title: p1-1_E02

description: SMART Seq2 with few modification

data_processing:
Sequencing reads from single-cell RNA-Seq libraries were aligned to the mouse reference genome (version mm10 from the UCSC) using Bowtie 2 (version 2.4.2) with default parameters for paired-end reads.
Supplementary files format and content: Expression values of each gene were quantified as TPM using RSEM (version 1.3.3)

source_name: colon

extract_protocol:
Colonic epithelial cells were stained with eBioscience™ Fixable Viability Dye eFluor™ 506 (65-0866-14, Invitrogen) in a 1:1000 ratio for dead cell exclusion. Cells were Fc-blocked using Purified Rat Anti-Mouse CD16/CD32 (Clone 2.4G2, 553142, BD Pharmingen™) for 10 minutes and washed with FACS buffer (Ca2+ and Mg2+-free DPBS supplemented with 0.5% BSA and 0.3% sodium azide). For surface marker staining, PE Rat Anti-Mouse Siglec-F (Clone E50-2440, 552126, BD Pharmingen™) antibody and APC anti-mouse CD326 (EpCAM) antibody (clone G8.8, 118214, Biolegend) were used in a 1:50 and 1:100 dilution ratio, respectively. Antibody staining was performed for 30 minutes. All procedures were conducted at 4°C in the dark. Tuft cells were acquired by BD FACSAriaII (BD Biosciences)
Single-cell RNA-Seq libraries were prepared using the Smart-seq2 protocol with few modifications. Single-cells were sorted using a BD FACSAriaII (BD Biosciences) into 96 well PCR plates (Thermo Scientific) containing 2μl of lysis buffer (0.1% Triton X-100, 1U/μl RNase Inhibitor (Enzynomics), 0.25μM oligo-dT30VN primer) and stored at -80°C. The plates were thawed on ice and incubated for 3 min at 72 °C to lyse the cells. Revers transcription (40U/µl Maxima H minus transcriptase), template switching reaction and PCR pre-amplification (15 cycles) were performed according to the protocol. The PCR products in each well was cleaned up using 0.5X SPRI beads (2% Sera-Mag Speed Beads (Cytiva), 1M NaCl, 10mM Tris-HCl pH 8.0, 1mM EDTA, 0.01% NP40, 0.05% Sodium Azide, 22% w/v PEG 8000). To exclude empty wells and low-quality libraries, cDNA libraries were assessed by quantitative PCR with a primer pair of GAPDH, a housekeeping gene (forward: 5′-GTCGTGGAGTCTACTGGTGTCTTCAC-3′; reverse: 5′-GTTGTCATATTTCTCGTGGTTCACACCC-3′). Samples showing a high threshold cycle (Ct) value (>35 cycles) or no PCR amplification were discarded. 50–200 pg of each cDNA library were used to generate the Illumina sequencing library using EZ-Tera XT DNA library preparation kits (Enzynomics). After the final PCR amplification, samples were pooled and size-selected by SPRI beads (removing DNA bound to 0.3X beads and taking DNA bound to subsequent 0.6X beads). Pooled sequencing libraries were sequenced on an Illumina NextSeq 500 instrument using a 38-bp paired-end reads setting.

value: Female

value: wt

value: tuft


title: Th17_ROR_WT_2

status: Public on Oct 26 2022

type: SRA

city: Duarte

first: Xiancai

last: Zhong

state: CA

address: 1500 E Duarte Rd

department: Immunology & Theranostics

country: USA

institute: Beckman Research Institute of City of Hope

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for Novaseq output and RTA version was 3.4.4.
Files for each group are associated and subjected to data processing using Partek® Flow®.
ChIP-seq reads were aligned to the mm10 genome using BWA version 0.7.17.
Reads were filtered by removing unaligned reads, singletons, and duplicates. Files (BAMPE format) were then reformatted to BigWig files.
Peaks were called uing MACS2 v2.1.1 with the significance cut-off q-value <=0.05.
Sequence reads were quantified and normalized to fragments per kilobase million (FPKM).
Assembly: mm10
Supplementary files format and content: BigWig files showing binding peaks

molecule: genomic DNA

organism: Mus musculus

source_name: Spleen

growth_protocol: ROR-KO CD4+ T cells isolated from mouse spleen were stimulated with 0.25 ug/mL anti-CD3 and 1 ug/mL anti-CD28 antibodies overnight in a 24-well plate coated with anti-hamster secondary antibody.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was fragmented using a ChIP-IT Express Enzymatic kit (Active motif).
ChIP-seq libraries were prepared using the KAPA DNA HyperPrep Library Preparation Kit complemented with xGen Stubby Adapter and Unique Dual Index Primer Pairs from IDT. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Flag-tagged WT or K256R mutated RORgt were retrovirally transduced to acitivated CD4+ T cells. Th17 differentiation was subsequenctly induced by the supplementation of 2 ng/mL TGF-beta, 20 ng/mL IL-6, and 20 ng/mL of IL-23 in the presence of 2 ug/mL anti-IL-4 and 2 ug/mL anti-IFN-gamma antibodies.

