title: STRT_03.H1.2c.DOXminus

tag: cell line

tag: cell type

value: Control


title: IPA_CYTO_Silv_n3

status: Public on Mar 16 2022

type: SRA

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

country: France

institute: Institut Curie

description: replicate 3

library_source: transcriptomic

data_processing:
library strategy: 3'-seq
Raw reads were trimmed to remove uninformative nucleotides due to primer sequences.
Trimmed reads of 25 bp or more were aligned on the human reference genome (hg19) using Bowtie2 (version 2.2.5) (Langmead and Salzberg 2012). Only reads with a mapping quality score (MAPQ) of 20 or more were retained (Samtools version 1.1) for downstream analysis.
Reads were then clustered along the genome using Bedtools (version 2.17.0) (Quinlan and Hall 2010), allowing a maximum distance of 50 bp and a minimum number of 5 reads per peak.
Peaks with a stretch of 6 consecutive As (or 8 As out of 9 nucleotides) within 50 bp downstream were filtered out, as they are likely due to internal priming of oligo-dT.
Genome_build: hg19
Supplementary_files_format_and_content: .bed

molecule: polyA RNA

organism: Homo sapiens

source_name: T lymphocytes_healthy donor

growth_protocol: Isolated T cells from PBMCs were cultured in RPMI (Eurobio Scientific, France) supplemented with 10% (v/v) fetal bovine serum (PAN Biotech, Germany), 2 mM L-glutamine (Eurobio Scientific, France) and maintained at 37°C in 5% CO2. They were stimulated with ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator (StemCell #10990) and IL-2 (Peprotech 200-02) for 72 hours.

extract_protocol:
For preparation of polysomal and whole cytosolic fractions, cells were incubated at 37 °C with 100 μg/mL cycloheximide in fresh medium for 5 min. Cells were then washed, scraped into ice-cold PBS supplemented with 100 μg/mL cycloheximide, centrifuged at 400g. for 5 min. The cell pellets were resuspended into 400 μL of LSB buffer (20 mM Tris, pH 7.4, 100 mM NaCl, 3 mM MgCl2, 0.5 M sucrose, 1 mM DTT, 100 U/mL RNasOUT and 100 μg/mL cylcoheximide). After homogenization, 400 μL LSB buffer supplemented with 0.5 % Triton X-100 and 0.5% sodium deoxycholate was added. Samples were incubated on ice for 30 min and centrifuged at 12,000 g for 15min at 4 °C. The lysates were then loaded onto a 5-50 % sucrose density gradient and centrifuged in an SW41 Ti rotor (Beckman) at 36,000 rpm for 2 h at 4 °C. Fractions were monitored and collected using a gradient fractionation system (Isco). RNA was extracted from the five heaviest polysomal fractions (pooled). RNA from whole or fractionated cell lysates were extracted with TRIzol Reagent (TRIzol-LS for polysomes; ThermoFischer Scientific) according to the manufacturer’s instructions, and 1 µl of GlycoBlue (ThermoFisher Scientific) was added for RNA precipitation. RNA was treated with TURBO DNase I (ThermoFisher Scientific) and quantified using a Nanodrop 2000 spectrophotometer (ThermoFischer Scientific). For sequencing, RNA samples were analyzed using an RNA 2100 Bioanalyzer (Agilent).
3’-seq libraries were prepared with QuantSeq 3’ mRNA-Seq Library Prep Kit REV for Illumina (Lexogen) using 500 ng (for polysomal or whole cytosolic RNAs) of DNase 1 treated RNA (n=3 for each condition) following manufacturer’s instructions. Purified libraries were quantified with Quant-iT Picogreen dsDNA kit (ThermoFisher Scientific) and run on Experion automated electrophoresis system (BIO-RAD). Pooled libraries were quantitated by qPCR (KAPA Library Quantification Kits Illumina Platforms, Roche), diluted to 12 pM, and subjected to single-end, 51 bp sequencing using the NovaSeq 2500 machine (Illumina).

treatment_protocol: Treatment with silvestrol (Medchmexpress HY-13251), resuspended in DMSO, was performed at a final concentration of 10 nM for 2 hours aside treatment with DMSO (control) alone for 2 hours.

tag: treatment

value: Silvestrol 2 hours

tag: extract

value: Whole Cytosol


title: wt_adgerm_batch02_rep06

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

state: CA

address: 329 sinsheimer labs

country: USA

institute: University of California at Santa Cruz

description: 20-60 gonads dissected from 1st day adult hermaphrodites.

data_processing:
Libraries were sequenced and demultiplexed at the QB3 Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.
Illumina reads were mapped to the ce10 genome and  92 ERCC spike-in sequences  (Life Technologies, #4456740) using HISAT2 (v2.2.1) and parameters: --no-unal, --no-discordant, --no-mixed.  Known exons and splice sites were extracted from an Ensembl ce10 (WS220) GTF annotation file and given to HISAT2 for read mapping. Reads were de-duplicated using Samtools (v1.10) and then counted over exons and at the gene level (same ce10 annotation) using featureCounts from the Subread package (Liao et al., 2014).
Low quality transcript profiles from PGCs and EGCs were filtered from the dataset using scuttle in R (v1.2.0) (McCarthy et al., 2017). All PGCs and EGCs were used to calculate Median Absolute Deviations (MADs) for library size, number of detected features (genes), and % of library that aligned to ERCC spike-in transcripts. Samples were considered outliers and filtered from the dataset if they had a library size >3 MADs lower than the median, or a number of detected features >3 MADs lower than the median, or a % of library that aligned to ERCC spike-in transcripts >3 MADs greater than the median.
Scaling factors to normalize raw read counts were calculated using scran in R (v1.20.1) (Lun et al., 2016) for PGCs and EGCs and using DESeq2 (v1.32.0) (Love et al., 2014) for gonads. A matrix of normalized counts for samples of PGCs and EGCs is included in this submission: pgc_egcs_countsNormalized.txt
Differentially expressed genes were identified using DESeq2 (v1.32.0) (Love et al., 2014) as those with a Benjamini Hochberg-adjusted p-value < 0.05.
Assembly: ce10
Supplementary files format and content: allsamples_rawcounts_matrix.txt is a matrix containing raw gene-level counts over exons annotated in a Ensembl ce10 (WS220) GTF file that also includes entries for 92 ERCC spike-in transcripts. Counts were generated using featureCounts from the subread package (Liao et al. 2014). pgcs_egcs_countsNormalized_matrix.txt contains normalized counts for all samples of PGCs and EGCs. adgerm_batch01_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch01".  adgerm_batch02_countsNormalized_matrix.txt contains normalized counts for adult gonad samples sequenced in "adgerm_batch02".

organism: Caenorhabditis elegans

source_name: Gonads (distal half)

growth_protocol: Animals were reared at 20˚C using standard protocols.

extract_protocol:
Single sets of 2 Primordial Germ Cells (PGCs) or 2 Early Germ Cells (EGCs) were dissected from L1 larvae or L2 larvae, respectively. PGCs and EGCs were used directly as starting material for library preparation. 20-60 gonads were dissected from 1st day adult hermaphrodites and then cut at the gonad bend. Only the distal halves were kept to exclude oocytes and several somatic gonad cells from our analysis. Gonads were vortexed in Trizol and stored at -80˚C. RNAs were then extract from those gonads using 1-bromo-3-chloropropane (Sigma #B9673), precipitated using isopropanol, pelleted by a 13,000 rcf spin for 15 minutes at 4˚C, and washed using ethanol.
Libraries were constructed according to manufacturer's recommendation. PGCs/EGCs: RNAs were converted into double-stranded cDNAs using a modified smart-seq2 protocol (Picelli et al., 2014). Illumina sequencing libraries were then prepared from those cDNAs using Illumina's Nextera XT kit. Gonads: mRNAs were isolated from total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then used to prepare Illumina sequencing libraries using the NEBNext Ultra RNA Library Prep Kit (#E7530).

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: 1st day adult hermaphrodite

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: wt_adgerm_batch02_rep05


title: ScRNA Pt1 Pre

city: Nashville

first: Young

last: Kim

state: TN

address: 2220 Pierce Ave PRB 654

institute: Vanderbilt University Medical Center

data_processing:
Samples were processed to generate single-cell gene expression profiles (scRNA-Seq) using the 10X Chromium 3’ Library and Gel Bead Kit (10X Genomics), following the manufacturer’s user guide
Illumina NovaSeq 6000 Sequencing System
Gene expression data were processed with “cellranger count” on the pre-built human reference set of 30,727 genes to generate counts matrices
Cell Ranger performed default filtering for quality control, and produced for each sample a barcodes.tsv, genes.tsv, and matrix.mts file containing counts of transcripts for each sample, such that the expression of each gene is in terms of the number of unique molecular identifiers (UMIs) tagged to cDNA molecules corresponding to that gene
These data were loaded into the R version 3.6.1 programming environment, where the publicly available Seurat package v3.0 was used to further quality-control filter cells to those with fewer than 10% mitochondrial RNA content, more than 1,500 unique UMI counts, and fewer than 15,000 unique UMI counts
Genome_build: hg38
Supplementary_files_format_and_content: Cell Ranger Output files containing matrix + gene + UMI counts
bulk RNA-seq:
Illumina Dragen RNA Pipeline
NEBNext® rRNA depletion kit was used for library preparation
Sequencing was performed at Paired End 150 bp on the Illumina NovaSeq 6000 targeting an average of 50M reads per sample
Supplementary_files_format_and_content: Tab delimited matrix table for each sample

molecule: total RNA

source_name: Head And Neck Oral Cavity Squamous Cell Carcinoma

extract_protocol:
Pre-nivolumab biopsies and post-nivolumab tumors were surgically resected from patients
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Patients were treated with nivolumab every 2 weeks for one month

tag: tissue

value: Tumor

tag: tissue type

tag: time point

value: pre


title: ScRNA Pt1 Post

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

value: post


title: Head & Neck tissue (X4090082011_D)

type: RNA

city: Dallas

first: Xiaoyu

last: Wang

state: Texas

address: ND3 200, 6001 Forest Park Rd

department: Cancer Center

institute: Ut Southwestern Medical Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was background subtracted and quantile-normalized using the MBCB algorithm, and then log-transformed (base 2).

