title: Healthy_5

description:
small RNA
C2_C1

value: Cow 11


title: Low_SCC_5

status: Public on Mar 16 2022

type: SRA

city: Zurich

first: Maria

middle: Desemparats

last: Saenz-de-Juano

address: Universitatstrasse 2

country: Switzerland

institute: ETH Zurich

description:
small RNA
C6_L2

library_source: transcriptomic

data_processing:
Remove Adapter:  Tool “Clip” from Galaxy
Remove short reads (<25 nucleotides):  Tool “Clip” from Galaxy
Remove Low Quality reads:  Tool "FASTQ Quality Trimmer" from Galaxy
Remove PCR duplicates:  Tool “Collapse” from galaxy
Filtering:  "Count Per Million (CPM) Filter" from Galaxy
miRNA Aligment:  Aligment was performed using "blastn-short". Only alignments without any mismatch were included.
IsomiRs grouping:  IsomiRs  were grouped in their canonical form and their counts were sum, using the tool "Group on data" from Galaxy
Genome_build: miRBase database v22.1.
Supplementary_files_format_and_content: Normalization of read counts was done using TMM and GLM robust (estimateGLMRobustDisp) included in edgeR

molecule: total RNA

organism: Bos taurus

source_name: Milk EV

extract_protocol:
miRNeasy MicroKit  (QIAGEN) following manufacturer's instructions
NEXTflex™ Small RNA-Seq Kit v3 (Bioo Scientific)  following manufacturer's instructions

tag: type

tag: animal

value: Cow 15

tag: sample type

value: Milk EV


title: hippocampus, YC76

city: Houston

first: Yi-Ting

last: Cheng

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
Quality control was performed on fastq files using fastQC and multiQC. Paired end reads were mapped to the mouse genome (mm10) using STAR (v2.5.0a).
Reads Per Million (RPM) were calculated using GenomicAlignments (v1.16.0) and DESeq2 (v1.20.0) was used for read count normalization and differential gene expression between different samples.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM normalized abundance measurements from astrocytes

organism: Mus musculus

source_name: hippocampus

extract_protocol:
Tissue was dissociated as previously described. (Lin et al., Nat Neurosci 2017)
Illumina sequencing libraries were constructed from 500pg - 1ng of total RNA using the Trio RNA-seq (Nugen)

tag: tissue

value: hippocampus

tag: cell type

value: astrocyte

tag: age


title: KO_C_3

city: Montréal

first: Vincent

last: Giguère

state: QC

address: 1160 Pine Ave West, McIntyre Bldg Room 710

department: Goodman Cancer Centre

country: Canada

institute: McGill University

data_processing:
Reference mouse genome mm10 and gene model annotation files were directly downloaded from the genome website browser (NCBI/UCSC/Ensembl)
The STAR (Spliced Transcripts Alignment to a Reference) software was used to align paired-end clean reads to the reference genome, and to count number reads per gene while mapping.
FPKM (Fragments per kilobase of transcript sequence per millions base pairs sequenced) of each gene was calculated based on the length of the gene and read counts mapped to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

growth_protocol: Mice fed a standard normal diet.

extract_protocol:
Total RNA was extracted from frozen liver and skeletal muscle using a RNeasy Mini Kit (QIAGEN) and a RNeasy Fibrous Tissue Mini Kit (QIAGEN), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For liver RNA-sequencing of insulin stimulation, ERRα WT or KO mice on a C57BL/6N genetic background were randomly assigned to two groups and fasted for 12 h overnight followed by intraperitoneal injection of saline or 1 unit/kg insulin.

tag: strain

value: Liver

tag: genotype

value: Err-alpha KO

tag: treatment

value: control


title: Healthy_2

description:
small RNA
C1_C1

value: Healthy

value: Cow 9


title: WT_C_2

value: WT


title: WT_C_1


title: WT_INS_3

value: insulin


title: cortex, YC47

source_name: cortex

value: cortex


title: hippocampus, YC74


title: Healthy_3

description:
small RNA
C1_C3


title: shZfp207_3

city: Nanjing

first: Xu

last: Wang

state: Jiangsu

address: Longmian road 639

department: Center for New Drug Safety Evaluation and Research

country: China

institute: China pharmaceutical university

data_processing:
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 ploy-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. And 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.
Genome_build: mm10
tab-delimited excel files include readcount and FPKM values for each sample
Genome_build: mm10
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: Mouse HCC cell line

growth_protocol: Hepa1-6 cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% Penicillin-Streptomycin  at 37 ℃ in a humidified 5% CO2 incubator.

extract_protocol:
RNA was harvested using Trizol reagent. RNA purity was checked using the NanoPhotomete spectrophotometer (IMPLEN, CA, USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Zfp207 knockdown

value: Tumor


title: Healthy_1

description:
small RNA
C2_C2


title: WT_C_3


title: WT_INS_2


title: Low_SCC_2

description:
small RNA
C5_L2

value: Cow 14


title: shZfp207_1


title: WT_INS_1


title: shNC_1


title: KO_C_2


title: WT_C_4


title: Low_SCC_1

description:
small RNA
C4_L2

value: Cow 8


title: D30_WT_SBNX_8 [H9_Triple-i_Day 30]

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.

organism: Homo sapiens

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: cell line

tag: protocol

value: Triple-i

value: Day 30

value: Brain Organoid


title: shZfp207_2


title: cortex, YC30


title: shNC_3


title: cortex, YC39


title: cortex, YC45


title: shNC_2


title: cortex, YC44


title: D0_Embryonic stem cells WT 1 [H9_hESCs_Day 0]

source_name: hESCs

value: hESCs

value: Day 0


title: cortex, YC48

value: astrocyte


title: D30_WT_SBN_8 [H9_Dual SMAD-i_Day 30]

value: Dual SMAD-i


title: cortex, YC34


title: sictrl_EtOH

city: Wuhan

first: Ge

last: Sun

state: Hubei

address: Shizi Mountain Street No.1

institute: Huazhong Argriculture University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ATAC-seq reads were aligned to the human genome hg38 assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg38
Supplementary files format and content: bw files were generated using python

molecule: genomic DNA

source_name: Breast cancer

growth_protocol: MCF7 cells were cucltured into DMEM medium with 10% FBS

extract_protocol:
Primary analyze of ATAC-seq: The threshold of the number of the valid peak was selected within a false discovery rate (FDR) of 0.01. We used the default parameters from HOMER to distinguish genomic distribution, while promoter peaks were defined as those with peak center falling between 100 bp downstream and 5,000 bp upstream of transcript start sites (TSS). Exon, intron, and transcript terminate site (TTS) regions were exported from the National Center for Biological Information (NCBI), and the other regions were suggested as intergenic regions. To define meaningful BAP18 binding sites, we defined the fold enrichment of a peak was larger than 2 in IP versus input and the fold change (FC) of tag density was considered at least p<10e-5.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For BAP18 ATAC-seq, 1*10e7 MCF7 cells were contained in a 9ml DMEM medium fixed with 243ul paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 15 min at room temperature. Then the crosslinks were stopped by 2.5M glycine to a final concentration of 0.125M. Cells were rinsed with icily PBS and performed in Wuhan Seqhealth Tech Co. LTD.

value: Luminal

value: MCF7 cells

value: EtOH


title: siBAP_EtOH


title: siBAP_E2

value: estrogen


title: input_minus (E2 control)

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the human genome hg38 assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Assembly: hg38
Supplementary files format and content: bw files were generated using python

extract_protocol:
Primary analyze of ChIP-seq: The threshold of the number of the valid peak was selected within a false discovery rate (FDR) of 0.01. We used the default parameters from HOMER to distinguish genomic distribution, while promoter peaks were defined as those with peak center falling between 100 bp downstream and 5,000 bp upstream of transcript start sites (TSS). Exon, intron, and transcript terminate site (TTS) regions were exported from the National Center for Biological Information (NCBI), and the other regions were suggested as intergenic regions. To define meaningful BAP18 binding sites, we defined the fold enrichment of a peak was larger than 2 in IP versus input and the fold change (FC) of tag density was considered at least p<10e-5.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For BAP18 ChIP-seq, 1*10e7 MCF7 cells were contained in a 9ml DMEM medium fixed with 243ul paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 15 min at room temperature. Then the crosslinks were stopped by 2.5M glycine to a final concentration of 0.125M. Cells were rinsed with icily PBS and performed in Wuhan Seqhealth Tech Co. LTD.