tag: tissue

value: Spleen

tag: cell type

value: CD4+ T cells

tag: genotype

tag: treatment

value: TGF-β, IL-6. IL-23

tag: chip antibody

value: sigma F1804


title: TU-NK [chip3_1851035015_site_25]

city: New Delhi

first: Smriti

last: Chawla

address: Okhla Industrial Estate, Phase III, near Govind Puri Metro Station

country: India

institute: Indraprastha Institute of Information Technology,

library_source: transcriptomic

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie
Quantified gene expression levels in counts using RSEM v1.2.44
Genomic mappings(GM) performed with TopHat 2 v2.0.135 and GM percentages calculated using resulting alignments
Raw sequencing read data aligned to the human rRNA sequences using bowtie 2 v2.2.46, and calculated percentage of reads aligned to rRNA as reads aligned to sequences divided by the total reads
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated csv files include RSEM TPM values for each Sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: MDA-MB-231 cells (triple-negative breast carcinoma, ATCC® HTB-26 ™) were cultured using the DMEM (high modified) culture medium supplemented with 10% inactivated fetal bovine serum and 1% penicillin/streptomycin, replicating the culture every three days, keeping the culture at a confluence of 40% at the time of passage, at 37°C in a humid atmosphere at 5% CO2. The adherent cells were dissociated with the TrypLE reagent (Gibco) and resuspended in the complete culture medium. NK-92MI cells (human NK cells genetically modified to produce interleukin 2, ATCC® CRL-2408) were cultured using the AMEM (Alpha Minimum Essential medium) culture medium, plus 0.2 mM inositol, 0.1 mM mercaptoethanol, 0.02 mM folic acid, 12.5% fetal bovine serum and 12.5% horse serum. The cells were homogenized in order to separate the clusters of NKs prior to the replication of the culture into a new 25 cm² flask (1mL of cells cultured previously + 9mL new culture medium). Both cell lines were cultured separately for the subsequent cell-cell interaction experiment using the Polaris equipment (Fluidigm, South San Francisco, USA).

extract_protocol:
NA
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Preparation Kit (FC-131-1096), using the cDNA synthetized from total isolated RNA.

treatment_protocol: Activation was assessed after 24 and 48 hours of cell incubation in a proportion of 3 NK cells for each MDA-MB-231 by evaluating the markers (CD25, CD69, and CD314) expressed from cell-cell contact, using flow cytometry (Sony SH800S).

value: Cancer-NK doublet

tag: cell line


title: NK [chip3_1851035015_site_26]

value: NK cell


title: TU-NK [chip3_1851035015_site_24]


title: p1-1_E01

city: Daejeon

first: Hanseul

last: Yang

address: 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: SMART Seq2 with few modification

library_source: transcriptomic single cell

molecule: polyA RNA

value: colon

tag: age

value: 11 weeks old

tag: Sex


title: Th17_ROR_K256R_2


title: RORgt-K256R_Th17_EGFP+ (biol rep 3)

data_processing:
Partek® Flow®
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow (version 9.0.20.0629; quality score limit: 20)
Trimmed sequence reads were aligned to GRCm38/mm10 using "STAR" method.
Aligned sequence reads were quantified to annotation model and noise reads were filtered out by exluding max <= 1.0.
Sequence reads were normalized to counts per million (CPM) and 0.0001 was added.
Assembly: mm10
Supplementary files format and content: A tab-delimited text file including CPM values for all samples.

growth_protocol: CD4+ T cells isolated from mouse spleen were stimulated with 0.25 ug/mL anti-CD3 and 1 ug/mL anti-CD28 antibodies overnight in a 24-well plate coated with anti-hamster secondary antibody.

extract_protocol:
Total RNA was extracted using RNAeasy mini kit (QIAGEN).
RNA libraries were constructed by Novogene.

treatment_protocol: Th17 differentiation was induced by the supplementation of 2 ng/mL TGF-beta, 20 ng/mL IL-6, and 20 ng/mL of IL-23 in the presence of 2 ug/mL anti-IL-4 and 2 ug/mL anti-IFN-gamma antibodies.


title: RORgt-K256R_Th17_EGFP+ (biol rep 1)


title: T7291,VilgemA,T8,V1N

city: Columbus

first: Anna

last: Vilgelm

state: OH

address: 460 W 12th Ave

department: Pathology

institute: The Ohio State University

data_processing:
Individual FASTQ files were trimmed for adapter sequences and filtered for a minimum quality score of Q20 using AdapterRemoval v2.2.0.
Preliminary alignment using HISAT2 v2.0.6 was performed to a composite reference of rRNA, mtDNA, and PhiX bacteriophage sequences obtained from NCBI RefSeq. Reads aligning to these references were excluded in downstream analyses.
Primary alignment was performed against the mouse genome reference GRCm38p4 using HISAT2.
Gene expression values for genes described by the GENCODE Gene Transfer Format (GTF) release M14 (mouse) were quantified using the featureCounts tool of the Subread package v1.5.1 58 in stranded mode.
expression values in the processed data file were ‘sequencing depth normalized’ by DESeq2 package
Assembly: mm10
Supplementary files format and content: Excel spreadsheet includes raw normalized counts for each Sample

source_name: Tumor

growth_protocol: B16F10 cells were maintained in F12 -DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy@mini kit
libraries were generated with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext rRNA Depletion Kit (NEB #E7405) with an input amount of 100 ng total RNA per sample.

treatment_protocol: C57Bl/6 mice were injected subcutaineously with 50000 B16F10 cells and treated with with 100 mg/kg navitoclax (BCLi), 25 mg/kg of alisertib (AURKAi), a combination of both drugs (same doses), or drug vehicles for 11 days by daily oral gavage.

value: Tumor

value: Melanoma

value: Wild

value: Alisertib+Navitoclax

tag: strain

value: C57Bl/6 mice


title: WT_Th17_EGFP+ (biol rep 3)


title: Th17_ROR_EV


title: TU-NK [chip3_1851035015_site_23]


title: RORgt-K256R_Th17_EGFP+ (biol rep 2)


title: p1-1_D12

description: SMART Seq2 with few modification


title: p1-1_D11

description: SMART Seq2 with few modification


title: WT_Th17_EGFP+ (biol rep 2)


title: p1-1_D10

description: SMART Seq2 with few modification


title: WT_Th17_EGFP+ (biol rep 1)


title: Unknown [chip3_1851035015_site_20]

source_name: Unknown

value: Unknown


title: p1-1_D09

description: SMART Seq2 with few modification

value: Female


title: Bone marrow young rep 9 (RNA-Seq)

