

value: Day 13 200 nM citalopram


title: YZ10

value: MaPR172H/-; Rosa26LSL-TdTomato/+


title: YZ7


title: 4T1, Day4, single cell 338


title: HS360-Day13-CIT100-scRNA-seq

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
13-D13-CIT100

value: day 13, end of self-pattering stage, exposed to 100 nM citalopram

value: Day 13 100 nM citalopram


title: Mild_1

value: mild


title: Control3


title: Control1


title: 4T1, Day4, single cell 337


title: HPSC,Input2

value: hematopoietic stem cell


title: Control2


title: HS360-Day13-CIT50-scRNA-seq

description:
Day 13", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
12-D13-CIT50

value: day 13, end of self-pattering stage, exposed to 50 nM citalopram

value: Day 13 50 nM citalopram


title: YZ4


title: 4T1, Day4, single cell 336


title: vector control strain (pSPG), 48 h old TYD culture, pooled sample

city: Samsun

first: ASLIHAN

middle: KURT

last: KIZILDOĞAN

address: ONDOKUZ MAYIS ÜNİVERSİTESİ, -

department: Agricultural Biotechnology

country: Turkey

institute: Ondokuz Mayıs University

description: pSPG

data_processing:
Firstly, we filter the low quality reads, reads with adapters and reads with unknown bases to get the clean reads. Then we map those clean reads to reference genome, followed with novel gene prediction,  SNP  &  INDEL  calling. Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations.
SOAP was used to align and filter the reads which mapped to the rRNA reference.
The  raw data  for sequencing included low quality, adapter contamination, and reads with unknown base N content, which need to be removed prior to data analysis to ensure reliable results. We use internal software for filtering, the specific steps are as follows:
1) Remove the reads containing the joints;
2) Remove the reads with unknown base N content greater than 5%;
3) Remove low-quality reads (we define reads with a quality value below 10 in the proportion of the total number of bases in the reads greater than 20% for low-quality reads).
HISATwas used to align the filtered clean reads to the genome
FirstlyBowtie2 (http://bowtie-bio.sourceforge.net/Bowtie2/index.shtml) was used to align clean reads to reference genes. The gene expression level was then calculated using theRSEM[5](official website:http://deweylab.biostat.wisc.edu/RSEM) software package
Sample correlation was done using the cor function in the R software.
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000148465.1
Supplementary files format and content: tab limited text file includes raw counts and FPKMs for each sample

organism: Streptomyces clavuligerus

source_name: vector control (pSPG) strain of Streptomyces clavuligerus NRRL3585

growth_protocol: All bacteria were grown in 100 ml of TYD cultures at 28 °C at 220 rpm for 48 h

extract_protocol:
Two ml of samples were taken from 48 h old TYD cultures of S. clavuligerus NRRL 3585, S. clavuligerus ΔadpA, S. clavuligerus pSPGadpA and S. clavuligerus pSPG and sonicated. RNA extractions were carried out using Nucleospin® RNA Kit (Macherey-Nagel GmbH & Co, Germany) according to the manufacturer's protocol.
1. rRNA removal: rRNA were removed from the total RNA;
2. RNA fragmentation: RNA molecules were fragmented into small pieces using fragmentation reagent;
3.cDNA Synthesis: First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis with/without dUTP instead of dTTP;(For stranded library, using dUTP instead of dTTP for second-strand cDNA synthesis)
4. End Repair, Add A and adapter ligation: the synthesized cDNA was subjected to end-repair and then was 3’ adenylated.
5. Adapters were ligated to the ends of these 3’ adenylated cDNA fragments;
6. PCR: cDNA fragments were amplified and the PCR products were purified with Ampure XP Beads (AGENCOURT), and dissolved in EB solution.
7. Circularization: The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) were generated as the final library;
8. Sequencing: The library was amplified with phi29 to make DNA nanoball (DNB) and the DNBs were loaded into the patterned nanoarray for PE100(or PE150) sequencing on DNBseq platform.

