title: Fig4 double positive, P12, replicate 1 [E1_Fig4pp_P12_1]

value: sciatic nerve

tag: genotype


title: HCC tumor from patient MDA_026

status: Public on Jan 01 2024

type: protein

city: Houston

first: Ju-Seog

last: Lee

state: Texas

address: 6565 MD Anderson Blvd

country: USA

institute: UT MD Anderson Cancer Ctr.

hyb_protocol: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.  Printed proteins in slides were probed with 201 validated primary antibodies followed by corresponding secondary antibodies (goat anti-rabbit IgG, goat anti-mouse IgG, or rabbit anti-goat IgG)

scan_protocol: Slides were scanned on a flatbed scanner to produce 16-bit tiff images. Spots from tiff images were identified and their densities were quantified by MicroVigene. Relative protein levels for each sample were determined by interpolation of each dilution curve from the standard curve (supercurve) of the slide (antibody). Supercurve is constructed from a script in R written by the informatics department. These values are given as Normalized values.

data_processing: Expression data was normalized for possible unequal protein loading, taking into account the signal intensity for each sample for all antibodies tested. Log2 values were media-centered by protein to account for variability in signal intensity by time and were calculated using the formula log2 signal to  log2 median. Principal component analysis was used to check for a batch effect and feature-by-feature two-sample t-tests were used to assess differences between treatment and control groups. We also used feature-by-feature one-way analysis of variance (ANOVA) followed by the Tukey test to perform pair comparisons for all groups. Beta-uniform mixture models were used to fit the resulting p value distributions to adjust for multiple comparisons. The cutoff p values and number of significant proteins were computed for several different false discovery rates (FDRs).

molecule: protein

organism: Homo sapiens

source_name: primary HCC tumor

growth_protocol: Collected primary tumors

extract_protocol: protein was extracted from tumors using an RPPA lysis buffer (1% Triton X-100, 50 nmol/L HEPES, pH 7.4, 150 nmol/L NaCl, 1.5 nmol/L MgCl2, 1 mmol/L EGTA, 100 nmol/L NaF, 10 nmol/L sodium pyrophosphate, 10% glycerol, 1 nmol/L phenylmethylsulfonyl fluoride, 1 nmol/L Na3VO4, 10 µg/mL aprotinin). Lysis buffer was used to lyse frozen tumors with a Precellys homogenizer (Bertin Instruments). Tumor lysates were adjusted to a concentration of 1 g/L as determined using a bicinchoninic acid assay and boiled with 1% sodium dodecyl sulfate.

treatment_protocol: Not treated

tag: organ

value: liver

tag: age (years)

tag: Sex

value: M

tag: death

value: dead

tag: follow-up (month)


title: HCC tumor from patient MDA_030

label_protocol: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.  Printed proteins in slides were probed with 201 validated primary antibodies followed by corresponding secondary antibodies (goat anti-rabbit IgG, goat anti-mouse IgG, or rabbit anti-goat IgG)

value: F

value: alive


title: Sarcoma tumor tissue, Sample 43

type: SRA

first: Jennifer

last: Wang

state: TX

address: 1515 Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
Raw RNA sequencing reads of the samples were mapped to the hg19 reference genome using the STAR aligner.
RSEM was used to quantify aligned reads and produce raw counts of known transcripts
The raw count of transcripts in the samples were then converted to transcripts per million that normalize counts for library size and gene length.
Assembly: hg19
Supplementary files format and content: rawcounts and TPMs

molecule: polyA RNA

source_name: Sarcoma tumor tissue

extract_protocol:
RNA was extracted by NORGEN Total RNA Purification Kit (Cat. 37500) (NORGEN BIOTEK CORP). The extracted RNA was treated with DNase I. The treated RNA then was cleaned-up using the AMPure XP beads (Beckman Coulter Life Sciences) and eluted into 1x TE buffer. The purified RNA was quantified using Quant-iT™ RiboGreen™ RNA Assay Kit (ThermoFisher SCIENTIFIC) and the RNA quality was accessed using Agilent RNA 6000 Nano Kit and the 2100 Bioanalyzer Instrument (Agilent Technologies).
Up to 200 ng of each cDNA sample based on the PicoGreen quantification was sheared (mechanically fragmented) using the E220 Focused-ultrasonicator Covaris (Covaris). The sonication was performed under the following conditions: Peak Incident Power 200, Duty Cycle 25%, Cycles per Burst 50, and duration 10 seconds for 120 iterations. To ensure the proper fragment size, samples were examined on TapeStation 4200 using the DNA High Sensitivity kit (Agilent Technologies). The sheared cDNA was proceeded to library preparation using SureSelect XT Low Input Reagent Kit with indexes 1-96 (Agilent Technologies) as automated method on the Sciclone G3 NGSx Workstation (PerkinElmer, Inc.).This protocol consists of 3 enzymatic reactions for end repair, A-tailing and Adaptor ligation, followed by barcode insertion by PCR using Herculase II Fusion DNA Polymerase (8 to 14 cycles, based on input DNA quality and quantity). PCR primers were removed by using 1x volume of Agencourt AMPure PCR Purification kit (Agencourt Bioscience Corporation). The quality and quantity of the prepared libraries were evaluated using TapeStation 4200 and the DNA High Sensitivity kit (Agilent Technologies) to verify correct fragment size and to ensure complete removal of primer dimers.

tag: tissue

value: Sarcoma tumor tissue

tag: disease state

value: Soft-Tissue Sarcoma

tag: treatment

value: Immune checkpoint blockade

tag: collected date

tag: collected

value: Surgery

tag: age

tag: outcome

value: SD

tag: grade

value: High Grade


title: UPFL2

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

description: bulk RNA

data_processing:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
Illumina Novaseq_6000 for scRNAseq base calling
Transcript abundance estimates for cell were performed using cell ranger
Supplementary files format and content: Tab-delimited text files include Normalized count values for each sample
Supplementary files format and content: H5 format files of cell ranger output for each scRNAseq samples
Assembly: mm10

molecule: total RNA

organism: Mus musculus

source_name: bladder tumor

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
scRNAseq libraries were prepared using Chromium Single Cell 3' Reagent Kits (v3.1 Chemistry)

tag: strain

value: bladder tumor

tag: tissue type

value: primary UPFL tumor

value: untreated


title: HCC tumor from patient MDA_025

description: Protein lysate from each sample was spotted to nitrocellulose-coated slides and probed with over 200  antibodies.


title: Tumor tissue from patient with Ovarian cancer [P24newrepeat]

type: genomic

city: Athens

first: Georgios

last: Tsaousis

state: Attiki

address: Spaton 52, Ave., Gerakas

department: Bioinformatics

country: Greece

institute: Genekor Medical SA

hyb_protocol: After amplification, the fragments are subjected to HAEIII endonuclease digestion and hybridized to OncoScan® CNV  assay on Affymetrix Genechip® Hybridization Oven 645 (Thermo Fisher Scientific, Waltham, MA, USA) set at 49, 60rpm for 16-18h (overnight)

scan_protocol: The Arrays were  scanned using a GeneChip Scanner 3000 7 G (cat no. 00-0218 Thermo Fisher Scientific Inc.)

data_processing: Scanning results from both arrays (AT/GC) are combined and subjected to further analysis in Chromosome Analysis Suite (Thermo Fisher Scientific, Waltham, MA, USA).

label: biotin

molecule: genomic DNA

label_protocol: Biotin

growth_protocol: All samples were collected from the second Department of Surgery, Aretaieion Hospital, Medical School, National and Kapodistrian University of Athens.

extract_protocol: Genomic DNA was extracted from the FFPE tumor biopsies using the MagMAX™ Total Nucleic Acid Isolation Kit (cat no. AM1840; Thermo Fisher Scientific Inc.)

tag: disease

value: ovarian cancer


title: HCC tumor from patient MDA_024


title: Tumor tissue from patient with Ovarian cancer [P22]


title: UPFL1

description: bulk RNA


title: Tumor tissue from patient with Ovarian cancer [P21]


title: Sarcoma tumor tissue, Sample 44


title: Sarcoma tumor tissue, Sample 40

value: baseline

value: PD


title: Sarcoma tumor tissue, Sample 39


title: Tumor tissue from patient with Ovarian cancer [P20]


title: Tumor tissue from patient with Ovarian cancer [P19]


title: high-fat diet, replicate 3, scRNAseq

city: Wuxi

first: Hao

last: Kan

address: The number of 1800 ,Li Hu Road

country: China

institute: jiangnan university

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)

source_name: aorta

extract_protocol:
aortas were cut and digested with an enzyme solution (0.2% type IA collagenase [Sigma, USA] and 200 U/ml DNase [Sigma, USA]) for 30 min at 37°C. The cell suspension was strained through a 40-μm filter (STEMCELL Technologies, China), treated with ACK lysis buffer for 1 minute at room temperature (Sigma, USA), and washed thrice with PBS. The cells were resuspension in PBS with 0.04% bovine serum albumin (Beyotime, China), and their viability was greater than 80%.
Qualified aortic cell suspensions (500–1000 living cells per microliter as determined by Count Star) were loaded onto a Single-cell Controller (10x Genomics GemCode Technology, CA) to generate single-cell gel beads in emulsion (GEMs, Single cell 3′ Library, Gel Bead Kit V2 and Chromium Single Cell B Chip Kit [10x Genomics]). Briefly, the single-cell suspensions, gel beads, reagents and partitioning oil were loaded onto each channel. Single-cell RNA was barcoded through reverse transcription in individual GEMs. Barcoded cDNA was pooled, and a general library was prepared using Single Cell 3′ Library and Gel Bead Kit V2. The library was finally sent for sequencing.

value: high-fat diet

value: aorta


title: Sarcoma tumor tissue, Sample 38

value: M


title: high-fat diet, replicate 2, scRNAseq

description: 10x Genomics


title: high-fat diet, replicate 1, scRNAseq

description: 10x Genomics


title: Sarcoma tumor tissue, Sample 37

value: F


title: Sarcoma tumor tissue, Sample 41


title: Tumor tissue from patient with Ovarian cancer [P17]


title: HCC tumor from patient MDA_021

value: liver

value: dead


title: Tumor tissue from patient with Ovarian cancer [P16]


title: Control, replicate 3, scRNAseq

description: 10x Genomics

value: Control


title: Control, replicate 2, scRNAseq

description: 10x Genomics


title: Sarcoma tumor tissue, Sample 36

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade


title: Sarcoma tumor tissue, Sample 35

value: Surgery

value: SD

value: High Grade


title: HCC tumor from patient MDA_020

value: alive


title: Control, replicate 1, scRNAseq

description: 10x Genomics


title: Tumor tissue from patient with Ovarian cancer [P14]

value: ovarian cancer


title: Tumor tissue from patient with Ovarian cancer [P15]


title: HCC tumor from patient MDA_017


title: HCC tumor from patient MDA_018


title: HCC tumor from patient MDA_023


title: KO, Naïve T, 1- 6

city: Xiamen

first: Guo

last: Fu

address: No. 422, Siming South Road, Xiamen, Fujian, China.