city: Buffalo

first: Jonathan

middle: E

last: Bard

state: New York

address: 701 Ellicott Street

department: Genomics and Bioinformatics Core

institute: University at Buffalo

description:
BM_Y9
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt

data_processing:
Illumina RTA 2.2.68 Basecaller
Cellranger 3.0.1 mkoutput with Bcl2Fastq 2.20.0.422
Cellranger 3.0.1 Count against mm10 genome to produce count matrix
Seurat 4.0.1 used for marker gene analysis and visualization
Feature Counts to DESeq2 for BULK-RNA analysis
Assembly: mm10
Supplementary files format and content: CSV File containing UMI corrected read counts for scRNA-seq samples; featureCounts txt file for bulkRNA-seq samples

source_name: Femur

extract_protocol:
Chromimum Single Cell 3' v2 (10x Genomics)
TruSeq Stranded RNA (illumina)

value: Femur bone marrow

value: Wildtype

value: 6 month


title: Bone marrow young rep 6 (RNA-Seq)

description:
BM_Y6
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Bone marrow young rep 5 (RNA-Seq)

description:
BM_Y5
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Th17_ROR_K256R_1

value: Spleen

value: CD4+ T cells


title: Bone marrow young rep 2 (RNA-Seq)

description:
BM_Y2
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Bone marrow young rep 1 (RNA-Seq)

description:
BM_Y1
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: TU [chip3_1851035015_site_18]

value: Cancer cell


title: Bone marrow young rep 10 (RNA-Seq)

description:
BM_Y10
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: TU [chip3_1851035015_site_22]


title: Bone marrow old rep 6 (RNA-Seq)

description:
BM_O7
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt

value: 24 Month


title: p1-1_D06

description: SMART Seq2 with few modification

value: wt

value: tuft


title: p1-1_D07

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old


title: TU [chip3_1851035015_site_21]


title: p1-1_D04

description: SMART Seq2 with few modification


title: TU-NK [chip3_1851035015_site_16]

value: Cancer-NK doublet


title: p1-1_D05

description: SMART Seq2 with few modification


title: Bone marrow old rep 5 (RNA-Seq)

description:
BM_O6
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Bone marrow old rep 3 (RNA-Seq)

description:
BM_O4
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: TU-NK [chip3_1851035015_site_15]


title: Bone marrow old rep 4 (RNA-Seq)

description:
BM_O5
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Bone marrow old rep 1 (RNA-Seq)

description:
BM_O1
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: TU-NK [chip3_1851035015_site_17]


title: Bone marrow old rep 2 (RNA-Seq)

description:
BM_O2
Wildtype Femur Bone marrow
bonemarrow_young_old_featureCounts.txt


title: Femur Conditional KO (scRNA-Seq)

description:
cTTPKO
Femure Bonemarrow TTP KO

value: cTTPKO

value: 3 Month


title: TU-NK [chip3_1851035015_site_14]


title: p1-1_D03

description: SMART Seq2 with few modification


title: TU-NK [chip3_1851035015_site_13]


title: TU [chip3_1851035015_site_19]


title: Femur Wildtype (scRNA-Seq)

description:
Control
Wildtype Femure Bonemarrow


title: Sample 3 sepsis sample

city: Changsha, Hunan

first: Yufan

state: China

address: No. 86 Ziyuan Road

country: China

institute: Hunan Children's Hospital

description: one sample from heart tissue

data_processing:
The Cell Ranger software pipeline provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells
mm10
Matrix table with raw gene counts for every gene and every cell

source_name: heart

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: heart

value: all cells in heart

value: cecal ligation and puncture operation


title: Sample 4 sepsis + low level tagus stimulation sample

description: one sample from heart tissue

value: low-level tragus stimulation


title: Femur TTP KO (scRNA-Seq)

description:
TTPKO
Femure Bonemarrow TTP KO

value: Femur bone marrow

value: TTPKO


title: p1-1_D01

description: SMART Seq2 with few modification

value: Female


title: Sample 2 sham sample

description: one sample from heart tissue

value: sham


title: NK [chip3_1851035015_site_12]

value: NK cell


title: p1-1_C12

description: SMART Seq2 with few modification


title: NK [chip3_1851035015_site_11]


title: p1-1_C11

description: SMART Seq2 with few modification


title: NK [chip3_1851035015_site_10]


title: Sample 1 control sample

description: one sample from heart tissue

value: control


title: p1-1_C09

description: SMART Seq2 with few modification

value: wt


title: NK [chip3_1851035015_site_09]


title: primary hepatocytes ALKBH1-IP DNA

city: Chengdu

first: Liping

last: Luo

state: Sichuan

address: 783#，Xindu Avenue

department: School of Bioscience and Technology

institute: Chengdu Medical College

data_processing:
Raw data was filtered by Trimmomatic (version 0.36).
Clean reads were mapped to mouse genome (GRCm38) using STAR software (version 2.5.3a).
The RSeQC (version 2.6) was used for reads distribution analysis. The MACS2 software (Version 2.1.1) was used for peak calling. The bedtools (Version 2.25.0) was used for peaks annotation and peak distribution analysis.
The differentially binding peaks were identified by a python script, using fisher test. P-value less than 0.05 was judged statistically significant enrichment.
Genome_build: mm10
Supplementary_files_format_and_content: peak txt files

source_name: Mouse primary hepatocytes

growth_protocol: Primary heaptocytes were isolated and cultured in 12-well plate  (typically 2.8 × 105 cells per well) in  MEMα supplemented with 10% fetal bovine serum  FBS plus 100 U/ml of penicillin and 100 mg/ml of streptomycin  at 37 °C for 4 hours and then kept in serum-free medium until the treatment.