label: biotin

source_name: Head & Neck tissues

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment in accordance the manufacturer’s protocol (QIAGEN Inc., Valencia, CA). Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Male

value: Floor of mouth

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: surgical margin pos

value: No

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Liver

value: Dead

value: Distant metastasis


title: IPA_CYTO_Silv_n2

description: replicate 2

tag: cell line

tag: treatment

value: Silvestrol 2 hours

tag: extract

value: Whole Cytosol


title: Head & Neck tissue (X4090082011_C)

value: Pyriform Sinus

value: Hypopharynx

value: no nodes

tag: lymphovascular invasion

tag: vascular invasion

value: Lung, Bone


title: STRT_01.H1.2a.DOXminus

city: Yokohama

first: Shruti

last: Bhagat

state: Kanagawa

address: W424, RIKEN Yokohama Campus, 1-7-22 Suehiro-cho, Tsurumi-ku

department: RIKEN Center for Integrative Medical Sciences

country: Japan

institute: RIKEN, Yokohama

description: STRT_H1_H9_hESC_19_BO4855_TFE_RawNormCounts_Diffexp.csv

data_processing:
The sequenced STRT raw reads were processed using the STRTprep pipeline (Krjutskov et al., Hum. Reprod. 2016) (v3dev branch commit 91a62d2 available at https://github.com/shka/STRTprep/tree/v3dev). Low-quality reads and redundant reads were excluded, and the processed nonredundant reads were aligned to hg19 human reference genome sequences, ERCC spike-in sequences and human ribosomal DNA unit (GenBank: U13369) with RefSeq transcript alignments as a guide of exon junctions. For TFE-based statistics, the mapped reads were assembled according to the alignments, and uniquely mapped reads within the first exons of the assembled transcripts were counted, as described in Töhönen et al. 2015. For gene-based statistics, uniquely mapped reads within (i) the 5’-UTR or the proximal upstream (up to 500 bp) of the RefSeq protein coding genes, and (ii) within the first 50 bp of spike-in sequences, were counted. Prior to  downstream analysis, low quality samples (or cells) were filtered out based on (i) ERCC spike-in read counts, (ii) human genome mapped / ERCC spike-in read counts (this represents the relative abundance of poly (A) transcripts), (iii) percentage of ERCC spike-in 5’-end reads, and (iv) percentage of reads mapping to the 5’-end of coding genes were excluded. Based on these parameters, sample SV1.21.H9.4c.DOXminus.excluded.fq.gz was excluded. Details about these parameters have been provided here: (https://github.com/shka/STRTprep/blob/master/doc/result.md).
Assembly: hg19
Supplementary files format and content: Raw and normalized gene count table in csv format.

source_name: Embryo

growth_protocol: hESC lines H1 (WA01) and H9 (WA09) were maintained on Geltrex, hESC-qualified, reduced growth factor basement membrane matrix-coated tissue culture dishes in Essential 8 culture medium and passaged every three to five days by 3-5-min incubation with 0.5 mM EDTA (all from Thermo Fisher Scientific).

extract_protocol:
The libraries were prepared using the STRT method as described in Krjutskov et al., Hum. Reprod. 2016 with minor modifications. Briefly, RNA samples were placed in a 48-well plate in which a universal primer, template-switching oligos, and a well-specific 8 bp barcode sequence were added to each well (Krjutskov et al., Hum. Reprod. 2016). The synthesized cDNAs from the samples were then pooled into one library and amplified by single-primer PCR with the universal primer sequence. The resulting amplified library was then sequenced using an Illumina NextSeq500 instrument.
RNA-seq (Bulk STRT)

treatment_protocol: TetOn-DUX4 hESCs either with or without doxicycline treatment were washed with PBS and incubated with TrypLE for 5 min, detached, and suspended into cold FACS buffer (5% FBS in PBS).  The cell suspension was filtered through Cell strainers to remove any cell clumps and centrifuged at 800 rpm for 5 min. The cell pellets from Dox (+) and Dox (-) cultures were suspended in the cold FACS buffer and placed on ice. EmGFP (-) cells from the Dox (-) and EmGFP (+) cells from the Dox (+) suspension were sorted into cold FACS buffer using a Sony SH800Z Cell Sorter with blue laser (488) and 100 μm nozzle. Total RNA was isolated from FAC-sorted DUX4-TetOn hES cells using the RNAqueous Total RNA Isolation Kit (AM1912; Thermo Fisher Scientific). 20 ng of total RNA from each sample was used for library preparations.

tag: cell type

value: human embryonic stem cells (hESC)

value: Control


title: Head & Neck tissue (X4090082011_B)

value: Male

value: Pyriform sinus

value: Tumor

value: No evidence of disease


title: IPA_CYTO_DMSO_n3

description: replicate 3

value: Vehicle (DMSO)


title: mes4_adgerm_batch01_rep03

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M+Z- V

tag: stage and sex

value: 1st day adult hermaphrodite

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: wt_adgerm_batch01_rep02

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I


title: IPA_HP_DMSO_n3

description: replicate 3

value: Heavy polysomes


title: Head & Neck tissue (X4090082011_F)

tag: gender

value: Female

value: Gingiva lower

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension

value: No

tag: extracapsular extension. extra neural extension

value: Yes

tag: perineural invasion

tag: primary. recurrence date

tag: neck.recurrence date

value: Dead

value: Local recurrence+Local regional recurrence


title: mes4_adgerm_batch01_rep01


title: HCT_Keratinocyte_H3K27ac_Rep2

city: Philadelphia

first: Satish

last: Sati

state: Pennsylvania

address: 421 Curie Blvd, BRB 1039

department: Dermatology

institute: University of Pennsylvania

library_source: genomic

data_processing:
Library strategy: HiCuT
Datasets were analysed by HiC-Pro pipeline (https://github.com/nservant/HiC-Pro)
Genome_build: hg19
Supplementary_files_format_and_content: The processed datasets are valid pairs from HiC-Pro pipeline

molecule: genomic DNA

growth_protocol: GM12878 cells were cultured in RPMI. Both media were suppelemented with 10% FBS, 1 mM of glutamax (ThermoFisher, Cat.N: 35050-038), 50U of penicillin and streptomycin. Keratinocytes were grown in supplemented 50:50 keratinocyte media, a 50:50 mixture of keratinocytes-SFM (Thermo Scientific) and Medium 154 (Thermo Scientific).

extract_protocol:
HiC was carried out using the in-situ method as described previously (Rao et. al., 2014) with minor modifications.  In brief, cells were digested for 2 hours at 37C using 50U of DpnII. After biotin filling, proximity ligation was carried out for 2-4 hours at room temperature with 200U T4 DNA Ligase. After proximity ligation nuclei were then proceeded for Cut&Tag protocol as decribed previously (Kaya-Okur., et al, 2019)
Library protocol was included in the CuT&Tag assay as decribed earlier (Kaya-Okur., et al, 2019).

value: primary keratinocyte

tag: chip antibody


title: wt_adgerm_batch01_rep03


title: HCT_Keratinocyte_H3K27ac_Rep1


title: IPA_CYTO_Silv_n1

description: replicate 1

tag: cell line

tag: treatment

value: Silvestrol 2 hours

tag: extract

value: Whole Cytosol


title: IPA_HP_DMSO_n2

description: replicate 2

value: Vehicle (DMSO)


title: IPA_CYTO_DMSO_n1

description: replicate 1


title: IPA_HP_DMSO_n1

description: replicate 1


title: Head & Neck tissue (X4090082011_E)

value: Male

value: Hypopharyngeal wall

value: Hypopharynx

value: yes

tag: surgical margin pos

tag: vascular invasion

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Bone

value: Tumor

value: Distant metastasis


title: mes4_adgerm_batch01_rep02

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M+Z- V

tag: stage and sex

value: 1st day adult hermaphrodite

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: STRT_05.H1.2b.DOXplus

tag: cell type

value: human embryonic stem cells (hESC)

value: Doxycycline treated


title: HCT_Keratinocyte_H3K27ac_Rep3


title: wt_adgerm_batch02_rep04

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I


title: STRT_02.H1.2b.DOXminus

value: Control


title: IPA_HP_Silv_n2

description: replicate 2

value: Silvestrol 2 hours

value: Heavy polysomes


title: met1_l1pgcs_rep12

description: Single set of sister Primordial Germ Cells (2 cells) dissected from an L1 larva (fed for 30-60 minutes immediately after hatching).

source_name: Primordial Germ Cells

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva


title: Head & Neck tissue (X4068811085_A)

tag: gender

value: Male

value: Epiglottis

tag: site

value: Larynx

tag: n

tag: extra neural extension

tag: extracapsular extension. extra neural extension

value: Yes

value: No

tag: lymphovascular invasion

value: Alive

value: No evidence of disease


title: HCT_GM12878_RNA_polymerase_II_Rep3

value: GM12878 cell line

tag: chip antibody


title: wt_adgerm_batch01_rep01

description: 20-60 gonads were dissected from 1st day adult hermaphrodites.

value: 1st day adult hermaphrodite

value: no


title: Head & Neck tissue (X4068811084_D)

value: Female

value: Tonsillar fossa

value: Oropharynx

tag: extracapsular extension

value: yes

tag: surgical margin pos

tag: perineural invasion

tag: primary. recurrence

tag: neck.recurrence date

value: Dead

value: Tumor

value: Local regional recurrence


title: met1_l1pgcs_rep08

tag: source strain

tag: genotype

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva


title: met1_l1pgcs_rep07

tag: stage and sex

tag: sequencing batch


title: Head & Neck tissue (X4068811084_F)

value: Oral Tongue

value: Oral Cavity

tag: vascular invasion

tag: any.recurrence_local recurrence.or.local regional recurrence


title: Head & Neck tissue (X4068811084_C)

tag: gender

value: Epiglottis suprahyoid

tag: site

value: Larynx

value: no nodes

value: No


title: met1_l1pgcs_rep10

tag: outliers filtered from analysis

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations greater than the median of all PGCs and EGCs.


title: met1_l1pgcs_rep09

value: no


title: Head & Neck tissue (X4068811085_C)

value: Male

value: Floor of mouth

tag: n

tag: extracapsular extension. extra neural extension

value: Local recurrence+Local regional recurrence


title: met1_l1pgcs_rep11


title: Head & Neck tissue (X4068811084_B)

value: Female

value: Pyriform Sinus

value: Hypopharynx

value: yes

value: Yes

value: Alive

value: No evidence of disease


title: met1_l1pgcs_rep06

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva


title: Head & Neck tissue (X4068811085_E)

value: Epiglottis

value: Larynx

value: Dead

value: Tumor


title: Head & Neck tissue (X4068811085_F)

value: Soft palate and uvula

value: Oropharynx

value: no nodes

value: No

tag: lymphovascular invasion

tag: primary. recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Local recurrence+Local regional recurrence+Distant metastasis


title: Head & Neck tissue (X4068811084_E)

value: Male

value: Oral tongue

value: Oral Cavity

tag: extracapsular extension

tag: surgical margin pos

value: no

tag: perineural invasion

tag: primary. recurrence


title: MC2: Negative control_2

city: Seongnam

first: JeongMan

last: Park

address: 689, Sampyeong-dong, Bundang-gu, Seongnam-si

country: South Korea

institute: CHA university

description: Gene expression data of MKN74 cell lines treated scrambled siRNA

data_processing:
Assessing average base quality per cycle using FastQC v0.11.7.
The raw data for each sample and the trimmed read that went through the preprocessing process were compared with the total data amount and Q30 (phred score, base quality 30% or more) value, respectively.
The preprocessed trimmed reads were mapped to a known reference genome using the HISAT2 version 2.1.0, Bowtie2 2.3.4.1.
After read mapping, transcript assembly was performed through  StringTie version 2.1.3b.
Genome_build: Genome Reference Consortium Human Build 37 patch release 13 (GRCh37.p13)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MKN74 was purchased from Korean Cell Line Bank (KCLB) and cultured in RPMI-1640 (Gibco) supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (Gibco). Cells were grown at 37°C in a 5% CO2 incubator under humidified conditions.