institute: Xiamen University

description:
Mars-seq
cell_metadata.csv

data_processing:
ScRNA-seq libraries (pooled at equimolar concentrations) were sequenced on an Illumina NextSeq 500.MARS-seq reads were processed using the MARS-seq2.0 pipeline (Keren-Shaul et al., 2019).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Lung and spleen of co-transfer WT and cKO CD8+ T cells were  purified by FACS sorting.
Single-cell cDNA libraries were prepared using the MARS-Seq method, as described (Jaitin et al., 2014; Keren-Shaul et al., 2019)

tag: cell type

value: T cell

value: Spleen

value: Naive T (control)

tag: infection


title: Tumor tissue from patient with Ovarian cancer [P13]


title: Sarcoma tumor tissue, Sample 33

value: baseline


title: HCC tumor from patient MDA_016

tag: organ

tag: age (years)

value: M


title: HCC tumor from patient MDA_015

tag: Sex

tag: death


title: Tumor tissue from patient with Ovarian cancer [P12]


title: KO, Naïve T, 1- 4

description:
Mars-seq
cell_metadata.csv

tag: tissue


title: Sarcoma tumor tissue, Sample 31

tag: disease state


title: KO, Naïve T, 1- 5

description:
Mars-seq
cell_metadata.csv

tag: treatment


title: Sarcoma tumor tissue, Sample 32

tag: collected date


title: HCC tumor from patient MDA_019

tag: follow-up (month)


title: Tumor tissue from patient with Ovarian cancer [P11]


title: Tumor tissue from patient with Ovarian cancer [P10]


title: Tumor tissue from patient with Ovarian cancer [P8]


title: HCC tumor from patient MDA_022


title: Sarcoma tumor tissue, Sample 29

tag: collected

tag: age


title: HCC tumor from patient MDA_014


title: HCC tumor from patient MDA_013


title: HCC tumor from patient MDA_012


title: KO, Naïve T, 1- 3

description:
Mars-seq
cell_metadata.csv


title: HCC tumor from patient MDA_011

value: F


title: Sarcoma tumor tissue, Sample 30

tag: outcome

tag: grade


title: KO, Naïve T, 1- 2

description:
Mars-seq
cell_metadata.csv

tag: strain


title: Sarcoma tumor tissue, Sample 34


title: KO, Naïve T, 1- 1

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 28


title: WT, Naïve T, 1- 6

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 26


title: WT, Naïve T, 1- 5

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 27


title: Tumor tissue from patient with Ovarian cancer [P5]

tag: disease


title: HCC tumor from patient MDA_010

value: liver


title: Tumor tissue from patient with Ovarian cancer [P6]


title: WT, Naïve T, 1- 4

description:
Mars-seq
cell_metadata.csv

tag: cell type


title: Sarcoma tumor tissue, Sample 25

value: PR


title: Sarcoma tumor tissue, Sample 24


title: HCC tumor from patient MDA_007


title: WT, Naïve T, 1- 3

description:
Mars-seq
cell_metadata.csv

tag: infection


title: HCC tumor from patient MDA_009

tag: organ

value: dead


title: WT, Naïve T, 1- 2

description:
Mars-seq
cell_metadata.csv


title: Tumor tissue from patient with Ovarian cancer [P1]


title: HCC tumor from patient MDA_008

tag: age (years)


title: Tumor tissue from patient with Ovarian cancer [P7]


title: Sarcoma tumor tissue, Sample 23

value: Sarcoma tumor tissue

tag: Sex


title: Sarcoma tumor tissue, Sample 22

value: Soft-Tissue Sarcoma


title: Tumor tissue from patient with Ovarian cancer [P3]


title: Tumor tissue from patient with Ovarian cancer [52f]


title: KO, Lung, 3- 3

description:
Mars-seq
cell_metadata.csv

source_name: Lung

value: Lung

value: o-transfer cKO CD8+ T cells


title: Tumor tissue from patient with Ovarian cancer [51f]


title: WT, Naïve T, 1- 1

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 21

value: Immune checkpoint blockade

value: PD


title: HCC tumor from patient MDA_005

tag: death


title: KO, Lung, 3- 2

description:
Mars-seq
cell_metadata.csv

tag: tissue


title: HCC tumor from patient MDA_004


title: HCC tumor from patient MDA_006


title: HCC tumor from patient MDA_003


title: Tumor tissue from patient with Ovarian cancer [50f]


title: Sarcoma tumor tissue, Sample 20

tag: disease state

value: Surgery

value: SD

value: High Grade


title: Sarcoma tumor tissue, Sample 19

tag: treatment


title: KO, Lung, 3- 1

description:
Mars-seq
cell_metadata.csv

value: T cell


title: KO, Lung, 2- 3

description:
Mars-seq
cell_metadata.csv


title: Tumor tissue from patient with Ovarian cancer [46f]

value: ovarian cancer


title: HCC tumor from patient MDA_002

value: alive


title: Sarcoma tumor tissue, Sample 18

tag: collected date

value: baseline

value: M


title: KO, Lung, 2- 2

description:
Mars-seq
cell_metadata.csv


title: cyc1K79A Hyphae 2h-3

city: Singapore

first: Guisheng

last: Zeng

address: 8A Biomedical Grove, #05-13 Immunos Building, Immunos

department: Infectious Diseases Labs

country: Singapore

institute: Agency for Science, Technology and Research

data_processing:
The raw paired-end reads were trimmed using SeqPrep.
The raw paired-end reads were quality-controlled using Sickle.
The clean reads were mapped to C. albicans reference genome SC5314 (assembly ASM18296v3) using the STAR aligner (version 2.2.1)
Mapped reads were summarized to the gene level with the featureCounts software (version 1.6.3).
Gene differential analysis was done using the Bioconductor R package edgeR in R (version 3.6.2).
Assembly: C. albicans reference genome SC5314 (assembly ASM18296v3)
Supplementary files format and content: Tab-delimited text files include raw counts for each sample
Supplementary files format and content: Tab-delimited text files include  RPKM value for each sample

organism: Candida albicans SC5314

source_name: Whole cell

growth_protocol: C. albicans strains were grown in YPD at 30°C overnight.

extract_protocol:
Total RNA was extracted using the Trizol reagent according to the manufacturer’s instructions (Invitrogen).
RNA-seq transcriptome library was prepared from 1 mg of total RNA using Illumina’s TruSeq RNA sample preparation kit.

treatment_protocol: Overnight yeast cultures were diluted (1 :20) to fresh YPD medium containing 10% fetal bovine serine (FBS) and incubation at 37°C for 1-2 h.

value: Whole cell

value: Hyphal-induced cell

tag: genotype

value: Hyphal-induced culture


title: Normal，scRNAseq

city: guangzhou

first: xu

last: dong

state: Guangdong

address: wushan

institute: South China Agricultural University

description: 10× Genomics

data_processing:
Cell Ranger (v7.1.0) as the official companion software of 10x Genomics provides upstream analysis of its single cell sequencing data, first the raw data obtained from sequencing (raw base call, BCL) was demultiplexed into FASTQ file by the cellranger mkfastq process. The FASTQ file generated by mkfastq was used for comparison (based on STAR), filtering, and UMI counting through the cellranger counting process to obtain clean data. Then, the reference genome and annotation files of the Gallus_gallus were downloaded from Ensembl (https://www.ensembl.org/) to generate the chicken genome through the cellranger mkgtf process to generate the chicken single-cell transcriptome reference genome (GRCg7b). It is worth stating that the annotation information for the mitochondrial genes needs to be added here manually. Subsequently, we then determined gene expression counts using unique molecular identifiers (UMIs) for each cell barcode-gene combination, generated a gene-barcode matrix using cell barcode, and three standard files, namely barcodes.tsv, features.tsv, and matrix.mtx, for each sample to be used in the samples for clustering, gene expression analysis, and so on.
Assembly: Gallus_gallus.bGalGal1.mat.broiler.GRCg7b
Supplementary files format and content: Tab-separated values files and matrix files

organism: Gallus gallus

source_name: Peritoneum

extract_protocol:
According to the manufacturer’s instructions for the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1(10x Genomics), single cell sequencing libraries were constructed. The cell suspension was loaded onto the Chromium Next GEM Chip G and ran the Chromium Controller to generate single-cell gel beads in the emulsions (GEMs) according to the manufacturer’s recommendation. Captured cells were lysed and the released RNA was barcoded through reverse transcription in individual GEMs. Barcoded, full-length cDNA was generated and libraries were constructed according to the performer’s protocol.
Next, the Qubit 4.0 was used to detect the concentration of cDNA products and libraries; the Agilent 2100 was used to check the integrity of cDNA libraries; and q-PCR was used to accurately quantify the effective concentration of libraries. After passing library inspection, sequencing was performed on the Illumina NovaSeq 6000 PE15 with a sequencing depth of at least 50,000 reads per cell (performed by Biomarker Technologies Corporation, Beijing, China).

value: Peritoneum


title: cyc1K79A Hyphae 2h-2


title: KO, Lung, 2- 1

description:
Mars-seq
cell_metadata.csv


title: HCC tumor from patient MDA_001

value: liver

value: F

tag: follow-up (month)


title: Tumor tissue from patient with Ovarian cancer [P2]


title: Sarcoma tumor tissue, Sample 17

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

tag: collected

tag: age


title: Sarcoma tumor tissue, Sample 16

value: Immune checkpoint blockade

tag: outcome

value: PD

tag: grade


title: WT, Lung, 3- 1

description:
Mars-seq
cell_metadata.csv

value: Lung

tag: strain

value: co-transfer WT CD8+ T cells


title: Mtb, control, rep2

city: Cologne

first: Raphael

last: Gries

address: Robert-Koch-Straße 21

country: Germany

institute: University Hospital Cologne

description:
Sample 3 and 4 were processed for relative expression compared to Samples 1 and 2 (controls)
sample name:
161580

data_processing:
Sequenced reads were aligned to the M. tuberculosis reference genome (GenBank ID: NC_000962.3) using Bowtie2 version 2.3.4.1 (Langmead and Salzberg, 2012).
Known gene transcripts were quantified using featureCounts 1.5.0-p1 (Liao et al., 2014), i.e. the number of reads assigned to an annotated gene feature.
Count data normalization and differential expression testing was performed with DESeq2 version 1.34 (Love et al., 2014).
Genes were defined as differentially expressed with a fold-change >=2 and an adjusted p-value cutoff (FDR) of <=0.5. Results were visualized in R with the EnhancedVolcano version 1.12 (Kevin Blighe, 2022) and pheatmap version 1.0.12 packages.
Assembly: GenBank ID: NC_000962.3
Supplementary files format and content: featurecounts

organism: Mycobacterium tuberculosis

source_name: bacteria

growth_protocol: Mtb were innoculated at an OD600 of 0.1 and cultivated for 48h at 37°C in 7H9c medium.

extract_protocol:
Mtb were mechanically lysed by beating previously frozen cells (-80 °C) using a cell disruptor (Disruptor Genie; Scientific Industry, Bohemia, USA) and 150 - 212 µm glass beats. Lysates were then mixed with RLT lysis buffer (QIAGEN, Venlo, Netherlands) containing 1% β-mercaptoethanol (AppliChem GmbH, Darmstadt, Germany) and ethanol (Th. Geyer GmbH & Co. KG, Renningen, Germany) (3:2) and extracted using the RNeasy kit (QIAGEN, Venlo, Netherlands) according to its protocol.
RNA samples were first depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit (Bacteria) (New England Biolabs, Ipswich, USA). The following strand specific library creation was done using 1000 ng total RNA and the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, USA). Next generation sequencing was then performed using a NovaSeq600 (Illumina, Inc, San Diego, USA) sequencer at 10 million reads per sample.