extract_protocol:
Lysates were clarified from sonicated nuclei and ALKBH1-flag-DNA complexes were isolated with anti-flag antibody using a SimpleChIP Enzymatic Chromatin IP Kit (Cell signaling, Danvers, USA, #9003) .
DNA libraries were prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, #ND607). The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: Hepatocytes  was transfected with ALKBH1-expressing plasmid for 48 hours to overexpress an ALKBH1-flag fusion protein.

value: Mouse primary hepatocytes

value: 3 months

value: wildtype

value: Flag (Cell Signaling, #14793)


title: NK [chip3_1851035015_site_08]


title: p1-1_D02

description: SMART Seq2 with few modification

value: colon

value: 11 weeks old

value: tuft


title: primary hepatocytes input DNA

value: transfected with ALKBH1-expressing plasmid for 48 hours


title: T1

city: Los Angeles

first: Fei

last: Pei

address: 2250 Alcazar St

institute: USC

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 3.1.0.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene

source_name: trigeminal ganglion

extract_protocol:
Briefly, samples were dounce homogenized with a tight pestle in the ice-cold detergent lysis buffer
cDNA libraries were prepared for sequencing using standard 10X Genomics protocols

value: trigeminal ganglion


title: p1-1_C08

description: SMART Seq2 with few modification


title: NK [chip3_1851035015_site_07]


title: p1-1_C06

description: SMART Seq2 with few modification


title: control heaptocytes rep1

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic (vesion 0.36) and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the mouse genome (GRCm38) using HISAT2 (vesion 2.2.1.0). FPKM of each gene was calculated using Cufflinks, and the read counts of each gene were obtained by HTSeq-count (vesion 0.9.1).
Differential expression analysis was performed using the DESeq (vesion 1.18.0). P value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression.
Genome_build: mm10
Supplementary_files_format_and_content: txt files include FPKM values for each Sample

extract_protocol:
Hepatocytes were removed and RNA was harvested using Trizol reagent.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions, and were prepared for sequencing using on an illumina Nova seq 6000 platform and 150 bp paired-end reads were generated

treatment_protocol: Hepatocytes  was treated with 0.2 mM palmitic acid for 24 hours.

value: Alkbh1 f/f

value: 0.2 mM palmitic acid


title: AKO heaptocytes rep1

value: Alkbh1 f/f, Albumine-cre


title: control heaptocytes rep3


title: AKO heaptocytes rep2

value: Alkbh2 f/f, Albumine-cre


title: AKO heaptocytes rep3

value: Alkbh3 f/f, Albumine-cre


title: NK [chip3_1851035015_site_06]

value: NK cell


title: S2

city: Guangzhou

first: canzhen

last: liu

state: Guangdong

address: Jingxi Street  Guangzhou Baiyun District China

department: Nanfang Hospital

institute: Southern Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In   this step, clean data (clean reads) were obtained by removing reads containing adapter, reads   0 containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC   content the clean data were calculated. All the downstream analyses were based on the clean   data with high quality
Reference genome and gene model annotation files were downloaded from genome website   directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean   reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the   mapping tool for that Hisat2 can generate a database of splice junctions based on the gene   model annotation file and thus a better mapping result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then   FPKM of each gene was calculated based on the length of the gene and reads count mapped   to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per   Millions base pairs sequenced, considers the effect of sequencing depth and gene length for   the reads count at the same time, and is currently the most commonly used method for   estimating gene expression levels
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the DESeq2   R package (1.20.0). DESeq2 provide statistical routines for determining differential expression   in digital gene expression data using a model based on the negative binomial distribution. The   resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling   the false discovery rate . Genes with an adjusted P-value <0.05 found by DESeq2 were   assigned as differentially expressed
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample

source_name: Kidney

extract_protocol:
Total RNA was extracted from the kidney using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, sequencing was performed with an Illumina Novaseq 6000 instrument.

value: BALB/c

value: kidney

value: intraperitoneal injections of PA-S14


title: S1


title: p1-1_C04

description: SMART Seq2 with few modification

value: Female

value: wt


title: UIRI_3

value: intraperitoneal injections of vehicle


title: NK [chip3_1851035015_site_05]


title: p1-1_C03

description: SMART Seq2 with few modification

value: colon


title: UIRI_2


title: S3


title: NK [chip3_1851035015_site_04]


title: UIRI_1


title: control heaptocytes rep2

value: Mouse primary hepatocytes

value: 3 months


title: S-3


title: p1-1_B10

description: SMART Seq2 with few modification

value: 11 weeks old

value: epithelial


title: NK [chip3_1851035015_site_03]


title: p1-1_C02

description: SMART Seq2 with few modification

value: tuft


title: C-3


title: S-2


title: p1-1_B09

description: SMART Seq2 with few modification


title: NK [chip3_1851035015_site_02]


title: KV22928

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: shRor2-1 rep 3

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using HISAT2 (Galaxy tool version2.1.0+galaxy5). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.3).  UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

source_name: Lineage-depleted tumor cells from tumor organoid model, Ror2 knockdown

growth_protocol: After a 4-day culture period, shLUC and shRor2 organoids were retrieved from the matrix by digesting in 2mg/ml of collagenase for 20 minutes at 150 rpm at 37 °C.

extract_protocol:
Organoids were then washed twice in 1X DPBS for immediate RNA isolation using the Arcturus PicoPure RNA Isolation Kit. RNA was subjected to sample quality control by the Genomics and RNA Profiling Core of Baylor College of Medicine using the Nanodrop ND-1000 and a Bioanalyzer Nano Chip.
RNA samples representing biological replicates from shLUC and shRor2 groups were then subjected to library preparation and Illumina Next Generation Sequencing on a NovaSeq 6000 (100 bp Paired-End Sequencing, 68 million reads per sample).

