title: Sph-AU565-UP-3

value: AU565 cells, liquid overlay spheroid large


title: 10 μM BPA 3h_rep 3

status: Public on Jul 31 2023

type: SRA

city: MONTRÉAL

first: Barbara

last: Hales

state: QC

address: 3655 Promenade Sir-William-Osler

department: Pharmacology and Therapeutics

country: Canada

institute: McGill University

description:
A10_3vsAC_3.txt
A10033

library_source: transcriptomic

data_processing:
Base calling was performed using Illumina CASAVA (v1.8)
Sequences were filtered for reads containing adapter or of low quality, then mapped to mm10 using STAR (v2.5, mismatch=2)
Quantification was performed using HTSeq (v0.6.1, -m union)
Differential analysis was performed using DESeq2 (v2_1.6.3, q-value < 0.05)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table containing raw count, FPKM value, and normalized abundance output (from DESeq2) of each gene for each sample and each treatment group

molecule: total RNA

organism: Mus musculus

source_name: Embryonic forelimb

growth_protocol: Forelimbs of each gestational day 13 embryo were excised, pooled, and placed in glass bottles containing 6 mL of a culture medium consisting of 75% BGJb medium (Gibco, ThermoFisher Scientific), 25% salt solution, supplemented with ascorbic acid (0.16 mg/mL) and gentamycin (50 mg/mL, Wisent Bioproducts, QC, Canada). Limbs from male and female embryos were cultured together.

extract_protocol:
Total RNA was extracted using the Rneasy Mini kit (Qiagen). The concentration and purity of extracted RNA was assessed using NanoDrop 2000 spectrophotometer (Thermofisher).
mRNA was purified from 1ug of total RNA using poly-T oligo-attached magnetic beads and fragmented randomly in a fragmentation buffer. First-strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-); second-strand cDNA was subsequently synthesized using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of the 3' ends of DNA fragments, NEBNext Adaptor was ligated to prepare for hybridization. The library fragments were purified with AMPure XP system. The final library was obtained by PCR amplification and purification of PCR products using AMPure XP beads.

treatment_protocol: Culture bottles were gassed for two minutes with 5% CO2, 50% O2 balanced with N2. Each bottle subsequently received one of two treatments: dimethyl sulfoxide (DMSO, vehicle control) or bisphenol A (BPA 10 or 50 μM).  Limbs were then cultured at 37° for 3 hours.

tag: strain

tag: gestation day

value: GD 13

tag: tissue

value: limb bud

tag: treatment

value: 10 uM BPA

tag: treatment length

value: 3 hours


title: 8plex-SSNseq-CAR-T-in-vitro, mRNA-derived cDNA

city: Houston

first: Pawel

last: Mazur

state: Texas

address: 6565 MD Anderson Blvd

country: USA

institute: MD Anderson Cancer Center

description:
mRNA
Sample 3-1
Exp3_barcodes.tsv.gz
Exp3_features.tsv.gz
Exp3_matrix.mtx.gz

data_processing:
Gene expressing reads were aligned to the GRCh38 genome (human) and/or mm10 genome (mouse) using the 10x Genomics Cell Ranger, with the pipeline cellranger count. Small RNA counts were retrieved through cellranger count using the pattern containing group barcodes and sequences derived from constant regions of corresponding small RNAs.
Assembly: GRCh38, mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: SSN-Seq

organism: Homo sapiens

source_name: Human CAR T cells

extract_protocol:
Lentiviral barcoded multi-type cell lines and/or primary T cells were pooled and loaded into a Chromium Controller (10X Genomics).
10x Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (with Feature Barcoding technology for CRISPR Screening) was used to construct the mRNA and small RNA libraries, according to the manufacturer’s protocol (CG000205 Rev D).

tag: cell type

value: Human CAR T cells


title: E3.5-RNA-3

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were first organized by specific cell barcode information attached in the read 2 of pair-ended reads. Second, unique molecular identifier (UMI) information were added into the corresponding read 1 which were then trimmed to remove template switch oligo (TSO) sequence and polyA tails. Subsequently, we also removed reads with adapter contaminants and low-quality bases (N>10%).
Third, the cleaned reads were aligned to the mm10 genome by Hisat2. Fourth, uniquely mapped reads were counted using htseq-count of the HTSeq package and grouped by cell-specific barcode.  Based on UMI information, duplicated transcripts of each gene were removed. Finally, within a given cell, distinct UMIs of each gene were counted as the transcript number of that gene.
The expression levels TPM, where TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include theTPM values of RefSeq genes.

molecule: polyA RNA

source_name: E3.5 embryo

growth_protocol: E2.5 Klf2-H2bmcherry mouse embryos were extracted at M2 (Sigma, M7167-50ML). Then embryos were transferred to drops of KSOMaa with HEPES (Zenith biotech, ZEHP-050) covered with mineral oil (Sigma, M8410) in the petri dish (Ibidi, 81501), cultured in the tissue incubator (37℃, 5% CO2) (Thermo Fisher , Forma371) with static and shaking culture.

extract_protocol:
Single-cell RNA-seq library preparation was performed using an optimized Smart-seq2 protocol. Klf2-H2Bmcherry mouse line was used to acquire the mcherry positive embryos. Then, single-cell from blastomeres was picked into scRNA lysis buffer by mouth pipette. Oligo (dT) primer with an 8 nt specific barcode and an 8 nt random sequence as unique molecular identifiers (UMIs) were used in reverse transcription, and TSO oligo was used to synthesize the second strand.
All products of the first 17-cycle PCR were pooled together, and additional 5 cycles of PCR reaction were performed using a biotinylated primer to introduce a library specific index. Subsequently, the cDNA was sheared to acquire ~300 bp fragments, and 3’ terminal fragments of the cDNA were captured by Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher). Finally, NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB E7370) was used to construct the scRNA-seq library. All the Single-cell RNA-seq libraries were subjected to 150 bp paired-end sequencing on an Illumina HiSeq 4000 or X-TEN platform for an average sequencing depth of 200 million reads per library.

treatment_protocol: The zona pellucida were dissociated with 0.5% w/v Proteinase E (Sigma, P8811) in KSOMaa supplemented with 0.5% PVP-40 (Sigma, P0930) at the blastocyst stage. The embryos without zona pellucida were placed into KSOMaa without Ca2+ and Mg2+ for 10 min at 37℃ to dissociate blastomeres. Subsequently the blastomeres were also dissociated into single cells at room temperature with one microinjection needle made by the micropipette puller.

value: embryo

tag: developmental stage


title: Sph-AU565-UP-2

city: Albany

first: Ramon

last: Bossardi Ramos

state: Ny

address: 43 New Scotland Avenue

department: Department of Molecular and Cellular Physiology

institute: Albany Medical College

data_processing:
RNA-seq libraries were prepared using Illumina’s TruSeq protocol and were sequenced on an Illumina NextSeq 500. Reads were aligned to the hg38 genome using Rsubread v1.5.3. Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation. Gene symbols were provided by NCBI gene annotation. Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: CSV files containing read counts values for each Sample

source_name: epithelium

growth_protocol: AU565 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol extraction method
RNA-seq libraries were prepared using Illumina’s TruSeq protocol

treatment_protocol: liquid overlay + 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction

tag: cell line

value: epithelium

value: WT

tag: condition


title: 10 μM BPA 3h_rep 4

description:
A10_3vsAC_3.txt
A10034


title: Sph-AU565-UP-1

value: 5% matrigel following trastuzumab treatment, 96 hours incubation prior to rna extraction


title: RNA-seq for PBS conditionally treated monocytes

first: Yuzhuo

last: Yang

address: Zheng Yutong Building room D311

institute: Tsinghua University

data_processing:
(Ribo-seq) Cutadapt program was used to trim the 3’ adaptor in the raw reads from Ribo-seq
(Ribo-seq) RPF reads with length between 25 and 35 nt were extracted
(Ribo-seq) Low quality reads with Phred quality score >20 (>50% of bases) were removed using the FASTX-Toolkit
(Ribo-seq) Sequencing reads originating from rRNAs were identified and discarded by aligning the reads to rRNA sequences of the particular species using Bowtie 1.1.2 with no mismatch allowed.
(Ribo-seq) The remaining reads were mapped to the genome by STAR with end-to-end read alignment and maximum 1 mismatch was allowed.
(Ribo-seq) Reads aligned to the first 15 and last 5 codons were excluded from the counting of RPF.
(Ribo-seq) Only the reads uniquely mapped to the coding regions were counted for RPF
(RNA-seq) Datasets were excluded owing to low-quality reads.
(RNA-seq) Bowtie2 and STAR were used to map clean reads to reference gene and genome respectively
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include read counts of genes for each sample.

source_name: Buffy coat

extract_protocol:
(Ribo-seq) Treated cells were lysed with lysis buffer and treated with nuclease. Ribosome-protected fragments (RPF) were separated with a sucrose-cushion. Footprint fragments were purified and used to generate deep sequencing libraries.  (RNA-seq) Treated cells were lysed with TRIzol and total RNA was used to generate deep sequencing libraries.
(Ribo-seq) DNA was PCR amplified with Illumina primers for 12 cycles and library fragments of ~175 bp were band isolated from a polyacrylamide TBE-urea 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. (RNA-seq) Total RNA was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations

treatment_protocol: Human monocytes were cultured with killing supernatant  for 5 days and treated with metoprolol or PBS prophylactically or conditionally

value: Human CD14+ monocytes

tag: disease state

value: Healthy

value: PBS


title: E3.5-RNA-2


title: TFEB_OE_#2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
TFEB_OE_UR_2022_unique
Transcriptome profile of TFEB overexpressing, biological rep2

data_processing: Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq. Sequence reads were trimmed BBDuk (sourceforge.net/projects/bbmap/) to remove adapter sequences and low-quality end bases (Q < 20). Alignment was performed with STAR 2.6.0a(1) on the Hg38 reference provided by UCSC Genome Browser (2). Alignment to mm10, and rn6 reference genome assembly (1), and counting by gene (3) using Ensembl assembly (release 93). Gene expression levels were determined with HTseq-count 0.9.1(3). Differential expression analyses were performed using edgeR (4) a statistical package based on generalized linear models, suitable for multifactorial experiments. The threshold for statistical significance chosen was False Discovery Rate (FDR)<0,05.

source_name: isolated murine pancreatic islets

growth_protocol: Upon mouse sacrifice, pancreas were perfused using a collagenase solution and digested. Islets were isolated by density gradient.