treatment_protocol: After 44 h of cultivation test compounds were added to the medium.

value: Erdman

tag: cell type

value: bacteria

value: WT

value: 0.1% DMSO


title: cyc1K79A Hyphae 2h-1


title: ctm1∆/∆ Hyphae 2h-3

value: ctm1 deletion


title: Mtb, S3, rep1

description:
Sample 3 and 4 were processed for relative expression compared to Samples 1 and 2 (controls)
sample name:
161586

value: 20 uM S3


title: Mtb, S3, rep2

description:
Sample 3 and 4 were processed for relative expression compared to Samples 1 and 2 (controls)
sample name:
161588


title: WT, Lung, 3- 3

description:
Mars-seq
cell_metadata.csv

value: T cell

tag: infection


title: Sarcoma tumor tissue, Sample 15

value: SD

value: High Grade


title: Sarcoma tumor tissue, Sample 13

value: baseline


title: ctm1∆/∆ Hyphae 2h-1

value: Whole cell

value: Hyphal-induced cell

value: Hyphal-induced culture


title: Mtb, control, rep1

description:
Sample 3 and 4 were processed for relative expression compared to Samples 1 and 2 (controls)
sample name:
161577


title: ctm1∆/∆ Hyphae 2h-2


title: WT, Lung, 3- 2

description:
Mars-seq
cell_metadata.csv


title: WT, Lung, 1- 3

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 12

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade

value: M


title: HVP，scRNAseq

description: 10× Genomics

value: Peritoneum


title: Sarcoma tumor tissue, Sample 11

value: F

value: PD


title: Sarcoma tumor tissue, Sample 10


title: WT C.albicans Hyphae 2h-3

value: WT


title: WT, Lung, 1- 1

description:
Mars-seq
cell_metadata.csv

value: Lung

value: co-transfer WT CD8+ T cells


title: WT C.albicans Hyphae 2h-1


title: WT, Lung, 1- 2

description:
Mars-seq
cell_metadata.csv

value: T cell


title: KL Lung tumor, 10 weeks, rep 2

city: Wuhan, China

first: Ci

last: Yang

address: 115 East Lake Road

institute: Wuhan University

data_processing:
CutadaptData filteringAt least 10 bp overlap (agatcggaag), allowing a base error rate of 20%
Library quality inspection (2100 detection of library size, fluorescence quantitative detection of total library concentration < quantifluor st fluorometer, Promega, e6090; quant it PicoGreen dsDNA assay kit, Invitrogen, p7589) >, qPCR quantitative detection of effective library concentration < Thermo Scientific steponeplus real time PCR systems >)
All RNA-seq data wrer aligned to Mus musculus GRCm38 genome with Ensembl byTophat2 microexon-search and library-type=fr-firststrand
Illumina NovaSeq 6000
Quantitative gene expression using union scheme in HTSeq
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: excel with FPKM for every gene and every sample

source_name: lung

growth_protocol: KL and KL25 mice were intranasally injected with Ad-Cre for 10 weeks.Tumor-burdened lungs from KL and KL25 mice were perfused through alveolar lavage and cardiac lavage with PBS and the lung tumors were collected. Single-cell suspensions were obtained from the lung tumors with the gentleMACS followed by incubation with CD45 magnetic beads for 15 min.

extract_protocol:
The cells were homogenized in 2 ml of TRIzol (Invitrogen). Total RNAs were prepared and the quality of RNAs was determined by agarose gel electrophoresis and spectrophotometer analysis.
TruSeq Stranded mRNA LT Sample Prep Kit was used to synthesized the first strand cDNA through the action of random primers and reverse transcriptase, the second strand cDNA is synthesized with the first strand cDNA as the template, cDNA library construction followed by sequencing on an Illumina NovaSeq 6000 platform.  RNA-sequencing reads were first trimmed to remove poly(A) and unqualified reads with cutadapt, then aligned to Mus musculus GRCm38 genome with Ensembl. The numbers of counts were summarized at the gene level using HTseq.

value: lung

value: CD45- lung tumor cells

value: 10 weeks after  intranasal injection of Ad-Cre


title: Sarcoma tumor tissue, Sample 9

value: baseline

value: SD

value: High Grade


title: KL Lung tumor, 10 weeks, rep 1


title: WT C.albicans Hyphae 2h-2

value: Whole cell

value: Hyphal-induced cell

value: Hyphal-induced culture


title: KL25 Lung tumor, 10 weeks, rep 2


title: WT, Spleen, 1- 3

description:
Mars-seq
cell_metadata.csv

value: Spleen


title: cyc1K79A Hyphae 1h-3


title: Sarcoma tumor tissue, Sample 14

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade

value: Surgery

value: M


title: Sarcoma tumor tissue, Sample 8

value: PD


title: WT, Spleen, 1- 2

description:
Mars-seq
cell_metadata.csv

value: T cell

value: co-transfer WT CD8+ T cells


title: KL25 Lung tumor, 10 weeks, rep 1

value: lung

value: CD45- lung tumor cells


title: cyc1K79A Hyphae 1h-1


title: cyc1K79A Hyphae 1h-2


title: WT, Spleen, 2- 3

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 6

value: baseline


title: WT, Spleen, 1- 1

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 7

value: Relapse

value: SD


title: ctm1∆/∆ Hyphae 1h-3

value: Whole cell

value: ctm1 deletion


title: Sarcoma tumor tissue, Sample 5

value: High Grade


title: WT, Spleen, 2- 2

description:
Mars-seq
cell_metadata.csv

value: Spleen


title: ctm1∆/∆ Hyphae 1h-2

value: Hyphal-induced cell

value: Hyphal-induced culture


title: Sarcoma tumor tissue, Sample 4

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade


title: WT, Spleen, 2- 1

description:
Mars-seq
cell_metadata.csv


title: WT, Spleen, 3- 3

description:
Mars-seq
cell_metadata.csv


title: WT, Spleen, 3- 2

description:
Mars-seq
cell_metadata.csv


title: Sarcoma tumor tissue, Sample 3

value: Surgery

value: M


title: WT C.albicans Hyphae 1h-2

value: WT


title: MSC-ABs-CoCl2-rep1

type: RNA

city: Shanghai

first: Qiuyu

last: Zhao

address: 639 Zhi Zao Ju Road,

institute: Shanghai Ninth People’s Hospital, Shanghai JiaoTong University School of Medicine

description: Induction of miRNA expression in apoptotic vesicles harvested from MSC by STS after 24hr of stimulation with oxygen environment

hyb_protocol: 1.5 µg of Cy3-labeled cRNA (specific activity greater than 10.0 pmol Cy3/ug cRNA) was reacted in the hybridization reaction volume for 5 minutes at 100°C according to the manufacturer's instructions, followed immediately by 5 minutes in an ice bath. Then hybridize to The Agilent Human miRNA Microarray in an Agilent hybridization oven at 55°C for 20 hours. After hybridization, the microarrays were washed with GE Wash Buffer 1 (Agilent) for 5 min at room temperature and with GE Wash Buffer 2 (Agilent) at 37°C for 5 min, then immediately dried by brief centrifugation.

scan_protocol: Slides were cleaned and immediately scanned on an Agilent DNA microarray scanner (G2505C).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hMSC-ABs, CoCl2, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity(RIN) was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: adipose tissue


title: WT C.albicans Hyphae 1h-3


title: MSC-ABs-CoCl2-rep3

source_name: hMSC-ABs, CoCl2, replicate 3


title: MSC-ABs-H2O2-rep2

source_name: hMSC-ABs, H2O2, replicate 2


title: MSC-ABs-H2O2-rep3

source_name: hMSC-ABs, H2O2, replicate 3


title: Sarcoma tumor tissue, Sample 1

value: PD


title: WT, Spleen, 3- 1

description:
Mars-seq
cell_metadata.csv

value: T cell

value: co-transfer WT CD8+ T cells


title: WT, Lung, 2- 3

description:
Mars-seq
cell_metadata.csv

value: Lung


title: MSC-ABs-H2O2-rep1

source_name: hMSC-ABs, H2O2, replicate 1


title: MSC-ABs-CoCl2-rep2

source_name: hMSC-ABs, CoCl2, replicate 2


title: sh6

city: Xi’an

first: QICHAO

last: HUANG

address: Changle Western Road

institute: Fourth Military Medical University

library_source: genomic

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low quality reads using Trimmomatic v0.38(non-default parameters: SLIDINGWINDOW:4:15 LEADING:10 TRAILING:10 MINLEN:36)
Then FastQC[2](with default parameters) is used to ensure high reads quality. The clean reads were mapped to the mouse genome (assembly GRCm38) using the Bowtie2 v2.3.4.1(non-default parameters: -N 1 -L 25 -X 2000 --no-mixed --no-discordant) software. Alignments with low mapping quality scores (MAPQ < 30) were removed using samtools
Duplicate reads were then removed using picard MarkDuplicates (http://broadinstitute.github.io/picard)
Peak detection was performed using the MACS v2.1.2 [5](non-default parameters: -g mm -q 0.05 –nomodel --keep-dup all) peak finding algorithm with 0.05 set as the q-value cutoff
Genome_build: hg38
Supplementary_files_format_and_content: bw

source_name: HCC cell lines

extract_protocol:
50,000 intact live cells were extracted, and trypan blue was used to detect the number of live cells, 1ul of 0.4% trypan blue, 9ul of cell suspension, stained for 3-5min, and microscopic examination. Add 50ul of pre-chilled RSB (add 0.1% NP40, 0.1% Tween-20, 0.01% digitonin), invert 3 times, and incubate on ice for 3 min. Add 1ml of pre-chilled RSB (only add 0.1% Tween-20), invert 3 times and mix, centrifuge at 500xg for 5min at 4°C, discard the supernatant.
Cells were lysed using cold lysis buffer (10Mm Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were spun at 500 × g for 10 minutes at 4℃ and the supernatant was discarded. Immediately the pellet was resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Qiagen Minelute kit. Following purification, we amplified library fragments using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by thermocycling at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute，Last extension at 72℃ for 5min.The libraries were purified using a Qiagen PCR cleanup kit yielding a final library。

value: shTFAM

tag: cell line

value: HCC cell lines


title: cyc1K79A Yeast-2

value: Whole cell

value: Yeast cell

value: Yeast culture


title: sh5


title: WT, Lung, 2- 2

description:
Mars-seq
cell_metadata.csv


title: ctm1∆/∆ Hyphae 1h-1

value: Hyphal-induced cell

value: ctm1 deletion

value: Hyphal-induced culture


title: cyc1K79A Yeast-3


title: MSC-ABs-PBS-rep3

source_name: hMSC-ABs, PBS, replicate 3


title: cyc1K79A Yeast-1


title: sh4


title: Sarcoma tumor tissue, Sample 2

source_name: Sarcoma tumor tissue

value: Sarcoma tumor tissue

value: Soft-Tissue Sarcoma

value: Immune checkpoint blockade

value: F

value: SD

value: High Grade


title: KO, Spleen, 3- 3

description:
Mars-seq
cell_metadata.csv

value: T cell

value: Spleen

value: o-transfer cKO CD8+ T cells


title: MSC-ABs-PBS-rep2

source_name: hMSC-ABs, PBS, replicate 2

value: adipose tissue


title: MSC-ABs-PBS-rep1

source_name: hMSC-ABs, PBS, replicate 1


title: NC3

value: shCtrl

value: HCC cell lines


title: Zebrafish Transcriptome - mecp2 Wild Type 10

city: Madison

first: Nicholas

middle: Joel

last: Santistevan

state: WI

address: 145 Noland Hall, 250 N Mills St

department: Department of Integrative Biology

institute: University of Wisconsin – Madison

data_processing:
Bioinformatic analysis of transcriptomic data adhere to recommended ENCODE guidelines and best practices for RNA-Seq. Alignment of adapter-trimmed (Skewer v0.1.123) 2x150 (paired-end; PE) bp strand-specific Illumina reads to the Danio rerio GRCz11 genome (assembly accession GCF_000002035.6) was achieved with the Spliced Transcripts Alignment to a Reference (STAR v2.5.3a) software, a splice-junction aware aligner, using annotation modifications (v4.3.2) made by Lawson et al 2020. Expression estimation was performed with RSEM v1.3.0 (RNASeq by Expectation Maximization).
Assembly: GRCz11
Supplementary files format and content: CSV file of gene expression value (counts) by gene and sample.