tag: strain

value: NRRL 3585

value: bacterial cell

value: pSPG vector control


title: YZ2

value: Mouse mammary tumor


title: 4T1, Day4, single cell 335

tag: host


title: HS360-Day13-scRNA-seq

description:
Day 13", "male", "self-patterning", "NPCs", "control
11-D13-CTRL

tag: cell line

value: day 13, end of self-pattering stage

value: Day 13 control


title: YZ3


title: AdpA overexpressed strain (pSPGadpA), 48 h old TYD culture, pooled sample

description: pSPGadpA

source_name: pSPGadpA carrying recombinant Streptomyces clavuligerus NRRL3585

tag: cell type

value: adpA overexpressed


title: HS360-Day10-CIT400-scRNA-seq

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT400", "400 nM citalopram
10-D10-CIT400

value: day 10, middle of self-pattering stage, exposed to 400 nM citalopram

value: Day 10 400 nM citalopram


title: HS360-Day10-CIT200-scRNA-seq

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT200", "200 nM citalopram
9-D10-CIT200

value: day 10, middle of self-pattering stage, exposed to 200 nM citalopram

value: Day 10 200 nM citalopram


title: 4T1, Day4, single cell 334

value: Female BALB/c mice

value: metastatic tumor cells


title: Brain fasting 24 hours

city: Lausanne

first: Federico

last: Santoni

address: Chemin du Bugnon 27

country: Switzerland

institute: CHUV

data_processing:
Data were process with Cellranger version 3.1.0 (10X Genomics)
Assembly: mm10
Supplementary files format and content: raw sequencing files are fastq file. Processed data are output from cellranger; raw barcodes, features and matrix, filtered barcodes, features and matrix

source_name: brain

extract_protocol:
Ressection of mouse brain third ventricle. Dissociation with Worthington papain (manufacturer instruction) follow by 10X single-cell RNA seq protocol with a Chromium Next GEM chip B.
Libraries prepared according to 10X guidelines (protocol CG000183 revA)

tag: tissue

value: brain

value: fasting 24 hours


title: HS360-Day10-CIT100-scRNA-seq

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT100", "100 nM citalopram
8-D10-CIT100

value: day 10, middle of self-pattering stage, exposed to 100 nM citalopram

value: Day 10 100 nM citalopram


title: YZ6

value: MaPR172H/-; Rosa26LSL-TdTomato/+


title: 4T1, Day4, single cell 333


title: wild type strain, 48 h old TYD culture, pooled sample

source_name: wild type, Streptomyces clavuligerus NRRL3585

value: NRRL 3585

value: bacterial cell

value: wild type


title: HS360-Day10-CIT50-scRNA-seq

description:
Day 10", "male", "self-patterning", "NPCs", "citalopram", "CIT50", "50 nM citalopram
7-D10-CIT50

value: day 10, middle of self-pattering stage, exposed to 50 nM citalopram

value: Day 10 50 nM citalopram


title: Brain fasting 12 hours

value: fasting 12 hours


title: HS360-Day10-scRNA-seq

description:
Day 10", "male", "self-patterning", "NPCs", "control
6-D10-CTRL

value: day 10, middle of self-pattering stage

value: Day 10 control


title: 4T1, Day4, single cell 332


title: 4T1, Day4, single cell 331


title: Input DNA fragments of HPCs with RUNX1-Y287X heterozygous mutation and transfected vector expressing WT FLI1

city: Yokohama

first: Yuki

last: Tanaka

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

description:
Input DNA fragments of HPCs with RUNX1-Y287X heterozygous mutation and transfected vector expressing wild-type FLI1 (pCW57.1-FLI1), CUT&RUN
Y287X-FLI1-HPC-input

data_processing:
*library strategy: CUT&RUN
Adapter trimming: cutadapt 3.2 with Python 3.9.2
Quality control: PRINSEQ-lite 0.20.4 with the following options, -trim_qual_left 30 -trim_qual_right 30
Genome alignment: Bowtie 2
Duplicated reads, reads mapped to the mitochondrial genome, and reads shoter than 25 bp were removed using SAMtools and command lines in Linux.
Assembly: hg38
Supplementary files format and content: MACS2 peakcalling bed files

source_name: 610B1 human iPS cells

growth_protocol: 610B1 human iPSC cells (RIKEN BRC, HPS0331) were maintained on Corning Matrigel hESC-Quantified Matrix (Corning) in mTeSRTM Plus-cGMP medium (STEMCELL Technologies Inc.) and were passaged every 6-7 days using an enzyme-free reagent, ReLeSR (STEMCELL Technologies Inc.).