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and the concentration was calculated using Quant-IT RiboGreen (Invitrogen).
Total RNA (0.5 µg) was used to construct a library using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina). After removing the rRNA, fragmentation was performed with mRNA under elevated temperatures. First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) and random primers. Second-strand cDNA synthesis was performed using DNA Polymerase I, Rnase H, and dUTP. These cDNA fragments go through an end repair process mediated by the addition of a single ‘A’ base and ligation of the adapters. The products were purified and enriched by PCR to create the final cDNA library.
The libraries were quantified using KAPA Library Quantification Kits for Illumina Sequencing platforms according to the qPCR Quantification Protocol Guide (KAPA BIOSYSTEMS, #KK4854) and qualified using the TapeStation D1000 ScreenTape (Agilent Technologies, #5067-5582). Indexed libraries were then submitted to Illumina NovaSeq (Illumina), and the paired-end (2 × 100 bp) sequencing was performed by Macrogen Incorporated (Seoul, Republic of Korea).

treatment_protocol: The LOC441461 siRNA oligonucleotide (si-LOC441461; BIONEER) and negative control scrambled siRNA (N.C, BIONEER) were transfected into MKN74 cells using Lipofectamine™ RNAiMAX (Invitrogen) and Opti-MEM (Gibco) at a final concentration of 100 nM. After 24 h, cells were harvested.

tag: cell line

tag: cell type

value: Gastric cancer cell

tag: transfection

value: Scrambled negative control siRNA


title: IPA_HP_Silv_n1

description: replicate 1

tag: treatment

value: Silvestrol 2 hours

tag: extract

value: Heavy polysomes


title: HCT_GM12878_H3K27ac_Rep3

value: GM12878 cell line

tag: chip antibody


title: HCT_GM12878_RNA_polymerase_II_Rep1


title: HCT_GM12878_RNA_polymerase_II_Rep2


title: IPA_HP_Silv_n3

description: replicate 3


title: HCT_GM12878_CTCF_Rep3

value: CTCF


title: HCT_GM12878_H3K27ac_Rep1


title: MC3: Negative control_3


title: Head & Neck tissue (X4068811084_A)

tag: gender

value: Base of Tongue

tag: site

value: yes

value: Yes

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: No evidence of disease


title: HCT_GM12878_H3K27ac_Rep2


title: HCT_GM12878_CTCF_Rep1


title: Head & Neck tissue (X4068811067_E)

value: Gingiva

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: No

tag: lymphovascular invasion

tag: vascular invasion


title: met1_l1pgcs_rep02

tag: source strain

tag: genotype

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L1 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis


title: Head & Neck tissue (X4068811067_F)

value: Male

value: Larynx NOS

value: Larynx

tag: extracapsular extension

tag: surgical margin pos

tag: primary. recurrence

value: Alive


title: NET-CAGE_H9hESC_dox_biologicalRep1

data_processing:
Reads were split by barcode using the MOIRAI package. Cutadapt v 1.1.8 (http://code.google.com/p/cutadapt/) was used to trim reads to 73 bp and remove reads below base quality 33 and ‘N’ bases. Reads aligning to ribosomal RNA sequences (GenBank U13369.1) were removed using the rRNAdust script within the MOIRAI package. The resulting reads were aligned to the human genome (hg19) using STAR v 2.5.0a with Gencode v27lift37 (“comprehensive”) as the reference gene model. Mapping was performed with the following parameters: --runThreadN --outSAMtype BAM SortedByCoordinate --out FilterMultimapNmax 1. Following alignment, the re-sequenced replicates were merged using the Picard Toolkit v 2.0.1 with the MergeSamFiles program (Broad Institute, Picard Toolkit, 2018. http://broadinstitute.github.io/picard). BAM files were converted to bed files using BEDTools v 2.2.27. TSSs were identified for all CAGE and NET-CAGE samples according to http://fantom.gsc.riken.jp/5/sstar/Protocols:HeliScopeCAGE_read_alignment. The TSSs bed files were converted to strand specific bedGraph files and subsequently to bigWig files using the UCSC software bedGraphtobigWig.
Genome_build: hg19
Supplementary_files_format_and_content: CAGE-based bed 6 file for transcription start sites. Scores represent aggregated tags with same starting position.

molecule: other

extract_protocol:
NET-CAGE: Nascent RNA from flash-frozen cells was isolated as described by Hirabayashi et al. 2019 Nat. Genet. with the following exceptions: (i) DNase I enzyme (50 Units, Thermo Fisher Scientific) was used to prepare the DNase I solution (50 μl), (ii) the samples were incubated for up to 1 h at 37°C while being pipetted up and down several times every 10 min, and (iii) RNA quality was measured using a TapeStation 4200 (Agilent).
CAGE-based libraries were generated according to the no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) protocol (Murata et al 2014; Methods Mol. Biol.).

treatment_protocol: hESCs were incubated with StemPro Accutase (Thermo Fisher Scientific) until the edges of the colonies started to curl up. The Accutase was aspirated and the cells were gently detached in cold 5% FBS (Thermo Fisher Scientific) 1×PBS (Corning) and counted. One million cells were centrifuged at 107×g for 5 min and the pellet was transferred into 120 μl of R-buffer containing 1 μg of pB-tight-DUX4-ires-EmGFP-pA-PGK-Puro, 0.5 μg of pBASE and 0.5 μg of rtTA-M2-IN plasmids. 100 μl of the cell-plasmid suspension was electroporated with two pulses of 1100V, 20 ms pulse width, using Neon Transfection system (Thermo Fischer Scientific). The electroporated cells were plated on Geltrex-coated dishes in Essential 8 medium with 10 μM ROCK inhibitor Y27632 (Selleckhem). The following day, the medium was exchanged with fresh Essential 8 medium without ROCK inhibitor. The cells were selected with Puromycin at 0.3 μg/ml.  The TetOn-DUX4 hESC clones were picked manually on Geltrex-coated 96-well plates, expanded and selected again with Puromycin. Appearance of the EmGFP reporter protein was tested using Doxycycline at concentrations ranging from 0.2 μg/ml to 1.0 μg/ml and detected using an EVOS FL Cell imaging system (Thermo Fisher Scientific). For the experiments presented in this paper, the DUX4 TetOn hESCs have been treated with 1μg/ml of Doxycycline for 4 hours.

tag: cell line

value: H9 hESC

tag: treatment

value: Doxycycline treated

tag: rna population

value: Nascent RNA


title: Day 80 Triple-i ZIP8K8  Organoid-2

city: Berlin

first: Yechiel

last: Elkabetz

address: Ihnestraße 63-73

country: Germany

institute: Max Planck Institute for Molecular Genetics

data_processing:
scRNA-Seq libraries were sequenced on Illumina NovaSeq 6000. Bulk RNA-Seq libraries were sequenced on Illumina HiSeq 2500.
Single cell RNA-Seq sequencing data from day 50 organoids was processed using Cell Ranger software version 3.1.0 reference genome hg38 and ensembl reference transcriptome version 93 (http://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz).
Single cell RNA-Seq sequencing data from day 80 organoids was processed using Cell Ranger software version 6.0.1 reference genome hg38 and ensembl reference transcriptome version 93 (http://ftp.ensembl.org/pub/release-93/gtf/homo_sapiens/Homo_sapiens.GRCh38.93.gtf.gz).
For bulk RNA-Seq of H9-derived organoids, raw RNA-Seq reads were mapped to the human reference genome hg19 using STAR mapper version 2.6.1d. Generated bam files were filtered for uniquely mapped reads using Samtools version 1.10 and read counts were generated using HTSeq version 0.10.0 (parameters: -m intersection-strict --nonunique all -r pos -s reverse). For further analysis, all mitochondrial genes were removed from the data. RPKM values were calculated by dividing the number of counts by gene length and sequencing depth, followed by multiplying by 10E9. For data normalization, only RefSeq-annotated genes were considered and their RPKM values were normalized by bringing the samples to the same RPKM sum.
DESeq2 version v1.26.0 was run on the bulk RNA-Seq count data across three pairwise treatment comparisons for wild type organoids, Triple-i vs Dual SMAD-i, Triple-i vs Inhibitor-free, and Dual SMAD-i vs Inhibitor-free, using 8 biological replicates of individual organoids from each protocol. DESeq2 version v1.26.0 was run on the raw count data to compare day 17 and day 30 heterozygous and homozygous microcephaly pooled organoids vs wild type pooled organoids across Triple-i, Dual SMAD-i and Inhibitor-free organoids.
Genome_build: scRNA-Seq: hg38; bulk RNA-Seq: hg19
Supplementary_files_format_and_content: Count matrices in the form of gzipped tab-delimited text files for each scRNA-Seq sample. RPKM expression tables in an Excel table for all bulk RNA-Seq samples. DESeq2 differential expression analysis in an Excel table for bulk RNA-Seq samples.

source_name: Brain Organoid

growth_protocol: Undifferentiated hESC or iPSC cells were dissociated, counted and plated at a concentration of 9000 cells per 150µl of PSC growth medium (see Methods for details) and plated on a 96 well U-bottom low attachment plate till aggregates were formed. Medium was changed from day 2 and on, every other day with pathway inhibitors supplemented at day 2 according to the differentiation protocol using SB-431542 (10µM), Noggin (250 ng/ml) and XAV-939 (3.3 µM). On day 6, organoids were transferred into low attachment 24 well plate along with Neural induction medium (see Methods for details) and continued to be cultured with Neural induction medium and inhibitors according to derivation method. On day 11, organoids (500-600 µm in size) were embedded in Matrigel droplets and transferred into a 6 well low attachment plate containing Neural induction medium and neurobasal medium (see Methods for details) B-27 without retinoic acid. Same medium was given every other day till the end of the experiment. On day 15 organoid dishes were transferred onto an orbital shaker, and medium was changed one to two days.