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Nextseq6000 (Illumina) with a read length of 100 bp.

treatment_protocol: Islets were lysed directly after isolation.

value: freshly isolated pancreatic islets

tag: gender

value: male

tag: genotype/variation

value: TFEB overexpressing


title: 10 μM BPA 3h_rep 5

description:
A10_3vsAC_3.txt
A10035


title: 8plex-SSNseq-CAR-T-in-vivo, SSN-derived cDNA

description:
small RNA
Sample 4-2
Exp4_barcodes.tsv.gz
Exp4_features.tsv.gz
Exp4_matrix.mtx.gz


title: Ribo-seq for metoprolol conditionally treated monocytes

description:
ribosome-protected mRNA
Conditional_metoprolol_RPF

data_processing:
Library strategy: Ribo-seq
(Ribo-seq) Cutadapt program was used to trim the 3’ adaptor in the raw reads from Ribo-seq
(Ribo-seq) RPF reads with length between 25 and 35 nt were extracted
(Ribo-seq) Low quality reads with Phred quality score >20 (>50% of bases) were removed using the FASTX-Toolkit
(Ribo-seq) Sequencing reads originating from rRNAs were identified and discarded by aligning the reads to rRNA sequences of the particular species using Bowtie 1.1.2 with no mismatch allowed.
(Ribo-seq) The remaining reads were mapped to the genome by STAR with end-to-end read alignment and maximum 1 mismatch was allowed.
(Ribo-seq) Reads aligned to the first 15 and last 5 codons were excluded from the counting of RPF.
(Ribo-seq) Only the reads uniquely mapped to the coding regions were counted for RPF
(RNA-seq) Datasets were excluded owing to low-quality reads.
(RNA-seq) Bowtie2 and STAR were used to map clean reads to reference gene and genome respectively
Genome_build: hg38
Supplementary_files_format_and_content: Excel files include read counts of genes for each sample.

value: metoprolol


title: TFEB_OE_#1

description:
TFEB_OE_UR_1998_unique
Transcriptome profile of TFEB overexpressing, biological rep1


title: Ribo-seq for PBS conditionally treated monocytes

description:
ribosome-protected mRNA
Conditional_PBS_RPF


title: Control_#4

description:
TFEB_CTR_UR_2021_unique
Transcriptome profile of control, biological rep4

value: Control


title: AU565-L-O-1

value: AU565 cells, liquid overlay spheroid small


title: AU565-L-O-3


title: AU565-L-O-2


title: E4-M77e

city: Orangeburg

first: Paul

last: Mathews

state: NY

address: 140 Old Orangeburg Rd.

department: Psychiatry

institute: New York University Grossman School of Medicine

data_processing:
Sequenced reads quality was assessed using Fastqc version 0.11.823 and were trimmed as necessary by Trimmomatic 0.3924. If QC passed and showed no adapter contamination, this step was skipped.
Reads were aligned to the mouse reference genome (Gencode GRCm38-mm10) using STAR Aligner (2.7.0). Aligned reads were quantified using the read summarization algorithm Feature Counts.
The resulting count matrix was tested for differential gene expression using negative binomial generalized regression model from the “DESeq2” package. All genes with fewer than 10 raw read counts across all samples (low expressed genes) were filtered out from the analysis.
P-values were generated by wald test and corrected for multiple testing using the Benjamini and Hochberg false discovery rate (FDR) method.
Genome_build: GRCm38-mm10
Supplementary_files_format_and_content: EXCEL format; Matrix table with raw gene counts for every gene and every sample

source_name: APOE4/APOE4_mouse hemibrain

extract_protocol:
Hemibrains were removed, flash frozen on dry ice, and RNA was harvested using the miRNeasy mini kit. Subsequent validation was done for quality and quantity utilizing RNA 6000 Nano kit on the Agilent 2100 bioanalyzer.
RNA-Seq libraries were prepared robotically on a Beckman Biomek Fxp liquid handler using the Illumina TruSeq Stranded mRNA Library Prep kit (catalog # 20020595) starting from 500 ng of total RNA with 10 cycles of final PCR amplification.
All libraries were pooled equimolar and sequenced as Single-read 50 across three lanes of an Illumina HiSeq4000 flowcell.

tag: genotype

tag: Sex

value: M

value: Mouse hemibrain


title: RNA-seq for metoprolol conditionally treated monocytes


title: AU565-2D-UP-3

value: AU565 cells, monolayer


title: RNA-seq for metoprolol prophylactically treated monocytes


title: E4-M76e


title: E4-M78e


title: AU565-2D-UP-2


title: Control_#2

description:
TFEB_CTR_UR_2010_unique
Transcriptome profile of control, biological rep2


title: Control_#3

description:
TFEB_CTR_UR_2012_unique
Transcriptome profile of control, biological rep3


title: TFEB_OE_#3

description:
TFEB_OE_UR_2023_unique
Transcriptome profile of TFEB overexpressing, biological rep3


title: Control_#1

description:
TFEB_CTR_UR_2008_unique
Transcriptome profile of control, biological rep1


title: AU565-2D-UP-1


title: Ribo-seq for metoprolol prophylactically treated monocytes

description:
ribosome-protected mRNA
Prophylactic_metoprolol_RPF


title: Ribo-seq for PBS prophylactically treated monocytes

description:
ribosome-protected mRNA
Prophylactic_PBS_RPF


title: E4-F30d

value: F


title: E3.5-RNA-1

value: embryo


title: hyg_3

city: London

first: Michalis

last: Barkoulas

address: SAF Building, South Kensington

country: United Kingdom

institute: Imperial College London

data_processing:
Reads were aligned to C. elegans genome WS283
Reads were counted using Kallisto
Transcript abundance was quantified using the Sleuth and Wald test
Assembly: WormBase Release WS283
Supplementary files format and content: H5 files having raw TPM counts for all genes

organism: Caenorhabditis elegans

source_name: N2 (icbEx360) (hygromycin resistant) L4

growth_protocol: All strains were prepared by bleaching gravid adults to isolate embyros which were grown until L4 stage

extract_protocol:
TRIzol (Life Technologies)
By BGI (Hongkong) and Novogene (Cambridge)

treatment_protocol: Nematode Growth Media agar plates supplemented with E. coli OP50 at 20°C

value: Whole animal


title: E4-F44f


title: RNA-seq for PBS prophylactically treated monocytes


title: hyg_2


title: hyg_1


title: E3-F1g

source_name: APOE3/APOE3_mouse hemibrain


title: E3-F82f


title: dpy_3

source_name: dpy-7p::old-1 L4


title: E3-F88f


title: dpy_2


title: siTFEB/TFE3_Fast #1

description: Transcriptome profile of silenced TFEB and TFE3, Fast biological rep1

source_name: Endoc-BH1 cells

growth_protocol: Cells were grown in 75cm² flasks using OptiB1 medium

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

treatment_protocol: Cells were plated on 12-well plates and treated with full medium (GC) or Minimum Essential Medium (Fast) for 16h (overnight).

value: human insulinoma derived cell line Endoc-BH1

value: silenced TFEB and TFE3

value: Fast


title: E3-M71e


title: siTFEB/TFE3_Fast #2

description: Transcriptome profile of silenced TFEB and TFE3, Fast biological rep2


title: siTFEB/TFE3_GC #4

description: Transcriptome profile of silenced TFEB and TFE3, GC biological rep4

value: GC


title: siTFEB/TFE3_Fast #3

description: Transcriptome profile of silenced TFEB and TFE3, Fast biological rep3


title: siTFEB/TFE3_Fast #4

description: Transcriptome profile of silenced TFEB and TFE3, Fast biological rep4


title: E4-F79f


title: dpy_1


title: siTFEB/TFE3_GC #2

description: Transcriptome profile of silenced TFEB and TFE3, GC biological rep2


title: oe_control_C

source_name: N2(icbIs5) - non-transgenic L4 from MBA1013


title: E3-M54e


title: siTFEB/TFE3_GC #3

description: Transcriptome profile of silenced TFEB and TFE3, GC biological rep3


title: E2-M25

source_name: APOE2/APOE2_mouse hemibrain


title: siTFEB/TFE3_GC #1

description: Transcriptome profile of silenced TFEB and TFE3, GC biological rep1


title: oe_control_A


title: Control_for siTFEB_siTFE3_Fast #4

description: Transcriptome profile of siscramble, Fast biological rep4

value: control


title: E2-M21c


title: old-1oe_C

source_name: old-1p::old-1 L4


title: E2-M20c


title: Control_for siTFEB_siTFE3_Fast #3

description: Transcriptome profile of siscramble, Fast biological rep3


title: Control_for siTFEB_siTFE3_Fast #2

description: Transcriptome profile of siscramble, Fast biological rep2


title: 10 μM BPA 24h_rep 3

description:
A10_24vsAC_24.txt
A10243

value: GD 13

value: limb bud

value: 10 uM BPA

value: 24 hours


title: E2-F86c


title: E3-M67e


title: old-1oe_A


title: Control_for siTFEB_siTFE3_Fast #1

description: Transcriptome profile of siscramble, Fast biological rep1


title: old-1_Ext_C

source_name: old-1(ok1273) L4 + Extract


title: Control_for siTFEB_siTFE3_GC #4

description: Transcriptome profile of siscramble, GC biological rep4


title: Scer_40C_BR2

city: Chicago

first: D Allan

last: Drummond

state: IL

address: 929 E 57th Street

institute: University of Chicago

data_processing:
Raw reads were first processed using TrimGalore v0.6.10 to remove Illumina sequencing adapters using default settings.
All genomic DNA sequences and GTF files were downloaded from NCBI using the following versions (Saccharomyces cerevisiae: GCF_000146045.2_R64, Saccharomyces kudriavzevii: GCA_947243785.1_Skud-ZP591, Kluyveromyces_marxianus: GCA_001417885.1_Kmar_1.0).
These files were then used by STAR v2.7.10b to generate indices (--sjdbOverhang 99 --sjdbGTFtagExonParentTranscript transcript_id --sjdbGTFfeatureExon CDS --sjdbGTFtagExonParentGene gene_id --genomeSAindexNbases 10).
Mapping of the filtered and trimmed fastqs was also done with STAR v2.7.10b (--alignMatesGapMax 20000).
The reads mapping to each gene were quantified using HTSeq v2.0.2 (--stranded=no --type=CDS --idattr=gene_id).
Assembly: GCF_000146045.2_R64, GCA_947243785.1_Skud-ZP591, GCA_001417885.1_Kmar_1.0
Supplementary files format and content: tab-separated value format; includes raw counts
Supplementary files format and content: tab-separated value format; includes TPMs

organism: Saccharomyces cerevisiae

growth_protocol: Each species (strains BY4742, FM1389, DMKU3-1042) was grown at its optimum growth temperature (33C, 34C, and 37C, respectively) until OD600 was between 0.2-0.4 in YPD with 2% dextrose.

extract_protocol:
Total RNA was extracted using Direct-zol RNA Miniprep kit (Zymo cat. no R2052) with Ambion TRI-reagent (Fisher cat. no. AM9738) and Zirconia/Silica 0.5 mm homogenization beads (Biospec cat. no. 11079105Z). Samples were treated with Dnase I (NEB M0303S).
Sequencing libraries were prepared by Novogene (https://www.novogene.com/us-en/). Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification. Paired-end sequencing of the library was then performed on an Illumina instrument.

treatment_protocol: Using cells between OD600 of0.2-0.4: 1.2 mL of cells were transferred to a 1.5 mL tube and treated at either the control temperature (optimal growth temperature) or their maximum heat shock temperature for 8 minutes (BY = 40C, FM = 31C, DMKU = 46C). Cells were then centrifuged at 3,000 g for 1 minute at room temperature, and the supernatant was removed. Cells were flash frozen and stored at -80°C.

tag: temperature

tag: biological replicate


title: Control_for siTFEB_siTFE3_GC #3

description: Transcriptome profile of siscramble, GC biological rep3


title: oe_control_B


title: old-1oe_B


title: old-1_Ext_A


title: E2-F3


title: E2-F35


title: Control_for siTFEB_siTFE3_GC #2

description: Transcriptome profile of siscramble, GC biological rep2


title: Scer_40C_BR1


title: old-1_Ext_B


title: Control_for siTFEB_siTFE3_GC #1

description: Transcriptome profile of siscramble, GC biological rep1


title: Scer_33C_BR2


title: old-1_B


title: TFEB OE Fast #4

description:
hTFEBv5_Earl_4_unique
Transcriptome profile of TFEB overexpressing, Fast biological rep4

growth_protocol: Cells were grown in 75cm² flasks using OptiB1 medium.