treatment_protocol: Lineage-depleted tumor cells were derived from 2153L basal-like TP53 null mammary tumor models and transduced overnight with shLUC and shRor2 lentiviruses (MOI-30) in low-attachment 24-well plates at a density of 500,000 cells per well.  The following day, aggregated/transduced organoids were embedded in a 2 mg/ml Type I collagen matrix. Eight-well chamber slides were first coated with a thin layer of neutralized Type I collagen (5 μl) and allowed to polymerize for 30 minutes at 37 °C. Aggregated organoids after overnight transduction were washed twice in 1X Dulbecco’s Phosphate Buffered Saline (DPBS) before suspending in 2mg/ml neutralized Type I collagen at a density of 50,000 cells/50 μl volume of collagen. Within each chamber, 50μl of cell suspension was plated and allowed to polymerize at 37 °C for 1 hour. Cultures were then overlaid with 500μl of growth media.

value: 2153L basal-like TP53null organoid

tag: knockdown

value: Ror2 knockdown


title: p1-1_C01

description: SMART Seq2 with few modification


title: TU [chip2_1851035011_site_48]

value: Cancer cell


title: NK [chip3_1851035015_site_01]


title: S-1


title: C-2


title: p1-1_C05

description: SMART Seq2 with few modification


title: KV22926

description: shRor2-1 rep 1


title: TU [chip2_1851035011_site_47]


title: KV22925

description: shLUC-1 rep 3

source_name: Lineage-depleted tumor cells from tumor organoid model, luciferase control

value: luciferase control


title: C-1


title: KV22927

description: shRor2-1 rep 2


title: p1-1_B04

description: SMART Seq2 with few modification


title: p1-1_B06

description: SMART Seq2 with few modification


title: KV22924

description: shLUC-1 rep 2


title: TU [chip2_1851035011_site_46]


title: KV17830

description: shRor2 rep3

data_processing:
Sequenced reads in FASTQ files were mapped to mm10 whole genome using STAR (Galaxy Version 2.6.0b-1). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.2). UCSC known transcripts were supplied in GTF format file.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *gene_expression.tabular.txt: Tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

treatment_protocol: Lineage-depleted tumor cells were derived from 2225L basal-like TP53 null mammary tumor models and transduced overnight with shLUC and shRor2 lentiviruses (MOI-30) in low-attachment 24-well plates at a density of 500,000 cells per well. The following day, aggregated/transduced organoids were embedded in a 2 mg/ml Type I collagen matrix. Eight-well chamber slides were first coated with a thin layer of neutralized Type I collagen (5 μl) and allowed to polymerize for 30 minutes at 37 °C. Aggregated organoids after overnight transduction were washed twice in 1X Dulbecco’s Phosphate Buffered Saline (DPBS) before suspending in 2mg/ml neutralized Type I collagen at a density of 50,000 cells/50 μl volume of collagen. Within each chamber, 50μl of cell suspension was plated and allowed to polymerize at 37 °C for 1 hour. Cultures were then overlaid with 500μl of growth media.

value: 2225L basal-like TP53 null organoid

value: Lineage-depleted tumor cells

tag: shRNA


title: KV22923

description: shLUC-1 rep 1


title: TU [chip2_1851035011_site_45]


title: KV17829

description: shRor2 rep2


title: p1-1_B03

description: SMART Seq2 with few modification


title: p1-1_B02

description: SMART Seq2 with few modification


title: TU [chip2_1851035011_site_43]


title: p1-1_B01

description: SMART Seq2 with few modification


title: p1-1_A12

description: SMART Seq2 with few modification


title: KO-Drug-3

city: Baltimore

first: Som

last: Dev

state: MD

address: 725 N, Wolfe St

department: Physiology, School of Medicine

institute: Johns Hopkins University

data_processing:
Reads quality was checked with FastQC v0.11.7 and trimmed with trimmometric 0.38
Trimmed reads mapped to reference genome UCSC mm10 using HISAT2v 2.1.0 (~50 million mapped reads/sample)
The transcripts were assembled by StringTie v.2.1.3b with aligned reads
Expression profiles were represented as read count and FPKM (Fragments Per Kilobase of transcript per Million mapped reads)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include, read count & FPKM values for each Sample ...

source_name: Liver

extract_protocol:
Liver tissues piece were removed, flash frozen on dry ice, and RNA was harvested using RNeasy mini kit (Qiagen). Illumina TruSeq Stranded Total RNA Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: KO-Drug

value: 20 wk


title: KV17828

description: shRor2 rep1


title: KO-Drug-1


title: KO-Drug-4


title: KV17827

description: shLUC rep3

value: shLUC


title: KV17826

description: shLUC rep2


title: p1-1_A08

description: SMART Seq2 with few modification

value: Female

value: wt


title: p1-1_A10

description: SMART Seq2 with few modification

value: colon


title: KO-Drug-2


title: KO-6

value: KO


title: TU [chip2_1851035011_site_40]


title: TU [chip2_1851035011_site_39]


title: KO-4


title: KO-2


title: p1-1_A04

description: SMART Seq2 with few modification


title: Het-4

value: Het


title: p1-1_A05

description: SMART Seq2 with few modification

value: 11 weeks old


title: TU [chip2_1851035011_site_42]


title: Het-3


title: TU-NK [chip2_1851035011_site_44]

value: Cancer-NK doublet


title: Het-2


title: p1-1_A03

description: SMART Seq2 with few modification

value: epithelial


title: Unknown [chip2_1851035011_site_38]

value: Unknown


title: TU [chip2_1851035011_site_37]


title: KV17825

description: shLUC rep1


title: Unknown [chip2_1851035011_site_41]


title: p1-1_A02

description: SMART Seq2 with few modification


title: KSCR

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:  -MT% < 20%;   -Cell Gene Number < Median Gene Number * 2;  -Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each cell

source_name: Kras, Tp53, Setd2 triple mutant mice

growth_protocol: Feeding in SPF

extract_protocol:
Leukocytes of pancreatic tumor were isolated using collagenase digestion method described for ﬂow cytometry analysis. In brief, pancreatic tumor tissue were cut into pieces and digested in FACS Buffer (HBSS +10% FCS) containing 2 mg/ml collagenase type IV (Yeasen Biotech ). The tissues were incubated at 37 °C water bath for 30 min and vortexed every 10 min, and then passed through a 70 μm filter.
RNA libraries were generated by 10xGenomics Single Cell 3’ Library Gel Bead Kit V3 and prepared for sequencing using standard Illumina protocols

treatment_protocol: Pancreatic tissues were isolated and digested immediately, and performed single cell sequencing.