extract_protocol:
CUT&RUN Assay Kit (#86652S; Cell Signaling Technologies)
DNA Library Prep Kit for Illumina Systems (ChIP-seq, CUT&RUN; Cell Signaling Technologies)

treatment_protocol: STEMdiff Hematopoietic Kit (STEMCELL Technologies Inc.) was used for in vitro hematopoietic differentiation.

value: 610B1 human iPS cells

value: hematopoietic progenitor cells

value: RUNX1-Y287X heterozygous mutation

value: Doxycycline addition


title: Brain fed

value: brain

value: fed


description:
Input DNA fragments of HPCs with RUNX1-Y287X heterozygous mutation and transfected empty vector (pCW57.1-FLI1), CUT&RUN
Y287X-mock-HPC-input


title: 4T1, Day4, single cell 330

value: Female BALB/c mice

value: metastatic tumor cells


title: 4T1, Day4, single cell 374


description:
Input DNA fragments of wild-type hematopoietic progenitor cells, CUT&RUN
WT-HPC-input

value: WT


title: HS360-Day6-CIT400-scRNA-seq

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
5-D6-CIT400

value: day 6, neural induction, exposed to 400 nM citalopram

value: Day 6 400 nM citalopram


title: RNA_T66_SD_T66S2_L

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

institute: University of Lausanne

data_processing:
Gene quantification was performed as follow for liver samples: Illumina reads were filtered using fastp to keep high quality reads and remove adapter sequences. Reads were aligned on the mouse reference genome mm10 (GRCm38) using STAR v2.7.0e with default parameters. Read counts was done by STAR using “--quantMode GeneCounts”, taking only reverse strand mapped reads. Genes with low counts (mean counts overall samples < 10) were filtered and normalization was performed with edgeR. Batch effects were corrected by ComBat.
Assembly: mm10
Supplementary files format and content: Gene expression [log2 CPM]

source_name: Liver

growth_protocol: Mice were housed under standard conditions according to the Swiss Animal Protection Act, under a 12h:12h light/dark cycle, with food accessible ad libitum at all times.

extract_protocol:
Mice were anesthetized with isoflurane prior to decapitation. Liver was rapidly dissected and flash frozen in liquid nitrogen. Frozen Liver of each individual was ground in liquid nitrogen and stored at -140°C until further use.
Total RNA was extracted using the miRNeasy kit (Qiagen; Hilden, Germany) following the manufacturer's instructions. RNA-seq libraries were prepared using 10 ng/μl of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, CA, USA). Libraries were sequenced on the Illumina HiSeq 4000 sequencer, producing >24 million mappable single-end reads.

treatment_protocol: Mice for tissue collection were divided into two experimental cohorts, sleep deprived (SD) and non-sleep deprived (controls, Ctr). After a one-week habituation to the experimental setting, at the age of 11-12 weeks, the SD mice were sleep-deprived by gentle handling for 6 hours starting at light onset (zeitgeber time ZT0-ZT6), and allowed to recover according to the tissue collection schedule.