extract_protocol:
For scRNA-Seq, day 50 organoids (N=4-6 pooled organoids per a processed sample) derived by Triple-i (from ZIP8K8, ZIP13K5, KUCG2 and FOK1 iPSC cell lines), Dual SMAD-i (from ZIP8K8, ZIP13K5, KUCG2 and FOK1 iPSC cell lines), and Inhibitor-free (from ZIP8K8 and ZIP13K5 cell lines) treatments; day 80 individual organoids derived by Triple-i (ZIP8K8 cell line, N=3 individually processed organoids) and Dual SMAD-i (ZIP8K8 cell line, N=3 individually processed organoids), as well as pooled Triple-i organoids (ZIP13K5 cell line, 1  experiment across N=3 pooled organoids); all were dissociated into single cells using papain dissociation kit (Worthington). Organoids were dissected using needle into small pieces, then incubated with papain and DNase I solution for 35-45 min, and later triturated to single cells. Cell suspension was passed twice through 40-micron filter to obtain single cell suspension. Cells were centrifuged at 300g for 5 min, re-suspended in 0.4% BSA in Dulbecco’s Phosphate Buffer Solution (DPBS), counted for viability (>80% were viable) and 1000 cells/ µL were used for generating libraries using 10X Chromium single cell 3’ reagent kit V3.1 chemistry. For bulk RNA-Seq, RNA was purified using the miRNeasy™ RNA MiniPrep (Qiagene).
For scRNA-Seq, roughly 17,400 single live cells were suspended in 0.4% BSA in DPBS buffer (1000 cells/µL) and subjected for GEM generation and barcoding. Library preparation was performed according to the recommended procedures of the manufacture Chromium Single Cell 3’ reagent Kit V3.1 chemistry. In day 50 organoids, 10,000 cells were targeted for capturing and 9 cycles were used for cDNA amplification, while 12 cycles were performed for library formation. For day 80 organoids, 11 cycles are used both for cDNA amplification and library formation. Bulk RNA-Seq libraries were generated using the Illumina TruSeq RNA Library Preparation Kits.

treatment_protocol: We compared organoids generated by the standard, inhibition-free protocol (Lancaster et al., Nature 501, 373-379 (2013) (denoted as Inhibitor-free), to those generated by WNT inhibitor XAV939 alone (WNT-i) or TGF-β/BMP inhibitors SB-431542/Noggin together (Chambers et al. Nat Biotechnol 27, 275-280 (2009)) (Dual SMAD-i) as controls, as well as to organoids made by combined Dual SMAD and WNT inhibition (Triple-i) as the most directed cortical differentiation paradigm (See Methods for details).

tag: protocol

value: Triple-i

tag: age

value: Day 80

tag: cell type

value: Fibroblast-derived iPSCs


title: mes3_l2germ_rep12

description: Set of 2 Early Germ Cells dissected from an L2 larva (fed for ~20 hours immediately after hatching).

source_name: Early Germ Cells

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L2 hermaphrodite larva

value: no


title: Head & Neck tissue (X4068811067_D)

tag: gender

value: AFP and RMT

tag: site

value: Oral Cavity

tag: n

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: perineural invasion

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: No evidence of disease


title: mes3_l2germ_rep11

tag: source strain

tag: genotype

tag: stage and sex

tag: sequencing batch


title: met1_l1pgcs_rep05

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva

tag: outliers filtered from analysis


title: NET-CAGE_H9hESC_dox_biologicalRep2

tag: cell line

value: H9 hESC

value: Doxycycline treated


title: Head & Neck tissue (X4068811067_A)

value: Female

value: Hypopharyngeal wall

value: Hypopharynx

tag: extracapsular extension

tag: surgical margin pos

value: No

tag: primary. recurrence


title: Day 80 Dual SMAD-i ZIP8K8  Organoid-3

tag: protocol

value: Dual SMAD-i

tag: age

value: Day 80

value: Fibroblast-derived iPSCs


title: HCT_GM12878_CTCF_Rep2

tag: cell type

value: GM12878 cell line

tag: chip antibody

value: CTCF


title: LOC1: si-LOC441461_1

description: Gene expression data of MKN74 cell lines treated si-LOC441461

value: Gastric cancer cell

tag: transfection

value: siencing RNA (siRNA) targeting LOC441461


title: met1_l1pgcs_rep03

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations greater than the median of all PGCs and EGCs and the number of detected features (genes) was >3 median absolute deviations lower than the median of all PGCs and EGCs.


title: MC1: Negative control_1

value: Scrambled negative control siRNA


title: met1_l1pgcs_rep01

value: met-1(bn200) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: no


title: mes3_l2germ_rep10

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L2 hermaphrodite larva


title: Day 80 Triple-i ZIP8K8  Organoid-3

value: Triple-i


title: NET-CAGE_H9hESC_control_biologicalRep2

value: H9 hESC

tag: treatment

value: Control

tag: rna population

value: Nascent RNA


title: Day 80 Dual SMAD-i ZIP8K8  Organoid-2

value: Dual SMAD-i


title: NET-CAGE_H9hESC_control_biologicalRep1


title: LOC3: si-LOC441461_3


title: met1_l1pgcs_rep04

value: L1 hermaphrodite larva


title: LOC2: si-LOC441461_2


title: mes3_l2germ_rep09


title: Head & Neck tissue (X4019614109_F)

tag: gender

value: Male

value: Oral Tongue

tag: site

value: Oral Cavity

tag: n

value: No

tag: extracapsular extension. extra neural extension

tag: perineural invasion

value: yes

tag: vascular invasion

value: Yes

tag: primary. recurrence date

tag: neck.recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local recurrence+Local regional recurrence+Distant metastasis


title: Day 80 Triple-i ZIP8K8  Organoid-1

tag: cell line

tag: protocol

tag: age

value: Day 80

value: Fibroblast-derived iPSCs


title: CAGE_H9hESC_dox_biologicalRep2

extract_protocol:
CAGE: Total RNA from flash-frozen cells was isolated as described by Hirabayashi et al. 2019 Nat. Genet. RNA quality was measured using a TapeStation 4200 (Agilent).
CAGE-based libraries were generated according to the no-amplification non-tagging CAGE libraries for Illumina next-generation sequencers (nAnT-iCAGE) protocol (Murata et al 2014; Methods Mol. Biol.).

value: H9 hESC

value: Doxycycline treated

value: Total RNA


title: Head & Neck tissue (X4019614109_E)

value: Pyriform Sinus

value: Hypopharynx

tag: extracapsular extension

tag: surgical margin pos

tag: lymphovascular invasion

value: no

tag: primary. recurrence

value: Alive

value: Local regional recurrence


title: Head & Neck tissue (X4068811067_C)

tag: gender

value: Female

value: Floor of mouth

tag: site

value: Oral Cavity

value: No

value: Local recurrence


title: mes3_l2germ_rep08

tag: source strain

tag: genotype

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis


title: Head & Neck tissue (X4019614116_F)

value: Male

value: Gingiva lower

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: yes

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Tumor

value: No evidence of disease


title: Head & Neck tissue (X4068811067_B)

value: Pyriform Sinus

value: Hypopharynx

value: Dead


title: CAGE_H9hESC_control_biologicalRep1

tag: cell line

value: H9 hESC

tag: treatment

value: Control

tag: rna population

value: Total RNA


title: mes3_l2germ_rep06

value: no


title: CAGE_H9hESC_dox_biologicalRep1

value: Doxycycline treated


title: Head & Neck tissue (X4019614109_D)

value: Female

value: Oral tongue

value: Oral Cavity

value: No

tag: perineural invasion

value: Alive


title: Day 50 Triple-i FOK1 Pooled Organoids

tag: protocol

value: Triple-i

tag: age

value: Day 50

tag: cell type

value: PBMC-derived iPSCs


title: gfpTAI: GFP transduced cortical culture tail lengths

city: Berkeley

first: Timothy

middle: J

last: Eisen

state: CALIFORNIA

address: Stanley Hall

institute: UC Berkeley

data_processing:
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Eichhorn et al., 2014). PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths according to the pipeline available on github (https://github.com/kslin/PAL-seq/tree/tailSeqPipeline); transcript models available for download (Eichhorn et al., 2014) with 3' end annotations included in this manuscript (Bartel lab website)
Illumina 1.5; Conventional base calls
filtered for only thosed that passed the chastity filter; removed first 8 nt of the read (randomized 5p adapter)
reads aligned with STAR v2.4.2: --alignIntronMax 1 --clip3pAdapterSeq TCGTATGCCGTCTTCTGCTTG --runThreadN 30 --outFilterMultimapNmax 1 --outFilterMismatchNoverLmax 0.04 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSJfilterReads Unique
assigned to features with intersectBed: -wb -s
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPM and RPKM values for each sample. PAL-seq processed files include tab-delimited files of reads.

organism: Mus musculus

source_name: cortical culture DIV 14

extract_protocol:
RNA-seq and RPF libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)
PAL-seq V2 and TAIL-seq libraries were constructed and processed according to the methods.
For RNA-seq or RPF libraries, detailed protocols are available (Subtelny et al., 2014 and Bartel lab website). Detailed protocols are also available for library construction for PAL-seq V2 and TAIL-seq (Eisen et al., 2020; Chang et al., 2014; and Bartel lab website).