extract_protocol:
Total RNA was quantified using the Qubit 2.0 fluorimetric Assay (Thermo Fisher Scientific). For RNA-seq analysis, library preparation was performed with a total of 100ng of RNA from each sample using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen) according to manufacturer's instructions. Amplified fragmented cDNA of 300bp in size was sequenced in single-end mode by NovaSeq 6000 (Illumina) with a read length of 100bp
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions.
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the Novaseq6000 (Illumina) with a read length of 100 bp.

value: Human insulinoma derived cell line

value: TFEB overexpressing

value: Fasting


title: Scer_33C_BR1


title: TFEB OE Fast #3

description:
hTFEBv5_Earl_3_unique
Transcriptome profile of TFEB overexpressing, Fast biological rep3


title: old-1_A


title: OsbHLH002-FLAG-IP

city: Hangzhou

first: Yang

last: lijia

address: 866 Yuhangtang Rd

institute: Zhejiang University

library_source: genomic

data_processing:
Illumina TruSeq sequencing libraries were constructed and sequenced by using the NovaSeq6000 platform in the PE150 sequencing mode.
The ChIP-seq datasets were mapped to the rice genome (version MSU 7.0) using bowtie2 (version 2.4.2) with the default parameters.
Unmapped reads were then filtered using samtools view (version 1.3.1) with options -b -F 3852 -f 2 and -q 30, and duplicated reads were removed using picard MarkDuplicates (version 2.22.4).
The clean reads were supplied to macs2 (version 2.2.7.1) for peak calling with the default parameters.
Peaks were matched with genes if they were located within the region of the gene in genome annotation file.
Assembly: MSU 7.0
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Oryza sativa

source_name: Osbhlh002-1 gOsbHLH002-3FLAG

extract_protocol:
Plant tissues were fixed in 1x PBS with 1% formaldehyde for 15 min under vacuum and ground to fine power under liquid nitrogen. Nuclei were purified using a one-step Percoll gradient centrifugation and sonicated to obtain DNA fragments of 300–500 bp using a Covaris M220 (Covaris).
The reverse crosslinked DNA was end-repaired, dA-tailed, ligated to Y-adapters, and PCR amplified prior to sequencing.

value: Osbhlh002-1 gOsbHLH002-3FLAG

value: Rice transgenic plants

tag: chip antibody

value: FLAG (Sigma Cat# F3165)


title: N2_Ext_C

source_name: wild-type L4 + Extract


title: OsbHLH002-FLAG-Input


title: TFEB OE Fast #2

description:
hTFEBv5_Earl_2_unique
Transcriptome profile of TFEB overexpressing, Fast biological rep2


title: N2_Ext_A


title: N2_Ext_B


title: TFEB OE Fast #1

description:
hTFEBv5_Earl_1_unique
Transcriptome profile of TFEB overexpressing, Fast biological rep1


title: N2A, SR59230A, 4

city: Firenze

first: Gianluca

last: Mattei

state: FI

address: Via di S. Marta, 3

institute: Università degli Studi di Firenze

data_processing:
Counts were retrieved using Salmon
DESeq2 was used to perform normalization and statistical analyses
Assembly: GRCm39
Supplementary files format and content: Salmon normalized counts

source_name: Tumor

growth_protocol: Murine neuroblastoma N2A tumor cells (1x10^6) were subcutaneusly injected in A/J mice

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen). 500 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina) following manufacturer's protocols.

treatment_protocol: When a palpable tumor mass was present, mice were treated i.p. twice a day with vehicle or SR59230A 10 mg/kg

value: Tumor

value: Neuroblastoma


title: N2A, SR59230A, 3


title: N2_C

source_name: wild-type L4

value: Whole animal


title: N2A, SR59230A, 1


title: old-1_C


title: N2_B


title: TFEB OE GC #1

description:
hTFEBv5_GC_2_unique
Transcriptome profile of TFEB overexpressing, GC biological rep1

value: Growing


title: N2A, SR59230A, 2


title: TFEB OE GC #2

description:
hTFEBv5_GC_3_unique
Transcriptome profile of TFEB overexpressing, GC biological rep2


title: TFEB OE GC #3

description:
hTFEBv5_GC_4_unique
Transcriptome profile of TFEB overexpressing, GC biological rep3


title: N2_A


title: N2A, vehicle, 3

value: mock


title: Control Fast #4

description:
CTL_Earl_4_unique
Transcriptome profile of wild type, Fast biological rep4

value: Control


title: N2A, vehicle, 2


title: Control Fast #3

description:
CTL_Earl_3_unique
Transcriptome profile of wild type, Fast biological rep3


title: dCas9-VPR_rep2

first: Isaac

last: Hilton

address: 6500 Main Street

department: Bioengineering

institute: Rice University

data_processing:
Reads were aligned to the human genome (hg38) Gencode Release 36 reference using STAR aligner (v2.7.3a). Transcript levels were quantified to the reference genome using a Bayesian approach. Normalization was done using counts per million (CPM) method. Differential expression was done using DESeq2 (v3.5) with default parameters. Genes were considered significantly differentially expressed based upon a fold change >2 or <-2 and an FDR <0.05.
Assembly: hg38- Gencode Release 36
Supplementary files format and content: individual tab-delimited text files for all replicates corresponding to each sample includes Counts per million (CPM) values

growth_protocol: HEK293T (ATCC, CRL-11268) were cultured in  ATCC-recommended DMEM media supplemented with 10% FBS (Sigma-Aldrich) and 1% pen/strep (100units/ mL penicillin, 100µg/ mL streptomycin; Gibco) at 37° C and 5% CO2.

extract_protocol:
72 hours post-transfection RNA was isolated using the RNeasy Plus mini kit (Qiagen). RNA integrity was assessed using a Bioanalyzer 2200 (Agilent)
RNA-seq libraries were constructed using the TruSeq Stranded Total RNA Gold (Illumina, RS-122-2303).The qualities of RNA-seq libraries were verified using the Tape Station D1000 assay (Tape Station 2200, Agilent Technologies) and the concentration of RNA-seq libraries were checked again using real time PCR (QuantStudio 6 Flex Real time PCR System, Applied Biosystem). Libraries were normalized and pooled prior to sequencing. Sequencing was performed using an Illumina Hiseq 3000 with paired end 75 base pair reads.

treatment_protocol: Approximately 125000 HEK293T cells were plated the day before transfection and then transfected using Lipofectamine 3000 (Invitrogen, USA) as per manufacturer’s instruction in 24-well plates using 375ng of dCas9 (for dCas9-VPR) expression plasmid and 125ng of equimolar pooled gRNAs for HBG1/HBG2. For two component systems Control- (dCas9 + MCP-mCherry), DREAM- (dCas9 + MCP-MSN), and SAM- (dCas9-VP64 + MCP-p65-HSF1) 187.5ng of each plasmid was used and 125ng of equimolar pooled gRNAs for HBG1/HBG2 (MS2- modified) was used.

value: Human embryonic kidney cells

value: Transfected with dCas9-VPR  in presence of HBG1/HBG2 gRNA pool


title: N2A, vehicle, 1


title: Control Fast #2

description:
CTL_Earl_2_unique
Transcriptome profile of wild type, Fast biological rep2


title: NLF cells, siNTC, replicate 2

city: Philadelphia

first: Sharon

last: Diskin

state: PA

address: 3501 Civic Center Blvd

institute: Children's Hospital of Philadelphia

data_processing:
Sample and read quality was assessed using FastQC.
Reads were mapped to hg19 using STAR_2.4.2a.
Read counts and gene expression quantification was identified using StringTie 1.3.3.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: neuroblastoma

growth_protocol: NLF neuroblastoma cell lines were  grown in RPM1-1640 with HEPES, L-glutamine and phenol red, supplemented with 10% FBS, 1% L-glutamine in an incubator at 37°C with 5% CO2.

extract_protocol:
Total RNA was extracted from cells using the miRNeasy kit (Qiagen). 1000 ng/sample was used as input for library preparation.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit from Illumina (with Ribo-Zero treatment).

treatment_protocol: NLF cells were treated for 48hours with siTBX2-AS1, siTBX2, and non-targeting control samples, siNTC, (three biological replicates per condition).

value: neuroblastoma

value: NLF

value: neural crest

value: WT

value: siNTC


title: APP_hNS1 differentiation rep 3

city: Majadahonda

first: Victoria

last: López-Alonso

address: Crta Majadahonda Pozuelo km 2

department: Computational Biology

country: Spain

institute: Institute of Health Carlos III

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome GRCh38 using STAR
Measures of gene level expression with HT-Seq raw read counts.
Differential expression analysis was performed using DESeq2 v. 1.10.1
Assembly: GRCh38
Supplementary files format and content: Matrix table with normalized gene counts (DESeq2) for every gene and every sample

source_name: human fetal forebrain-derived

growth_protocol: Human stem cell (HSC) medium supplemented with 20 ng/ml epidermal growth factor (EGF; PetroPech) and 20 ng/ml basic fibroblast growth factor (FGF2; PetroPech)

extract_protocol:
RNeasy Mini extraction kit (Qiagen, Valencia, CA, USA). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were proliferated in an incubator set to 37 °C and 5% CO2. Cultures were differentiated on poly-L-lysine- (10–30 μg/ml; Sigma) coated plastic or glass coverslips, by withdrawal of growth factors (EGF and FGF2) and addition of 0.5% heat-inactivated fetal bovine serum (FBS) for 4 days.

tag: develomental stage

value: differentation day4

value: 4ug of 335 pcDNA3-APP695 plasmid


title: N2A, vehicle, 0


title: SAM_rep1

value: Transfected with dCas9-VP64 + MCP-p65-HSF1 in presence of HBG1/HBG2 gRNA (MS2) pool


title: SAM_rep2


title: APP_hNS1 differentiation rep 1


title: Control Fast #1

description:
CTL_Earl_1_unique
Transcriptome profile of wild type, Fast biological rep1

value: Human insulinoma derived cell line

value: Fasting


title: Control GC #4

description:
CTL_GC_4_unique
Transcriptome profile of wild type, GC biological rep4


title: APP_hNS1 differentiation rep 2


title: Kmarx_46C_BR2

organism: Kluyveromyces marxianus

tag: strain


title: Control GC #3

description:
CTL_GC_3_unique
Transcriptome profile of wild type, GC biological rep3


title: DREAM_rep2

value: Transfected with dCas9 + MCP-MSN in presence of HBG1/HBG2 gRNA (MS2) pool


title: hNS1 differentiation rep 2


title: Kmarx_46C_BR1


title: DREAM_rep1


title: Control_rep1

value: Transfected with dCas9 + MCP-mCherry in presence of HBG1/HBG2 gRNA (MS2) pool


title: hNS1 differentiation rep 3


title: Kmarx_37C_BR2


title: Control GC #1

description:
CTL_GC_1_unique
Transcriptome profile of wild type, GC biological rep1

value: Growing


title: Control_rep2


title: Control GC #2

description:
CTL_GC_2_unique
Transcriptome profile of wild type, GC biological rep2


title: dCas9-VPR_rep1

value: Transfected with dCas9-VPR  in presence of HBG1/HBG2 gRNA  pool


title: LX2 rep2

city: Nanjing

first: Peiliang

last: Shen

address: Xianlin Road 138#

institute: Nanjing university of Chinese Medcine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: hepatic stellate  cell