title: E2_minus


title: D30_WT_SBNX_6 [H9_Triple-i_Day 30]


title: cortex, YC46


title: D30_WT_SBNX_7 [H9_Triple-i_Day 30]


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female06

type: RNA

city: Toronto

first: Elena

last: Comelli

state: Ontario

address: 1 king's college circle, MSB5354

department: Nutritional Sciences

institute: University of Toronto

hyb_protocol: 200 ng of total RNA per sample, was first hybridized with capture and reporter probes which then hybridize to the target molecules, using Nanostring miRNA assay kit and following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.).

scan_protocol: Following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.)

data_processing:
miRNA expression data were processed using nSolverTM Analysis Software V4.0 (NanoString Technologies). Background hybridization was corrected by subtracting the geometric mean of the negative controls. Data were then normalized to the mean of all probes, and finally, log2 transformed.
Nanostring digital analyzer was used for raw data collection, while nSolverTM Analysis Software V4.0 (NanoString Technologies) was used for data analysis

label: Fluorescent barcode and biotin moiety

source_name: Mouse mammary gland

label_protocol: Not supplied

growth_protocol: Not applied

extract_protocol: Total RNA was extracted from the 4th left of the mammary gland using the mirVana™ miRNA Isolation Kit (catalog no. AM1561, Invitrogen™, Thermo Fisher Scientific, Vilnius, Lithuania), following the manufacturer’s protocol

treatment_protocol: Not applied

value: Mammary gland-4th left

tag: treatment group


title: D30_WT_SBNX_5 [H9_Triple-i_Day 30]


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female05


title: sictrl_E2


title: cortex, YC43

value: cortex


title: RNA_St6_2_ISC

city: Bethesda

first: Han-Yu

last: Shih

state: MD

address: 10 Center Drive Rm 5S261

institute: National Eye Institute

data_processing:
ATAC-seq:
Omni-ATAC-seq reads from biological replicates were mapped to the mouse genome (mm10 assembly) using Bowtie 1.3.0 with parameters -v 2 -m 1 --pairtries 200.
Peaks were called using Macs1 (version 1.4.3) with a p-value cutoff of 1E-5. Peak files were merged for each condition using homer’s mergePeaks command with parameter -d given. Peak files were converted to bed format using HOMER’s pos2bed.pl function and compared using bedtools (version 2.30.0). Only regions called in both replicates were used in downstream analysis. A master list of peaks was generated using HOMER’s mergePeaks function with -d given, and annotated using HOMER’s annotatePeaks.pl function, with reference genome mm10, -size given, and tag counts from tag directories created previously.
RNA-seq:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. Read counts were generated using HTSeq (version 0.11.4), with parameters -m union, --stranded=reverse, and the mm10 genes.gtf file from UCSC.
Differential gene expression analysis was performed using DESeq2 (version 1.30.1) in RStudio (version 1.4.1106) using R (version 4.0.4).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files for ATAC-seq and RNA-seq

source_name: colon crypt cell

extract_protocol:
cell isolation protocol: For colon crypt cell isolation, take colon carefully and put into 10 cm dish containing cold PBS, associated fat tissue was removed carefully. Flush the lumen of the intestine with cold PBS, cut the colon longitudinally with scissors and place in a 50ml tube with 25ml cold PBS, invert 10~15 times and remove PBS (repeat until the supernatant no longer contains any visible debris), cut the colon into around 5mm pieces and place into cold 10ml 5mM EDTA-PBS. Vigorously triturate the fragments by pipetting up and down into a 10ml pipette 15 times, Let the fragments settle by gravity for 30 sec, aspirate the supernatant (Be careful to avoid the intestinal fragments). Replace with 10ml 5mM EDTA-PBS and place at 4°C on roller for 15 min and remove the EDTA-PBS from the tube by aspiration. Wash with PBS twice and add 3ml Basal media (RPMI 1640) containing 500U/ml Collagenase Type IV and pipette up and down 5 times using 5ml pipette. Place the tubes in 37°C water bath for 30-40min. Add 10ml cold PBS and then vigorously vortex with a 10ml pipette (x10 times), Collect this 10 ml supernatant fraction in a separate tube. Repeat the cold PBS/vortex 2 more times, and combined 2nd and 3rd round wash into 50ml tube to gather crypt cells.
Omni-ATAC protocol (Corces et al., 2017). Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. ImmediWe followed the Omni-ATAC protocol (Corces et al., 2017). Briefly, 50000 cells were washed and lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500g for 10 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. ately after lysis, nuclei were spun at 500g for 10 min to remove the supernatant. Nuclei were then incubated with the Tn5 transposome and tagmentation buffer (20 mM Tris-HCl (pH 7.6), 10 mM MgCl2, 20% Dimethylformamide) containing 0.1% Tween-20 and 0.005% Digitonin at 37 °C for 30 min. After the tagmentation, the stop buffer was added directly into the reaction to end the tagmentation. PCR was performed to amplify the library.
ATAC-seq: PCR was performed to amplify the library. After the PCR reaction, libraries were purified with SPRI (Beckman) beads and deep sequencing was performed by Sequencing Facility in NCI.
For RNA-seq, the mRNA from fresh isolated 2-5 million colon crypt ISCs was isolated by using RNeasy Plus Micro Kit (Qiagen, cat:74034) and the concentration and QC was determined by Agilent technologies.
RNA-Seq samples were pooled and sequenced on NextSeq using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

value: Colon

tag: genotype/variation

tag: culture condition

value: ex vivo

value: intestinal epithelial cells.


title: cortex, YC167

description: Gabbr1_integrated_seurat_labelled.rds, Gabbr1_integrated_seurat_labelled_AS.EN.IN.rds

data_processing:
Sample alignment was done by 10X Cell Ranger (v3.0.2)
Quality control was performed using Seurat (v4.1.0) by following criteria: nUMI/cell threshold > 200, gene/cell threshold > 250, log10gene/UMI threshold > 0.8, mitochondria ratio < 0.3, and ribosome ration > 0.01
DoubletFinder, cluster, and annotate clusters -> save this file as Gabbr1_integrated_seurat_labelled.rds
isolate sub-culsters, astrocyte, interneuron, and excitatory neurons
FindMarkers by Seurat -> saved as Gabbr1_integrated_seurat_labelled_AS.EN.IN.rds
CellChat
Assembly: mm10
Supplementary files format and content: rds files include FPKM values from astrocytes

extract_protocol:
Tissue was dissociated by using MACS neural dissociation kit
Illumina sequencing libraries were prepared by Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics)

value: Gabbr1 control


title: D30_WT_XAV_2 [H9_WNT-i_Day 30]

value: WNT-i


title: D30_WT_SBN_7 [H9_Dual SMAD-i_Day 30]

value: Day 30


title: Mammary Gland- 3.67% Flaxseed Oil-female06

value: 3.67% Flaxseed Oil


title: cortex, YC168

value: Gabbr1 cKO


title: Mammary Gland- 3.67% Flaxseed Oil-female01


title: Mammary Gland- 3.67% Flaxseed Oil-female02


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female03


title: E2_plus


title: D30_WT_NT_7 [H9_Inhibitor-free_Day 30]

value: Inhibitor-free

value: Brain Organoid


title: cortex, YC42

value: astrocyte


title: D30_WT_NT_6 [H9_Inhibitor-free_Day 30]


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female04


title: Mammary Gland- 10% Flaxseed-female06

value: 10% Flaxseed


title: Mammary Gland- 10% Flaxseed-female05


title: Mammary Gland- 10% Flaxseed-female04


title: PDX O8378, acq resistance, rep2

city: montpellier

first: stanislas

middle: P

last: du manoir

address: 280 rue des apothicaires

country: France

institute: IRCM

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on the Affymetrix® U133+PM Array in the GeneAtlas oven.

scan_protocol: StripChips were washed and stained on the fluidic station of the Affymetrix GeneAtlas system using GeneAtlas Hybridization Wash & Stain kit.

data_processing: Data were generated with Affymetrix Expression Console v 1.4.1 and GCRMA algorithm. The Final processed data table was obtained by collapsing expression values from multiple input ids that map to a single target gene with the CollapseDataset instruction from GenePattern suite.

label: Biotin

source_name: Acquired-resistance after multiple CBP treatment cycles from PDX O8378

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix GeneAtlas IVT PLUS protocol from 200 ng total RNA (GeneAtlas 3'IVT PLUS Technical Manual, 2013-2015, P/N703210 Rev2 Affymetrix).