tag: tissue

value: cortical culture DIV 14

tag: stimulated

tag: libraryprepmethod

value: TAIL-seq

tag: experiment type

value: microRNA experiment


title: Head & Neck tissue (X4019614109_A)

tag: gender

value: Male

value: Floor of mouth

tag: site

tag: extracapsular extension

value: yes

value: Yes

tag: surgical margin pos

tag: primary. recurrence

tag: neck.recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local regional recurrence+Distant metastasis


title: m15TAI: miR-155 transduced cortical culture tail lengths


title: Day 80 Dual SMAD-i ZIP8K8 Organoid-1

tag: cell line

value: Dual SMAD-i

value: Day 80

value: Fibroblast-derived iPSCs


title: CAGE_H9hESC_control_biologicalRep2

value: H9 hESC

tag: treatment

value: Control

tag: rna population

value: Total RNA


title: Day 50 Dual SMAD-i KUCG2 Pooled Organoids

tag: protocol

tag: age

value: Day 50


title: mes3_l2germ_rep05

tag: source strain

tag: genotype

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: mes3_l2germ_rep07


title: Day 80 Triple-i ZIP13K5 Pooled Organoids

value: Triple-i

tag: cell type


title: Day 50 Inhibitor-free ZIP13K5 Pooled Organoids

value: Inhibitor-free


title: mi1TAI: miR-1 transduced cortical culture tail lengths

tag: tissue

value: cortical culture DIV 14

tag: stimulated

tag: libraryprepmethod

value: TAIL-seq

tag: experiment type

value: microRNA experiment


title: mes3_l2germ_rep03


title: mes3_l2germ_rep02


title: Head & Neck tissue (X4019614067_E)

tag: gender

value: Male

value: Alveolar ridge

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: surgical margin pos

value: No

tag: primary. recurrence

tag: primary. recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: Local recurrence


title: Day 50 Triple-i KUCG2 Pooled Organoids

tag: cell line

tag: protocol

tag: age

value: Day 50

value: Fibroblast-derived iPSCs


title: embhp_TAI: Embryonic hippocampus tissue tail lengths [PAL-seq V2]

source_name: Embryonic hippocampus

value: Embryonic hippocampus

value: PAL-seq V2

value: Tissue dissection


title: Day 50 Dual SMAD-i FOK1 Pooled Organoids

value: Dual SMAD-i

tag: cell type

value: PBMC-derived iPSCs


title: Day 50 Dual SMAD-i ZIP13K5 Pooled Organoids


title: Head & Neck tissue (X4019614109_B)

value: Female

value: Epiglottis

value: Larynx

value: No evidence of disease


title: aduco_TAI: Adult cortex tissue tail lengths

source_name: Adult cortex

tag: tissue

value: Adult cortex

value: TAIL-seq


title: aduhp_TAI: Adult hippocampus tissue tail lengths [PAL-seq V2]

source_name: Adult hippocampus

value: Adult hippocampus

tag: stimulated


title: Head & Neck tissue (X4019614067_F)

value: Male

value: AFP and RMT

value: Oral Cavity

tag: extra neural extension

value: yes

value: Yes

tag: neck.recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Dermal

value: Dead

value: Local recurrence+Local regional recurrence+Distant metastasis


title: mes3_l2germ_rep01

tag: source strain

tag: genotype

value: mes-3(bn199) M-Z- glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: Head & Neck tissue (X4019614067_C)

tag: gender

value: Female

value: Gingiva upper

tag: site

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

tag: surgical margin pos

tag: primary. recurrence

value: No

value: Alive

value: Tumor


title: mes3_l2germ_rep04


title: Head & Neck tissue (X4019614067_D)

value: Pyriform Sinus

value: Hypopharynx

tag: extracapsular extension

tag: lymphovascular invasion

tag: any.recurrence_local recurrence.or.local regional recurrence

value: No evidence of disease


title: Day 50 Triple-i ZIP13K5 Pooled Organoids

tag: cell line

tag: protocol

value: Triple-i

tag: age

value: Day 50

tag: cell type

value: Fibroblast-derived iPSCs


title: Head & Neck tissue (X4019614109_C)

value: Male

value: Tonsillar fossa

value: Oropharynx

tag: extra neural extension

value: yes

value: Yes


title: mes4_l2germ_rep15

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L2 hermaphrodite larva

value: no


title: Head & Neck tissue (X4019614067_A)

tag: gender

value: Epiglottis

value: Larynx

value: No

tag: neck.recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Local regional recurrence+Distant metastasis


title: LightStim1hrSample3: LightStim visual cortex 1hr Sample 3 tail lengths [PAL-seq V2]

source_name: LightStim visual cortex 1hr

tag: tissue

value: visual cortex

tag: stimulated

tag: libraryprepmethod

value: PAL-seq V2

tag: experiment type

value: Light stimulation experiment


title: Day 50 Dual SMAD-i ZIP8K8 Pooled Organoids

value: Dual SMAD-i

value: Day 50

value: Fibroblast-derived iPSCs


title: mes4_l2germ_rep14

tag: sequencing batch

tag: outliers filtered from analysis


title: mes4_l2germ_rep12


title: LightStim1hrSample1: LightStim visual cortex 1hr Sample 1 tail lengths [PAL-seq V2]


title: mes4_l2germ_rep13


title: LightStim1hrSample2: LightStim visual cortex 1hr Sample 2 tail lengths [PAL-seq V2]


title: LightStim0hrSample4: LightStim visual cortex 0hr Sample 4 tail lengths [PAL-seq V2]

source_name: LightStim visual cortex 0hr


title: Day 50 Inhibitor-free ZIP8K8 Pooled Organoids

tag: cell line

tag: protocol

value: Inhibitor-free


title: T_4432

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description: mRNA expression in human frontal cortical brain cells

data_processing:
Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with unique gene counts over 9,000 or less than 300, cells with unique molecular identifiers (UMI) count over than 50,000, and cells with high fraction of mitochondrial reads (> 5%).
Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
Seurat v3.0 (Butler et al., 2018) R package used for analysis.
Genome_build: hg38 genome

source_name: single nuclei from frozen postmortem human tissue

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)

tag: Sex

value: M

tag: diagnosis

value: GBA N370S/WT  - heterozygous for GBA


title: LightStim1hrSample4: LightStim visual cortex 1hr Sample 4 tail lengths [PAL-seq V2]

value: Yes


title: Head & Neck tissue (X1951406076_B)

value: Female

value: Epiglottis suprahyoid

tag: site

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

tag: surgical margin pos

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Tumor

value: No evidence of disease


title: mes4_l2germ_rep11

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L2 hermaphrodite larva

value: no


title: mes4_l2germ_rep10


title: LightStim0hrSample3: LightStim visual cortex 0hr Sample 3 tail lengths [PAL-seq V2]

tag: tissue

value: visual cortex

tag: stimulated

value: No

tag: libraryprepmethod

value: PAL-seq V2

tag: experiment type


title: T_779

value: F

value: GBA WT/WT - control


title: LightStim0hrSample2: LightStim visual cortex 0hr Sample 2 tail lengths [PAL-seq V2]

value: Light stimulation experiment


title: Day 50 Triple-i ZIP8K8 Pooled Organoids

tag: cell line

tag: protocol

value: Triple-i

tag: age

value: Day 50

tag: cell type

value: Fibroblast-derived iPSCs


title: Head & Neck tissue (X1951406076_E)

tag: gender

value: Female

value: Floor of mouth

tag: site

value: Oral Cavity

tag: n

value: no nodes

tag: vascular invasion

value: Yes

tag: primary. recurrence date

value: Dead

value: Local recurrence


title: Head & Neck tissue (X4019614067_B)

value: Male

value: Epiglottis

value: Larynx

tag: extracapsular extension

tag: extracapsular extension. extra neural extension

tag: surgical margin pos

tag: perineural invasion

value: no

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Tumor

value: No evidence of disease


title: T_3922

tag: Sex

value: M

tag: diagnosis

value: Diffuse Lewy Body disease, limbic or transitional type


title: Head & Neck tissue (X1951406072_E)

value: Base of Tongue

value: Oropharynx

value: No


title: Head & Neck tissue (X1951406076_F)

tag: extra neural extension

value: yes

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Distant metastasis


title: mes4_l2germ_rep09

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis


title: LightStim0hrSample1: LightStim visual cortex 0hr Sample 1 tail lengths [PAL-seq V2]

tag: tissue

value: visual cortex

tag: stimulated

tag: libraryprepmethod

value: PAL-seq V2

tag: experiment type

value: Light stimulation experiment


title: T_3860

value: GBA N370S/WT  - heterozygous for GBA


title: mes4_l2germ_rep08

value: no


title: Patient6_ESCC2

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

country: China

institute: Sichuan University

data_processing:
ScRNA-seq alignment process was completed by cellranger (version 3.0.0)
Seurat V3 workflow
Genome_build: hg19
Supplementary_files_format_and_content: txt files with gene counts for scRNA-seq

extract_protocol:
Preparation: collect the tumor tissue from ESCC patients. The samples were washed by 0.04% PBS-BSA. After Golu's iodine solution spraying, the uncolored region of tissue was used to lysis with shearing. Then, PBS was used to wash the samples more than 20 times. After the tissue preparation, collagen I (0.5mgml-1) and collagen IV (50mgml-1) was combined to lysis the samples with 2 hours in 37℃. The 400g centrifuge was used with 5 minutes. After discarding the supernatant, 10 ml trypsin was used to resuspend with 1 hour in 37℃. The 10% FBS was added to medium, and filter the mixture through 70μm. Then 400g centrifuge was used. After discarding the supernatant, 3ml 1XACK was used to resuspend the cells on the ice with 3 minutes. And 200 μl 0.04%BSA-PBS was used to resuspend cells. After quantifying the cell number, adjusting the concentration to the 800-1200 cells/μl and ensuring the cell activity > 85%, we used the 10X genomics platform to construct the single cell library of samples.
Follwed by v2 protocol of chemistry of the 3’ scRNA-seq 10X genomics platform

tag: patient

tag: disease state

value: esophageal squamous cell carcinoma


title: glugl_TAI: Glugly stim tail lengths

value: cortical culture DIV 14

value: Yes

value: TAIL-seq

value: BDNF/Glugly experiment


title: kcl10_TAI: KCl stim 10 min tail lengths

source_name: cortical culture DIV 10

value: cortical culture DIV 10

value: KCl experiment


title: kcl30_TAI: KCl stim 30 min tail lengths


title: mes4_l2germ_rep07


title: Head & Neck tissue (X1951406076_A)

tag: gender

value: Male

value: Epiglottis suprahyoid

tag: site

value: Larynx

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

tag: surgical margin pos

value: No

tag: perineural invasion

tag: primary. recurrence

tag: neck.recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: Local regional recurrence


title: mes4_l2germ_rep06

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis


title: mes4_l2germ_rep05

value: no


title: Head & Neck tissue (X1951406072_B)

value: Pyriform Sinus

value: Hypopharynx

tag: distant metastasis data

tag: distant metastasis site

value: Lung, Liver

value: Distant metastasis


title: Head & Neck tissue (X1951406072_D)

tag: gender

value: Posterior pharynx

value: no nodes

tag: lymphovascular invasion

tag: vascular invasion

value: No evidence of disease


title: cntrk_TAI: KCl stim control tail lengths

tag: tissue

value: cortical culture DIV 10

tag: stimulated

tag: libraryprepmethod

value: TAIL-seq

tag: experiment type

value: KCl experiment


title: Patient6_normal

tag: patient

tag: disease state

value: normal


title: Head & Neck tissue (X1951406072_A)

value: Male

value: Tonsillar fossa

tag: site

value: Oropharynx

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: surgical margin pos

value: No

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Alive


title: bdnfs_TAI: BDNF stim tail lengths

value: cortical culture DIV 14

value: BDNF/Glugly experiment


title: mes4_l2germ_rep04

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M-Z- V

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: Patient6_ESCC1

value: esophageal squamous cell carcinoma


title: wt_l2germ_rep14

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I


title: Patient3


title: Head & Neck tissue (X1951406072_C)