value: culture in a tumor-om-a-chip alone


title: Kmarx_37C_BR1


title: nc2_plasma_mRNA_lncRNA

status: Public on Jul 30 2023

city: Shenyang

first: Zhijie

last: Song

state: Liaoning

address: Huanghe North street No.146

institute: Shenyang Medical College

description: HG38_for_every_sample_in_plasma_(mRNA_and_lncRNA).xlsx

library_source: other

data_processing:
Pooled miRNA libraries were loaded and sequenced on BGISEQ-2000 (BGI) in single-end 50 bp mode, yielding an average of 2.39 Gb of reads from each library. Trimming primer-adaptor and filtering low-quality reads were performed using SOAPnuke v1.5.6 (with parameters -Q 2 -q -c 0), followed by alignment to the human reference genome (HG19) using Bowtie2 v2.2.9 (with parameters -q -L 16 -p 6 --phred64 --rdg 1,10 --rfg 1,10 -m 1), yielding an average of 732M clean reads per sample. The matched reads were aligned to known miRNA using miRbase version 20. Base quality and sequence length were checked using the fqcheck tool.  Pooled mRNA/lncRNA libraries were loaded and sequenced in pair-end 100 bp mode on the DNBSEQ platform (BGI). Sequences were processed by trimming primer-adaptor, and filtering low-quality reads using SOAPnuke v2.1.0 (with parameters -l 15 -Q 2 -q 0.2 -n 0.05) followed by aligning to the human reference genome GRCh38 (GENCODE v32/Ensembl 98) using HISAT2 version 2.1.0 (with parameters -k 1 -p 4). Then the expression level of each gene was calculated by the transcripts per million mapped reads (TPM) using StringTie v2.1.4 (with parameters -t -C -e -B -A -p 12 -G).
Assembly: HG19, HG38
Supplementary files format and content: Deep sequencing raw reads obtained upon alignment to HG19 and mapping to miRBase V.20 for 39 sample in leukocytes (miRNA) ,format:xlsx;Deep sequencing raw reads obtained upon alignment to HG38 for 39 sample in leukocytes (mRNA and lncRNA) ,format:xlsx ;Deep sequencing raw reads obtained upon alignment to HG38 for 25 sample in plasma (mRNA and lncRNA),format:xlsx ;The content of metabolites in all the samples (ng/ml),format:xlsx.

molecule: other

source_name: blood

extract_protocol: MRNA/lncRNA and miRNA were extracted from leukocytes and plasma using the RNeasy Mini Kit (no.74104, Qiagen, Germany) and miRNeasy Serum/Plasma Kit (no.163031715, Qiagen, Germany). The RNA concentration was determined using NanoDrop 2000 (Thermo Scientific) and Qubit 3.0 (Thermo Scientific). MRNA/lncRNA was converted into cDNA libraries using the MGIEasy RNA Library Prep Set (no. 1000006384, MGI, China) and MGIEasy rRNA removal kit (no. 1000005953, MGI, China). MiRNA was transformed into cDNA libraries using the MGIEasy Small RNA Library Prep Kit (no. 940-000196-00, MGI, China). Targeted metabolomics detection of SCFAs and neurotransmitters in plasma was performed by LC-MS/MS. Multi Reaction Monitoring (MRM) was the LC-MS/MS scanning mode.

tag: tissue

value: blood

value: plasma


title: nc6_plasma_mRNA_lncRNA


title: nc4_plasma_mRNA_lncRNA


title: nc16_plasma_mRNA_lncRNA


title: nc8_plasma_mRNA_lncRNA


title: nc3_plasma_mRNA_lncRNA


title: nc5_plasma_mRNA_lncRNA


title: nc7_plasma_mRNA_lncRNA


title: nc13_plasma_mRNA_lncRNA


title: nc10_plasma_mRNA_lncRNA


title: nc12_plasma_mRNA_lncRNA


title: nc11_plasma_mRNA_lncRNA


title: hNS1 differentiation rep 1


title: ad37_plasma_mRNA_lncRNA


title: nc1_plasma_mRNA_lncRNA


title: pd105_plasma_mRNA_lncRNA


title: ad36_plasma_mRNA_lncRNA


title: ad33_plasma_mRNA_lncRNA


title: ad34_plasma_mRNA_lncRNA


title: nc9_plasma_mRNA_lncRNA


title: ad35_plasma_mRNA_lncRNA


title: ad30_plasma_mRNA_lncRNA


title: ad31_plasma_mRNA_lncRNA


title: pd96_miRNA

description: HG19_and_mapping_to_miRBase_V.20_for_every_sample_in_Leukocytes_(miRNA).xlsx

value: leukocyte


title: ad29_plasma_mRNA_lncRNA


title: pd97_miRNA


title: pd99_miRNA


title: pd98_miRNA


title: nc15_plasma_mRNA_lncRNA


title: pd95_miRNA


title: pd108_miRNA


title: pd107_miRNA


title: pd104_miRNA


title: pd101_miRNA


title: pd103_miRNA


title: pd100_miRNA


title: pd105_miRNA


title: nc9_miRNA


title: ad32_plasma_mRNA_lncRNA


title: nc7_miRNA


title: nc5_miRNA


title: nc4_miRNA


title: nc3_miRNA


title: nc6_miRNA


title: nc12_miRNA


title: nc16_miRNA


title: ad38_miRNA


title: nc13_miRNA


title: nc11_miRNA


title: ad36_miRNA


title: nc15_miRNA


title: nc8_miRNA


title: ad35_miRNA


title: ad39_miRNA


title: nc1_miRNA


title: nc10_miRNA


title: pd102_miRNA


title: ad31_miRNA


title: ad29_miRNA


title: ad33_miRNA


title: nc2_miRNA


title: ad30_miRNA


title: ad32_miRNA


title: cHL, Patient 23

type: RNA

city: MADRID

first: Juan F

last: Garcia

state: MADRID

address: C/ ARTURO SORIA 270

institute: MD ANDERSON CANCER CENTER MADRID

data_processing:
parameters for quality control: Imaging QC = 85, Binding Density QC = 0.05-2.50, Positive Control Linearity QC = 0.90, and Positive Control Limit of Detection QC = 2 standard deviations above the mean of the negative controls
Housekeeping Gene Normalization performed automatically in nSolver,

label: Nanostring reporter probe

source_name: FFPE tumor sample

extract_protocol: RNA from diagnostic biopsies was isolated using the truXTRAC FFPE total NA kit (Covaris Inc., Woburn, MA)

tag: individual

value: Patient 23

value: classical Hodgkin lymphoma

tag: chl subtype

value: NS

tag: Stage

value: IV

tag: treatment response (favorable vs unfavorable)

value: U

tag: age

value: female

tag: iPS

tag: relapse

value: NO

value: tumor samples of lymph nodes affected by cHL


title: cHL, Patient 26

value: Patient 26

tag: disease state

tag: gender


title: cHL, Patient 40

value: Patient 40

value: OTHER

value: I-III

value: F


title: cHL, Patient 41

value: Patient 41


title: cHL, Patient 46

value: Patient 46


title: cHL, Patient 27

value: Patient 27


title: cHL, Patient 47

value: Patient 47

value: male

value: YES


title: ad37_miRNA

value: blood

tag: cell line

value: leukocyte

tag: cell type


title: cHL, Patient 28

value: Patient 28

value: classical Hodgkin lymphoma

value: NS

value: IV

value: U


title: ad34_miRNA


title: cHL, Patient 24

value: Patient 24

value: tumor samples of lymph nodes affected by cHL


title: cHL, Patient 20

value: Patient 20

value: NO


title: cHL, Patient 25

value: Patient 25

value: I-III

value: F

value: female


title: cHL, Patient 21

value: Patient 21

value: OTHER

value: male


title: cHL, Patient 17

value: Patient 17


title: cHL, Patient 22

value: Patient 22


title: cHL, Patient 18

value: Patient 18

value: classical Hodgkin lymphoma


title: cHL, Patient 16

value: Patient 16


title: cHL, Patient 14

value: Patient 14

value: IV

value: YES


title: cHL, Patient 15

value: Patient 15

value: NS

value: U

value: tumor samples of lymph nodes affected by cHL


title: cHL, Patient 10

value: Patient 10

value: I-III

value: F

value: NO


title: cHL, Patient 12

value: Patient 12

value: OTHER

value: female


title: cHL, Patient 7

value: Patient 7


title: cHL, Patient 5

value: Patient 5

value: classical Hodgkin lymphoma

value: male


title: cHL, Patient 6

value: Patient 6


title: cHL, Patient 19

value: Patient 19

value: YES


title: cHL, Patient 8

value: Patient 8

value: NS


title: cHL, Patient 13

value: Patient 13

value: U

value: tumor samples of lymph nodes affected by cHL


title: cHL, Patient 9

value: Patient 9

value: IV


title: WT.HT1.R4

city: Neuherberg

first: Yiming

last: cheng

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Munich

description:
sample40
HT1

data_processing:
The transcriptome assembly was build using all the sample reads. These transcriptome was translated into peptide and BLAST again human reference proteome to get the human gene count.
The low quality base pairs were trimmed with Trimomatic.
The gene read count values were quantified with custom script.
Assembly: NA
Supplementary files format and content: gene.count.txt: Matrix table with raw gene counts for every gene and every sample.

organism: Phodopus sungorus

source_name: Blood

extract_protocol:
Frozen blood pellets were thawed in 400 µl lysis buffer and RNA was isolated using the Mini NucleoSpin RNA Blood Kit according to the manufacturer's instruction (MACHEREY-NAGEL, Düren, Germany). RNA concentrations were quantified by NanoDrop fluorometer (Thermofisher Scientific, Waltham, MA, USA) and RNA integrity was assessed by Qubit and RNA IQ Assay (Thermofisher Scientific, Waltham, MA, USA). Samples passed internal quality control with a purity of 2.08 - 2.11 and RNA integrity number was 8.85 ± 0.76.
Additional quality controls using fragment analyser, random primed cDNA synthesis, and RNA sequencing by Next Generation Sequencing (NGS) were performed at Eurofins Genomics Europe Sequencing GmbH (Konstanz, Germany). NGS was done on an Illumina HiSeq 2500 platform in a paired-end configuration of 2 x 150bp with a minimum of 30M reads per sample.