organism: Danio rerio

source_name: Embryo; whole larvae

extract_protocol:
Embryos derived from incrosses of mecp2-Q63X homozygous adults or wild-type adults were pooled in groups of three and processed for RNA extraction at 4 dpf as previously described in Yoon et al 2022.
cDNA libraries were prepared using the TruSeq stranded mRNA library preparation protocol with poly-A selection and sequenced on the Illumina HiSeq. 2500. 10 biological replicates of each genotype, confirmed from raw sequencing data alignments using the Integrative Genomics Viewer, were analyzed.

value: Embryo; whole larvae

value: mecp2 Q63X

value: Embryo; 4dpf

value: mecp2 wild type


title: ctm1∆/∆ Yeast-3

value: Whole cell

value: Yeast cell

value: ctm1 deletion

value: Yeast culture


title: Zebrafish Transcriptome - mecp2 Wild Type 9


title: Zebrafish Transcriptome - mecp2 Wild Type 8


title: WT C.albicans Hyphae 1h-1

value: Hyphal-induced cell

value: WT

value: Hyphal-induced culture


title: KO, Spleen, 3- 2

description:
Mars-seq
cell_metadata.csv

source_name: Spleen

value: T cell


title: NC2


title: ctm1∆/∆ Yeast-2

source_name: Whole cell


title: Zebrafish Transcriptome - mecp2 Wild Type 7


title: KO, Spleen, 3- 1

description:
Mars-seq
cell_metadata.csv

value: Spleen


title: NC1


title: Zebrafish Transcriptome - mecp2 Wild Type 6


title: ctm1∆/∆ Yeast-1


title: SH_A6

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.
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: shTFAM


title: WT, Lung, 2- 1

description:
Mars-seq
cell_metadata.csv

source_name: Lung

value: Lung

value: co-transfer WT CD8+ T cells


title: WT C.albicans Yeast-3


title: SH_A5


title: Zebrafish Transcriptome - mecp2 Wild Type 5


title: KO, Spleen, 1- 2

description:
Mars-seq
cell_metadata.csv

value: o-transfer cKO CD8+ T cells


title: Zebrafish Transcriptome - mecp2 Wild Type 4

value: Embryo; whole larvae


title: KO, Spleen, 1- 1

description:
Mars-seq
cell_metadata.csv


title: WT C.albicans Yeast-2


title: Zebrafish Transcriptome - mecp2 Wild Type 3

value: mecp2 Q63X


title: WT C.albicans Yeast-1


title: ∆kmt1_oPf2_A replicate 2

city: Palaiseau

first: Nicolas

last: Lapalu

address: 22 place de l'agronomie

department: SPE

country: France

institute: INRAE

data_processing:
Quality of the reads was checked and improved using Trimmomatic.
The resulting reads were treated to remove adaptors and reads below 30 bp and filtered reads were mapped against the L. maculans genome using STAR (Dobin et al., 2013; Dutreux et al., 2018) with default parameters. Read alignments were stored in SAM format, and indexing, sorting, and conversion to BAM format were performed using SAMtools v0.1.19
Genes with a number of reads > 15 in at least one condition were kept for statistical analysis. Differential expression analyses were made using R (R Core Team, 2017) and the package EdgeR (Robinson et al., 2010). Genes with a log2 Fold Change ≤ -1.5 or ≥ 1.5 and an associated false discovery rate ≤ 0.05 were considered as differentially expressed (McCarthy et al., 2012).
Assembly: Leptosphaeria maculans JN3
Supplementary files format and content: tabulated txt file

organism: Plenodomus lingam

source_name: mycelium

growth_protocol: Samples were grown in Fries liquid medium during 7 days and harvested for RNA extraction

extract_protocol:
Two RNA extractions corresponding to two biological replicates were performed for each transformant. About 150 mg of mycelium was used per extraction.
Libraries were prepared from all biological replicates, individually, according to the Illumina TruSeq protocol (Illumina, San Diego, CA, USA). Libraries including polyA enrichment were performed and sequenced using 150 pb paired-end strategy on an HiSeq2000 Illumina sequencer at the Genewiz sequencing facility (Leipzig, Germany) with an input of 2 µg total RNA.

value: mycelium

tag: background

value: kmt1 mutant

value: oPf2 OE


title: Zebrafish Transcriptome - mecp2 Wild Type 2

value: Embryo; 4dpf

value: mecp2 wild type


title: KO, Spleen, 2- 3

description:
Mars-seq
cell_metadata.csv


title: NC_A3

value: shCtrl


title: KO, Spleen, 2- 2

description:
Mars-seq
cell_metadata.csv


title: Zebrafish Transcriptome - mecp2 Wild Type 1


title: ∆kmt1_oPf2_B replicate 2


title: Zebrafish Transcriptome - mecp2 Mutant 10


title: KO, Spleen, 2- 1

description:
Mars-seq
cell_metadata.csv


title: KO, Spleen, 1- 3

description:
Mars-seq
cell_metadata.csv


title: NC_A1


title: RNA-seq, Knockdown LGMN replicate 3

city: Odense

first: Alexander

last: Rauch

address: Campusvej 55

department: Department of Clinical Research

country: Denmark

institute: University of Southern Denmark and Odense University Hospital

data_processing:
RNA-seq reads were aligned to mm10 genome using STAR aligner and default settings.
Gene expression was quantified using HOMER (Heinz S, et al. 2010. Molecular Cell 38: 576-589) with the options -count exons -condenseGenes -noCondensing -noadj. Normalization and differential expression analysis was performed using DEseq2 (Love M I,  et al. 2014. Genome Biology 15: 550) comparing overexpressing cells  to control (T4_LGMN vs. T4_pBabe: padj_OE and logFC_OE) and knockdown cells to control (T4_shLGMN vs. T4_shCtrl: padj_KD and logFC_KD).
Genome_build: hg19
Supplementary_files_format_and_content: Txt file containing raw counts, DEseq2 derived normalized and rlog transformed counts as well as adjusted p values and logFC for overexpression (OE: T4_LGMN vs. T4_pBabe) and knockdown (KD T4_shLGMN vs. T4_shCtrl)

source_name: Immortalized human bone marrow stromal cells transduced with LGMN targeting shRNA

growth_protocol: Cells were cultured in MEM + 10% FBS + 1% pen/strep, Lysates were prepared at 80% confluency

extract_protocol:
RNA was extracted from cultured cells using Trizol combined with the Qiagen Rneasy Mini Kit (Qiagen)
RNA-seq was performed according to manufacturer’s instructions (TruSeq 2, Illumina) using 1 µg RNA for preparation of cDNA libraries.

treatment_protocol: Cells were not treated, from each clone lysats were prepared three times at 80% confluency.

value: hBM-MSC-TERT4 cells (Simonsen J L, et al. 2002. Nat Biotechnol 20:592-596) derived clone with LGMN targeting shRNA plasmid


title: KO, Lung, 1- 3

description:
Mars-seq
cell_metadata.csv


title: ∆kmt1_oPf2_B replicate 1


title: KO, Lung, 1- 2

description:
Mars-seq
cell_metadata.csv


title: RNA-seq, Knockdown LGMN replicate 2


title: Zebrafish Transcriptome - mecp2 Mutant 8


title: JN2_oPf2_B replicate 1

value: WT


title: Zebrafish Transcriptome - mecp2 Mutant 9


title: KO, Lung, 1- 1

description:
Mars-seq
cell_metadata.csv


title: JN2_oPf2_B replicate 2


title: RNA-seq, Knockdown LGMN replicate 1


title: SH_A4


title: Zebrafish Transcriptome - mecp2 Mutant 6


title: JN2_oPf2_A replicate 2


title: NC_A2


title: RNA-seq, Knockdown control replicate 2

source_name: Immortalized human bone marrow stromal cells transduced with control shRNA

value: hBM-MSC-TERT4 cells (Simonsen J L, et al. 2002. Nat Biotechnol 20:592-596) derived clone with control shRNA plasmid


title: RNA-seq, Knockdown control replicate 3


title: Zebrafish Transcriptome - mecp2 Mutant 7


title: ∆kmt1_oPf2_A replicate 1


title: Zebrafish Transcriptome - mecp2 Mutant 5


title: RNA-seq, Knockdown control replicate 1


title: JN2_oPf2_A replicate 1


title: ∆kmt1 replicate 2


title: RNA-seq, Overexpression LGMN replicate 3

source_name: Immortalized human bone marrow stromal cells transduced with LGMN plasmid

value: hBM-MSC-TERT4 cells (Simonsen J L, et al. 2002. Nat Biotechnol 20:592-596) derived clone with LGMN coding plasmid


title: RNA-seq, Overexpression LGMN replicate 2


title: ∆kmt1 replicate 1


title: JN2 replicate 2


title: RNA-seq, Overexpression LGMN replicate 1


title: Zebrafish Transcriptome - mecp2 Mutant 2


title: JN2 replicate 1


title: ∆LmPf2_B replicate 2

value: LmPf2 mutant


title: RNA-seq, Overexpression control replicate 3

source_name: Immortalized human bone marrow stromal cells transduced with empty plasmid

value: hBM-MSC-TERT4 cells (Simonsen J L, et al. 2002. Nat Biotechnol 20:592-596) derived clone with empty plasmid


title: ∆LmPf2_B replicate 1


title: RNA-seq, Overexpression control replicate 2


title: ∆LmPf2_A replicate 2


title: LW_Tes_1.smallRNAseq

city: Yunnan Kunming

first: Huo

last: Jinlong

address: Jinhei Road 95

institute: Yunnan Agricultural University

data_processing:
The SRs were aligned to the susScr11 reference genome using STAR (version 2.7.10a, parameters --alignEndsType EndToEnd --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All -- outSAMtype BAM).
Illumina paired-end short reads were quantified using Salmon (v1.9.0), and TPM values were summaized in the processed data table.
Illumina single-end small RNA reads were predicted potential miRNA using miRDeep2 (v0.1.3). Small RNA reads were mapped to mature miRNA and precursor miRNA from the prediction and miRbase (Release 22.1) using bowtie (v1.3.1).
Assembly: susScr11
Supplementary files format and content: tab-delimited text files include TPM values and RPM values for each Sample

organism: Sus scrofa

source_name: testis

growth_protocol: All samples were acquired from 12-month adult male pigs. Pigs were housed in a temperature (64-79°F) and humidity (30-70%) controlled room.