tag: gender

value: Pyriform Sinus

value: Hypopharynx

tag: neck.recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local regional recurrence+Distant metastasis


title: wt_l2germ_rep13


title: Patient5

tag: patient

tag: disease state


title: cntrb_TAI: BDNF and glugly stim control tail lengths

tag: tissue

tag: stimulated

tag: libraryprepmethod

value: TAIL-seq

tag: experiment type


title: Head & Neck tissue (X1951406071_D)

value: Female

value: Oral Tongue

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

tag: surgical margin pos

value: No

tag: perineural invasion

value: yes

tag: primary. recurrence

value: No evidence of disease


title: m15RPF: miR-1 transduced cortical culture RPF

value: cortical culture DIV 14

value: Ribosome profiling

value: microRNA experiment


title: Patient1

value: esophageal squamous cell carcinoma


title: wt_l2germ_rep12

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: Head & Neck tissue (X1951406071_B)

tag: gender

value: Male

value: Base of tongue

value: Oropharynx

tag: extracapsular extension

value: Yes

tag: lymphovascular invasion

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor


title: Patient2

tag: patient

tag: disease state


title: mi1RPF: miR-155 transduced cortical culture RPF

tag: tissue

tag: stimulated

tag: libraryprepmethod

tag: experiment type


title: Head & Neck tissue (X1951406071_C)

value: Oral tongue

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

tag: surgical margin pos

tag: perineural invasion

tag: vascular invasion

value: No

value: Alive


title: Patient4


title: gfpRPF: GFP transduced cortical culture RPF

value: cortical culture DIV 14

value: Ribosome profiling

value: microRNA experiment


title: HK-2 cells, CSE, t24h, rep3

city: Taipei

first: Yung-Li

address: 250 Wu-Hsing Street

country: Taiwan

institute: Graduate Institute of Clinical Medicine, Taipei Medical University

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic (v0.38) to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software (v2.1.0).
FeatureCounts (v1.6.0) was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq (v1.36.1) without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 (v1.22.1) with biological duplicate.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human kidney

growth_protocol: HK-2 cells were maintainedkept in Keratinocyte-serum-free medium (K-SFM) with bovine pituitary extract and human recombinant EGF (Invitrogen, CA), cultured at 37 °C/5% CO2

extract_protocol:
Total RNA was isolated using the EasyPrep Total RNA Kit (Cat:TB-DPT-BD19).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were seeded 24 hours before treatment on 6-cm dish at a density of 6x10^5 cells per well with 4 ml of medium per dish. Cells were treated at ~90% confluency with the required doses for the required timepoints. Control cells were exposed to an appropriate concentration of the control vehicle.

tag: cell type

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: treated with cigarette smoke extract for 24 hours


title: Head & Neck tissue (X1951406071_E)

tag: gender

value: Female

value: Epiglottis suprahyoid

value: Larynx

tag: primary. recurrence

value: No evidence of disease


title: wt_l2germ_rep11

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: wt_l2germ_rep09


title: m15RNA: miR-155 transduced cortical culture RNA

tag: tissue

tag: stimulated

tag: libraryprepmethod

value: RNA-seq


title: mi1RNA: miR-1 transduced cortical culture RNA

tag: experiment type


title: wt_l2germ_rep10


title: wt_l2germ_rep08


title: Head & Neck tissue (X1951406070_D)

value: Male

value: Pyriform Sinus

tag: site

value: Hypopharynx

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: lymphovascular invasion

tag: neck.recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local regional recurrence+Distant metastasis


title: Head & Neck tissue (X1951406056_F)

tag: gender

value: Female

value: Buccal mucosa

value: Oral Cavity

value: no nodes

tag: surgical margin pos

tag: primary. recurrence

tag: primary. recurrence date

value: No

value: Local recurrence


title: HK-2 cells, CSE, t24h, rep2

tag: cell type

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: treated with cigarette smoke extract for 24 hours


title: wt_l2germ_rep07

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: Head & Neck tissue (X1951406070_F)

value: Male

value: Hypopharyngeal wall

tag: site

value: Hypopharynx

tag: n

tag: extracapsular extension

tag: extracapsular extension. extra neural extension

value: yes

tag: perineural invasion

tag: vascular invasion

value: Yes

value: Lung, Bone

value: Distant metastasis


title: Head & Neck tissue (X1951406070_A)

tag: gender

value: Floor of mouth

value: Oral Cavity

tag: extra neural extension

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: No evidence of disease


title: wt_l2germ_rep06


title: Head & Neck tissue (X1951406056_E)

value: Larynx NOS

value: Larynx

tag: surgical margin pos

value: No

tag: lymphovascular invasion

tag: primary. recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Lung


title: aduco_RNA: Adult cortex tissue RNA

tag: tissue

value: Adult cortex

tag: stimulated

tag: libraryprepmethod

value: RNA-seq

tag: experiment type

value: Tissue dissection


title: wt_l2germ_rep05

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: Head & Neck tissue (X1951406070_E)

tag: gender

value: Male

value: AFP and RMT

tag: site

tag: n

tag: extracapsular extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

value: Distant metastasis


title: HK-2 cells, CSE, t24h, rep1

tag: cell type

value: immortalized human renal proximal tubular epithelial cells

tag: treatment

value: treated with cigarette smoke extract for 24 hours


title: D302T44 recombinant CSF-1

city: Paris

first: Elodie

last: Segura

address: 156 rue de Vaugirard

department: INSERM U1151

institute: INSERM

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Trimming was performed using Atropos.
Reads were aligned to the transcriptome using STAR
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using DESeq2.

source_name: human monocyte

growth_protocol: Human CD14+ monocytes were cultured with extracellular vesicles from MDA-MB-231 tumor cells (0.02  ng/ml) or recombinant CSF-1 (100  ng/ml) for 5 days.

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Stranded mRNA Library Prep Kit (Illumina). 500 ng of RNA was used for each sample.

tag: donor

value: recombinant CSF-1


title: aduco_RPF: Adult cortex tissue RPF

tag: tissue

value: Ribosome profiling


title: aduhp_RPF: Adult hippocampus tissue RPF

value: Adult hippocampus

tag: stimulated


title: gfpRNA: GFP transduced cortical culture RNA

value: cortical culture DIV 14

tag: libraryprepmethod

value: microRNA experiment


title: Head & Neck tissue (X1951406056_B)

value: Floor of mouth

value: Oral Cavity

tag: surgical margin pos

tag: primary. recurrence

value: No

tag: neck.recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local regional recurrence+Distant metastasis


title: D302T42 EV-poor

value: EV-poor


title: embhp_RPF: Embryonic hippocampus tissue RPF

value: Embryonic hippocampus

tag: experiment type

value: Tissue dissection


title: Head & Neck tissue (X1951406056_D)

tag: gender

value: Female

value: Pyriform Sinus

tag: site

value: Hypopharynx

value: yes

value: Yes

tag: perineural invasion

tag: primary. recurrence date

value: Local recurrence+Local regional recurrence


title: D302T43 concentrated conditioned medium

value: concentrated conditioned medium


title: wt_l2germ_rep04

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L2 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: wt_l2germ_rep03


title: wt_l1pgcs_rep23

value: L1 hermaphrodite larva


title: Head & Neck tissue (X1951406055_E)

value: Larynx NOS

value: Larynx

tag: n

tag: extra neural extension

tag: extracapsular extension. extra neural extension

value: No

value: Lung, Bone

value: Dead

value: Tumor


title: embhp_RNA: Embryonic hippocampus tissue RNA

tag: tissue

value: Embryonic hippocampus

tag: stimulated

tag: libraryprepmethod

value: RNA-seq

value: Tissue dissection


title: D302T41 EV-R

tag: donor

tag: treatment

value: EV-R


title: D302T40 recombinant CSF-1

value: recombinant CSF-1


title: Head & Neck tissue (X1951406055_F)

tag: gender

value: Male

value: AFP & RMT

value: Oral Cavity

value: yes

value: Yes

tag: surgical margin pos

tag: vascular invasion

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Local recurrence


title: Head & Neck tissue (X1951406055_A)

value: Larynx NOS

tag: site

tag: extracapsular extension

value: No evidence of disease


title: Head & Neck tissue (X1951406056_A)

value: Oral tongue

value: No

tag: neck.recurrence date

value: Local regional recurrence


title: kcl30_RPF: KCl stim 30 min RPF

value: cortical culture DIV 10

value: Ribosome profiling

tag: experiment type

value: KCl experiment


title: aduhp_RNA: Adult hippocampus tissue RNA

value: Adult hippocampus

value: RNA-seq

value: Tissue dissection


title: D302T38 EV-poor

value: EV-poor


title: D302T37 EV-R

value: EV-R


title: wt_l1pgcs_rep22

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

value: L1 hermaphrodite larva

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: wt_l1pgcs_rep19


title: D302T39 concentrated conditioned medium

value: concentrated conditioned medium


title: wt_l1pgcs_rep20


title: D302T36 recombinant CSF-1

value: recombinant CSF-1


title: wt_l1pgcs_rep18


title: Head & Neck tissue (X1922146132_C)

value: Male

value: Floor of mouth

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: Yes

tag: primary. recurrence date

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Local recurrence+Distant metastasis


title: Head & Neck tissue (X1922146132_F)

tag: gender

value: Female

value: Gingiva upper

value: yes

tag: surgical margin pos

value: No

value: Local recurrence


title: kcl10_RNA: KCl stim 10 min RNA

tag: tissue

value: cortical culture DIV 10

tag: stimulated

tag: libraryprepmethod

value: RNA-seq

value: KCl experiment


title: wt_l1pgcs_rep21

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva

value: no


title: cntrk_RPF: KCl stim control RPF

value: Ribosome profiling


title: Head & Neck tissue (X1922146132_D)

value: Male

value: Larynx NOS

tag: site

value: Larynx

tag: extracapsular extension

value: Yes

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: No evidence of disease


title: kcl10_RPF: KCl stim 10 min RPF

tag: experiment type


title: wt_l1pgcs_rep16

tag: source strain

tag: genotype

tag: stage and sex

tag: sequencing batch

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations higher than the median of all PGCs and EGCs.


title: D302T35 concentrated conditioned medium

tag: donor

tag: treatment

value: concentrated conditioned medium


title: Head & Neck tissue (X1922146132_B)

value: Gingiva

value: Oral Cavity

tag: n

value: yes

tag: extracapsular extension. extra neural extension

value: No

tag: lymphovascular invasion

tag: perineural invasion

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Dead

value: Tumor

value: Distant metastasis


title: wt_l1pgcs_rep17

value: DUP64 (i.e. "wild type")