value: Blood

tag: breed

value: Djungarian

tag: genotype

value: WT

value: Male

tag: condition

value: HT

tag: time point


title: WT.Control.HT7.R4

description:
sample38
Control.HT7

value: Female

value: NT


title: WT.HT16.R3

description:
sample41
HT16


title: WT.HT16.R4

description:
sample42
HT16


title: WT.HT4.R5

description:
sample48
HT4


title: WT.Control.HT1.R6

description:
sample37
Control.HT1


title: WT.HT16.R2

description:
sample39
HT16


title: WT.Control.HT4.R4

description:
sample30
Control.HT4


title: WT.Control.HT4.R3

description:
sample29
Control.HT4


title: WT.Control.R5

description:
sample27
Control

value: not provided

value: Control


title: WT.Control.HT7.R3

description:
sample32
Control.HT7


title: WT.Control.HT16.R4

description:
sample33
Control.HT16


title: WT.Control.HT1.R5

description:
sample35
Control.HT1


title: WT.Control.R4

description:
sample26
Control


title: cHL, Patient 1

value: Patient 1

value: classical Hodgkin lymphoma


title: cHL, Patient 2

value: Patient 2

value: OTHER

value: F

value: female

value: YES


title: cHL, Patient 4

value: Patient 4

value: I-III

value: NO

value: tumor samples of lymph nodes affected by cHL


title: cHL, Patient 3

value: Patient 3

value: IV

value: male


title: WT.HT1.R3

description:
sample21
HT1

value: Blood

value: Djungarian

value: WT

value: Female

value: HT


title: WT.HT1.R5

description:
sample45
HT1


title: WT.Control.HT7.R2

description:
sample19
Control.HT7

value: NT


title: WT.HT7.R4

description:
sample31
HT7


title: WT.Control.HT4.R2

description:
sample25
Control.HT4

value: Male


title: WT.Control.HT1.R3

description:
sample20
Control.HT1


title: WT.HT4.R4

description:
sample18
HT4


title: WT.Control.HT1.R4

description:
sample22
Control.HT1


title: WT.Control.R3

description:
sample24
Control

value: not provided

value: Control


title: WT.Control.HT4.R1

description:
sample16
Control.HT4


title: WT.Control.HT7.R1

description:
sample17
Control.HT7


title: WT.HT16.R1

description:
sample13
HT16


title: WT.Control.HT16.R3

description:
sample10
Control.HT16


title: WT.Control.HT16.R2

description:
sample05
Control.HT16


title: A549_M58R_Bulk_1

city: New York

first: Brad

middle: R

last: Rosenberg

address: 1 Gustave L Levy Place, Box 1124

department: Department of Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: Bulk RNAseq library

data_processing:
For single cell RNA sequencing experiments: Fastq files from bcl files for standard 10X 3' and 10X 5' libraries were generated using cellranger (v3.1.0, 10X Genomics) mkfastq. Fastqs for 5' libraries sequenced with the Extended R1 protocol were generated using bcl2fastq (v2.20.0, Illumina, Inc).Extended R1 fastqs were then separated into pseudo R1 fastqs, containing the cell barcode and UMI, and pseudo read 2 (R2) fastqs, containing cDNA sequence, using a customized Python/3.7.3 script (available at github link pending) as follows. The cell barcode and UMI are selected from the first 26 bp of R1. The subsequent 13 bp derive from the template switch oligonucleotide and are ignored. The remaining nucleotides (and corresponding quality scores) are reverse complemented and stored as pseudo R2. The read header of the pseudo R2 fastqs are modified to reflect the format for standard R2 fastqs.
For single cell RNA sequencing experiments: To control for differences in sequencing depth per library for Vero E6 samples, read depth per library was downsampled to approximately 50,000 reads multiplied by the number of cells in the library using seqtk (version 1.2). We do this by generating a whitelist of cell barcodes using a preliminary gene cell matrix generated using cellranger (v3.1.0, 10X Genomics) count with a combined African Green Monkey reference (ChlSab1.1) combined with SARS-CoV-2 transcripts  (NC_045512.2) with modifications for the USA/WA01 strain. This output was analyzed in R (v4.0.4) with the Seurat package (version 4.0.1) to filter out putative multiplets, empty droplets, and dead cells based on total UMIs/cell, number of genes/cell, and percent of mitochondrial gene expression per cell.
For single cell RNA sequencing experiments: Downsampled Vero E6 and unaltered ACE2-A549 fastq files were mapped and quantified using cellranger (v3.1.0, 10X Genomics) count to a combined African Green Monkey (ChlSab1.1) for Vero E6 cells or human (GRCh39 version 100) for ACE2-A549 cells and SARS-CoV-2 reference derived from empirically defined RNAs sequenced with long-read direct RNA Nanopore sequencing published by Kim et al, Cell 2020. These were downloaded from the UCSC Genome Table Browser after filtering for TRS-dependent transcripts and score > 900 and exporting to gtf format. Transcripts for previously unknown ORFs were excluded and an additional annotation for genomic RNA covering the entire length of the SARS-CoV-2 genome was added. Modifications the reference were made to match the USA/WA01 SARS-CoV-2 strain.
For single cell RNA sequencing experiments: To quantify SARS-CoV-2 RNAs, we developed single cell coronavirus sequencing (scCoVseq), which quantifies only unambiguous genomic RNA (gRNA)-derived reads and reads from subgenomic mRNAs (sgmRNAs) containing junctions between the 5' leader of the genome and sgmRNA. We did this using samtools (v1.11) to filter SARS-CoV-2 aligned reads to contiguous reads aligning upstream of sgmRNA-containing regions of the genome or to SARS-CoV-2 reads aligning in part the the 5' leader (defined as the 5' proximal 80 nt of the genome) and in part to the regions of the genome used by sgmRNAs with any gap length. Reads not matching these filters were excluded. Filtered SARS-CoV-2 reads were then merged with host reads and quantified using umi_tools (v1.0.0) and converted to a sparse matrix using a custom R (v3.5.3) script with the Matrix package (v1.2-18) and the readr package (v1.3.1). UMIs assigned to multiple genes were removed from the resulting matrix during downstream analysis.
For bulk RNA sequencing experiments: raw BCL files were converted to fastq files using bcl2fastq/2.20.0 (Illumina, Inc), and viral reqads were quantified using the periscope/0.1.2 package with the technology argument set to "illumina".
Assembly: custom build described above
Supplementary files format and content: bam: Reads from downsampled libraries mapped to combined African Green Monkey/SARS-CoV-2 or human/SARS-CoV-2 reference output by cellranger prior to filtering SARS-CoV-2 reads with scCoVseq; h5: gene x cell matrix output by cellranger in h5 format; rds: gene x cell matrix output by scCoVseq as R data file, rds; csv: periscope output for bulk RNAseq analysis of infected ACE2-A549 cells

source_name: ACE2-expressing human respiratory epithelial cell line

growth_protocol: Vero E6 cells were cultured with Dulbecco's Modified Eagle Medium (DMEM) with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (PSN) at 37°C and 5% CO2. Ace-2 A549 cells were cultured in DMEM with 10% FBS and penicillin/streptomycin at 37°C and 5% CO2.

extract_protocol:
For single cell RNA sequencing experiments: Vero E6 cultures were washed with calcium/magnesium-PBS and disassociated with TrypLE (Gibco # 12605010) for 5 minutes at 37°C. Cells were then centrifuged (200 x g for 5 minutes), resuspended in calcium/magnesium free PBS supplemented with 1% BSA and counted. Cells were then filtered through a 40μm FlowMi strainer (ScienceWare # H13680-0040) and counted again. Mock and infected samples were loaded on separate lanes of a 10X Genomics Chromium Controller, according to manufacturer's protocol, for either NextGem Single Cell 3' v3.1 (10X 3') or NextGEM Single Cell V(D)J v1.1 (10X 5'). For ACE2-A549 cells, cells were detached with TrypLE, washed with PBS, and passed through a 70 uM filter. For bulk RNA sequencing experiments: ACE2-A549 cells were lysed in Trizol reagent (Invitrogen), and total RNA was extracted using miRNeasy mini kit (Qiagen) per the manufacturer's instructions. DNAse treatment was performed on isolated RNA using RNA clean and Concentrator Kit (Zymo).
For single cell RNA sequencing experiments: mock and SARS-CoV-2 infected Vero E6 cells performed with either 10X Genomics Chromium Next GEM Single Cell 3' (10X 3') or 10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5'). Final 10X 3' mock and infected gene expression libraries and 10X 5' infected gene expression libraries were PCR amplified for 16 cycles, while the 10X 5' mock gene expression library was amplified for 14 cycles. 10X 3' libraries were pooled and sequenced according with the following read lengths: read1 28 nt, i7 index 8 nt, read2 130 nt. 10X 5' libraries were also pooled and sequenced on an Illumina NextSeq 500 with the following read lengths: read 1 26 nt, i7 index 8nt, read 2 132 nt. 10X 5' were also sequenced with our custom extended R1 protocol (read 1 158 nt, i7 index 8 nt, no read 2).  Ace2-A549 samples were prepared with  10X Genomics Chromium Next GEM Single Cell V(D)J (10X 5'). These libraries were amplified with 12 PCR cycles and sequenced on an Illumina NovaSeq with the following read lengths: read 1 200 nt, index 1 8 nt, and read 2 100 nt. For data analyzed as extended read 1 data, only read 1 was analyzed, and for data analyzed using conventional 10X 5' read 1 was truncated to 26 nts and read 2 was used (this data is denoted by "_trim_R1"). For bulk RNAseq data of Ace2-A549 cells: samples were prepared with SMART-Seq v4 PLUS Kit (Takara Bio) following manufacturer's instructions. Samples were amplified for 14 PCR cycles and sequenced on an Illumina NextSeq 500 with read lengths as follows: read 1 150 nt, i7 8 nt, i5 8 nt, and read 2 150 nt.

treatment_protocol: In 6 well plates, Vero E6 cells were infected with SARS-CoV-2 (USA-WA1/2020) at an MOI of 0.1 or mock infected with equivalent control media in reduced serum media (2% FBS, 1% PSN) for 24 hours. For Ace2-A549 cells, cultures were incubated with a recombinant SARS-CoV-2 ORF6 M58R expressing virus at an MOI of 2 in DMEM with 2% FBS, 1% non-essential amino acids, 1% HEPES, and 1% penicillin/streptomycin at 37°C and 5% CO2 for 4 hours. Supernatants were then removed and replaced with fresh media.

tag: infection

value: recombinant SARS-CoV-2 ORF6 M58R, MOI 2, 24 hours

tag: scrnaseq method

value: SMARTseq v4 PLUS kit (Takara Bio)

tag: sequencing method

value: Read 1 150 nt, i7 index 8 nt, i5 index 8 nt, read 2 150 nt


title: A549_M58R_Bulk_3

description: Bulk RNAseq library

value: ACE2-expressing human respiratory epithelial cell line


title: WT.Control.R2

description:
sample15
Control

tag: tissue


title: WT.HT7.R3

description:
sample28
HT7


title: WT.HT1.R2

description:
sample14
HT1


title: WT.HT4.R2

description:
sample09
HT4


title: WT.Control.R1

description:
sample08
Control


title: WT.HT4.R3

description:
sample12
HT4


title: BST2KO IFNg 3 [20072R-07-02]

first: Bailee

last: Kain

address: 1102 Bates Avenue

institute: Baylor College of Medicine

data_processing:
FASTQ files were preprocessed using HTS stream
RNA seq alignment (STAR)
Differential expression (DE) analysis of gene expression was performed using basespace
Normalized counts were used to perform gene set enrichment analysis (GSEA).
Assembly: NOT PROVIDED
Supplementary files format and content: deseq.counts

source_name: Bone marrow

growth_protocol: HSCs were isolated via whole bone marrow from naïve or IFNg-treated mice

extract_protocol:
Leg, pelvis and hips were used to HSC isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with rm-IFNg for 24 hours

value: Bone marrow

value: BST2 KO

value: Hematopoietic Stem Cells

tag: strain background

tag: treatment

value: 24 hour IFN-gamma (100 ug)


title: WT.Control.HT1.R2

description:
sample11
Control.HT1

value: Blood


title: 20190311NC_TIL5746_Library_16_screen_Lib16_CRISPRn_TIL_Donor_5746_D4_Time_point_0_509038_S1

city: Lexington

first: Micah

last: Benson

state: MA

address: 4 Maguire Rd

institute: KSQ Therapeutics

data_processing:
Read and UMI counts were tabulated using linux command line programs awk, sed, sort, uniq, zcat and paste
Sequencing-errors in guide and UMI sequences were suppressed by aggregating guides and UMIs with an edit-distance of one
UMIs that did not match the synthesized degenerate UMI-pattern were removed
UMIs potentially representing index-swapping between samples on the same sequencing run were removed
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Pooled CRISPR Screen