extract_protocol:
Total RNAs were extracted using Trizol followed by acid phenol extraction. rRNA depletion was done for Illumina RNAseq.
Illumina paired-end sequencing uses standard RNAseq library construction protocol. Illumina single-end sequencing library was constructed using TruSeq small RNA sample prep Kits (Illumina, SanDiego, USA)

value: testis

tag: breed

value: Large white


title: K562_TRIAC_rep2

first: Shanhe

last: Yu

address: 197# Rui Jin Road II

institute: Shanghai Institute of Hematology，Rui Jin Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Bowtie2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . RSEM was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Genome_build: GRCh38

growth_protocol: K562 were grown in RPMI 1640 supplemented with 10% FBS, at 37 °C in a humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent. 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: 10 uM Hemin was used for erythroid differentiation of K562 cells. 20 uM TRIAC or DMSO was incubated with K562 cells for 48 hours.

value: human erythroleukemic cells

value: TRIAC


title: L-pipecolic acid producing LPA-5 C.

city: Saarbruecken

first: Michael

last: Kohlstedt

address: Campus A1.5

institute: Saarland University

description:
cell biomass
exponential growth
LPA-5 C

hyb_protocol: Agilent hybridisation kit

scan_protocol: Agilent SureScan S2600D Microarray Scanner

data_processing: GeneSpring 14.9 GC, Feature extraction, Statistical analysis (moderated t-test, p_corr < 0.05 (Benjamini-Hochberg), 2fold change), export

organism: Corynebacterium glutamicum

source_name: modified Corynebacterium glutamicum ATCC13032 (LPA-5)

label_protocol: Agilent labeling kit (one color)

growth_protocol: baffeled 500 mL shake flask, 50 mL potassium based minimal medium (10 g L-1 glucose), 30°C, 230 rpm, initial OD660 = 0.2

extract_protocol: mRNA extracted from harvested cell pellets (6 mg DCW) using Qiagen RNeasy kit and Turbo DNAfree kit

treatment_protocol: cells (500 µL) were harvested via centrifugation (30 sec, 4°C, 13.000 x g) and snap-frozen in liquid nitrogen

tag: phenotype

value: OD4 higher L-pipecolic acid producing


title: ∆LmPf2_A replicate 1

tag: tissue

value: mycelium


title: K562_TRIAC_rep1


title: DU_Tes_3.smallRNAseq

value: Western Duroc


title: L-pipecolic acid producing LPA-5 A.

description:
cell biomass
exponential growth
LPA-5 A


title: DU_Tes_1.smallRNAseq


title: K562_DMSO_rep1

value: DMSO


title: Zebrafish Transcriptome - mecp2 Mutant 3

value: Embryo; whole larvae

value: mecp2 Q63X

value: Embryo; 4dpf


title: K562_DMSO_rep2


title: Zebrafish Transcriptome - mecp2 Mutant 4


title: Zebrafish Transcriptome - mecp2 Mutant 1


title: RNA-seq, Overexpression control replicate 1


title: K326×GDH88-3 [KG8_3]

city: Guiyang

first: Renxiang

last: Liu

state: Guizhou

address: Huaxi

institute: Guizhou University

description:
Nicotiana tabacum L.
Leaf_18
KG8_3

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep(https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Then clean reads were separately aligned to reference genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome） with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)software.
The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml?t=example) .
RSEM （http://deweylab.github.io/RSEM/）establishes the maximum likelihood abundance estimation model based on the maximum expectation algorithm, and considers the paid end reads, the length of reads, the length distribution of fragments, and the quality value to distinguish which transcripts are different subtypes of the same gene. The results of expression quantification are expressed in TPM/FPKM. The homogenization process of TPM/FPKM makes the total expression amount in different samples consistent.
Assembly: Tobacco K326 Reference Genome（https://solgenomics.net/organism/Nicotiana_tabacum/genome）
Supplementary files format and content: all_ express.txt includes 15 transcriptome sequencing materials and 69500 gene expressions. The file can be opened in Excel for viewing.

organism: Nicotiana tabacum

source_name: Leaf

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent (Plant RNA Purification Reagent for plant tissue) according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) andquantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample(OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >1μg) was used to construct sequencing library.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. After quantified by TBS380, paired-end RNA-seq  sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 ×  150bp read length)

value: Leaf

value: 45 days after transplantation


title: K326×GDH88-2 [KG8_2]

description:
Nicotiana tabacum L.
Leaf_17
KG8_2


title: Non-L-pipecolic acid producing LPA-0 B.

description:
cell biomass
exponential growth
LPA-0 B

source_name: modified Corynebacterium glutamicum ATCC13032 (LPA-0)

value: OD4 non-L-pipecolic acid producing


title: LW_Tes_3.smallRNAseq


title: Non-L-pipecolic acid producing LPA-0 A.

description:
cell biomass
exponential growth
LPA-0 A


title: K326×GDH88-1 [KG8_1]

description:
Nicotiana tabacum L.
Leaf_16
KG8_1


title: GDH88-3 [G8_3]

description:
Nicotiana tabacum L.
Leaf_15
G8_3


title: L-pipecolic acid producing LPA-1 C

description:
cell biomass
exponential growth
LPA-1 C

source_name: modified Corynebacterium glutamicum ATCC13032 (LPA-1A)

value: OD4 low L-pipecolic acid producing


title: LW_Tes_2.smallRNAseq


title: L-pipecolic acid producing LPA-5 B.

description:
cell biomass
exponential growth
LPA-5 B


title: GDH88-2 [G8_2]

description:
Nicotiana tabacum L.
Leaf_14
G8_2


title: GDH88-1 [G8_1]

description:
Nicotiana tabacum L.
Leaf_13
G8_1


title: 2_6R

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

country: United Kingdom

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

data_processing:
Data was acquired and processed at GenXPro GmbH. Data was aligned using Bowtie2, Mouse Ensemble MM10. Data was normalised using TPM and analyses done with DESeq2. Cleaning was performed by duplicate removal based on TrueQuant unique molecular barcode.
Sequencing was performed on the platform: Illumina NextSeq500
Genome_build: MM10 (Mus musculus)
Supplementary_files_format_and_content: Prcessed data are provided as a single txt file,including the raw counts of sequencing reads for each gene

source_name: Knee cartilage

growth_protocol: 10 weeks-old C57BL/6 mice were maintained in standard diet. Extracellular vesicles (EVs) were produced by stimulation of human neutrophils with 50ng/ml TNFa for 20min at 37C. Human neutrophils were obtained using the double histopaque density method from healthy volunteers.

extract_protocol:
Total RNA was extracted from a single mouse joint (including cartilage surfaces and underlying subchondral bone). RNA was extracted using TRIzol reagent using manufacturer's protocol (Invitrogen) and tissues disrupted using Precellys steel beads; contaminating DNA was removed with TURBO DNAse kit (Ambion). Then, RNA was cleanued-uo with RNeasy Mini kit (Qiagen).
Library was constructed using the massive analysis of cDNA ends (MACE) 3' mRNA-Seq; stranded, single end (1x75bp)

treatment_protocol: Mice were treated with K/BxN serum to induce artritis (two intraperitoneal injections of 100ul on days 0 and day 2). For the therapeutic treatment, mice were treated with 100,000 EVs given intra-articularly. For Treated and Control groups of samples, EVs treatment and vehicle were applied to contralateral knees on the same mouse.

tag: group

value: Naive


title: Non-L-pipecolic acid producing LPA-0 C.

description:
cell biomass
exponential growth
LPA-0 C


title: Non-L-pipecolic acid producing LPA-0 C

description:
cell biomass
exponential growth
LPA-0 C


title: K326-3 [K_3]

description:
Nicotiana tabacum L.
Leaf_12
K_3


title: Non-L-pipecolic acid producing LPA-0 B

description:
cell biomass
exponential growth
LPA-0 B


title: 2_5R

value: Disease


title: K326-2 [K_2]

description:
Nicotiana tabacum L.
Leaf_11
K_2


title: 2_5L


title: Non-L-pipecolic acid producing LPA-0 A

description:
cell biomass
exponential growth
LPA-0 A


title: K326-1 [K_1]

description:
Nicotiana tabacum L.
Leaf_10
K_1


title: L-pipecolic acid producing LPA-1 B

description:
cell biomass
exponential growth
LPA-1 B


title: gut, 50 μg/L NIC exposure group, rep3

city: Changsha

last: Wu

address: Shuanghe Road 728, Kaifu District, Changsha

institute: Hunan Fisheries Science Institute

data_processing:
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.
Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Assembly: the reference genome of Pelodiscus sinensis (GenBank No. 309658)
Supplementary files format and content: tab-delimited txt file includes FPKM values for each sample

organism: Pelodiscus sinensis

source_name: gut

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: gut

value: WT

tag: treatment

value: 50 μg/L NIC


title: L-pipecolic acid producing LPA-1 A

description:
cell biomass
exponential growth
LPA-1 A


title: GDH94-2 [G9_2]

description:
Nicotiana tabacum L.
Leaf_8
G9_2


title: gut, 50 μg/L NIC exposure group, rep2


title: 2_4L

value: Control


title: DU_Tes_2.smallRNAseq

value: testis


title: 2_3R

value: Treated


title: GDH94-1 [G9_1]

description:
Nicotiana tabacum L.
Leaf_7
G9_1


title: 2_6L


title: gut, 50 μg/L NIC exposure group, rep1


title: 2_3L


title: VA116-3 [V_3]

description:
Nicotiana tabacum L.
Leaf_6
V_3


title: GDH94-3 [G9_3]

description:
Nicotiana tabacum L.
Leaf_9
G9_3


title: 2_4R


title: gut, 10 μg/L NIC exposure group, rep3

value: 10 μg/L NIC


title: 2_2R


title: VA116-2 [V_2]

description:
Nicotiana tabacum L.
Leaf_5
V_2


title: gut, 10 μg/L NIC exposure group, rep2


title: 2_2L


title: VA116-1 [V_1]

description:
Nicotiana tabacum L.
Leaf_4
V_1


title: 2_1R


title: gut, 10 μg/L NIC exposure group, rep1


title: 2_1L


title: MEF Spry124 KO repA 120 min

city: Evanston

first: Neda

last: Bagheri

state: IL

address: 2145 Sheridan Road, Tech E154

department: Chemical and Biological Engineering

institute: Northwestern University

description: Spry124-/- MEFs

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using background subtraction and quantile normalization with Illumina Genome Studio (v 1.9.0)

source_name: Immortalized MEF

label_protocol: Standard label protocol

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), according to manufacturer’s instructions

tag: spry status

value: No Spry expression (Spry1,2,4 are excised)

tag: culture genotype/variation

value: Serum Starved (DMEM + 0.2% BSA + 100 U/mL penicillin + 100ug/mL streptomycin)

tag: fgf treatment time (min)

tag: rep

value: A

tag: genotype/variation

value: KO


title: MEF Spry124 KO repC 120 min

description: Spry124-/- MEFs

value: C


title: MEF Spry124 KO repB 60 min

description: Spry124-/- MEFs

value: B


title: gut, control group, rep3

first: Hao

tag: genotype

value: control group


title: VA116×GDH94-3 [VG9_3]

description:
Nicotiana tabacum L.
Leaf_3
VG9_3

value: Leaf

tag: age

value: 45 days after transplantation


title: VA116×GDH94-1 [VG9_1]