growth_protocol: PDX tumors were established by grafting of patient HGOC tumor piece in the intrascapular compartment of NUDE mice.Detailed protocol was previously published (PMID:26334103). Once tumors developed and reached about 120 mm3, each PDX model (one per patient) was stratified into treatment vs no treatment.

extract_protocol: Total RNA was extracted with RNA easy minikit (Quiagen) according to supplier recommandations.

treatment_protocol:
PDX tumors that were in the treatment category received 2 doses of intraperitoneal combination chemotherapy once a week for four weeks.This regimen constitutes a  treatment cycle. PDX tumors that were in the control category received identical volume of Nacl 0.9 %. Therapy was 50 mg/kg of carboplatin.
At the end of one month treatment, both treated and untreated PDX mice were sacrificed according to IACUC protocol. Fresh tumor tissue was harvested and snap frozen in liquid nitrogen.

tag: design

value: Human ovarian PDX tumor

tag: pdx model

value: PDX O8378

value: multiple CBP treatment cycles

tag: phenotype

value: Acquired-resistance


title: D30_WT_NT_8 [H9_Inhibitor-free_Day 30]


title: PDX O8378, acq resistance, rep1


title: PDX O8378, treated regrowth

source_name: regrowth after one cycle of CBP treatment from PDX O3378

value: PDX O3378

value: one cycle of CBP treatment

value: regrowth


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female02

value: Mammary gland-4th left


title: D30_WT_SBN_5 [H9_Dual SMAD-i_Day 30]

value: Dual SMAD-i


title: Mammary Gland- 0.15% secoisolariciresinol diglucoside (SDG)-female01


title: Mammary Gland- 10% Flaxseed-female02


title: input_plus (E2 control)

value: Luminal

value: MCF7 cells


title: D30_WT_SBN_6 [H9_Dual SMAD-i_Day 30]

value: Day 30


title: Mammary Gland- Basel Diet-female06

value: Basal Diet-Control


title: Mammary Gland- 10% Flaxseed-female03


title: D30_WT_SBNX_4 [H9_Triple-i_Day 30]

value: Triple-i


title: Mammary Gland- 3.67% Flaxseed Oil-female03

value: 3.67% Flaxseed Oil


title: Mammary Gland- Basel Diet-female04


title: T-47d cells, miR-mimic negative control 6

city: Reykjavik

last: Bustos

address: Sturlugata 8

country: Iceland

institute: University of Iceland

description: Biotin-labelled miR-mimic negative control 6

data_processing:
Samples were appropriately pooled (up to 24 samples/pool/lane) and clustered on NovaSeq S4 v 1.0 flowcells using on-board clustering. Paired-end sequencing was performed using the XP workflow on NovaSeq6000 instruments with 2*125 cycles of incorporation and imaging in addition to 2*8 cycles for the dual indexes. Basecalling was perfomed in real-time using RTA v3.4.4. Demultiplexing of BCL files and generation of FASTQ files was performed using bcl2fastq2 v.2.20.
RNA-seq reads were aligned to the GRCh38 cDNA reference genome using Kallisto v0.45.0 with the parameters -t 8 -b 100
Normalized counts were generated using DESeq2 version 1.32.0
Assembly: GRCh38
Supplementary files format and content: a HDF5 binary file containing run info, abundance esimates, bootstrap estimates, and transcript length information length

source_name: Breast cancer cell line

growth_protocol: T-47d cells were cultured according to ATCC guidelines

extract_protocol:
miRNA:mRNA complexes were immunoprecipitated first with anti Ago2 antibody and secondly with streptavidin coated magnetic beads. RNA was isolated with  phenol-chloroform-isoamyl alcohol mixure.
cDNA libraries derived from mRNA were generated using Illumina´s TruSeq RNA v2 Sample Prep Kit with minor modifications. Briefly, the starting material (mRNA) was fragmented at 94°C in the presence of divalent cations, followed by first-strand cDNA synthesis using random hexamers and SuperScript IV reverse transcriptase (Invitrogen). Following second-strand cDNA synthesis, end repair, addition of a single A nucleotide, unique dual indexed adaptor ligation, AMPure bead purification, and PCR amplification, the resulting cDNA sequencing libraries were measured on the LabChip GX (Perkin Elmer), diluted to 3 nM and stored at -20 °C.

treatment_protocol: T-47d cells were transfected with biotin-labelled miR-190b mimic or biotin-labelled miR-mimic negative control for 48 hours prior to extraction

value: ER-positive breast cancer cell line

tag: transfection

value: Biotin labelled miR-mimic negative control

tag: rip antibody


title: Mammary Gland- Basel Diet-female01


title: D30_WT_SBNX_2 [H9_Triple-i_Day 30]

value: Brain Organoid


title: PDX O3312, acq resistance, rep1

source_name: Acquired-resistance after multiple CBP treatment cycles from PDX O3312

value: Human ovarian PDX tumor

value: PDX O3312


title: Mammary Gland- 3.67% Flaxseed Oil-female04


title: D30_WT_SBNX_1 [H9_Triple-i_Day 30]


title: PDX O8378, untreated, rep1

source_name: Untreated from PDX O8378

value: PDX O8378

value: untreated

value: naive


title: D30_WT_NT_5 [H9_Inhibitor-free_Day 30]

value: Inhibitor-free


title: Mammary Gland- 10% Flaxseed-female01

value: Mammary gland-4th left

value: 10% Flaxseed


title: D30_WT_SBNX_3 [H9_Triple-i_Day 30]


title: PDX O5588, CBP treated, rep1

source_name: One cycle CBP treated from PDX O5588

value: PDX O5588

value: carboplatin (CBP)


title: T-47d cells, miR-190b mimic replicate 6

description: Biotin-labelled miR-190b mimic replicate 6

value: Biotin labelled miR-190b mimic


title: PDX O3312, acq resistance, rep2

value: multiple CBP treatment cycles

value: Acquired-resistance


title: T-47d cells, miR-190b mimic replicate 5

description: Biotin-labelled miR-190b mimic replicate 5


title: D30_WT_SBN_2 [H9_Dual SMAD-i_Day 30]

value: Dual SMAD-i

value: Day 30


title: PDX O3312, treated regrowth

source_name: regrowth after one cycle of CBP treatment from PDX O3312

value: one cycle of CBP treatment

value: regrowth


title: T-47d cells, miR-mimic negative control 5

description: Biotin-labelled miR-mimic negative control 5

value: ER-positive breast cancer cell line

value: Biotin labelled miR-mimic negative control


title: T-47d cells, miR-mimic negative control 2

description: Biotin-labelled miR-mimic negative control 2


title: D30_WT_SBN_4 [H9_Dual SMAD-i_Day 30]

value: Brain Organoid


title: D30_WT_SBN_1 [H9_Dual SMAD-i_Day 30]


title: T-47d cells, miR-mimic negative control 4

description: Biotin-labelled miR-mimic negative control 4


title: PDX O5588, mock treated, rep2

source_name: One cycle mock treated from PDX O5588

value: Human ovarian PDX tumor

value: mock


title: T-47d cells, miR-mimic negative control 1

description: Biotin-labelled miR-mimic negative control 1


title: Mammary Gland- Basel Diet-female02

value: Basal Diet-Control


title: Mammary Gland- Basel Diet-female03

value: Mammary gland-4th left


title: PDX O5588, CBP treated, rep2


title: D30_WT_SBN_3 [H9_Dual SMAD-i_Day 30]


title: T-47d cells, miR-mimic negative control 3

description: Biotin-labelled miR-mimic negative control 3


title: T-47d cells, miR-190b mimic replicate 4

description: Biotin-labelled miR-190b mimic replicate 4


title: PDX O3312, untreated, rep1

source_name: Untreated from PDX O3312

value: PDX O3312

value: untreated

value: naive


title: T-47d cells, miR-190b mimic replicate 2

description: Biotin-labelled miR-190b mimic replicate 2

value: Biotin labelled miR-190b mimic


title: D30_WT_NT_4 [H9_Inhibitor-free_Day 30]

value: Inhibitor-free


title: PDX O3312, CBP treated, rep2

source_name: One cycle CBP treated from PDX O3312

value: carboplatin (CBP)


title: T-47d cells, miR-190b mimic replicate 1

description: Biotin-labelled miR-190b mimic replicate 1


title: D30_WT_XAV_1 [H9_WNT-i_Day 30]

value: WNT-i


title: RIP_Ishikawa cells_IP

city: Shenyang

first: Cuicui

state: Liaoning

address: Sanhao Street

institute: China Medical University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for protein binding site analysis. They were mapped to the reference genome of Homo_sapiens from Ensembl(ftp://ftp.ensembl.org/pub/release-87/fasta/homo_sapiens/dna/) using STAR software (version 2.5.3a) with default parameters.The RSeQC（version 2.6）was used for reads distribution analysis.
The exomePeak (Version 3.8) software was used for peak calling. Peaks were annotated using bedtools (Version 2.25.0). The deepTools (version 2.4.1) was used for peak distribution analysis. The differentially binding peaks were identified by a python script，using fisher test.
Sequence motifs enriched in peak regions were identified using Homer (version 4.10).
Assembly: GRCh38
Supplementary files format and content: txt

source_name: endometrial carcinoma

growth_protocol: Ishikawa cells were cultured in RPMI 1640 medium with 10% fetal bovine serum. All cells were cultured at 37°C in 5% CO2 with saturated humidity and routinely tested negative for mycoplasma.