extract_protocol:
Dissociated melanoma tumors from donor 110005746 were obtained from Conversant Bio and seeded at 1x56 cells/ml in TIL-CM (RPMI 1640 + 10% HI HS, 1X HEPES, GlutaMAX, 2-Mercaptoethanol, Pen/Strep, Gentamicin) containing 300ng/ml IL-2 in a 24 well tissue culture treated plate, and incubated at 37C.  Every other day, 300ng/ml IL-2 was added to cell culture assuming consumption.  On Day 5, suspension cells were harvested and re-seeded at 1.5x10e6/ml in TIL-CM combined 1:1 with XVIVO-15 and supplemented with 300ng/ml IL-2, with adherent cells observed to have disappeared from the wells.  Between Days 7 through Day 22, cells were expanded in IL-2 with a 1:1 ratio of TIL-CM:XVIVO-15 media supplemented with 300ng/ml IL-2 added every other day in order to maintain cell density at 1e6 cells/ml.  On Day 35, cellularity was evaluated, with composition found to be 66% CD8+, and 32% CD4+.  TIL5746 were frozen on Day 35 in CS10 freezing medium at 1x108 cells/ml.  On the first day of the screen (screen Day 0), 2x108 TIL were thawed, washed in 40ml XVIVO-15 media twice, and resuspended to 2x106 cells/ml in XVIVO-15 media containing 600ng/ml IL-2 and 1X DNase (Stemcell, Cat# 07900).  In parallel, non-tissue culture treated 6 well plates were coated with 20ug/ml retronectin in PBS and incubated overnight in preparation for transduction. On Day 1, TIL were transduced with pKSQ017 lentivirus driving expression of Lib16 under control of the human U6 promoter, as well as driving expression of tagRFP under control of a UBC promoter.  Semi-random barcodes were used to track individual clones. In parallel, an aliquot of TIL5746 were separately transduced with the KSQ041 lentivirus which drives expression of a sgRNA targeting the essential gene RPL10a under control of a human U6 promoter as well as mNeonGreen under control of a UBC promoter.  Transduced cells were incubated in 6 well plates at 37C in XVIVO-15 overnight.  On Day 2, TIL were combined from 6 well plates, spun at 300g for 5 minutes, supernatant removed, and TIL resuspended in complete XVIVO-15 media and rested overnight.  On Day 3, transduced TIL5746 were electroporated with Cas9 mRNA (Trilink #L-7206, lot# T1COL01A) using an Amaxa 4D-Nucleofector unit and pulse code CA137 with Buffer P3 according to the manufacturer’s instructions.  Following electroporation, 80l of pre-warmed XVIVO-15 media was added to each well, mixed, and wells combined and washed. TIL were re-suspended to 1x106 in complete XVIVO-15 media, and incubated overnight at 37C. On Day 4, 5x107 transduced TIL5746 were frozen to determine the input sgRNA Library distribution. The TIL Rapid Expansion Phase (REP) was initiated on 25x10e6 transduced and edited TIL with a 1:200 ratio of TIL to irradiated PBMCs derived from 5 pooled donors, 600ng/ml IL-2 and 30ng/ml OKT3 using XVIVO-15 media in a 5L Grex.  Cells were incubated at 37C.  On Days 8, 11 and 15, 2.5L of media was aspirated from the Grex and replaced with 2.5L complete XVIVO-15 media, with 3mgs of IL-2 added to the 5L Grex.  On Day 17, TIL were counted, with 13.2x109 TIL5746 obtained, and analyzed for cellularity on a FACS, with 85.5% of the TIL CD8+, and 12.9% of the TIL CD4+.
TIL were harvested for screen analysis by freezing three 5x10e7 cell pellets for gDNA preparations.

treatment_protocol: The ‘Lib16’ sgRNA library targeting 5,137 genes with 10sgRNAs/gene and 56,408 sgRNAs total, including controls, was cloned into pKSQ017 with semi-random barcodes (see Supplementary Methods for more information on library design and lentivirus production).  Lib16 includes sgRNAs targeting genes involved in T cell function, all predicted cell surface receptors, all known immune-related genes, and all genes demonstrating expression in blood.

tag: time

value: Day 4

tag: library

value: Cas9 Over-Expression


title: BST2KO IFNg 2 [20072R-09-08]

city: Houston


title: WT.HT7.R1

description:
sample03
HT7

value: Djungarian

value: WT


title: WT.HT4.R1

description:
sample07
HT4

value: HT


title: BST2KO untreated 1 [20072R-09-07]

value: naïve


title: WT.HT1.R1

description:
sample02
HT1

value: Male


title: WT.HT7.R2

description:
sample06
HT7

value: Female


title: WT IFNg treated 3 [20072R-09-06]


title: 20190311NC_TIL5746_Library_16_screen_Lib16_CRISPRn_TIL_Donor_5746_D17_50_million_proliferation_509039_S2

value: Day 17


title: WT.Control.HT1.R1

description:
sample04
Control.HT1

value: NT


title: WT.Control.HT16.R1

description:
sample01
Control.HT16


title: WT IFNg treated 1 [20072FL-06-01-04]


title: A549_M58R

description: scRNAseq Library

value: recombinant SARS-CoV-2 ORF6 M58R, MOI 2, 24 hours

value: 10X Genomics Chromium Next GEM Single Cell V(D)J v1.1

value: Read 1 200 nt, index 1 8 nt, read 2 100 np


title: A549_M58R_Bulk_2

description: Bulk RNAseq library

value: ACE2-expressing human respiratory epithelial cell line

value: SMARTseq v4 PLUS kit (Takara Bio)

value: Read 1 150 nt, i7 index 8 nt, i5 index 8 nt, read 2 150 nt


title: A549_Mock

description: scRNAseq Library

source_name: Human respiratory epithelial cell line

value: Human respiratory epithelial cell line

value: Mock


title: BST2KO Untreated 3 [20072FL-06-01-06]

value: Bone marrow

value: BST2 KO

value: Hematopoietic Stem Cells


title: BST2KO IFNg 1 [20072FL-06-01-07]

value: 24 hour IFN-gamma (100 ug)


title: BST2KO Untreated 2 [20072R-07-01]

value: naïve


title: pd98_mRNA_lncRNA

description: HG38_for_every_sample_in_Leukocytes_(mRNA_and_lncRNA).xlsx

value: blood

value: leukocyte


title: MeVa2.2.dOVA rep3

city: Amsterdam

first: PETROS

last: DIMITRIADIS

email: p.dimitriadis@nki.nl, d.rao@nki.nl

state: Noord-Holland

address: Plesmanlaan 121

country: Netherlands

institute: NETHERLANDS CANCER INSTITUTE - NKI

data_processing:
Mapped to mouse genome using STAR (v2.6.0c)
The read counts were computed with HTseq-count (v0.10.0) and were analyzed with DESeq2 (v1.30.1)
Assembly: Mus_musulus.GRCm38.99

source_name: skin, s.c tumor

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen) as per manufacturer's instructions
Strand-specific libraries were generated using TruSeq Stranded mRNA sample preparation kit (Illumina Inc.,) according to the manufacturer's instructions

treatment_protocol: cells were left untreated

value: skin, s.c tumor

value: murine melanoma cell line

value: WT

value: untreated


title: MeVa2.2.dOVA rep2


title: WT IFNg treated 2 [20072FL-06-01-03]


title: pd97_mRNA_lncRNA


title: heat-treated PIF4-L.2 seedlings rep3

city: Cerdanyola del Vallès

first: Guiomar

last: Martín

state: Barcelona

address: Vall Moronta

institute: Centre for Research in Agricultural Genomics

data_processing:
Gene expression (GE) quantification is performed using vast-tools. vast-tools maps the first 50 nucleotides of the forward read (if longer and paired end) to a library with one reference transcript per gene, the *.1 transcript according to the TAIR 10 nomenclature or else that with the lowest suffix (33,602 genes in total). GE levels are provided using the cRPKM metric (corrected [for mappability] Reads Per Kilobasepair and Million mapped reads), as detailed in Labbé et al., Stem Cells 2012. cRPKM can be converted to TPMs applying the following formula: TPM = 10^6 * cRPKM/sum_all(cRPKM).
Supplementary files format and content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Stratified seeds were irradiated with white light at 22ºC for 3 hours to induce germination, grown in darkness at 22ºC for 3 days, and then either placed at 37ºC or kept at 22ºC for 3 hours.

extract_protocol:
Total RNA (1 µg) was extracted from whole Arabidopsis seedlings using the innuPREP Plant RNA kit (Analytik Jena BioSolutions).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: 3 day-old

tag: growth conditions

value: heat (H)

tag: genetic backgroung

value: Columbia


title: WT untreated 3 [20072R-09-05]


title: heat-treated PIF4-L.1 seedlings rep2


title: WT untreated 2 [20072FL-06-01-02]


title: heat-treated PIF4-L.2 seedlings rep1


title: heat-treated PIF4-L.2 seedlings rep2


title: WT untreated 1 [20072FL-06-01-01]


title: pd99_mRNA_lncRNA

tag: cell line


title: heat-treated PIF4-L.1 seedlings rep1


title: pd96_mRNA_lncRNA

tag: cell type


title: heat-treated PIF4-L.1 seedlings rep3


title: MeVa2.2 rep2


title: MeVa2.2.dOVA rep1


title: pd108_mRNA_lncRNA


title: MeVa2.2 rep3


title: pd95_mRNA_lncRNA


title: heat-treated pif4 seedlings rep3


title: pd107_mRNA_lncRNA


title: heat-treated pif4 seedlings rep2


title: MeVa2.1.dOVA rep1


title: MeVa2.2 rep1


title: MeVa2.1.dOVA rep2


title: MeVa2.1.dOVA rep3


title: MeVa2.1 rep2


title: heat-treated WT seedlings rep3


title: pd103_mRNA_lncRNA


title: heat-treated WT seedlings rep1


title: pd105_mRNA_lncRNA


title: Input

city: Shijiazhuang

first: Lingxiao

last: Xing

state: Hebei

address: No.361 East Zhongshan Road

institute: Hebei Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low quality reads using Cutadapt v1.18[1] (non-default parameters: --max-n 0 --minimum-length 35) and Trimmomatic v0.38[2](non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:35).
ChIP-seq reads were aligned to the UCSC hg38 genome using the Bowtie2 v2.3.4.1[4](with default parameters) software. Duplicate reads were then removed using picard MarkDuplicates.
Peak detection was performed using the MACS v2.1.2 [5](non-default parameters: -f BAMPE -g hs/mm -p 0.01) peak finding algorithm with 0.01 set as the p-value cutoff.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Annotation of peak sites to gene features was performed using the ChIPseeker R package
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Cells were crosslinked with 1 % formaldehyde for 10 min at room temperature and quenched with 125 mM glycine. The fragmented chromatin fragments were pre-cleared and then immunoprecipitated with Protein A + G Magnetic beads coupled with anti-H3K18la.
After reverse crosslinking, ChIP and input DNA fragments were end-repaired and A-tailed using the NEBNext End Repair/dA-Tailing Module (E7442, NEB) followed by adaptor ligation with the NEBNext Ultra Ligation Module (E7445, NEB). The DNA libraries were amplified for 15 cycles and sequenced using Illumina Hi-Seq with paired-end 2x150 as the sequencing mode.