description:
Nicotiana tabacum L.
Leaf_1
VG9_1


title: MEF Spry124 WT repA 120 min

description: Spry124fl/fl MEFs

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)


title: MEF Spry124 WT repC 240 min

description: Spry124fl/fl MEFs


title: MEF Spry124 KO repC 240 min

description: Spry124-/- MEFs


title: MEF Spry124 WT repA 240 min

description: Spry124fl/fl MEFs


title: gut, control group, rep1

value: gut


title: MEF Spry124 WT repC 120 min

description: Spry124fl/fl MEFs

value: WT


title: MEF Spry124 KO repA 240 min

description: Spry124-/- MEFs


title: MEF Spry124 WT repC 60 min

description: Spry124fl/fl MEFs


title: MEF Spry124 KO repC 60 min

description: Spry124-/- MEFs


title: MEF Spry124 KO repB 240 min

description: Spry124-/- MEFs


title: MEF Spry124 WT repB 120 min

description: Spry124fl/fl MEFs


title: MEF Spry124 WT repB 60 min

description: Spry124fl/fl MEFs


title: gut, control group, rep2


title: VA116×GDH94-2 [VG9_2]

description:
Nicotiana tabacum L.
Leaf_2
VG9_2


title: MEF Spry124 WT repB 240 min

description: Spry124fl/fl MEFs


title: 1_6R

value: Naive


title: MEF Spry124 KO repA 60 min

description: Spry124-/- MEFs


title: MEF Spry124 WT repA 60 min

description: Spry124fl/fl MEFs


title: 1_6L


title: liver, 50 μg/L NIC exposure group, rep3

source_name: liver

value: liver

value: 50 μg/L NIC


title: liver, 50 μg/L NIC exposure group, rep1


title: 1_4L

value: Treated


title: liver, 10 μg/L NIC exposure group, rep2

value: 10 μg/L NIC


title: 1_5L

value: Disease


title: 1_4R

value: Control


title: 1_3R


title: liver, 50 μg/L NIC exposure group, rep2


title: MEF Spry124 KO repB 120 min

description: Spry124-/- MEFs

value: No Spry expression (Spry1,2,4 are excised)

value: Serum Starved (DMEM + 0.2% BSA + 100 U/mL penicillin + 100ug/mL streptomycin)


title: 1_3L


title: liver, 10 μg/L NIC exposure group, rep3


title: liver, control group, rep3


title: 1_2R


title: liver, 10 μg/L NIC exposure group, rep1


title: N2a,NPM1KD, rep3

city: Freiburg

first: Tanja

last: Vogel

address: Albertstr. 23

institute: University of Freiburg

data_processing:
The analyses were done on the usegalaxy.eu platform
Reads were trimmed using Porechop with default settings for Nanopore data
Trimmed reads were aligned to the reference genome (GRCm39) using minimap2 with the Oxford Nanopore default  mapping profile (-k15).
gene counts were quantified using featurecounts with long read settings.
Deseq2 was used to run to normalise the counts and run differential expression analysis.
Assembly: GRCm39
Supplementary files format and content: tabular DESEQ2 result table
Supplementary files format and content: tabular, normalised counts

growth_protocol: Mouse neuroblastoma cell line, Neuro-2a (N2a) was cultured and maintained at 37°C, 95% relative humidity and 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM, ThermoScientific, Schwerte, Germany) supplemented with 10% fetal bovine serum (FBS, ThermoScientific), 1% non-essential amino acids (NEAA, ThermoScientific), 1% L-glutamine, and 1% penicillin, streptomycin, and neomycin (PSN, ThermoScientific).

extract_protocol:
RNA was extracted using Qiagen Rneasy kit following the manufacturer's instructions.
Library Prep was performed with Oxford Nanopore SQK-PCB109 kit.
Long read barcoded RNA-Seq libraries were sequenced on GridION (Oxford Nanopore) at Max Planck Institute of Immunobiology and Epigenetics.

treatment_protocol: N2a cells were transfected with shNPM1 (NPM1 KD) or shControl plasmid (CTR) and were grown on 6 wells plates (~6 Mio cells) for 72h. Two independent biological replicates per conditions were used. The following plasmid were used for transfection: pLKO.1-shCTR (Sigma, Non Target #3), pLKO.1-shNpm1 (Sigma, TRCN0000115430). For NPM1 Knockd Down (NPM1 KD) experiments, N2a cells were selected with 9.3 µg/ml Puromycin starting 24hs after transfection and for the remaining time until RNA extraction.

value: neuro2a neuroblastoma cells

tag: div (days_in_vitro)


title: 1_5R


title: liver, control group, rep2


title: MEF Spry124 WT repC 15 min

description: Spry124fl/fl MEFs

value: C


title: MEF Spry124 KO repB 15 min

description: Spry124-/- MEFs

value: B

value: KO


title: 1_1R


title: 1_2L


title: MEF Spry124 KO repC 15 min

description: Spry124-/- MEFs


title: N2a,NPM1KD, rep1

tag: cell type


title: liver, control group, rep1

value: control group


title: N2a,NPM1KD, rep2


title: MEF Spry124 KO repA 15 min

description: Spry124-/- MEFs

value: A


title: 1_1L


title: N2a,control,rep2

value: control


title: MEF Spry124 KO repD 0 min

description: Spry124-/- MEFs

value: D


title: MEF Spry124 KO repC 0 min

description: Spry124-/- MEFs


title: N2a,control,rep1

value: WT


title: NRSF/REST_ChIPseq_Mm_Input

city: IRVINE

first: Shan

last: Jiang

address: 2300E Biological Sciences III

institute: UNIVERSITY OF CALIFORNIA, IRVINE

data_processing:
ChIP and input sequencing reads were aligned using Bowtie v.0.12.8
After alignment, peaks were detected using MACS v.1.4.2, retaining all statistically enriched regions ( p<10-4.5). Binding regions were considered reproducible when they were identified in both replicates. Consensus binding regions were then merged and called subpeaks using PeakSplitter_Cpp v.1.0. Subpeaks in 50bp were merged. Peaks having (1) higher signal in control than ChIP replicates in each species or (2) signal in control is higher than 1.4 RPM in each species or (3) in Blacklist (ENCODE Project Consortium. 2012) in human and mouse were filtered out as artificially high signal peaks.
Genome_build: GRCh37/hg19,GRCm38/mm10, CanFam3.1, EquCab2.0
Supplementary_files_format_and_content: peak calling results for each species in .txt format. (chromosome, start, end)

source_name: Macrophage cells

growth_protocol: Mouse macrophage cells (RAW264.7, ATCC, Manassas, VA) were grown in DMEM medium (30-2002, ATCC, Manassas, VA) supplemented with 10% FBS (VWR, Radnor, PA) and penicillin/streptomycin (Life Technologies). Dog myelomonocytic leukemia cells (ML2, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with 1000 mM Hepes, 10mM MEM NEAA, 100mM Sodium pyruvate, 55mM β- mercaptoethanol, 10% FBS and penicillin/streptomycin. Horse skin fibroblast (E.Derm, ATCC, Manassas, VA) were grown in EMEM(30-2003, ATCC, Manassas, VA) supplemented with 10% FBS and penicillin/streptomycin. Trypan Blue (VWR) staining was performed before harvesting the cells for each assay to make sure that at least 90% of the cells were viable.

extract_protocol:
We cross-linked about 20 million cells with 1% formaldehyde for each replicate. Cross-linked chromatin was sonicated into 200-300bp fragments. DNA fragments were incubated with Dynabeads protein G (Thermo Fisher Scientific) bound by NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11) overnight to perform immunoprecipitation. Then chromatin was reverse cross-linked to extract NRSF-bound DNA.
DNA fragments recovered from ChIPs were end-repaired, ligated to adapters, size selected (200 to 300bp) and PCR-amplified to make the libraries for sequencing. The libraries were made based on Myers Lab protocol v042211 (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v042211.pdf).

value: Macrophage cells

tag: passages

tag: strain

tag: chip antibody


title: NRSF/REST_ChIPseq_Mm_R1

description: NRSF/REST.peaks.Mm.txt

value: NRSF monoclonal antibody (Caltech Protein Expression Center, Pasadena, CA, USA, 12C11-1B11)


title: Active_UC_2

status: Public on Dec 31 2023

city: Kaunas

first: Rūta

last: Inčiūraitė

address: Mickeviciaus st. 9

country: Lithuania

institute: Lithuanian University of Health Sciences

data_processing:
Processing of the raw reads: nf-core/smrnaseq v1.0.0 analysis pipeline with default parameters and "illumina" protocol to process .fastq files (Nextflow version v20.01.0)
Trimming of adapter sequences: Trim Galore (v0.6.3) to remove 3’ adapter (5’ - TGGAATTCTCGGGTGCCAAGG - 3’) sequences from the reads
Collapsing and alignment of the reads: seqcluster to collapse reads with identical sequences and Bowtie1 v1.2.2 to align collapsed reads against mature and hairpin miRNA sequences in miRbase database v22.1
MiRNA annotation: mirTOP v0.4.23 to annotate miRNA
Genome_build: Ensembl build GRCh37
Supplementary_files_format_and_content: Tab-separated values (.tsv) file includes miRNA and iso-miRNA counts for all samples

source_name: Colon tissue

extract_protocol:
Standard protocol of miRNeasy Mini Kit (Qiagen)
TruSeq Small RNA Sample Preparation Kit (Illumina)

tag: gender

value: not applicable

tag: height (cm)

value: #N/A

tag: weigth (kg)

tag: stool frequency (mayo subscore)

tag: rectal bleeding (mayo subscore)

tag: endoscopic mayo subscore

tag: global assessment score (mayo subscore)

tag: mayo score


title: N2a,control,rep3

tag: cell line

tag: treatment


title: MEF Spry124 WT repB 15 min

description: Spry124fl/fl MEFs

tag: spry status

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

tag: culture genotype/variation

tag: fgf treatment time (min)

tag: rep

tag: genotype/variation


title: MEF Spry124 WT repA 15 min

description: Spry124fl/fl MEFs


title: NRSF/REST_ChIPseq_Mm_R2

description: NRSF/REST.peaks.Mm.txt

tag: cell type

tag: passages

tag: strain


title: MEF Spry124 WT repC 0 min

description: Spry124fl/fl MEFs


title: MEF Spry124 KO repA 0 min

description: Spry124-/- MEFs


title: MEF Spry124 WT repD 0 min

description: Spry124fl/fl MEFs


title: MEF Spry124 KO repB 0 min

description: Spry124-/- MEFs


title: R4_control_96h_2

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

country: Italy

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

description: ATRA-resistant cells

hyb_protocol: Samples were then hybridized ON using using the Affymetrix GeneChip Hybridization Oven 640 (Thermo Fisher Scientific)

scan_protocol: Samples were whashed, stained, and scanned using a Fluidic Station 450 and Scanner 3000 7G (Thermo Fisher Scientific)

data_processing: Quality control and normalization of Affymetrix .CEL files were performed using TAC software (v4.0; Thermo Fisher Scientific) by performing “Gene level SST-RMA” summarization method with human genome version hg38 (NCBI-Genome Reference Consortium Human Build 38).

source_name: APL cells, DMSO treated, 96h

label_protocol: RNA samples have been amplified, fragmented, and labeled for array hybridization according to the manufacturer’s instruction (Thermo Fisher Scientific).