extract_protocol:
The grinded cells was treated with cell lysis buffer. The 10% lysis sample was stored and named “input”, and 80% was used in immunoprecipitation reactions with Anti-IMP3 antibody (Abcam,cat. ab177477) and named “IP”, and 10% was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”，respectively. The RNA of input and IP was extracted using TRIzol reagent(Invitrogen, cat. NO 15596026).
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 300-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model

value: Ishikawa cells

value: anti-IGF2BP3 antibody (ab177477, Abcam, USA)


title: RIP_Ishikawa cells_input

value: none (input)


title: PDX O5588, mock treated, rep1

value: PDX O5588


title: Bulk RNA Pre-Treatment Pt43 [TJU0043_1]

city: Nashville

first: Young

last: Kim

state: TN

address: 2220 Pierce Ave PRB 654

institute: Vanderbilt University Medical Center

description: TJU_featurecounts_symbol.tsv (TJU0043_1)

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

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

value: Tumor

tag: tissue type

tag: time point

value: pre


title: Bulk RNA Post-Treatment Pt43 [TJU0043_2]

description: TJU_featurecounts_symbol.tsv (TJU0043_2)

tag: tissue

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

value: post


title: D30_WT_NT_2 [H9_Inhibitor-free_Day 30]

source_name: Brain Organoid

tag: age

value: Day 30

tag: cell type

value: Brain Organoid


title: PDX O3312, CBP treated, rep1

source_name: One cycle CBP treated   from PDX O3312

value: Human ovarian PDX tumor

value: PDX O3312


title: Bulk RNA Post-Treatment Pt40 [TJU0040_2]

description: TJU_featurecounts_symbol.tsv (TJU0040_2)


title: Bulk RNA Pre-Treatment Pt39 [TJU0039_1]

description: TJU_featurecounts_symbol.tsv (TJU0039_1)


title: PDX O3312, mock treated, rep2

source_name: One cycle mock treated from PDX O3312

value: mock


title: Bulk RNA Pre-Treatment Pt50 [TJU0050_1]

description: TJU_featurecounts_symbol.tsv (TJU0050_1)


title: Bulk RNA Post-Treatment Pt39 [TJU0039_2]

description: TJU_featurecounts_symbol.tsv (TJU0039_2)


title: Bulk RNA Post-Treatment Pt50 [TJU0050_2]

description: TJU_featurecounts_symbol.tsv (TJU0050_2)


title: D30_He_pooled_SBNX [H9 STIL +/-_Triple-i_Day 30]

value: H9 STIL +/-

value: Triple-i


title: T-47d cells, miR-190b mimic replicate 3

description: Biotin-labelled miR-190b mimic replicate 3

value: ER-positive breast cancer cell line

value: Biotin labelled miR-190b mimic


title: D30_WT_NT_1 [H9_Inhibitor-free_Day 30]

value: Inhibitor-free


title: Bulk RNA Pre-Treatment Pt37 [TJU0037_1]

description: TJU_featurecounts_symbol.tsv (TJU0037_1)


title: PDX O1047, CBP treated, rep1

source_name: One cycle CBP from PDX O1047

value: PDX O1047

value: carboplatin (CBP)


title: Bulk RNA Post-Treatment Pt37 [TJU0037_2]

description: TJU_featurecounts_symbol.tsv (TJU0037_2)


title: PDX O3312, mock treated, rep1


title: D30_WT_NT_3 [H9_Inhibitor-free_Day 30]


title: D30_He_pooled_SBN [H9 STIL +/-_Dual SMAD-i_Day 30]

value: Dual SMAD-i


title: PDX O1047, mock treated, rep1

source_name: One cycle mock treated from PDX O1047


title: Bulk RNA Post-Treatment Pt36 [TJU0036_2]

description: TJU_featurecounts_symbol.tsv (TJU0036_2)

value: Tumor


title: Bulk RNA Pre-Treatment Pt40 [TJU0040_1]

description: TJU_featurecounts_symbol.tsv (TJU0040_1)

value: pre


title: Bulk RNA Pre-Treatment Pt36 [TJU0036_1]

description: TJU_featurecounts_symbol.tsv (TJU0036_1)

value: Head And Neck Oral Cavity Squamous Cell Carcinoma


title: PDX O1047, CBP treated, rep2


title: Input for CCNE1 ChIP (ab7959, H9)

first: Yoshiaki

last: Tanaka

state: Québec

address: 5415 boul. l'Assomption

department: Medicine

institute: Centre de Recherche l'Hôpital Maisonneuve-Rosemont, Université de Montréal

description: Input for ChIP

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.1.0) with options “--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1”.
Peak regions were called by MACS2 (v2.1.0) with options "-g hs -q 0.05 --broad".
Genome_build: hg19
Supplementary_files_format_and_content: Peak files were formatted as bed

source_name: H9 hESCs

growth_protocol: hESCs were cultured in 5iLA medium

extract_protocol:
iDeal ChIP-seq kit for Transcription Factor
ThruPLEX® DNA-seq Kit

value: hESCs

tag: chip antibody


title: D30_He_pooled_NT [H9 STIL +/-_Inhibitor-free_Day 30]

value: Day 30


title: Bulk RNA Pre-Treatment Pt35 [TJU0035_1]

description: TJU_featurecounts_symbol.tsv (TJU0035_1)


title: CCNE1 ChIP (ab7959, H9)

description: Genomic binding of CCNE1

value: CCNE1 (ab7959, abcam)


title: PDX O1047, mock treated, rep2

value: Human ovarian PDX tumor

tag: treatment


title: D30_Ho_pooled_SBN [H9 STIL -/-_Dual SMAD-i_Day 30]

tag: cell line

value: H9 STIL -/-

value: Brain Organoid


title: Bulk RNA Post-Treatment Pt34 [TJU0034_2]

description: TJU_featurecounts_symbol.tsv (TJU0034_2)

value: post


title: CCNE1 ChIP (ab133266)

description:
YT149_CTTGTA_L004
processed data: CCNE1_peaks_combine.bed

source_name: H7 hESCs_genomic binding of CCNE1

value: H7 hESCs

value: Control shRNA KD

value: CCNE1 (ab133266, abcam)


title: 5iLA input

source_name: H7 hESCs_Input for ChIP

value: none (input)


title: D30_Ho_pooled_NT [H9 STIL -/-_Inhibitor-free_Day 30]

tag: protocol

value: Inhibitor-free


title: Bulk RNA Pre-Treatment Pt31 [TJU0031_1]

description: TJU_featurecounts_symbol.tsv (TJU0031_1)


title: Bulk RNA Post-Treatment Pt33 [TJU0033_2]

description: TJU_featurecounts_symbol.tsv (TJU0033_2)


title: Bulk RNA Post-Treatment Pt31 [TJU0031_2]

description: TJU_featurecounts_symbol.tsv (TJU0031_2)


title: Bulk RNA Pre-Treatment Pt33 [TJU0033_1]

description: TJU_featurecounts_symbol.tsv (TJU0033_1)


title: Bulk RNA Post-Treatment Pt35 [TJU0035_2]

description: TJU_featurecounts_symbol.tsv (TJU0035_2)


title: Input for CCNE1 ChIP (ab7959)

description:
H7_input
processed data: CCNE1_peaks_combine.bed

value: wild type control


title: Bulk RNA Post-Treatment Pt16 [TJU0016_2]

description: TJU_featurecounts_symbol.tsv (TJU0016_2)


title: D30_WT_pooled_SBNX [H9_Triple-i_Day 30]

value: Triple-i


title: Bulk RNA Pre-Treatment Pt16 [TJU0016_1]

description: TJU_featurecounts_symbol.tsv (TJU0016_1)

value: Tumor


title: D30_WT_pooled_SBN [H9_Dual SMAD-i_Day 30]

value: Dual SMAD-i


title: Bulk RNA Pre-Treatment Pt13 [TJU0013_1]

description: TJU_featurecounts_symbol.tsv (TJU0013_1)