value: Human  NSCLC cell line

tag: chip antibody

value: none; input


title: MeVa2.1 rep3

tag: genotype


title: MeVa2.1 rep1


title: heat-treated pif4 seedlings rep1


title: non-treated PIF4-L.2 seedlings rep2

value: darkness (D)


title: Anti-H3K18la

value: anti-H3K18la (1406, PTM)


title: pd102_mRNA_lncRNA


title: pd104_mRNA_lncRNA


title: rpkm_Panobinostat_15nM_12h

city: Berlin

first: Hedwig

middle: Elisabeth

last: Deubzer

state: Berlin

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charite - University Hospital Berlin

data_processing:
bcl2fastq 2.17.1.14 was used for base calling, cutadapt was used to cut 3' adapter AGATCGGAAGAG.
Reads were masked for low-complexity or low-quality sequence , STAR 2.3 was used for mapping against human genome 38 with default parameters and duplicates removed
Htseq-count --stranded=no against gencode.v24.annotation.gtf was used for counting
RPKM values were calculated from the HTSeq count values with a custom perl script. Briefly, total mapped reads in a sample and divide that number by 1,000,000 = "per million" scaling factor. Divide the read counts by the "per million" scaling factor. This normalizes for sequencing depth, giving you reads per million (RPM). Divide the RPM values by the length of the gene, in kilobases. The length of the gene was taken from the annotation gencode.v24 file. This gives the RPKM values.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include the raw count values for each Sample, RPKM values are includled in the file on the series record.

growth_protocol: Neuroblastoma BE(2)-C cell line was maintained in DMEM (Lonza, Basel, Switzerland), supplemented with 10% FCS (Sigma-Aldrich, Hamburg, Germany) and 1% non-essential amino acids (NEAA; Lonza) at 37° C and 5% CO2. Cell lines were monitored for infections using the PlasmoTest™ Kit (Invivo-Gen, according to the manufacturer’s instructions).

extract_protocol:
Total RNA was extracted using the RNeasy Mini Columns (Qiagen, Hilden, Germany) in accordance with manufacturer’s instructions including a purification step with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BE(2)-C cells were treated with 5 nM, 10 nM or 15 nM for 24h with the clinically approved histone deacetylase inhibitor, panobinostat in two independent duplicates.

value: neuroblastoma


title: rpkm_DMSO_control_12h

value: DMSO


title: rpkm_Panobinostat_10nM_12h


title: rpkm_Panobinostat_15nM_6h

value: 6 h


title: rpkm_Panobinostat_10nM_6h


title: rpkm_Panobinostat_5nM_12h


title: rpkm_Panobinostat_5nM_6h


title: pd101_mRNA_lncRNA


title: non-treated PIF4-L.1 seedlings rep3


title: non-treated PIF4-L.2 seedlings rep1


title: rpkm_DMSO_control_6h


title: non-treated PIF4-L.2 seedlings rep3


title: nc9_mRNA_lncRNA


title: heat-treated WT seedlings rep2


title: non-treated PIF4-L.1 seedlings rep1


title: nc8_mRNA_lncRNA


title: nc7_mRNA_lncRNA


title: pd100_mRNA_lncRNA


title: non-treated pif4 seedlings rep3


title: non-treated pif4 seedlings rep1


title: nc4_mRNA_lncRNA


title: nc6_mRNA_lncRNA


title: KSQ-IVP-0059_Input6_lib31_S10

data_processing:
Read and UMI counts were tabulated using linux command line programs awk, sed, sort, uniq, zcat and paste
Sequencing-errors in guide and UMI sequences were suppressed by aggregating guides and UMIs with an edit-distance of one
UMIs that did not match the synthesized degenerate UMI-pattern were removed
UMIs potentially representing index-swapping between samples on the same sequencing run were removed
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Library strategy: Pooled CRISPR Screen

source_name: PMEL

extract_protocol:
Cas9-Tg x TCR-Tg OT1 or PMEL CD8 T cells were isolated from freshly harvested mouse spleens and dissociated using a GentleMACS (Miltenyi), and with CD8 T cells purified by negative selection (EasySep Mouse CD8+ T cell isolation kit).  CD8s were then placed in T225 flasks at a concentration of 1M CD8s/ml and activated with CD3/CD28 Dynabeads and 2ng/ml mouse rIL-2.  The following day, T cells were transduced wither either lentivirus (OT1 B16-Ova screen) or retrovirus (PMEL / MC38-gp100 screen).  Dynabeads were removed the following day, with cells resuspended on cRPMI + 32ng/ml IL-2. On Day 4, transduced T cells were harvested and selected by positive selection using either Thy1.1 for OT1s or hCD2 for PMELs. 5x106 Thy1.1+ Cas9-Tg x OT1 CD8 T cells or 7x106 hCD2+ Cas9-Tg x PMEL CD8 T cells were injected into tumor-bearing mice i.v. via tail vein in 200L PBS, with 10x106 CD8+ T cells saved to determine the sgRNA distribution of the input population of T cells.  Group sizes were 7-8 mice per library.  At the indicated time (eg 11-21 days) following adoptive transfer of cells, mice were euthanized and blood was harvested in EDTA tubes, and stored at -80C. Tumors, spleens, tumor draining and non-draining lymph nodes were harvested and processed further for extraction of CD8 T cells using CD8a Microbeads (Miltenyi, cat# 130-049-401) from the spleen and CD45 Microbeads (Miltenyi, cat# 130-052-301) from the tumor. Tumors were digested using the Miltenyi Tumor Dissociation Kit (Cat# 130-096-730) according to the manufacturer’s instructions.
Genomic DNA was isolated using the Qiamp Blood Midi and Maxi kids, according to the manufacturer’s instructions.

treatment_protocol: The ‘Lib30’ sgRNA library targets 369 genes involved in T cell function with 10sgRNAs per gene and 3089 sgRNAs total, including controls, was cloned into pKSQ044.  Lib31 sgRNA library targets 1004 predicted CSR genes with 8 sgRNAs/gene and 11,148 sgRNAs total, including controls, was also cloned into pKSQ044 (see Supplementary Methods for more information on library design and lentivirus production).

value: PMEL

value: Day 0

tag: sampletype

value: input

value: Cas9 Over-Expression


title: KSQ-IVP-0059_Input5_lib31_S9


title: KSQ-IVP-0059_Input1_lib30_S5


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS3_S10

value: Day 14

value: endpoint


title: KSQ-IVP-0059_Input4_lib31_S8


title: KSQ-IVP-0059_Input2_lib30_S6


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS1_S8


title: KSQ-IVP-0059_Input3_lib30_S7


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS7_S14


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS6_S13


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS5_S12


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS2_S9


title: nc3_mRNA_lncRNA

value: blood

value: leukocyte


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS7_S7


title: nc5_mRNA_lncRNA


title: non-treated pif4 seedlings rep2

value: 3 day-old


title: non-treated WT seedlings rep3

value: WT

value: Columbia


title: non-treated PIF4-L.1 seedlings rep2


title: non-treated WT seedlings rep2


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS5_S5


title: nc2_mRNA_lncRNA


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS4_S4


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS3_S3


title: KSQ-IVP-0059_GP6_Tumor_CD45_MS4_S11


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS2_S2


title: non-treated WT seedlings rep1


title: nc16_mRNA_lncRNA


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS6_S6


title: KSQ-IVP-0059_GP5_Tumor_CD45_MS1_S1


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS4_S18


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS3_S22


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS2_S21


title: nc11_mRNA_lncRNA


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS7_S4


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS5_S2


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS6_S3


title: nc12_mRNA_lncRNA


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS4_S1


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS3_S17


title: nc13_mRNA_lncRNA


title: nc15_mRNA_lncRNA


title: nc10_mRNA_lncRNA


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS7_S19


title: nc1_mRNA_lncRNA


title: KSQ-IVP-0059_GP4_Tumor_CD45_MS1_S20


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS6_S18


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS5_S17


title: ad39_mRNA_lncRNA


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS2_S16


title: WT_1

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

institute: Wuhan university

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Human induced pluripotent stem cell

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: Human induced pluripotent stem cell

value: Cardiomyocytes

value: RPS3 WT

value: Ang II


title: WT_3


title: KSQ-IVP-0059_GP3_Tumor_CD45_MS1_S15


title: MUT_3

value: RPS3 S149 mutant


title: WT_2


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS6_S4


title: ad38_mRNA_lncRNA


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS4_S2


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS3_S1


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS5_S3


title: ad37_mRNA_lncRNA


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS1_S23


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS6_S22


title: MUT_2


title: MUT_1


title: ad35_mRNA_lncRNA


title: ad34_mRNA_lncRNA


title: ad36_mRNA_lncRNA


title: ad33_mRNA_lncRNA


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS5_S21


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS4_S20


title: Ets1 binding levels in the presence of Runx1

type: protein

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

hyb_protocol: Double-stranded microarrays were first pre-moistened in PBS / 0.01% Triton X-100 for 5 min and blocked with PBS / 2% (wt/vol) nonfat dried milk (Sigma) for 1 h. Microarrays were then washed once with PBS / 0.1% (vol/vol) Tween-20 for 5 min and once with PBS / 0.01% Triton X-100 for 2 min. Proteins were diluted to desired concentrations in a 175-μl protein binding reaction containing PBS / 2% (wt/vol) milk / 51.3 ng/μl salmon testes DNA (Sigma) / 0.2 μg/μl bovine serum albumin (New England Biolabs). Preincubated protein binding mixtures were applied to individual chambers of a four-chamber gasket cover slip in a steel hybridization chamber (Agilent), and the assembled microarrays were incubated for 1 h at room temperature. Microarrays were again washed once with PBS / 0.5% (vol/vol) Tween-20 for 3 min, and then once with PBS / 0.01% Triton X-100 for 2 min. Primary antibody to Ets1 (CST) or Runx1 (Abcam) was diluted with a dilution rate of 1:50 in PBS / 2% milk and applied to a single-chamber gasket cover slip (Agilent), and the assembled microarrays were again incubated for 1 h at 20°C. Alexa488-conjugated secondary antibody targeting the primary antibody was then applied with a dilution rate of 1:50.  Finally, microarrays were washed twice with PBS / 0.05% (vol/vol) Tween-20 for 3 min each, and once in PBS for 2 min. After each hour-long incubation step, microarrays and cover slips were disassembled in a staining dish filled with 500 ml of the first wash solution. All washes were performed in Coplin jars on an orbital shaker at 125 r.p.m. Immediately following each series of washes, microarrays were rinsed in PBS (slowly removed over approximately 10 seconds) to ensure removal of detergent and uniform drying.

scan_protocol: Protein-bound microarrays were scanned to detect Alexa-488-conjugated antibody (488 nm ex, 522 nm em) using at least three different laser power settings to best capture a broad range of signal intensities and ensure signal intensities below saturation for all spots. Microarray TIF images were analyzed using GenePix Pro version 6.0 software (Molecular Devices).

data_processing: To correct for any possible non-uniformities in protein binding, we adjusted the fluorescence signals according to their positions on the microarray. We calculated the median normalized intensity of the 15 x 15 block centered on each spot and divided the spot's signal by the ratio of the median within the block to the median over the entire chamber. For each unique sequence represented on the array, we then calculated the median over replicate spots and then normalized the signal for direct comparison between experiments.

label: Alexa 488

molecule: protein

organism: synthetic construct

source_name: Human Ets1, Human Runx1

label_protocol: Proteins were tagged with N-terminal GST by cloning. Protein-bound arrays were first incubated with primary antibody (CST 14069 for Ets1, Abcam 23980 for Runx1), and then Alexa-488-conjugated donkey-anti-rabbit secondary antibody (Invitrogen).