value: Pancreas

value: 13 weeks

value: Setd2 KO


title: KO-5


title: TU-NK [chip2_1851035011_site_34]


title: TU-NK [chip2_1851035011_site_35]


title: KCR

source_name: Kras, Tp53 double mutant mice

value: Setd2 WT


title: DH16076_2

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Assembly: Human sequenced genome GRCh38 v91
Supplementary files format and content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 49 or 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: time point

tag: library type

value: Low Input

value: NK cells


title: AK184_KO_Hyperoxia

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.20)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE vM19 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generarted by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: lung

extract_protocol:
Total RNA was harvested from frozen lungs using Trizol reagent and RNeasy column (Qiagen).
KAPA RNA HyperPrep with RiboErase HMR  was used for RNA library preparation.

treatment_protocol: Akap1 KO  and Wt mice were exposed to room air (Normoxia, 21% oxygen) or > 90% oxygen (hyperoxia) in airtight cages in a chamber (75x50x50 cm, Biospherix, NY) for 48h that was fitted with proOx p100 sensor to measure the concentration of oxygen was measure by (Biospherix, New York, NY).

value: lung

value: adult 7-9 weeks

value: hyperoxia


title: AK183_KO_Hyperoxia


title: AK188_KO_Hyperoxia


title: AK226_KO_Normoxia

value: normoxia


title: DH16044_2


title: TU-NK [chip2_1851035011_site_33]


title: AK222_Wt_Hyperoxia

value: wild-type


title: AK219_Wt_Hyperoxia


title: Unknown [chip2_1851035011_site_32]


title: CH19101_2


title: AK192_KO_Normoxia


title: AK190_KO_Normoxia


title: CH19101_1


title: TU [chip2_1851035011_site_31]

value: Cancer cell


title: AK217_Wt_Hyperoxia


title: TU-NK [chip2_1851035011_site_36]


title: Het-1

value: Het

value: 20 wk


title: AK223_Wt_Normoxia


title: NK [chip2_1851035011_site_30]

value: NK cell


title: AK204_Wt_Normoxia


title: AK224_Wt_Normoxia


title: CH19088_2


title: TU-NK [chip2_1851035011_site_29]

value: Cancer-NK doublet


title: DH16076_1


title: CH19078_3


title: Adipose derived cells Day 10

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was performed on Illumina NovaSeq
The reads from scRNA-seq were aligned to the mouse genome (mm10) using the cellranger pipeline.
Individual samples were merged to generate the digital expression matrix using cellranger aggr.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for each cell

source_name: White subcutaneous fat progenitor cell

extract_protocol:
For the generation of single-cell gel beads in emulsion, cells were loaded on a Chromium single cell instrument (10x Genomics) with an estimated targeted cell recovery of ~5,000 cells as per manufacturer’s protocol. Cells were partitioned with Gel Beads into emulsion in the Chromium instrument where cell lysis and barcoded reverse transcription of RNA occurred following amplification.
Single cell RNA-Seq libraries were prepared by using the Chromium single cell 3′ library and gel bead kit v3 (10x Genomics).

value: White subcutaneous fat progenitor cell undergoing cardiac transition

tag: day


title: Adipose derived cells Day 0

value: White subcutaneous fat progenitor cell


title: CH19083_2


title: TU-NK [chip2_1851035011_site_27]


title: NK [chip2_1851035011_site_28]


title: CH19088_3


title: Adipose derived cells Day 1


title: NK [chip2_1851035011_site_26]


title: TU-NK [chip2_1851035011_site_25]


title: CH19078_1


title: CH16023_3


title: TU-NK [chip2_1851035011_site_23]


title: CH19083_1


title: CH16013_2


title: MS patient 8B2

type: RNA

city: Copenhagen N

first: Atul

last: Anand

address: Ole Maaløes Vej 5, building 2, 3 floor

department: Department of Pathology

country: Denmark

institute: Rigshospitalet

hyb_protocol: 100 ng of total RNA was used for the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1.1, Agilent Technologies).  Additionally, the optional microRNA Spike-In kit (#5190-1934, Agilent Technologies) was added.

scan_protocol: scanned on an Agilent DNA Microarray Scanner C with SureScan Technology using the Agilent Microarray Scanner System user Guide

data_processing: Data from the Microarray Scanner C was extracted using Agilent Feature Extraction Software v. 12.03.1 (Agilent Technologies) and a Quality Control report for each microarray slide was provided after the data extraction

source_name: PAXgene Blood miRNA

extract_protocol: 210 full blood samples were collected in PAXgene tubes during the TREMEND (Tecfidera in Relapsing-Remitting Multiple Sclerosis: Endothelial Dysfunction) phase IV clinical trial from 52 RRMS patients and 22 controls from March 2014 to August 2016 and kept in 80oC. In 2020, the microRNA was extracted with Blood miRNA Kit from Qiagen. Quality and quantity assessment of extracted RNA on NanoDrop 2000c spectrophotometer (ThermoFischer) and 2100 bioanalyzer (Agilent).