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

value: pre


title: Bulk RNA Pre-Treatment Pt8 [TJU008_1]

description: TJU_featurecounts_symbol.tsv (TJU008_1)


title: 5iLA hESCs [GRO-seq]

data_processing:
library strategy: GRO-seq
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by Bowtie2 (v2.1.0) with options “--local -D 15 -R 3 -N 1 -L 20 -i S,1,0.50 -k 1”.
The output bam file was converted into bedGraph by genomecov function of Bedtools (v2.26) with -bg -split -ibam options.
The bedGraph file was then converted into wig format (500bp resolution) by normalizing read count with total number of mapped reads.
Finally, bigWig file was created with wigToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: Read distribution was formatted as BigWig.

source_name: 5iLA hESCs

growth_protocol: hESCs were cultured in primed or naïve (5iLA or t2iGo) medium

extract_protocol:
Global run-on was performed based on the method published (Kim et al., Genome Res, 2018).
Multi-indexing sequencing libraries were prepared by Illumina TruSeq Small RNA Library Prep Kit-set A (24 rxns, RS-200-0012).

tag: culture medium

value: naïve (5iLA) medium


title: Bulk RNA Post-Treatment Pt8 [TJU008_2]

description: TJU_featurecounts_symbol.tsv (TJU008_2)


title: Bulk RNA Post-Treatment Pt13 [TJU0013_2]

description: TJU_featurecounts_symbol.tsv (TJU0013_2)


title: D30_WT_pooled_XAV [H9_WNT-i_Day 30]

value: WNT-i

value: Day 30


title: Bulk RNA Pre-Treatment Pt34 [TJU0034_1]

description: TJU_featurecounts_symbol.tsv (TJU0034_1)


title: D17_He_pooled_SBNX [H9 STIL +/-_Triple-i_Day 17]

value: H9 STIL +/-

value: Day 17


title: Bulk RNA Pre-Treatment Pt24 [TJU0024_1]

description: TJU_featurecounts_symbol.tsv (TJU0024_1)


title: D30_WT_pooled_NT [H9_Inhibitor-free_Day 30]

value: Brain Organoid


title: Bulk RNA Post-Treatment Pt24 [TJU0024_2]

description: TJU_featurecounts_symbol.tsv (TJU0024_2)

value: post


title: Primed hESCs

description:
KY_12_AGTTCC_L004
processed data file: RPKM_table_primednaive.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were aligned to hg19 human genome by tophat2 (v2.3.0)
Gene expression was estimated by Cufflinks (v1.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-separated gene-sample matrix file

source_name: H7 hESCs_Primed hESCs

growth_protocol: hESCs were cultured in primed or naïve (5iLA or t2iGo) media.

extract_protocol:
RNeasy Mini Kit
Tru-Seq RNA library preparation kits

value: H7 hESCs

tag: state

value: Primed

value: No treatment

tag: time


title: D17_He_pooled_SBN [H9 STIL +/-_Dual SMAD-i_Day 17]


title: Primed hESCs [GRO-seq]

source_name: Primed hESCs


title: CCNE1 ChIP (ab7959)

description:
H7_abCCNE1
processed data: CCNE1_peaks_combine.bed

tag: genotype/variation

value: CCNE1 (ab7959, abcam)


title: Bulk RNA Post-Treatment Pt20 [TJU0020_2]

description: TJU_featurecounts_symbol.tsv (TJU0020_2)


title: pCCNE1 KD t2iGo

description:
KY_9_CAGATC_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_pCCNE1 KD t2iGo

value: H1 hESCs

value: t2iGo Naïve

value: shRNA KD for pCCNE1

value: 5 days after lentiviral infection


title: D17_He_pooled_XAV [H9 STIL +/-_WNT-i_Day 17]


title: D17_He_pooled_NT [H9 STIL +/-_Inhibitor-free_Day 17]

value: Inhibitor-free


title: Bulk RNA Pre-Treatment Pt19 [TJU0019_1]

description: TJU_featurecounts_symbol.tsv (TJU0019_1)

value: Tumor

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

value: pre


title: Bulk RNA Post-Treatment Pt22 [TJU0022_2]

description: TJU_featurecounts_symbol.tsv (TJU0022_2)


title: Bulk RNA Pre-Treatment Pt22 [TJU0022_1]

description: TJU_featurecounts_symbol.tsv (TJU0022_1)


title: Bulk RNA Post-Treatment Pt18 [TJU0018_2]

description: TJU_featurecounts_symbol.tsv (TJU0018_2)


title: 5iLA naïve hESCs

description:
H7-KY-4_CTTGTA_L004
processed data file: RPKM_table_primednaive.txt

source_name: H7 hESCs_5iLA naïve hESCs

value: 5iLA Naïve


title: Bulk RNA Pre-Treatment Pt20 [TJU0020_1]

description: TJU_featurecounts_symbol.tsv (TJU0020_1)


title: uCCNE1 KD t2iGo

description:
KY_10_CTTGTA_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_uCCNE1 KD t2iGo

value: shRNA KD for uCCNE1


title: D17_Ho_pooled_SBNX [H9 STIL -/-_Triple-i_Day 17]

value: H9 STIL -/-

value: Triple-i

value: Day 17


title: Bulk RNA Post-Treatment Pt19 [TJU0019_2]

description: TJU_featurecounts_symbol.tsv (TJU0019_2)

value: post


title: Ctrl t2iGo

description:
KY_8_GCCAAT_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_Ctrl t2iGo

value: Control shRNA KD


title: Bulk RNA Post-Treatment Pt15 [TJU0015_2]

description: TJU_featurecounts_symbol.tsv (TJU0015_2)


title: t2iGo hESCs [GRO-seq]

source_name: t2iGo hESCs

value: H7 hESCs

value: naïve (t2iGo) medium


title: Bulk RNA Pre-Treatment Pt15 [TJU0015_1]

description: TJU_featurecounts_symbol.tsv (TJU0015_1)

source_name: Head And Neck Oral Cavity Squamous Cell Carcinoma


title: D17_Ho_pooled_XAV [H9 STIL -/-_WNT-i_Day 17]

source_name: Brain Organoid

value: WNT-i

value: Brain Organoid


title: Bulk RNA Pre-Treatment Pt14 [TJU0014_1]

description: TJU_featurecounts_symbol.tsv (TJU0014_1)


title: Bulk RNA Post-Treatment Pt17 [TJU0017_2]

description: TJU_featurecounts_symbol.tsv (TJU0017_2)


title: Bulk RNA Pre-Treatment Pt18 [TJU0018_1]

description: TJU_featurecounts_symbol.tsv (TJU0018_1)


title: Bulk RNA Pre-Treatment Pt17 [TJU0017_1]

description: TJU_featurecounts_symbol.tsv (TJU0017_1)


title: D17_Ho_pooled_SBN [H9 STIL -/-_Dual SMAD-i_Day 17]

value: Dual SMAD-i


title: D17_WT_pooled_SBNX [H9_Triple-i_Day 17]


title: pCCNE1 KD Primed

description:
ACAGTG_ACAGTG
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_pCCNE1 KD Primed

value: H1 hESCs

value: Primed

value: shRNA KD for pCCNE1

value: 5 days after lentiviral infection


title: D17_WT_pooled_SBN [H9_Dual SMAD-i_Day 17]


title: Bulk RNA Post-Treatment Pt6 [TJU006_2]

description: TJU_featurecounts_symbol.tsv (TJU006_2)

value: Tumor

value: Head And Neck Oral Cavity Squamous Cell Carcinoma


title: pCCNE1 KD 5iLA

description:
KY_6_TGACCA_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H7 hESCs_pCCNE1 KD 5iLA

value: 5iLA Naïve


title: Bulk RNA Post-Treatment Pt14 [TJU0014_2]

description: TJU_featurecounts_symbol.tsv (TJU0014_2)


title: Bulk RNA Pre-Treatment Pt11 [TJU0011_1]

description: TJU_featurecounts_symbol.tsv (TJU0011_1)

value: pre


title: Bulk RNA Pre-Treatment Pt6 [TJU006_1]

description: TJU_featurecounts_symbol.tsv (TJU006_1)