growth_protocol: All the cell lines were grown in RPMI-1640 (Corning, NY, USA) supplemented with 10% heat-inactivated FBS (Thermo Fisher Scientific, Santa Clara, CA, USA), 2 mM L-Glutamine (Corning), 100 μg/mL penicillin and streptomycin (Corning). Cells were cultured at 37 °C in a humidified atmosphere of 5% CO2

extract_protocol: Live cells were resuspended in Invitrogen™ TRIzol™ Reagent (0.75 mL of TRIzol™ Reagent per 0.25 mL of sample; ~ 7.5×10^6 cells; Thermo Fisher Scientific) and stored at -80 °C. Total RNA was extracted following manufacturer's standard protocol (TRIzol™ Reagent).

treatment_protocol: Cells were seeded at a density of 5×10^5 cells/mL and treated with 4 μM of MK-8776 for 96 h or with DMSO used as control.

tag: tumor type

value: Acute promyelocytic leukemia (APL)

tag: tissue

value: Blood


title: R4_iCHK1_4uM_96h_1

description: ATRA-resistant cells

source_name: APL cells, MK-8776  treated, 96h


title: RH4_PFI90_24h_HiC

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

data_processing:
RNA-seq was mapped using STAR with hg19 as reference.
RNA-seq read abundance for each gene counted (TPM) using RSEM
RNA-seq raw reads normalized using DESeq2
ChIP-seq was mapped using BWA with hg19 as reference.
ChIP-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
ATAC-seq was mapped using BWA with hg19 as reference.
ATAC-seq peaks were called using MACS2. https://github.com/CBIIT/ChIP_seq.
scRNA-seq demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2
Hi-C was mapped to hg19 using omni-c_qc.sh from Dovetail Github (https://github.com/dovetail-genomics)
Hi-C Technical repliaces were merged using Pairtools' merge.
Assembly: hg19/GRCh37
Supplementary files format and content: ChIP-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: RNA-seq processed files are quantification matrices of TPM (transcripts per million) at the gene level.
Supplementary files format and content: ATAC-seq peak files are tab delimited bed text files for each sample.
Supplementary files format and content: scRNA-seq files are Tab delimited values files and matrix files
Supplementary files format and content: Hi-C files are merged processed .hic files

source_name: muscle

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation.

extract_protocol:
Bulk RNA is extracted using QIAGEN Rneasy Plus Mini Kit. ChIP samples were fixed with 1% formaldehyde for 15 mins, sonicated, immunoprecipitated using antibody and Dynabeads, washed, eluted, and reverse crosslinked.  ATAC samples were tagmented, PCR amplified, and purified. scRNA-seq samples were processed using the 10x Genomics Chromium Next GEM single cell 3' kit.  Hi-C samples were processed using the Dovetail Micro-C kit.
Illumina TruSeq Stranded mRNA and Total RNA library prep, Illumina TruSeq ChIP Library Prep, scRNA-seq using Chromium Next GEM single Cell 3' Reagent kits v3.1, ATAC library from tagmentation and PCR amplification, Hi-C library contructed using Dovetail Micro-C kit

treatment_protocol: Cells were treated with either DMSO or compound of interest for the specified amount of time.

value: muscle

value: Rhabdomyosarcoma

tag: genotype

value: wt

tag: time

value: 24 hr


title: C-S1 (salinity tolerant)

city: Nagoya

first: Joyce

last: Cartagena

address: Furo-cho, Chikusa-ku

country: Japan

institute: Nagoya University

description: same as GSM2132702

data_processing:
Adaptor sequences and low-quality reads/nucleotides were removed using trimmomatic (ver. 0.32).
Cleaned reads were used for mapping on reference sequence using bowtie (ver. 2-2.2.2) and tophat (ver. 2.0.11).
Assembly of transcripts and the calculation of the expression level were done using cufflinks (ver. 2.2.1).
Transcripts of all the samples obtained using cufflinks were assembled using cuffmerge (ver. 2.2.1).
Using cuffdiff (ver. 2.2.1), the expression level was compared among samples using the transcripts information obtained from the cuffmerge analysis.
Genome_build: IRGSP-1.0_genome.fa
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

organism: Oryza sativa

source_name: S-type lateral roots

growth_protocol: Growth condition: at 30°C/25°C, humidity of 70%/75% (day12h/night12h)

extract_protocol:
Total RNA was extracted from root tissues using RNeasy Plant Mini Kit (QIAGEN).
strand-specific mRNA-seq library (insert size 200 bp)

tag: cultivar

value: Mulai

value: S-type lateral roots

tag: phenotype

value: salinity tolerant


title: C-N (salinity sensitive)

description: same as GSM2309680

source_name: nodal roots

value: nodal roots

value: salinity sensitive


title: C-S (salinity sensitive)

description: same as GSM2309681


title: C-L1 (salinity tolerant)

description: same as GSM2132703

source_name: L-type lateral roots

value: L-type lateral roots


title: R4_iCHK1_4uM_96h_2

description: ATRA-resistant cells


title: C-L (salinity sensitive)

description: same as GSM2309682


title: GR-SD-R22

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

country: India

institute: Jawaharlal Nehru University

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning the reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Sorghum bicolor BTx623 v3.1.1 downloaded from Phytozome database
Supplementary_files_format_and_content: FPKM values in Excel format

organism: Sorghum bicolor

source_name: Stem Internode

growth_protocol: Seeds of Sorghum bicolor variety M35-1 were planted at ICAR - IARI, Pusa, New Delhi. For development stage samples, the seeds were directly sown into the prepared soil bed treated with nitrogen fertilizer. At three leaf stage, the plants were thinned. Weeding and watering was done at regular intervals.  For drought assay, 5-6 seeds were sown in a pot. At three leaf stage, plants were thinned so that only one healthy plant per pot was maintained.

extract_protocol:
Total RNA was isolated using a modified trizol method
Libraries were prepared using TruSeq® Stranded Total RNA kit using manufacturer’s instructions

treatment_protocol: Development samples were collected at four stages namely floral initiation, booting, milky stage and soft dough. For drought assay, at flag leaf stage, water was withheld and soil moisture was measured using Lutron PMS 175 soil moisture meter. Samples were harvested at Booting stage at three soil moisture readings which were ~13% (D1), ~7% (D2) and ~2% (D3).

value: Middle internode

tag: developmental stage

value: Soft dough


title: GR-SD-R12


title: GR-T3-R11

tag: stress

value: Drought stage D3 ~2% soil moisture


title: GR-T3-R21


title: C-N1 (salinity tolerant)

description: same as GSM2132701


title: MEF Spry124 WT repA 0 min

description: Spry124fl/fl MEFs

value: Serum Starved (DMEM + 0.2% BSA + 100 U/mL penicillin + 100ug/mL streptomycin)

value: A

value: WT


title: GR-FI-R11

value: Floral Initiation


title: CSS-T3-R11

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning the reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Sorghum bicolor BTx623 v3.1.1 downloaded from Phytozome database
Supplementary_files_format_and_content: FPKM values in excel format

growth_protocol: Seeds of Sorghum bicolor variety CSV24SS were planted at ICAR - IARI, Pusa, New Delhi. For development stage samples, the seeds were directly sown into the prepared soil bed treated with nitrogen fertilizer. At three leaf stage, the plants were thinned. Weeding and watering was done at regular intervals.  For drought assay, 5-6 seeds were sown in a pot. At three leaf stage, plants were thinned so that only one healthy plant per pot was maintained.


title: GR-T2-R21

value: Drought stage D2 ~7% soil moisture


title: MEF Spry124 WT repB 0 min

description: Spry124fl/fl MEFs

value: Wild-type Spry expression (Spry1,2,4 are floxed/floxed)

value: B


title: GR-T2-R11


title: GR-T1-R21

value: Drought stage D1 ~13% soil moisture


title: GR-MS-R22

value: Milky stage


title: GR-T1-R11


title: Symptomatic_control_33

tag: gender

value: not applicable

tag: age

value: #N/A

tag: height (cm)

tag: weigth (kg)

tag: endoscopic mayo subscore


title: GR-B-R12

value: Booting


title: GR-MS-R12


title: GR-B-R22


title: GR-FI-R21


title: CSS-SD-R21


title: CSS-FI-R21


title: Thymocytes, group3 KO

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm10 whole genome using Tophat v2.0.12 after filtering adaptor sequence and low-complexity or low-quality sequence.
FPKM(expected number of  Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) were calculated.
Genome_build: mm10
Supplementary_files_format_and_content: Text files include readcount and FPKM values for each sample

source_name: thymus

extract_protocol:
Single-cell suspension were prepared from thymus and stainned with CD69 and TCRβ. Then, group 2 (TCRβintCD69hi) and group 3 (TCRβhiCD69hi) subsets were sorted by Flow cytometry. The total RNA were extracted by Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

value: thymus

value: group 3 (TCRbetahiCD69hi) thymocytes


title: CSS-T2-R21

value: Middle internode


title: CSS-T3-R21


title: CSS-T2-R11


title: CSS-T1-R21


title: CSS-T1-R11


title: R4_control_96h_1

description: ATRA-resistant cells

value: Acute promyelocytic leukemia (APL)

value: Blood

tag: cell line


title: CSS-MS-R21


title: SW480 cells, E7386

city: Duarte

first: Ching

last: Ouyang

state: CA

address: 1500 E. Duarte Rd.

institute: City of Hope National Medical Center

data_processing:
Sequence reads passing quality check were preprocessed for adaptor and polyA removal using trimmomatic v.0.39 and fastp v.0.23.2.
Trimmed sequence reads were mapped to human reference genome hg38 with an index build containing the transcript/gene annotations using STAR v.2.7.9a.
Strand-specific read counts of each gene annotated in RefGene were calculated by featureCounts function in the Subread package v.1.6.4.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file containing read counts for each sample.

growth_protocol: SW480 colorectal cancer cells were maintained in DMEM 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).
Libraries were prepared with Kapa RNA mRNA HyperPrep kit (Kapa Biosystems) according to the manufacturer's protocol.