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva

tag: outliers filtered from analysis

value: no


title: Head & Neck tissue (X1922146132_A)

tag: gender

value: Male

value: Floor of mouth

tag: site

tag: extracapsular extension

tag: surgical margin pos

tag: primary. recurrence date

value: Lung, Bone

value: Local recurrence+Distant metastasis


title: kcl30_RNA: KCl stim 30 min RNA

tag: tissue

value: cortical culture DIV 10

tag: stimulated

value: Yes

tag: libraryprepmethod

value: RNA-seq

tag: experiment type

value: KCl experiment


title: D302T33 EV-R

tag: donor

tag: treatment

value: EV-R


title: bdnfs_RPF: BDNF stim RPF

value: cortical culture DIV 14

value: Ribosome profiling

value: BDNF/Glugly experiment


title: cntrk_RNA: KCl stim control RNA

value: No


title: D302T34 EV-poor

value: EV-poor


title: wt_l1pgcs_rep14

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

tag: stage and sex

tag: sequencing batch


title: cntrb_RPF: BDNF and glugly stim control RPF


title: glugl_RPF: Glugly stim RPF


title: Head & Neck tissue (X1922146024_E)

value: Gingiva

value: Oral Cavity

tag: n

value: yes

tag: extracapsular extension. extra neural extension

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: No evidence of disease


title: D302T32 recombinant CSF-1

value: recombinant CSF-1


title: Head & Neck tissue (X1922146024_C)

tag: gender

value: Male

value: Oral tongue

tag: site

tag: extracapsular extension

value: Yes

tag: lymphovascular invasion

tag: perineural invasion

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Distant metastasis


title: Head & Neck tissue (X1922146024_D)

value: Hypopharyngeal wall

value: Hypopharynx

tag: surgical margin pos


title: D302T31 concentrated conditioned medium

tag: donor

tag: treatment

value: concentrated conditioned medium


title: D302T30 EV-poor

value: EV-poor


title: wt_l1pgcs_rep15

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva

tag: outliers filtered from analysis

value: no


title: Nlrx_OE_T_3

city: Tianjin

first: Ling

last: Shuai

address: 38 Tong Yan Road, Jinnan district

department: State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy

institute: Nankai University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. Then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: mm10 (GRCm38)
Supplementary files format and content: *.txt: Tab-delimited text files include RPKM values for each Sample.

source_name: embryonic stem cells

extract_protocol:
WT-ESCs, Slc25a43-KO ESCs, and Nlrx1-OE ESCs were collected and RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250~300 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 m in followed by 5 min at 95 °Cbefore PCR. Then PCR was performed with Phusion High -Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: strain

tag: cell type

value: embryonic stem cells


title: glugl_RNA: Glugly stim RNA

tag: tissue

value: cortical culture DIV 14

tag: stimulated

tag: libraryprepmethod

value: RNA-seq

tag: experiment type

value: BDNF/Glugly experiment


title: bdnfs_RNA: BDNF stim RNA


title: D302T28 recombinant CSF-1

value: recombinant CSF-1


title: Slc3_T_1


title: C1.1_24hr_nuc_3

city: Kuopio

first: Mikko

middle: P

last: Turunen

address: Yliopistonranta 1 E

department: A. I. Virtanen Institute

country: Finland

institute: University of Eastern Finland

data_processing:
Our data analysis pipeline is based on the Tuxedo software package, which is a combination of open-source software and implements peer-reviewed statistical methods. In addition we employ specialized software developed internally at Exiqon to interpret and improve the readability of the final results. The components of our NGS RNA seq analysis pipeline include Bowtie2 (v. 2.2.2), Tophat (v2.0.11) and Cufflinks (v2.2.1).
Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns the sequencing reads to the reference genome using the sequence aligner Bowtie2. Tophat also uses the sequence alignments to identify splice junctions for both known and novel transcripts.
Cufflinks takes the alignment results from Tophat to assemble the aligned sequences into transcripts, constructing a map or a snapshot of the transcriptome. To guide the assembly process, an existing transcript annotation is used. In addition, we perform fragment bias correction which seeks to correct for sequence bias during library preparation (see Kasper et al., 2010 and Adam et al., 2011). The Cufflinks assembles aligned reads into different transcript isoforms based on exon usage and also determines the transcriptional start sites (TSSs).
When comparing groups, Cuffdiff is used to calculate the FPKM (number of fragments per kilobase per million mapped fragments) and test for differential expression and regulation among the assembled transcripts across the submitted samples using the Cufflinks output. Cuffdiff can be used to test differential expression at different levels, from CDS and gene specific, down to the isoform and TSS transcript level. For more information on the Cuffdiff module, see Trapnell et al., (2013).
When comparing groups with paired samples, featureCounts is used to calculate the counts of mapped reads in specific genes, and generalized linear model likelihood ratio test (glmLRT) implemented by edgeR is used to test for differential expression across the submitted samples using featureCounts output. For more information on featureCounts, (see Liao Y, 2014). For more information on edgeR and glmLRT, (see McCarthy, 2012).
As a final step, CummeRbund, which is an open source R package, will be used in combination with in-house custom software for post processing of Cufflinks and Cuffdiff results. We use these tools to generate a visual representation of your sequencing results to aid the interpretation of the sequencing data and the analysis results.
Genome_build: GRCm38
Supplementary_files_format_and_content: fastq files were generated by Exiqon A/S, Vedbaek, Denmark and further processed to xlsx file by authors

molecule: nuclear RNA

source_name: C1.1. mutant cell line

growth_protocol: C166 or C1.1 cells were grown on 150 mm cell culture dish in DMEM containing 10 % FBS and 1 % penicillin-streptomycin. Cells were split for experiments two days prior treatment so that they reach 80% confluency at the time of treatment.

extract_protocol:
Cells were fractionated into nuclear and cytoplasmic fractions and RNA isolated according to a protocol by Gagnon et al. (Gagnon K, Li L, Janowski BA, Corey DR. Analysis of nuclear RNA interference in human cells by subcellular fractionation and Argonaute loading. Nature Protocols 2014, vol. 9, no. 9, p.2045-60).
The library preparation was done using TruSeq® stranded total RNA sample preparation kit with rRNA depletion (Illumina inc).The starting material (300 ng) of total RNA was rRNA depleted using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal. The isolated mRNA was subsequently fragmented using enzymatic fragmentation. Then first strand synthesis and second strand synthesis were performed and the double stranded cDNA was purified (AMPure XP, Beckman Coulter). The cDNA was end repaired, 3’ adenylated and Illumina sequencing adaptors ligated onto the fragments ends, and the library was purified (AMPure XP). The mRNA stranded libraries were pre-amplified with PCR and purified (AMPure XP). The libraries size distribution was validated and quality inspected on a Bioanalyzer high sensitivity DNA chip (Agilent Technologies). High quality libraries were quantified using qPCR, the concentration normalized and the samples pooled according to the project specification (number of reads). The library pool(s) were re-quantified with qPCR and optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing on HiSeq2500) instrument using hiSeq v.4 reagents (51 cycles) (Illumina Inc.).(service from Exiqon A/S, Vedbaek, Denmark)

treatment_protocol: Cells were treated with hypoxia (2h or 24h) or normoxia (control). Hypoxia treatment was done using 1 % oxygen (InvivO2 Baker Ruskinn hypoxia chamber).

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

value: 24h hypoxia

tag: fraction

value: nucleus


title: Nlrx_OE_T_2


title: wt_l1pgcs_rep13

tag: stage and sex

tag: sequencing batch


title: D302T27 concentrated conditioned medium


title: cntrb_RNA: BDNF and glugly stim control RNA

value: No


title: Head & Neck tissue (X1922146024_A)

source_name: Head & Neck tissues

tag: gender

value: Male

value: Pyriform Sinus

tag: site

tag: n

tag: extra neural extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: lymphovascular invasion

tag: perineural invasion

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

value: Lung

value: Dead

value: Tumor

value: Distant metastasis


title: wt_l1pgcs_rep12

tag: source strain

value: DUP64 (i.e. "wild type")

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I

value: L1 hermaphrodite larva

tag: outliers filtered from analysis

value: yes:the % of library that aligned to ERCC spike-in transcripts was >3 median absolute deviations higher than the median of all PGCs and EGCs.


title: Head & Neck tissue (X1922146024_B)

value: Floor of mouth

value: Oral Cavity

tag: extracapsular extension

tag: surgical margin pos

tag: vascular invasion

tag: distant metastasis site

value: Lung, Bone, Liver


title: Head & Neck tissue (X1911480094_A)

tag: gender

value: Pyriform sinus

value: Hypopharynx

tag: primary. recurrence date

value: Local recurrence+Distant metastasis


title: Head & Neck tissue (X1718911493_F)

value: Male

value: Hard palate

tag: site

tag: n

value: no nodes

value: No

value: Alive

value: No evidence of disease


title: Head & Neck tissue (X1718911493_E)

value: Female

value: Larynx NOS

value: Larynx

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

value: Tumor


title: Head & Neck tissue (X1718911493_D)

value: Tonsillar fossa

value: Oropharynx

value: Dead


title: D302T29 EV-R

tag: donor

tag: treatment

value: EV-R


title: Slc1_T_1

tag: strain

tag: cell type

value: embryonic stem cells


title: D302T25 EV-R


title: C1.1_2hr_nuc_3

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

value: 2h hypoxia

tag: fraction

value: nucleus


title: WT_T_1

value: wild type diploid


title: C1.1_24hr_nuc_1

value: 24h hypoxia


title: Exp2_3D_WT050176_3

city: Medford

first: Nicholas

middle: James

last: Fiore

state: MA

address: 200 College Ave

department: Biomedical Engineering

institute: Tufts University

data_processing:
Illumina pipeline CASAVA v1.8.2 was used for base calling.
Raw sequencing data was uploaded to the Tufts University Galaxy Server for quality and adapter trimming with Trim Galore, read alignment with RNA STAR (reference human genome build 38), and read quantification with FeatureCounts using default settings.
Normalized read count tables, obtained by dividing the read counts by their size factors, were generated and extracted with the DESeq2 R package.
Genome_build: reference human genome build 38
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: dopaminergic neurons

growth_protocol: On day 0, a single cell suspension of hiPSCs (maintained with mTeSR1) was seeded in 50:50 (v/v) mTeSR1:floor plate specification medium (neurobasal medium (ThermoFisher 21103049) with 1X floor plate specification supplement (ThermoFisher A3146801)) supplemented with 10 μM Y-27632 (STEMCELL Technologies 72302) at a density of 2 x 10^5 cells/cm2 on 6-well plates coated with Matrigel. The next day, cells were washed with Dulbecco’s phosphate buffered saline (DPBS, ThermoFisher) and fresh specification medium was added. Medium was carefully changed every 48 hours. On day 11, floor plate progenitors (FPPs) were split 1:2 using Accutase (Innovative Cell Technologies AT104, San Diego, CA, USA) onto new Matrigel-coated 6-well plates with FPP expansion medium (ThermoFisher A3165801) + 10 μm Y-27642. FPPs were expanded (replacing FPP expansion medium every 48 hours) until cryopreservation on day 22 with Synth-a-Freeze reagent (ThermoFisher A1254201) to establish batches of cells for experimental consistency. For each individual experiment, FPPs were thawed and plated at a density of 6.25 x 10^5 cells/cm2 in Matrigel coated 6-well plates supplemented with 10 μM Y-27642. On day 28, FPPs were differentiated to DA neurons starting with a 72 hour treatment of maturation medium (DMEM/F12 (ThermoFisher 10565018) with 1X maturation supplement (ThermoFisher A3147401)) containing 1 μM PD0325901 (MilliporeSigma PZ0162, Burlington, MA, USA) and 5 μM SU5402 (MilliporeSigma SML0443). PD0325901 and SU5402 were employed to inhibit progenitor cell proliferation and promote neurogenesis.