title: Ctrl Primed

description:
CGATGT_CGATGT
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_Ctrl Primed


title: Ctrl 5iLA

description:
KY_5_CGATGT_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H7 hESCs_Ctrl 5iLA


title: D17_Ho_pooled_NT [H9 STIL -/-_Inhibitor-free_Day 17]

value: H9 STIL -/-

value: Inhibitor-free


title: uCCNE1 KD 5iLA

description:
KY_7_ACAGTG_L004
processed data file: RPKM_table_CCNE1.txt

source_name: H7 hESCs_uCCNE1 KD 5iLA

value: shRNA KD for uCCNE1


title: Bulk RNA Pre-Treatment Pt12 [TJU0012_1]

description: TJU_featurecounts_symbol.tsv (TJU0012_1)


title: Bulk RNA Post-Treatment Pt11 [TJU0011_2]

description: TJU_featurecounts_symbol.tsv (TJU0011_2)

value: post


title: D17_WT_pooled_NT [H9_Inhibitor-free_Day 17]

value: Day 17


title: uCCNE1 KD Primed

description:
TGACCA_TGACCA
processed data file: RPKM_table_CCNE1.txt

source_name: H1 hESCs_uCCNE1 KD Primed


title: Bulk RNA Post-Treatment Pt12 [TJU0012_2]

description: TJU_featurecounts_symbol.tsv (TJU0012_2)


title: Bulk RNA Post-Treatment Pt5 [TJU005_2]

description: TJU_featurecounts_symbol.tsv (TJU005_2)


title: 1-sh-NC

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data.
Raw reads were  filtered by Trimmomatic (version 0.36) according to several steps: 1) Removing adaptor sequence  if reads contains; 2) Removing low quality bases from reads 3’ to 5’ (Q < 20); 3) Removing low  quality bases from reads 5’ to 3’ (Q < 20); 4) Using a sliding window method to remove the base  value less than 20 of reads tail (window size is 5 bp); 5) Removing reads with reads length less  than 35 nt and its pairing reads. And the remaining clean data was used for further analysis.
Clean reads were mapped to the reference genome by HISAT2 (version 2.0) with default  parameters.
RSeQC (version 2.6.1) was used to statistics the alignment results
Gene expression values of the transcripts were computed by StringTie (version 1.3.3b).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includeTPM values for each Sample ...

source_name: endometrial carcinoma

extract_protocol:
Total RNA was extracted using the Total RNA Extractor（Trizol）kit (B511311, Sangon, China)  according to the manufacturer’s protocol, and treated with RNase-free DNase I to remove  genomic DNA contamination.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample  preparations. Sequencing libraries were generated using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for  Illumina®  following manufacturer’s recommendations and index codes were added to  attribute sequences to each sample

treatment_protocol: Hairpin-derived small RNAs (shRNAs) targeting LINC00958 was purchased from Shanghai GeneChem of China. Seventy-two hours after lentivirus infection, 2.5 µg/ml puromycin was applied to screen for stably infected cells.

value: Ishikawa cells

value: negative control


title: 2-sh-NC


title: Bulk RNA Pre-Treatment Pt5 [TJU005_1]

description: TJU_featurecounts_symbol.tsv (TJU005_1)


title: D17_WT_pooled_XAV [H9_WNT-i_Day 17]

value: WNT-i

value: Brain Organoid


title: Bulk RNA Pre-Treatment Pt4 [TJU004_1]

description: TJU_featurecounts_symbol.tsv (TJU004_1)


title: D0_Embryonic stem cells Ho [H9 STIL -/-_hESCs_Day 0]

source_name: hESCs

value: hESCs

value: Day 0


title: HeLa SUN1 rep3

city: Paris

first: Nicolas

last: Manel

address: 12 rue Lhomond

department: INSERM U932

institute: Institut Curie

hyb_protocol: Human Gene 2.0 ST from Affymetrix/Thermo were hybridized according to supplier recommendations

scan_protocol: Human Gene 2.0 ST array were scanned using a Genechip 7G scanner according to supplier recommendations

data_processing: Raw data were treated, normalized and summarized using oligo R package.

label: biotin

source_name: HeLa

label_protocol: A WT Plus amplification and labeling protocol was conducted with 100ng of total RNA

growth_protocol: HeLa cells were grown and expanded in DMEM medium with Glutamax, supplemented with 10% fetal bovine serum and 100 U/mL of penicillin-streptomycin, at 37°C with 5% CO2 and 95% humidity.

extract_protocol: Total RNA was extracted using the NucleoSpin RNA kit by Macherey Nagel, according to the manufacturer's protocol

treatment_protocol: HeLa cells were transduced with VSV-G pseudotypedlentiviral particle vectors for BFP, BFP-2A-SUN1 or BFP-2A-SUN2, in the presence of 1 µg/mL of protamine. Expression of proteins of interest was confirmed via flow cytometry detection of BFP signal and by Western Blot against human SUN1 and SUN2.

value: HeLa

tag: replicate

tag: lentivector


title: Ex Vivo HNCAF-1 Rep 3 [FIBR03]

description: fpkm_sample.xls, readcount.xls

source_name: Fibroblasts cultured from Head And Neck Oral Cavity Squamous Cell Carcinoma

growth_protocol: Fibroblasts were cultured from single cell suspension of tumor specimens for 3 passages before being sequenced


title: 2-sh-LINC00958

value: LINC00958 silenced


title: TAF4 GW3965

city: Madrid

first: Angel

middle: L

last: Corbí

state: Madrid

address: Ramiro de Maeztu 9

department: Molecular Microbiology and Infection Biology

country: Spain

institute: Consejo Superior de Investigaciones Científicas

data_processing:
BGISEQ-500 platform
Low quality reads were filtered using filtering software SOAPnuke (developed by BGI, Version v1.5.2, with parameters -l 15 -q 0.2 -n 0.05) to remove the reads containing the adaptor(adaptor pollution), the reads whose N content is greater than 5%, and low-quality reads (defined as those with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were saved in FASTQ format. Sequences were mapped to GRCh38 genome (version GCF_000001405.38_GRCh38.p12) using Bowtie2 with the following parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant  -p 1 -k 200
Gene expression levels were determined with software RSEM
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include Entrez Gene ID and FPKM values for each Sample

source_name: RNA from monocyte-derived macrophages 72 hours after culture with TAF and a 1hr pretreatment with GW3965

growth_protocol: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured  in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of either 50% Tumor-derived Ascitic Fluid (TAF) or 20% Synovial Fluid from patients with active Rheumatoid Arthritis (RASF),

extract_protocol:
Total RNA was extracted using the NucleoSpin RNA/Protein kit (Macherey-Nagel, Düren, Germany). Qualitative analysis of total RNAs were performed in a bioanalizer Agilent 2100.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: Monocytes from independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were treated with DMSO (vehicle), 1 micromolar GW3965 or 1 micromolar GSK2033 for 1 hour, and then cultured in RPMI 1640 10% FBS supplemented with either 50% Tumor-derived Ascitic Fluid (TAF) or 20% Synovial Fluid from patients with active Rheumatoid Arthritis (RASF), at 37°C in a humidified atmosphere with 5% CO2 and 21% O2. After 72 hours, cells were lysed and RNA isolated for transcriptional analysis.

value: Monocyte-derived macrophages

value: TAF; GW3965


title: 3-sh-LINC00958


title: HeLa SUN2 rep3


title: Bulk RNA Pre-Treatment Pt2 [TJU002_1]

description: TJU_featurecounts_symbol.tsv (TJU002_1)

value: Tumor

value: Head And Neck Oral Cavity Squamous Cell Carcinoma


title: Bulk RNA Post-Treatment Pt2 [TJU002_2]

description: TJU_featurecounts_symbol.tsv (TJU002_2)


title: D0_Embryonic stem cells WT 2 [H9_hESCs_Day 0]


title: 1-sh-LINC00958


title: HeLa SUN2 rep2


title: TAF3 GW3965


title: D0_Embryonic stem cells WT 3 [H9_hESCs_Day 0]


title: D0_Embryonic stem cells He [H9 STIL +/-_hESCs_Day 0]

value: H9 STIL +/-


title: Bulk RNA Post-Treatment Pt1 [TJU001_2]

description: TJU_featurecounts_symbol.tsv (TJU001_2)


title: Bulk RNA Pre-Treatment Pt1 [TJU001_1]

description: TJU_featurecounts_symbol.tsv (TJU001_1)

value: pre


title: AML cultured cells, Drug5

city: Columbus

first: Pearlly

last: Yan

state: Ohio

department: Comprehensive Cancer Center

institute: The Ohio State University

description:
Replicates of drug group
XRMDrug5

data_processing:
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the mouse genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release 25
Genome_build: GRCh38p7
Supplementary_files_format_and_content: TSV normalized counts table calculated with DESeq2

molecule: polyA RNA

source_name: Human Cultured AML Cells

growth_protocol: AML primary cells were cultured in StemSpan™ SFEM (Stemcell Technologies) or RPMI1640 (Life Technologies, Grand Island, NY) with 10% fetal bovine serum (FBS) (Sigma-Aldrich, St Louis, MO); 2mM L-glutamine; penicillin (100 U/ml); streptomycin (100 µg/ml) (Life Technologies) and supplemented with 10ng/ml IL3, GM-CSF and SCF (R&D Systems).