treatment_protocol: Blood samples of patients before and short- and long-term after DMF treatment of the the TREMEND (Tecfidera in Relapsing-Remitting Multiple Sclerosis: Endothelial Dysfunction) phase IV clinical trial

value: whole blood

tag: timepoint

value: Early group

value: female


title: TU-NK [chip2_1851035011_site_22]

data_processing:
RSEM index generated on hg19
Read data aligned to index using RSEM/bowtie
Quantified gene expression levels in counts using RSEM v1.2.44
Genomic mappings(GM) performed with TopHat 2 v2.0.135 and GM percentages calculated using resulting alignments
Raw sequencing read data aligned to the human rRNA sequences using bowtie 2 v2.2.46, and calculated percentage of reads aligned to rRNA as reads aligned to sequences divided by the total reads
Genome_build: hg19
Supplementary_files_format_and_content: Comma separated csv files include RSEM TPM values for each Sample


title: MS patient 9D2

label_protocol: 100 ng of total RNA was used for the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1.1, Agilent Technologies).  Additionally, the optional microRNA Spike-In kit (#5190-1934, Agilent Technologies) was added.

value: 1-year group


title: MS patient 9D1


title: MS patient 8D


title: Adipose derived cells Day 7


title: MS patient 9C

value: Intermediate group


title: TU-NK [chip2_1851035011_site_21]


title: Chickpea Flower 4

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

data_processing:
Low-quality reads and reads containg adaptor/primer contamination were filtered using NGS QC Toolkit v2.3
Fragments per exon kilobase per million (FPKM) value was calculated for all the genes in each tissue sample
Genome_build: Kabuli chickpea genome (v1.0; Varshney et al., 2013)
Supplementary_files_format_and_content: tab delimited text files include FPKM values for each sample

organism: Cicer arietinum

source_name: Mature plant

growth_protocol: Plants were grown in the culture room/greenhouse or under the field conditions.

extract_protocol:
Tissue samples were collected and frozen in liquid nitrogen. Total RNA was isolated using TRI reagent from Sigma.
Libraries were prepared using True-Seq Sample Prep kit (Illumina) according to the manufacture’s protocol.

treatment_protocol: Different tissues/organs were harvested from vegetative and reproductive stages.

value: Flower


title: MS patient 8A

value: Baseline group


title: MS patient 9A


title: Chickpea Flower 5


title: TU-NK [chip2_1851035011_site_20]

extract_protocol:
NA
Libraries were prepared according to Illumina's instructions accompanying the Nextera XT DNA Library Preparation Kit (FC-131-1096), using the cDNA synthetized from total isolated RNA.


title: CH16013_3

value: Blood

value: Low Input

value: NK cells


title: MS patient 6D


title: MS patient 7E

value: Long term group


title: MS patient 7D


title: MS patient 8B1


title: MS patient 6B


title: TU-NK [chip2_1851035011_site_19]


title: MS patient 6A


title: MS patient 7A


title: TU-NK [chip2_1851035011_site_18]


title: TU-NK [chip2_1851035011_site_24]


title: Chickpea Flower 2


title: MS patient 5C


title: Chickpea Flower 3


title: MS patient 5A


title: Chickpea Flower bud 4

value: Flower bud


title: MS patient 5D


title: TU-NK [chip2_1851035011_site_16]


title: MS patient 5E


title: TU-NK [chip2_1851035011_site_17]


title: TU [chip2_1851035011_site_15]

value: Cancer cell


title: Chickpea Flower bud 3


title: MS patient 56E

value: male


title: TU-NK [chip2_1851035011_site_14]

value: Cancer-NK doublet


title: Chickpea Flower bud 1


title: MS patient 56D


title: Chickpea Flower 1


title: TU-NK [chip2_1851035011_site_13]


title: MS patient 56B2


title: MS patient 56B1


title: Adipose derived cells Day 3

value: White subcutaneous fat progenitor cell undergoing cardiac transition


title: MS patient 54B


title: MS patient 55A


title: MS patient 55E


title: MS patient 56A


title: MS patient 55D


title: MS patient 55B


title: NK [chip2_1851035011_site_12]

value: NK cell


title: NK [chip2_1851035011_site_11]


title: Chickpea SAM

source_name: Seedling

value: SAM


title: Chickpea Young leaf

value: Young leaf


title: Chickpea Mature leaf

value: Mature leaf


title: NK [chip2_1851035011_site_10]


title: Chickpea Flower bud 2


title: MS patient 51D

value: whole blood

value: 1-year group

value: female


title: Chickpea Shoot

value: Root


title: MS patient 54A

value: Baseline group


title: NK [chip2_1851035011_site_09]


title: MS patient 51B2

value: Early group


title: Chickpea Root


title: MS patient 53D


title: MS patient 53B


title: NK [chip2_1851035011_site_08]


title: MS patient 51B1


title: MS patient 53A


title: Chickpea Germinating Seedling

value: Germinating Seedling


title: MS patient 51A


title: MS patient 50B


title: Chickpea Endosperm

value: Endosperm


title: NK [chip2_1851035011_site_06]


title: MS patient 50A


title: Chickpea Bracteole

value: Bracteole


title: MS patient 4A


title: MS patient 49E

value: Long term group


title: Chickpea Embryo

value: Embryo


title: NK [chip2_1851035011_site_05]


title: MS patient 49D


title: TU-NK [chip2_1851035011_site_04]

value: Cancer-NK doublet


title: MS patient 4D


title: MS patient 4B


title: MS patient 49A


title: NK [chip2_1851035011_site_03]


title: NK [chip2_1851035011_site_02]


title: MS patient 48D


title: NK [chip2_1851035011_site_07]


title: Chickpea Seed Coat

value: Seed Coat


title: MS patient 47D


title: Chickpea Pedicel

value: Pedicel


title: MS patient 47B


title: MS patient 48A


title: MS patient 47E


title: MS patient 48B


title: MS patient 47C

value: Intermediate group


title: NK [chip1_1851035014_site_48]