value: Liver

tag: ztime

tag: condition

value: SD

tag: batch


title: RNA_T60_SD_T60S3_L

tag: time


title: 4T1, Day4, single cell 329


title: RNA_T6_NSD_T6N4_L

value: NSD


title: Human FLI1-binding sites in HPCs with RUNX1-Y287X heterozygous mutation and transfected vector expressing WT FLI1

description:
Human FLI1-binding sites in HPCs with RUNX1-Y287X heterozygous mutation and transfected vector expressing wild-type FLI1 (pCW57.1-FLI1), CUT&RUN
Y287X-FLI1-HPC


title: adpA deleted strain, 48 h old TYD culture, pooled sample

description: DadpA

source_name: DadpA mutant of Streptomyces clavuligerus NRRL3585

value: NRRL 3585

value: bacterial cell

value: adpA mutant


title: HS360-Day6-CIT200-scRNA-seq

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
4-D6-CIT200

value: day 6, neural induction, exposed to 200 nM citalopram

value: Day 6 200 nM citalopram


description:
Human FLI1-binding sites in HPCs with RUNX1-Y287X heterozygous mutation and transfected empty vector (pCW57.1-FLI1), CUT&RUN
Y287X-mock-HPC

value: 610B1 human iPS cells

value: hematopoietic progenitor cells

value: RUNX1-Y287X heterozygous mutation


title: HS360-Day6-CIT100-scRNA-seq

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT100", "100 nM citalopram
3-D6-CIT100

value: day 6, neural induction, exposed to 100 nM citalopram

value: Day 6 100 nM citalopram


title: RNA_T6_NSD_J76N2_L


title: 4T1, Day4, single cell 327

value: Female BALB/c mice

value: metastatic tumor cells


description:
Human FLI1-binding sites in wild-type hematopoietic progenitor cells, CUT&RUN
WT-HPC

value: WT


title: 4T1, Day4, single cell 328


title: HS360-Day6-CIT50-scRNA-seq

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT50", "50 nM citalopram
2-D6-CIT50

value: day 6, neural induction, exposed to 50 nM citalopram

value: Day 6 50 nM citalopram


title: RNA_T42_SD_T42S6_L

value: Liver

value: SD


title: HS360-Day6-scRNA-seq

description:
Day 6", "male", "neural rosettes", "neural induction
1-D6-CTRL

value: day 6, neural induction

value: Day 6 control


title: 4T1, Day4, single cell 326


title: S23_Control_Female [133_3_S23]

first: Tina

middle: Oak

last: Findley

address: 6431 Fannin Street, MSB 3.224

department: Pediatrics

institute: University of Texas Health Science Center at Houston

data_processing:
Cutadatp
Raw mRNA sequence reads were processed usingCutadatpand the bases with quality scores less than 20 were removed.
Filtered RNA-sequence reads were aligned to the human reference genome (GRCh38.102) and gene read counts were generated by STAR.
Assembly: GRCh38.102
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Blood

extract_protocol:
RNA-stabilized samples were thawed and incubated for a minimum of 2 hours at room temperature to allow for complete lysis of blood cells.
Total RNA extraction was performed using RNeasy®blood kits in accordance with themanufacturer’s protocol (Qiagen, Germantown, Maryland).

value: Blood

tag: gender

value: Female

tag: group

value: Control


title: 4T1, Day4, single cell 325


title: RNA_T36_SD_T36S1_L


title: Skin Muscat_3 rep1

first: Yongzhou

address: No. 28, Gangwan Road, Guancheng District

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

data_processing:
sequence reads were obtained by filtering out reads containing adapters, poly-N sequences, and low-quality reads. Transcriptome analysis involved mapping the clean reads to a reference genome (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030704535.1/)
Gene expression levels were calculated by fragments per kilobase of transcript per million mapped reads (FPKM) values
Assembly: GCF_030704535.1
Supplementary files format and content: Tab-delimites text files include raw counts for each sample

source_name: grape skin

extract_protocol:
Store to -80 °C with skin retained.RNA extraction and subsequent sequencing were done by igenebook Biology (Wuhan, China).
RNA library were prepared for sequence using stabdard  DNBSEQ-T7 protocol

value: grape skin

value: Muscat grape

tag: Stage


title: S22_Control_Female [62_1_S22]