extract_protocol:
Trizol reagent was used to extract total RNA from 5 million cells per sample
Manufacturer protocol, Illumina TruSeq Stranded mRNA Sample Prep Kit

value: AML cultured cells


title: AML cultured cells, Drug4

description:
Replicates of drug group
XRMDrug4


title: Bulk RNA Post-Treatment Pt4 [TJU004_2]

description: TJU_featurecounts_symbol.tsv (TJU004_2)

value: post


title: Ex Vivo HNCAF-1 Rep 2 [FIBR02]

description: fpkm_sample.xls, readcount.xls

value: Fibroblasts cultured from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: AML cultured cells, Drug6

description:
Replicates of drug group
XRMDrug6


title: HeLa SUN1 rep2


title: HeLa Control rep2

value: control


title: D30_Ho_pooled_SBNX [H9 STIL -/-_Triple-i_Day 30]

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.

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.

value: H9 STIL -/-

value: Triple-i

value: Day 30


title: AML cultured cells, Control3

description:
Replicates of control group
XRMControl3

value: Control


title: Ex Vivo HNCAF-1 Rep 1 [FIBRO01]

description: fpkm_sample.xls, readcount.xls


title: HeLa SUN2 rep1


title: TAF2 GW3965


title: HeLa Control rep3


title: TAF1 GW3965


title: AML cultured cells, Control2

description:
Replicates of control group
XRMControl2


title: HeLa SUN1 rep1


title: Ex Vivo HNCAF-0/3 Rep 3


title: AML cultured cells, Control1

description:
Replicates of control group
XRMControl1


title: TAF4 DMSO

source_name: RNA from monocyte-derived macrophages 72 hours after culture with TAF and a 1hr pretreatment with DMSO

value: TAF; DMSO


title: Ex Vivo HNCAF-0/3 Rep 2


title: TAF2 DMSO


title: Sorted CAFS1-S4 Rep 16

source_name: Fibroblasts sorted from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: HeLa Control rep1

value: HeLa


title: Ex Vivo HNCAF-0/3 Rep 1


title: Sorted CAFS1-S4 Rep 15

value: Fibroblasts sorted from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: TAF3 DMSO

value: Monocyte-derived macrophages


title: TAF1 DMSO


title: RASF6 GSK2033

source_name: RNA from monocyte-derived macrophages 72 hours after culture with RASF and a 1hr pretreatment with GSK2033

value: RASF; GSK2033


title: RASF5 GSK2033


title: Sorted CAFS1-S4 Rep 13

value: Tumor


title: Sorted CAFS1-S4 Rep 14


title: A172-shHDAC2 Cell line_DOX(+), biological rep1

city: SEOUL

first: Kyung-Chul

last: Choi

address: Sonpa-gu

department: Biomedical Sciences

country: South Korea

institute: University of Ulsan college of Medicine

hyb_protocol: 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human  2.0 ST Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Raw data were extracted automatically in Affymetrix data extraction protocol using the software provided by Affymetrix GeneChip® Command Console® Software (AGCC). After importing CEL files, the data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

source_name: A172 Cell line-shTETON HDAC2 virus infection

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Cells were used DMEM media containing 10% FBS and 1% Antibiotic. A172 Cell line is grown in 37°C and 5% co2 environments.

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

treatment_protocol: The cells were treated with doxycycline two days before harvest.

value: Brain cancer

value: shTETON vector for HDAC2 siRNA expression with Doxycyclin.


title: A172-shHDAC2 Cell line_DOX(-), biological rep2

source_name: A172 Cell line-shTETON Control virus infection

value: shTETON vector for HDAC2 siRNA expression.


title: A172-shHDAC2 Cell line_DOX(+), biological rep2


title: A172-shHDAC2 Cell line_DOX(-), biological rep1


title: A172-shControl Cell line_DOX(+), biological rep2

value: shTETON vector for control siRNA expression with Doxycyclin.


title: Sorted CAFS1-S4 Rep 12


title: Head & Neck tissue (X4291571009_F)

city: Dallas

first: Xiaoyu

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).

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: Oral tongue

tag: site

value: Oral Cavity

tag: n

tag: extra neural extension

value: yes

tag: extracapsular extension. extra neural extension

value: Yes

tag: surgical margin pos

value: No

tag: perineural invasion

tag: primary. recurrence

tag: primary. recurrence date

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

value: Dead

value: Local recurrence


title: RASF4 GSK2033

tag: cell type

tag: treatment


title: Head & Neck tissue (X4257903069_E)

value: Larynx NOS

value: Larynx

value: no nodes

tag: lymphovascular invasion

value: no

value: No evidence of disease


title: Head & Neck tissue (X4257903069_F)

value: Tonsillar fossa

value: Oropharynx

tag: extracapsular extension

tag: vascular invasion

tag: distant metastasis data

tag: distant metastasis site

value: Lung, Liver

value: Tumor

value: Distant metastasis


title: A172-shControl Cell line_DOX(+), biological rep1

tag: tissue

value: Brain cancer

tag: cell line

value: shTETON vector for control siRNA expression with Doxycyclin.


title: RASF3 GSK2033

value: Monocyte-derived macrophages

value: RASF; GSK2033


title: STRT_24.H9.4c.DOXplus

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 samples was SV1.21.H9.4c.DOXminus.excluded.fq.gz 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.

value: human embryonic stem cells (hESC)

value: Doxycycline treated


title: Head & Neck tissue (X4257903087_D)

tag: gender

value: Male

value: AFP and RMT

tag: site

value: Oral Cavity

tag: n

value: yes

value: Yes

value: No

value: Dead


title: Head & Neck tissue (X4257903069_D)

value: Oral tongue

tag: extracapsular extension. extra neural extension

tag: surgical margin pos

value: no

value: No evidence of disease


title: Sorted CAFS1-S4 Rep 10

value: Tumor

tag: tissue type

value: Fibroblasts sorted from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: STRT_23.H9.4b.DOXplus

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.


title: A172-shControl Cell line_DOX(-), biological rep2

value: Brain cancer

value: shTETON vector for control siRNA expression.


title: RASF1 GSK2033

value: Monocyte-derived macrophages

value: RASF; GSK2033


title: Sorted CAFS1-S4 Rep 9


title: RASF6 DMSO

source_name: RNA from monocyte-derived macrophages 72 hours after culture with RASF and a 1hr pretreatment with DMSO

value: RASF; DMSO


title: STRT_22.H9.4a.DOXplus

value: human embryonic stem cells (hESC)

value: Doxycycline treated


title: Sorted CAFS1-S4 Rep 11


title: RASF5 DMSO


title: Sorted CAFS1-S4 Rep 8


title: RASF2 GSK2033


title: Head & Neck tissue (X4189251077_F)

value: Male

value: Oral Cavity

tag: perineural invasion

tag: primary. recurrence

value: Alive


title: STRT_21.H9.4c.DOXminus.excluded

description: Excluded from STRT_H1_H9_hESC_19_BO4855_TFE_RawNormCounts_Diffexp.csv

tag: cell type

value: Control


title: Head & Neck tissue (X4189251077_E)

value: Larynx NOS

value: Larynx

value: yes

value: Yes

value: No

tag: primary. recurrence date

tag: neck.recurrence date

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

value: Lung

value: Dead

value: Local recurrence+Local regional recurrence+Distant metastasis


title: A172-shControl Cell line_DOX(-), biological rep1

value: Brain cancer

tag: treatment

value: shTETON vector for control siRNA expression.


title: RASF4 DMSO

value: Monocyte-derived macrophages

value: RASF; DMSO


title: Sorted CAFS1-S4 Rep 7

value: Tumor

value: Fibroblasts sorted from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: STRT_20.H9.4b.DOXminus