growth_protocol: Gateway-compatible clones containing the full-length genes for Ets1 and Runx1 were respectively transferred into pDEST15 vector using the LR Clonase reaction (Life Technologies). pDEST15 vector enables the production of N-terminally GST-tagged proteins. Cells were grown in LB broth to an OD600 of 0.4 to 0.6 and then expression was induced with IPTG at 30° to 37° C. Pelleted cells were frozen, stored at -20 C, and thawed cells were lysed with lysozyme.

extract_protocol: GST-tagged protein was purified from the soluble portion of the lysate using GST resin (GE Healthcare) according to manufacturer’s instructions.

tag: transcription factor

value: Ets1, Runx1

tag: ets1 concentration

tag: runx1 concentration


title: Multipled-HashTag_Fibroblast Line E01 to E05, scRNAseq

city: Baltimore

first: Rong

last: Li

state: MD

address: 855 N. Wolfe St., Suite 440.

department: Cell Biology

institute: Johns Hopkins School of Medicine

description: 10x genomics

library_source: transcriptomic single cell

data_processing:
Data were uploaded and analyzed using Cell Ranger Cloud from 10x genomics (Ver 7.1.0)
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value files, per sample(CMO) output files, and matrix files

source_name: colon

growth_protocol: cDMEM (10% FBS-HI, 1x Anti-Anti in 1x DMEM high glucose)

extract_protocol:
Treated fibroblasts were dissociated using 0.05% Trypsin-EDTA and resuspended in cDMEM. Cells are labelled with CMO barcodes and sorted using PI stain and resuspended in loading buffer (PBS + 0.1% BSA). Finally, cells are pooled and loaded for single cell 3’ HT V3.1.
Library was performed according to the manufacter’s instructions (single cell 3’ HT V3.1, dual-index, multiplex barcode)

value: colon

value: fibroblast

tag: passage

value: mixed


title: Multipled-HashTag_Fibroblast Line H01 to H05, scRNAseq

description: 10x genomics

tag: tissue


title: Multipled-HashTag_Fibroblast Line F01 to F05, scRNAseq

description: 10x genomics


title: Multipled-HashTag_Fibroblast Line G01 to G05, scRNAseq

description: 10x genomics


title: Runx1 binding levels

source_name: Human Runx1


title: Ets1 binding levels

source_name: Human Ets1


title: KSQ-IVP-0059_GP2_Tumor_CD45_MS2_S24

value: PMEL

value: Cas9 Over-Expression


title: Runx1 binding levels in the presence of Ets1

source_name: Human Runx1, Human Ets1

value: Runx1, Ets1


title: ad32_mRNA_lncRNA

value: blood


title: miRNA_Panobinostat_5 nM_replicate_2

description:
257015612085_1_3
replicate 2

hyb_protocol: 100ng of Cy3 labeled miRNA sample were hybridized for at least 20 hr at 55°C on Agilent human miRNA Microarray V21.0, 8x60k according to manufacturer's instructions.

scan_protocol: Gene Expression Microarrays were scanned using the Agilent Scanner G2505C. The scanned images were analyzed with Feature Extraction Software (Agilent technologies) using default settings.

data_processing: Data extraction was done for all beads individually, and outliers are removed when the absolute difference to the median is greater than 2.5 times MAD(2.5 Hampel’s method). All remaining bead level data points are than quantile normalized. As test for significance the student’s t-test is used on the bead expression values of the two groups of interest. In the case of significance of expression against background we tested for greater than all negative beads for this sample and in the case of comparing separate groups we tested for inequality of the means of the groups. In both cases Benjamini-Hochberg correction was applied to the complete set of p-values of all ProbeIDs on the chip.

source_name: BE(2)-C cells

label_protocol: Fluorescently-labeled miRNA were prepared according to Agilent protocol  miRNA Complete Labeling and Hyb Kit.

extract_protocol: Total RNA was extracted using the RNeasy Mini Columns (Qiagen, Hilden, Germany) in accordance with manufacturer’s instructions including a purification step with DNase I.

treatment_protocol: BE(2)-C cells were treated with 5 nM, 10 nM and 15 nM for 24h with the clinically approved histone deacetylase inhibitor, panobinostat in two independent duplicates.

value: BE(2)-C cells

value: 5 nM panobinostat

tag: time point

tag: tumor entity

value: neuroblastoma


title: ad31_mRNA_lncRNA

value: leukocyte


title: miRNA_DMSO_control_replicate_2

description:
257015612085_1_1
replicate 2

tag: treatment

value: DMSO


title: Multipled-HashTag_Fibroblast Line D01 to D05, scRNAseq

description: 10x genomics


title: miRNA_Panobinostat_15 nM_replicate_2

description:
257015612085_2_1
replicate 2

value: 15 nM panobinostat


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS3_S19

tag: time

value: Day 14

tag: library

value: endpoint


title: miRNA_Panobinostat_10 nM_replicate_2

description:
257015612085_1_4
replicate 2

value: 10 nM panobinostat


title: Multipled-HashTag_Fibroblast Line C01 to C05, scRNAseq

description: 10x genomics


title: ad30_mRNA_lncRNA


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS2_S18


title: Multipled-HashTag_Fibroblast Line A01 to A05, scRNAseq

description: 10x genomics


title: KSQ-IVP-0059_GP1_Tumor_CD45_MS1_S17


title: miRNA_Panobinostat_15 nM_replicate_1

description:
257015612081_2_1
replicate 1


title: Multiplexed-Fibroblast Line H01 to H05, scRNAseq

description: 10x genomics


title: 3AO cells, LOC646029 biol rep 3

city: Beijing

first: Pengfei

last: Zhao

address: No.17, Panjiayuan Nanli, South Huawei Road

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (version 0.36) (parameter- ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE)
Clean Reads were further treated with UMI_soft (in-house) to eliminate duplication bias introduced in library preparation and sequencing on using UMI. (Default Parameter developed by Wuhan Seqhealth Co., Ltd.)
The de-duplicated consensus sequences were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts (Version 1.5.1) (parameter -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: 3AO cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following manufacturer's protocols.

value: epithelial ovarian cancer cells

value: LOC646029 overexpression

value: lentiviral infection


title: miRNA_Panobinostat_10 nM_replicate_1

description:
257015612081_1_4
replicate 1


title: Multiplexed-Fibroblast Line G01 to G05, scRNAseq

description: 10x genomics

value: colon

value: fibroblast

value: mixed


title: Multipled-HashTag_Fibroblast Line B01 to B05, scRNAseq

description: 10x genomics


title: 3AO cells, LOC646029 biol rep 2


title: ad29_mRNA_lncRNA


title: 3AO cells, LOC646029 biol rep 1


title: Multiplexed-Fibroblast Line E01 to E05, scRNAseq

description: 10x genomics


title: 3AO cells, EV biol rep 3

value: EV


title: 3AO cells, EV biol rep 2


title: Multiplexed-Fibroblast Line D01 to D05, scRNAseq

description: 10x genomics


title: Multiplexed-Fibroblast Line F01 to F05, scRNAseq

description: 10x genomics


title: Multiplexed-Fibroblast Line C01 to C05, scRNAseq

description: 10x genomics


title: Cxadr_ko mouse #4, MEP population

city: Vienna

first: Lukas

last: Kazianka

address: Währinger Gürtel 18-20

department: Medicine I, Div. of Hematology

country: Austria

institute: Medical University of Vienna

data_processing:
R/Python computing environment
Biomedical Sequencing Facility, Vienna, Austria
reads were aligned to the us musculus GRCm38/mm10 genome using STAR
aligned reads and normalized counts were analyzed using the DESeq2 package in R
Assembly: Mus musculusGRCm38/mm10 Reference Genome Assembly (December 2011)
Supplementary files format and content: normalized counts are presented in an .xlsx Excel sheet

source_name: bone marrow

extract_protocol:
TRIzol extraction with chloroform and isopropanaol precipitation
NEBNextSingle Cell/Low Input RNA Library Prep Kit for Illumina according to manufacturer's recommendation

treatment_protocol: cells were directly sorted into TRIzol followed by downstream RNA isolation

tag: animal

value: Cxadr_ko mouse #4

value: bone marrow

value: MEP

value: Cxadr ko (Mx1-Cre+ Cxadrfl/fl)


title: Cxadr_ko mouse #3, LSK population

value: Cxadr_ko mouse #3

value: LSK


title: Cxadr_ko mouse #4, CMP population

value: CMP


title: Cxadr_ko mouse #4, GMP population

value: GMP


title: Cxadr_ko mouse #3, MEP population


title: miRNA_DMSO_control_replicate_1

description:
257015612081_1_1
replicate 1

value: BE(2)-C cells

value: DMSO

value: neuroblastoma


title: Cxadr_ko mouse #4, LSK population


title: miRNA_Panobinostat_5 nM_replicate_1

description:
257015612081_1_3
replicate 1

value: 5 nM panobinostat


title: KSQ-IVP-0027_GP6_Tumor_M4_S15

source_name: OT-I

value: OT-I

tag: group

value: day 14

value: Cas9 Over-Expression


title: KSQ-IVP-0027_GP6_Tumor_M5_S16


title: KSQ-IVP-0027_GP6_Tumor_M6_S17


title: KSQ-IVP-0027_GP6_Tumor_M3_S14


title: KSQ-IVP-0027_GP6_Tumor_M7_S18


title: 3AO cells, EV biol rep 1

tag: cell line

value: epithelial ovarian cancer cells

value: lentiviral infection


title: KSQ-IVP-0027_GP6_Tumor_M1_S12

tag: cell type


title: Multiplexed-Fibroblast Line B01 to B05, scRNAseq

description: 10x genomics

value: colon

value: fibroblast

value: mixed


title: HuH-7_RIP_Input

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 (for RIP-seq) or Bowtie (for MeRIP-seq)
Gene annotated in NCBI were quantified using featureCounts
Peaks were identified using the MACS2 peak caller
Assembly: hg38
Supplementary files format and content: txt, counts for each RIP-seq sample
Supplementary files format and content: txt, MeRIP-seq peak (except for Input sample)

growth_protocol: HuH-7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (BasalMedia, Shanghai, China) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
Total RNA from HuH-7 cells were extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's instructions.
For the RIP-seq, the sequencing library was prepared deploying NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs, USA) and sequenced on the Illumina HiSeq 3000 platform.  For the MeRIP-seq, the library was prepared by smart-seq method. Both the input samples without IP and the m6A IP samples were subjected to 150-bp, paired-end sequencing on an Illumina NovaSeq 6000 sequencer.

value: HCC

tag: ip antibody


title: Cxadr_ko mouse #3, CMP population

value: Cxadr_ko mouse #3

value: bone marrow

tag: genotype

value: Cxadr ko (Mx1-Cre+ Cxadrfl/fl)


title: Cxadr_ko mouse #3, GMP population

value: GMP


title: HuH-7_RIP_IGF2BP1

value: IGF2BP1, Proteintech, 22803-1-AP


title: KSQ-IVP-0027_GP1_Tumor_M5_S5


title: KSQ-IVP-0027_GP1_Tumor_M6_S6


title: Cxadr_ko mouse #2, MEP population

value: Cxadr_ko mouse #2

value: MEP


title: KSQ-IVP-0027_GP6_Tumor_M2_S13


title: Cxadr_ko mouse #2, LSK population

value: LSK


title: Multiplexed-Fibroblast Line A01 to A05, scRNAseq

description: 10x genomics


title: Cxadr_ko mouse #2, CMP population

value: CMP


title: Cxadr_ko mouse #1, MEP population

value: Cxadr_ko mouse #1


title: Cxadr_ko mouse #2, GMP population