title: B8 OI-COL1A2

first: Peikai

address: 1 Haiyuan 1st Rd, Futian District

institute: The University of Hong Kong - Shenzhen Hospital

description:
control group 2
B8

data_processing:
The fastq read-pairs were aligned to human reference genome using the HISAT2 aligner
The resulting SAM files were sorted and re-formatted as BAM files using SAMTOOLS (0.1.18)
The BAM files were quantified to human gene model by GENCODE (v25) using Cufflinks and HTSeq-count
Genome_build: GRCh38
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample for all genes

source_name: OI

extract_protocol:
Cells were lysised using Trizol (Invitrogen) and RNA was extracted according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Male

value: Left femur


title: HS360-Day0-RNA-seq-rep3

description:
Day 0", "male", "hESCs", "control
345-D0-CTRL-C

data_processing:
BBDuk (BBMap v. 34.56) was used to reomve and trim low-quality reads and adaptor sequences with the following configurations: ktrim=r k=23 mink=11 hdist=1 tbo tpe qtrim=r trimq=15 maq=15 minlen=36 forcetrimright=149
Reads were mapped to the human genome/transcriptome ENSEMBL GRCh38 2020-A using hisat2 v2.1.0
FeatureCounts v.1.4.6-p1 was used to count the reads mapping to the features using default configurations
Downstream normalisation and differential expression analysis was performed using R software EdgeR package v3.38.4.
Assembly: ENSEMBL GRCh38 2020-A release-98
Supplementary files format and content: Count file with data matrix with unnormalized counts for each sample. Additionaly, "cpm.csv" contains a normalized count matrix (counts per million) for all samples.

extract_protocol:
Total RNA was extracted from cultured cells using Norgen RNA/DNA purification kit or Qiagen RNeasy kit and treated with DNase according to manufacturer´s instructions.
Illumina TruSeq Stranded mRNA Library Prep kit was used to contruct the sequencing library according to manufacturer´s instructions. Libraries were sequenced on an Illumina Novaseq 6000 S1 flow cell with 100bp pair end reads.

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13.  For cells that were exposed to either 50-400 nM citalopram, fresh media with citalopram was added every day from Day 1 until collection day (Day 6, 10 and 13)

value: day 0, hESCs undifferentiated

value: Day 0 control


title: RNA_T3_NSD_T3N2_L

value: NSD


title: 4T1, Day4, single cell 324

value: Female BALB/c mice

value: metastatic tumor cells


title: RNA_T24_NSD_T0N9_L


title: S21_Control_Female [78_1_S21]


title: 4T1, Day4, single cell 323


title: HS360-Day0-RNA-seq-rep1

description:
Day 0", "male", "hESCs", "control
343-D0-CTRL-A


title: HS360-Day6-CIT400-RNA-seq-rep6

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
342-D6-CIT400-F

value: day 6, neural induction, exposed to 400 nM citalopram

value: Day 6 400 nM citalopram


title: S19_Hypoxic_Female  [260_1_S19]

value: Hypoxic


title: S20_Hypoxic_Male  [159_2_S20]


title: RNA_T24_NSD_J70N2_L

value: Liver


title: HS360-Day6-CIT400-RNA-seq-rep5

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
341-D6-CIT400-E


title: S18_Control_Female [253_2_S18]


title: HS360-Day6-CIT400-RNA-seq-rep4

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT400", "400 nM citalopram
340-D6-CIT400-D


title: 4T1, Day4, single cell 320


title: RNA_T24_NSD_T0N5_L


title: S17_Control_Female [252_1_S17]


title: S16_Hypoxic_Female  [244_3_S16]


title: RNA_T18_NSD_T18N7_L


title: HS360-Day6-CIT200-RNA-seq-rep6

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
339-D6-CIT200-F

value: day 6, neural induction, exposed to 200 nM citalopram

value: Day 6 200 nM citalopram


title: 4T1, Day4, single cell 319


title: 4T1, Day4, single cell 318


title: S15_Hypoxic_Male  [221_2_S15]

value: Blood


title: RNA_T0_NSD_T0N2_L


title: HS360-Day6-CIT200-RNA-seq-rep5

description:
Day 6", "male", "neural rosettes", "neural induction", "citalopram", "CIT200", "200 nM citalopram
338-D6-CIT200-E