extract_protocol:
Total RNA was isolated from independent cultures using the RNeasy mini kit (Qiagen 74106, Hilden, Germany) utilizing the on-column DNA-digestion procedure according to manufacturer’s instructions. To improve extraction efficiency, the 2D cultures and 3D constructs were gently sonicated in the kit’s lysis buffer prior to extraction (ThermoFisher model no. FB120, 20% power, 1 second on followed by 1 second off for 10 pulses total). Sample purity and concentration was measured with a Nanodrop (ThermoFisher) spectrophotometer and 1 μg RNA per sample with a 260/280 nm reading greater than 2 were sent to Novogene for additional quality control tests, library preparation, and sequencing. First, RNA degradation and contamination were assessed on 1% agarose gels and RNA purity was checked using a NanoPhotometer spectrophotometer (Implen, Munich, Germany). RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, CA, USA).
Library preparation was achieved using the NEBNext Ultra RNA library prep kit for Illumina systems following manufacturer’s recommendations (New England Biolabs, Ipswich, MA, USA) and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand complementary DNA (cDNA) was synthesized using random hexamer primer and M-MuLV reverse transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptors with a hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Brea, CA, USA). Then 3 μL USER Enzyme (New England Biolabs) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by 5 minutes at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system, Beckman Coulter) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on an Illumina Novaseq sequencer according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on the same machine and paired-end reads were generated at a read depth of 20 million reads.

treatment_protocol: On day 31, cells were pre-differentiated DA neurons were seeded into 2D and 3D culture condition

value: hiPSC-derived dopaminergic neurons

value: Wild Type

tag: parkinson's disease (pd) status

value: Healthy

tag: culture condition

value: Three dimensional (3D)

tag: experiment number


title: D302T26 EV-poor

value: EV-poor


title: Exp2_3D_WT050176_2

tag: genotype


title: C1.1_24hr_nuc_2


title: S22854_404_c140_vino_pd1

city: Milan

first: Francesco

last: Bertolini

state: I am not in the U.S. or Canada

address: Via Giuseppe Ripamonti, 435

country: Italy

institute: European Institute of Oncology (IEO)

data_processing:
FASTQ files were converted to digital gene-cell count matrices using a Singularity- dependent Snakemake pipeline (https://github.com/raveancic/scRNAaltas_TNBC_mm/tree/master/cl_crt_FASTQ2countmat) employing the Cell Ranger v4 software. As reference, the Mus musculus reference genome GENCODE vM23/Ensembl98 was used. Market Exchange Format (MEX) for sparse matrices generated from the pipeline were loaded, merged, processed and analyzed using Seurat package.
Genome_build: mm10 (GENCODE vM23/Ensembl98)
Supplementary_files_format_and_content: Market Exchange Format (MEX) for sparse matrices

source_name: Cd45+ tumoral microenvironment

extract_protocol:
Tumours of three mice were dissociated and pooled together to generate the single cell suspension. The cell suspensions were then prepared for cell sorting with FACS Fusion sorter (BD bioscience). Only Cd45 + DAPI - (alive immune cells) were sorted and purity evaluated
10X Genomics protocol

tag: cell line

tag: condition

value: C140 + V + alphaPD-1

tag: 10x chemistry version


title: C1.1_2hr_nuc_1


title: C1.1_0hr_nuc_3

value: normoxia


title: S24237_461_cispl_pd1

value: P(Cisplatin) + alphaPD-1


title: Exp2_3D_LRRK050779_2

value: LRRK2 G2019S

value: PD


title: Head & Neck tissue (X1718911492_D)

tag: gender

value: Male

value: Epiglottis suprahyoid

value: Larynx

tag: extracapsular extension

value: yes

value: Yes

tag: surgical margin pos

value: No

tag: primary. recurrence

tag: neck.recurrence date

tag: any.recurrence_local recurrence.or.local regional recurrence

tag: distant metastasis data

tag: distant metastasis site

value: Lung, Subcutaneous

value: Dead

value: Tumor

value: Local regional recurrence+Distant metastasis


title: Slc2_T_1

tag: strain

tag: cell type

value: embryonic stem cells


title: Exp2_3D_WT050176_1

value: hiPSC-derived dopaminergic neurons

value: Wild Type

tag: parkinson's disease (pd) status

value: Healthy

value: Three dimensional (3D)


title: S21976_358_pacli_pd1

value: T(Paclitaxel) + alphaPD-1


title: C1.1_0hr_nuc_2

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

tag: treatment

value: normoxia

tag: fraction

value: nucleus


title: Head & Neck tissue (X1718911396_F)

value: Male

value: Gingiva upper

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

tag: perineural invasion

tag: primary. recurrence date

value: Local recurrence+Local regional recurrence


title: C1.1_0hr_nuc_1


title: Head & Neck tissue (X1718911492_F)

tag: gender

value: Epiglottis suprahyoid

value: Larynx

tag: extracapsular extension

value: yes

value: Yes

value: No

value: Lung

value: Alive

value: Distant metastasis


title: S21975_357_doxo_pd1

tag: cell line

tag: condition

value: D(Doxorubicin) + alphaPD-1

tag: 10x chemistry version


title: Exp2_3D_LRRK050779_1

value: hiPSC-derived dopaminergic neurons

tag: genotype

value: LRRK2 G2019S

value: PD

tag: culture condition

value: Three dimensional (3D)

tag: experiment number


title: Head & Neck tissue (X1718911492_C)

value: Female

value: Larynx NOS

tag: surgical margin pos

tag: lymphovascular invasion

tag: primary. recurrence

tag: any.recurrence_local recurrence.or.local regional recurrence

value: Dead

value: Tumor

value: Local recurrence


title: Exp2_3D_LRRK050401-01_2

tag: cell type

tag: parkinson's disease (pd) status


title: Head & Neck tissue (X1718911492_B)

value: Male

value: Oral Tongue

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: no

value: No evidence of disease


title: S21974_356_c140_pd1

value: C140 + alphaPD-1


title: C166_24hr_nuc_2

source_name: C166 endothelial cell line

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)

tag: treatment

value: 24h hypoxia

tag: fraction

value: nucleus


title: Exp2_3D_LRRK050401-01_1

value: hiPSC-derived dopaminergic neurons

value: LRRK2 G2019S

value: PD


title: S21973_355_c140

tag: cell line

value: C140 (Cyclophosphamide)


title: C1.1_2hr_nuc_2

value: yolk sac -derived endothelial cells (ATCC:CRL-2581) with CRISPR-mediated removal of mmu-miR-466c

value: 2h hypoxia


title: C166_24hr_nuc_3


title: S21972_354_pd1

tag: condition


title: C166_24hr_nuc_1


title: C166_2hr_nuc_3


title: Head & Neck tissue (X1718911396_D)

tag: gender

value: Female

tag: extracapsular extension

value: yes

value: Yes

value: No

tag: perineural invasion

tag: vascular invasion

tag: primary. recurrence date

tag: neck.recurrence date

value: Dead

value: Tumor

value: Local recurrence+Local regional recurrence


title: S22853_403_c140_vino

value: C140 + V (Vinorelbine)

tag: 10x chemistry version


title: Exp2_2D_WT050176_1

tag: genotype

value: Wild Type

value: Healthy

tag: culture condition

value: Two dimensional (2D)

tag: experiment number


title: hSKP-HPC NASH + ELA 60 µM 2

city: Brussels

first: Joost

last: Boeckmans

address: Laarbeeklaan 103

department: In Vitro Toxicology & Dermato-Cosmetology (IVTD)

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

hyb_protocol: 1) 12.5 µg fragmented aRNA was hybridized to Affymetrix Human Genome U133 plus 2.0 chips with hybridization cocktail solution.  2) Chips were incubated in an Genechip Hybridization Oven-645 (Affymetrix) (60 RPM / 45 °C /16h)  3) Chips were washed on a Genechip Fluidics Station-450 (Affymetrix)  4) Chips were stained with the Affymetrix HWS kit

scan_protocol: The chips were scanned with an Affymetrix Gene-Chip Scanner-3000-7G.

data_processing: Robust Multichip Average (RMA) Express was used for normalization and summarization.

source_name: foreskin

label_protocol: RNA (100 ng) was amplified using the GeneChip 3' IVT PLUS Reagent Kit (Affymetrix). The amplified RNA was purified using magnetic beads and 15 µg Biotin-aRNA was treated with fragmentation reagent.

growth_protocol: Cell cultures and exposures were performed according to Rodrigues et al. (2014) (DOI: 10.1089/scd.2013.0157) and Boeckmans et al. (2020) (DOI: 10.1007/s10565-020-09544-2)

extract_protocol: Total RNA was extracted using the GenElute Mammalian Total RNA Purification Miniprep Kit (Sigma-Aldrich).

value: 'NASH' triggers + elafibranor 60 µM

tag: cells

value: hSKP-HPC


title: Exp2_2D_LRRK050779_1

tag: cell type

value: hiPSC-derived dopaminergic neurons

value: LRRK2 G2019S

tag: parkinson's disease (pd) status

value: PD


title: hSKP-HPC NASH + ELA 60 µM 1

tag: treatment


title: PHH NASH + ELA 60 µM 3

source_name: liver

value: PHH


title: S24236_460_pacli_pd1

value: T(Paclitaxel) + alphaPD-1


title: hSKP-HPC NASH + ELA 60 µM 3


title: C166_0hr_nuc_3

value: yolk sac -derived endothelial cells (ATCC:CRL-2581)

value: normoxia

tag: fraction

value: nucleus


title: PHH NASH + ELA 60 µM 2