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 parameter, 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.

value: human embryonic stem cells (hESC)


title: Head & Neck tissue (X4189251077_C)

value: Female

value: Oral Tongue

value: Oral Cavity

tag: extracapsular extension

value: Local recurrence+Local regional recurrence


title: Sorted CAFS1-S4 Rep 6


title: Sorted CAFS1-S4 Rep 5


title: Head & Neck tissue (X4221353012_E)

value: Floor of mouth

value: no nodes

value: yes

value: Alive

value: No evidence of disease


title: Head & Neck tissue (X4189251077_D)

value: Buccal mucosa

value: No

value: Yes


title: Head & Neck tissue (X4189251077_B)

value: Gingiva

value: Dead


title: STRT_18.H9.3c.DOXplus

value: Doxycycline treated


title: STRT_19.H9.4a.DOXminus

value: Control


title: STRT_17.H9.3b.DOXplus

value: human embryonic stem cells (hESC)


title: RASF2 DMSO

value: Monocyte-derived macrophages

value: RASF; DMSO


title: Head & Neck tissue (X4189251021_F)

value: Male

value: Base of tongue

value: Oropharynx

tag: extra neural extension

value: no

value: Tumor


title: Sorted CAFS1-S4 Rep 3

tag: tissue

value: Fibroblasts sorted from Head And Neck Oral Cavity Squamous Cell Carcinoma


title: Sorted CAFS1-S4 Rep 4


title: STRT_16.H9.3a.DOXplus

tag: cell line


title: RASF3 DMSO


title: Sorted CAFS1-S4 Rep 2


title: STRT_15.H9.3c.DOXminus


title: Root Local White

city: Islamabad

first: Muhammad Ramzan

last: Khan

state: pakistan

address: Park Road, National Agricultural Research Center (NARC)

department: National Institute Of Genomics And Advanced Bio-Technology (NIGAB)

country: Pakistan

institute: National Agricultural Research Centre

data_processing:
Qaulity of raw sequenced data was checked by fastQC tool and low quality and adapter sequences were trimmed by Trimmomatic tool. Cleaned reads were mapped to reference genome by HISAT2 tool.
The mapping results were assembled into transcripts using a reference guided by StringTie tool.
Differential gene expression analysis with sequenced data was performed using R package edgeR
Genome_build: The International Wheat Genome Sequencing Consortium (IWGSC) RefSeq v1.0
Supplementary_files_format_and_content: Counts values for each Sample

organism: Triticum aestivum

source_name: Roots

growth_protocol: Seeds of six genotypes were germinated on moist germination paper. After 72 h of germination, four germinated seeds of each genotype were shifted in soiled filled pots. The seedlings were grown under well-watered condition for 35 days.

extract_protocol:
Total RNA of six genotypes was firstly isolated using GeneJET™ Plant RNA Purification Mini Kit and treated with RNase-free DNase I to remove any contaminating genomic DNA according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Under Normal conditions

value: Roots

tag: development stage

value: 35 days old seedling stage

tag: cultivar

value: Local White

tag: phenotype

value: drought tolerant


title: Sorted CAFS1-S4 Rep1


title: Head & Neck tissue (X4189251021_C)

tag: gender

value: Oral tongue

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: No

tag: lymphovascular invasion

value: yes

value: Alive

value: No evidence of disease


title: Root UZ-11-CWA-8


title: Head & Neck tissue (X4189251077_A)

value: Female

tag: surgical margin pos

tag: perineural invasion

tag: vascular invasion

tag: primary. recurrence


title: Root Syn-22


title: Head & Neck tissue (X4189251021_B)

value: Tonsillar fossa

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


title: ScRNA Pt3 Post

source_name: Head And Neck Oral Cavity Squamous Cell Carcinoma

tag: tissue type

tag: time point

value: post


title: Head & Neck tissue (X4189251021_D)

value: Male

tag: extracapsular extension

value: Yes

value: Dead


title: STRT_13.H9.3a.DOXminus

tag: cell line

tag: cell type

value: human embryonic stem cells (hESC)

tag: treatment

value: Control


title: STRT_14.H9.3b.DOXminus


title: STRT_12.H1.8c.DOXplus

value: Doxycycline treated


title: ScRNA Pt4 Post

tag: tissue

value: Tumor

value: Head And Neck Oral Cavity Squamous Cell Carcinoma


title: STRT_11.H1.8b.DOXplus


title: Root Batis

value: Roots

tag: development stage

value: 35 days old seedling stage

tag: cultivar

value: Batis

tag: phenotype

value: drought susceptible


title: ScRNA Pt2 Post


title: ScRNA Pt4 Pre

value: pre


title: Head & Neck tissue (X4090082067_B)

tag: gender

value: Oral Tongue

tag: site

value: Oral Cavity

tag: n

value: No

tag: extracapsular extension. extra neural extension

value: yes

tag: distant metastasis data

tag: distant metastasis site

value: Lung

value: Distant metastasis


title: Head & Neck tissue (X4090082067_D)

value: Male

value: Buccal mucosa

value: Yes

tag: surgical margin pos

tag: lymphovascular invasion

value: no

tag: perineural invasion

tag: primary. recurrence

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

value: Dead


title: Root Chakwal-50

value: drought tolerant


title: STRT_10.H1.8a.DOXplus

tag: cell line

tag: cell type

value: human embryonic stem cells (hESC)

value: Doxycycline treated


title: Root Blue Silver

tag: tissue

value: Roots

value: 35 days old seedling stage

value: Blue Silver


title: Head & Neck tissue (X4090082067_C)

value: Female

value: Epiglottis suprahyoid

value: Larynx

tag: extra neural extension

value: Tumor

value: No evidence of disease


title: ScRNA Pt3 Pre

tag: tissue type

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

tag: time point

value: pre


title: mes4lin15b_adgerm_batch02_rep02

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

state: CA

address: 329 sinsheimer labs

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

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M+Z- V; lin-15B(n744) M-Z- X

tag: stage and sex

value: 1st day adult hermaphrodite

tag: sequencing batch

tag: outliers filtered from analysis


title: Head & Neck tissue (X4189251021_A)

tag: gender

value: AFP and RMT

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension. extra neural extension

value: no nodes

value: No


title: RASF1 DMSO

value: Monocyte-derived macrophages

tag: treatment

value: RASF; DMSO


title: STRT_08.H1.8b.DOXminus

value: human embryonic stem cells (hESC)

value: Control


title: Head & Neck tissue (X4090082067_A)

value: Male

value: Pyriform Sinus

value: Hypopharynx

tag: extracapsular extension

value: yes

value: Yes

tag: surgical margin pos

tag: lymphovascular invasion

tag: perineural invasion

tag: vascular invasion

tag: primary. recurrence

tag: primary. recurrence date

tag: neck.recurrence date

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

value: Dead

value: Local recurrence+Local regional recurrence


title: STRT_09.H1.8c.DOXminus

tag: cell line

tag: cell type


title: Head & Neck tissue (X4090082052_E)

value: Tumor

value: Local recurrence


title: STRT_07.H1.8a.DOXminus


title: STRT_06.H1.2c.DOXplus

value: Doxycycline treated


title: ScRNA Pt2 Pre

tag: tissue

tag: tissue type

value: Head And Neck Oral Cavity Squamous Cell Carcinoma

tag: time point

value: pre


title: mes4lin15b_adgerm_batch02_rep03

tag: source strain

tag: genotype

value: glh-1(sams24[glh-1::GFP::3xFLAG]) I; mes-4(bn73) M+Z- V; lin-15B(n744) M-Z- X

tag: stage and sex

value: 1st day adult hermaphrodite

tag: sequencing batch

tag: outliers filtered from analysis

value: no


title: STRT_04.H1.2a.DOXplus

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, samples 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.

value: human embryonic stem cells (hESC)

tag: treatment


title: IPA_CYTO_DMSO_n2

city: Orsay

first: Céline

middle: M.

last: Labbé

address: Rue Henri Becquerel

description: replicate 2

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

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.

value: Vehicle (DMSO)

tag: extract

value: Whole Cytosol


title: mes4lin15b_adgerm_batch02_rep01


title: Head & Neck tissue (X4090082024_F)

last: Wang

tag: gender

value: Male

value: Gingiva lower

tag: site

value: Oral Cavity

tag: n

tag: extracapsular extension

tag: extracapsular extension. extra neural extension

tag: surgical margin pos

value: No

value: Alive

value: No evidence of disease