treatment_protocol: CBP/β-catenin antagonism was induced by treatment of cells with C82, ICG001 and E7386 for 24h

tag: cell type

value: Colorectal cancer cells

tag: treatment

value: CBP/β-catenin antagonism


title: SW480 cells, ICG001


title: SW480 cells, DMSO

value: Control


title: CSS-B-R22


title: SW480 cells, C82


title: CSS-B-R12


title: CSS-MS-R11


title: CSS-SD-R12

value: Soft dough


title: FpM_1

description: Transcriptome

data_processing:
Low-quality reads with Phred score<30 were filtered
Adapter triming using cutadapt 1.8.1
ribosomal RNA sequences removal by aligning thea reads with silva database using bowtie2 (2.2.9)
read alignment o the genome using Hisat2 program (version 2.0.5)
estimation of gene expression and transcript abundance using String_Tie program (version 1.3.3b)
pairwise differential expression analysis using cuffdiff
Genome_build: Phytozome v3.3.2
Supplementary_files_format_and_content: FPKM values in excel format

growth_protocol: Sweet Sorghum ICSA38  plants were raised in an open field

tag: line


title: CSS-FI-R12

value: Floral Initiation


title: Thymocytes, group2 KO

tag: strain


title: FpP_2

description: Transcriptome

tag: tissue

value: Physiological maturity


title: FpP_1

description: Transcriptome


title: FpM_2

description: Transcriptome


title: Thymocytes, group3 WT

value: group 2 (TCRbetaintCD69hi) thymocytes

tag: genotype

value: wild type


title: Thymocytes, group2 WT


title: RNAseq_CTR_for_RUVBL2-R1

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: RNA-seq experiment

data_processing:
ChIP-seq analysis: Alignment: Sequence reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) without the option -m.
ChIP-seq analysis: Peak detection was performed with MACS (PubMed ID: 18798982). Peaks were reported in BED format. ChIP-seq genome-wide profiles were normalized by the total number of reads of each sample.
RNA-seq analysis: Alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
ATAC-seq analysis: Sequence reads of the samples were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000. ChIP-seq genome-wide profiles were normalized by the total number of reads of each sample.
Genome_build: hg19
Supplementary_files_format_and_content: Files *.bdg.gz (BedGraph, genome-wide ChIP-seq/RNA-seq)
Supplementary_files_format_and_content: Files .bed (BED, ChIP-seq signal enriched regions)

growth_protocol: MDA-MB-231 cells (ATCC No.: HTB-26) were cultured in Dulbecco’s modified Eagle’s medium (Biowest; L0106-500) supplemented with 1% penicillin/streptomycin (Gibco; 15140122), 2 mM L-glutamine (Biowest; X0550-100), and 10% FBS (Gibco; 10270106) at 37ºC in 5% CO2.

extract_protocol:
RNA was extracted with RNeasy Mini Kit (Qiagen; 74104) following manufacturer's instruction
Libraries were prepared according to Illumina instructions.

treatment_protocol: MDA-MB-231 cells were infected with lentiviral particles for shControl or shRUVBL2 and selected for 48 hr with 2.5 µg/ml puromycin. At 48 hr post-selection

tag: chip antibody

tag: knockdown

value: shControl


title: RNAseq_shRUVBL2-R2

description: RNA-seq experiment


title: RNAseq_shRUVBL2-R1

description: RNA-seq experiment


title: RNAseq_CTR_for_RUVBL2-R2

description: RNA-seq experiment


title: RNAseq_CTR_for_LOXL2-R2

description: RNA-seq experiment


title: ATACseq_CTR

description: ATAC-seq experiment

extract_protocol:
About 50,000 cells of each condition were treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina), and DNA was purified using MinElute PCR Purification Kit (Qiagen; 28006). Transposed DNA was amplified by PCR using NEBNextHigh-Fidelity 2 PCR Master Mix (New Englands Labs; M0541S) and primers containing a barcode
Libraries were prepared according to Illumina instructions.

treatment_protocol: MDA-MB-231 cells were infected with lentiviral particles for shControl or shRUVBL2 and selected for 48 hr with 2.5 µg/ml puromycin. At 48 hr post-selection ATAC-seq experiment was performed


title: RNAseq_shLOXL2-R2

description: RNA-seq experiment


title: RNAseq_shLOXL2-R1

description: RNA-seq experiment


title: ATACseq_shRUVBL2

description: ATAC-seq experiment


title: RNAseq_CTR_for_LOXL2-R1

description: RNA-seq experiment


title: ChIPseq_H2AZ

description: ChIP-seq experiment

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody and incubated with protein-A agarose beads.
Libraries were prepared according to Illumina instructions.

value: H2AZ (abcam ab4174)


title: ChIPseq_H3K4ox-R2

description: ChIP-seq experiment

value: H3K4ox (handmade)


title: ChIPseq_H3K4ox-R1

description: ChIP-seq experiment


title: n2l3_wtype_xxxxx_az043

status: Public on Dec 22 2023

city: Santa Cruz

first: Alan

middle: M

last: Zahler

address: 1156 High St.

department: MCD Biology

institute: UC Santa Cruz

data_processing:
150 x 150 paired end reads. Sequencing libraries N2-1, N2-2, N2-3, DG3430-1, DG3430-2 and DG3430-3 were strand-specific (read2 is the coding strand). Libraries N2-4, N2-5, N2-6, SZ454-1, SZ454-2, SZ454-3 were not strand-specific.
Reads were mapped with Bowtie2 to the RepeatMasker library of C.elegans repeat elements.
After removing reads with both ends mapped to repeat elements, the remaining reads were mapped to the ce10 genome assembly using STAR.
Potential PCR duplicates were removed with samtools rmdup.
Splice junctions were extracted from the bam files by examining the CIGAR string, resulting in a non-redundant set of introns spanned by these splice junctions.
Alternative splicing events of types A5,A3 were identified from the splice junctions found in sequencing libraries N2-1, N2-2, N2-3, DG3430-1, DG3430-2 and DG3430-3 .
A5 events: A custom script was employed to identify junctions that define alternative 5' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
A3 events: A custom script was employed to identify junctions that define alternative 3' ss separated by <50bp across the libraries mapped to the indicated genome assembly.
Alternative splicing events of types SE, RI, MS, MX, AF, AL were extracted from the ce10 EnsemblArchive65 transcript annotation using junctionCounts:infer_pairwise_events (github ajw2329/junctionCounts)
The program junctionCounts (github ajw2329/junctionCounts) was used to determine PSI (percent spliced in) for all events in all samples. The option "suppress_eij_use" was used for the A5,A3 events. The option "--forward_read unstranded" was used for the not-strand-specific samples.
The junctionCounts PSI estimates for a sample were merged into a gtf with the scores for the 2 alternative transcripts of an event representing (1000 times) its PSI (and 1-PSI) values. If junctionCounts reported a non-zero span of the PSI estimate, these scores were reduced by a factor of (1-spanPSI).
Assembly: Oct. 2010 (WS220/ce10)
Supplementary files format and content: The ensArch65 gtf file for a sample contains the 2 alternative transcripts for each event of type SE, RI, MS, MX, AF, AL derived from the ce10 EnsembleArchive65 annotation. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. This score is modified by a factor of (1-spanPSI) if there is a non-zero span in the estimate of PSI.
Supplementary files format and content: The libIntrons gtf file for a sample contains the 2 alternative transcripts for each event of type A3, A5 derived from the introns found in all sample sequencing libraries. The score field of a transcript is 1000 times the PSI (1-PSI) value for the "included" ("excluded") transcript. For these event types the span in the estimate of PSI is always zero.

organism: Caenorhabditis elegans

growth_protocol: Indicated strains were grown at 20C on NGM agar plates fed OP50 E. coli

extract_protocol:
Worms were lysed in Trizol and total RNA was cleaned by Zymo RNA Clean and Concentrator according to manufacturer's protocol.
mRNA libraries for high throughput sequencing were prepared by rRNA depletion by Azenta. Paired 150 nt reads, Illumina

treatment_protocol: Embryos were isolated by bleach treatment, grown for 34hours, at which time RNA was extracted

tag: tissue type

value: whole worm - L3


title: n2l3_mog5x_sz454_az046


title: ChIPseq_RUVBL2

description: ChIP-seq experiment

value: RUVBL2 (abcam ab36569)


title: n2l3_mog5x_sz454_az045


title: n2l3_mog5x_sz454_az044


title: n2l3_wtype_xxxxx_az041


title: n2l3_wtype_xxxxx_az042


title: n2l3_sacy1_dg3430_az026


title: n2l3_sacy1_dg3430_az024


title: Patient 4, scRNAseq from skin and blood

status: Public on Dec 20 2023

city: Vienna

first: Johanna

last: Strobl

address: Währinger Gürtel 18-20

department: Department of Dermatology

country: Austria

institute: Medical University of Vienna

description: 10x Genomics single cell RNA-seq using cell hashing technique for blood and skin cell distinction

data_processing:
Single-end reads were trimmed for low quality bases and removal of low-quality reads using ReadTools
Trimmed reads were mapped to the Homo sapiens genome (GRCh38.92 assembly) using STAR (v2.5.3a) mapper
The reads mapped in multiple genomic locations were eliminated by using Samtools (v1.4)
Read counts for features (exons) were generated using the featureCounts function from the Subread package (v 1.22.1)
Cell Ranger (v3.0.2) mkfastq method demultiplexed raw base call (BCL) files generated by Illumina sequencers into FASTQ files., Cell Ranger (v3.0.2) count method took FASTQ files from cellranger mkfastq and performs alignment to the Homo sapiens genome (GRCh38.92 assembly), filtering, barcode counting, and UMI counting.
Assembly: hg38
Supplementary files format and content: Cell Ranger (v3.0.2) aggr method was used to aggregate the outputs from three runs of cellranger count.
Supplementary files format and content: Raw gene count matrix was generated using featureCounts function from the Subread package (v 1.22.1) with Ensembl Known Gene models (version GRCh38.92) as reference annotations

source_name: Skin and peripheral blood

extract_protocol:
Human skin tissue was digested for 2h in Collagenase and DNAse passed through 70-μm mesh filters and rinsed with 10% FBS in PBS. Peripheral blood mononuclear cells were isolated from the blood using Ficoll gradients.
Single-Cell 5’ Library & Gel Bead Kit v2 (10X Genomics) according to the manufacturer’s instructions

tag: disease state

value: human acute Graft-versus host disease (GVHD)

value: Skin and peripheral blood

value: Skin cells, peripheral blood leukocytes

value: naive


title: n2l3_wtype_xxxxxx_az022


title: n2l3_sacy1_dg3430_az025


title: Patient 5, scRNAseq from skin and blood


title: n2l3_wtype_xxxxxx_az023


title: Patient 3, scRNAseq from skin and blood


title: n2l3_wtype_xxxxxx_az021


title: UPCI:SCC-090 WT 1

status: Public on Dec 18 2023

city: Liverpool

first: Lekh

last: Dahal

address: Sherrington Building, Ashton Street

institute: University of Liverpool

data_processing:
FastQ Screen v0.13.0
Raw sequence reads were trimmed for contaminating sequence adapters and poor quality bases using the program FastP1. Bases with an average Phred score lower than 15 were trimmed. Reads that were trimmed to less than 54 bases were discarded.
The sequenced reads where checked for other species contamination using the Fastq-Screen program, which selects a sample of the reads and aligns them to a selection of reference genomes that are routinely sequenced at Glasgow Polyomics. The quality trimmed reads were aligned to the reference genome using the program Hisat2 and the transcript abundance estiamted using Stringtie.
Assembly: Ensembl
Supplementary files format and content: tab-deliminated text file includes raw counts for each sample

extract_protocol:
RNA was harvested using total RNA Miniprep kit (NEB) following the manufacturer's protocol.
RNA libraries for RNA-seq were prepared using QuantSeq Library Prep Kit following the manufacturer's protocol.

value: HNSCC

value: HPV+


title: UPCI:SCC-090 WT 2


title: UPCI:SCC-090 WT 3


title: ChIPseq_INPUT

description: ChIP-seq experiment


title: UPCI:SCC-154 WT 3


title: UPCI:SCC-154 WT 1


title: UM-SCC-47 WT 2


title: FaDu WT 3

source_name: FaDu

value: FaDu

value: HPV-


title: UM-SCC-81B WT 3


title: UM-SCC-47 WT 3


title: UM-SCC-47 WT 1


title: UM-SCC-81B WT 1


title: UM-SCC-11B WT 2


title: FaDu WT 1


title: UM-SCC-11B WT 3


title: UM-SCC-81B WT 2


title: UM-SCC-1 WT 2


title: UM-SCC-1 WT 1