value: NK cell


title: Chickpea Pod Shell

value: Pod Shell


title: NK [chip2_1851035011_site_01]


title: MS patient 47A

value: whole blood


title: MS patient 46E


title: Unknown [chip1_1851035014_site_47]

source_name: Unknown

value: Unknown


title: Chickpea Nodule

value: Nodule


title: Chickpea Root tip

value: Root


title: TU [chip1_1851035014_site_46]

value: Cancer cell


title: Chickpea Seed (10 dap)

value: Seed


title: MS patient 46D

value: 1-year group

value: female


title: Chickpea Root Hair

value: Root Hair


title: MS patient 45D


title: MS patient 46B

value: Early group


title: TU [chip1_1851035014_site_45]


title: MS patient 45C


title: MS patient 45B


title: Chickpea Seed (5 dap)


title: TU [chip1_1851035014_site_44]


title: Chickpea Gynoecium

value: Gynoecium


title: Chickpea Androecium

value: Androecium


title: TU [chip1_1851035014_site_43]


title: TU [chip1_1851035014_site_42]


title: MS patient 45A

value: Baseline group


title: MS patient 44D


title: MS patient 49C


title: MS patient 44C1


title: MS patient 44C2


title: MS patient 44B


title: Chickpea Sepal

value: Sepal


title: MS patient 44A


title: TU [chip1_1851035014_site_40]


title: NK [chip1_1851035014_site_41]


title: Chickpea Seed (20 dap)


title: Chickpea Seed (30 dap)


title: MS patient 42B2


title: MS patient 43A


title: KGN/MLT (10-9M) + 4P-PDOT (10-9M)

city: Québec

first: Asma

last: Arjoune

state: Québec

address: 3326,rue de la monnerie, Appertement 1

department: Animal sciences

country: Canada

institute: Laval University

data_processing:
Ensembl was used as the source of annotated genes and transcript isoforms. Trimming of adapters was performed using Trimmomatic; sequencing adapters were removed, and base calls with a quality score below 30 were removed from the end of the reads. Trimming was performed with the minimal length set at 32nt and these reads were kept for further processing. Pseudoalignment of all transcripts described in release 91 of ENSEMBL cdna gene annotation was accomplished by the kallisto tool, Differential expression of genes was then assessed using pairwise comparisons in EdgeR. Because of the lack of replicates, dispersion within EdgeR was evaluated by grouping samples for similar comparisons (first for control, then for melatonin (MLT) and FSK samples) and dropping the factor with the lowest impact, as suggested by the EdgeR manual
Assembly: Ensembl (release 91)
Supplementary files format and content: tab-delimited text files include log Fold change, p-value, adjsuted p-value for each Sample

source_name: KGN cells

growth_protocol: KGN cells were thawed on day 1, placed in a cell culture flask (25 cm3, Sigma-Aldrich) and sub-cultured on day 3. Confluence was never over 80%. On day 6, viable cells were placed in a 12-well dish at the density of 1.5x10^5 per well in 1.5 ml of medium and grown for 72 h.

extract_protocol:
Total RNA was isolated with AllPrep DNA/RNA Mini Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer’s instructions. Total RNA integrity and concentration were evaluated on a 2100-Bioanalyzer (Agilent Technologies, Palo Alto, CA)
The total RNA input used for sequencing was 270 ng for each treatment, a pool of 90 ng for each biological replicates. mRNA was isolated from total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module (E7490S; NEB). PolyA-selected mRNA was fragmented to a mean size of 200 nt, reverse transcribed to generate double-stranded cDNA, and converted to a paired-end library using NEBNext Ultra RNA Library Prep kit for Illumina (E7530S; NEB) according to the manufacturer’s instructions, using Agencourt AMPure XP beads and NEBNext Mutliplex Oligos for Illumina (set1, E7335S; NEB).

treatment_protocol: cells were cultured for 24 h in the presence of melatonin alone (10-7 M), melatonin alone (10-9M), melatonin (10-9 M) plus a MT1 specific agonist (NAS, 10-9 M), melatonin (10-9 M) plus a specific MT1 antagonist (S26131, 10-9 M), melatonin (10-9 M) plus a MT2 specific agonist (IIK7, 10-9 M), or melatonin (10-9 M) plus a specific MT2 antagonist (4P-PDOT, 10-9 M) for 24 h. The control consisted in the addition of ethanol at less than 0.05% of the final culture volume.

value: KGN cells

value: Granulosa cells

value: 1 nmol of melatonin L-1 + 1 nmol of 4P-PDOT L-1


title: MS patient 43B

value: whole blood


title: MS patient 42C

value: Intermediate group


title: MS patient 42B1


title: MS patient 42E

value: Long term group


title: TU [chip1_1851035014_site_37]

first: Smriti

address: Okhla Industrial Estate, Phase III, near Govind Puri Metro Station

institute: Indraprastha Institute of Information Technology,


title: TU [chip1_1851035014_site_39]


title: Chickpea Petal

value: Petal


title: KGN/MLT (10-9M) + S26131 (10-9M)

value: 1 nmol of melatonin L-1 + 1 nmol of S26131 L-1


title: MS patient 41D


title: TU-NK [chip1_1851035014_site_36]

value: Cancer-NK doublet


title: TAA+SDX3

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: liver

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

treatment_protocol: Mice were fed with TAA-containing water (400mg/L) for 12 weeks to induce liver fibrosis and then administered with Sulodexide or Vehicle daily while continuing to receive TAA-containing water for an additional 4 weeks.

value: liver

value: sulodexide-treated TAA


title: MS patient 41B

value: female


title: TU-NK [chip1_1851035014_site_34]

last: Chawla


title: MS patient 41A


title: KGN/MLT (10-9M) + NAC (10-9M)

value: 1 nmol of melatonin L-1 + 1 nmol of NAC L-1


title: TU-NK [chip1_1851035014_site_35]


title: MS patient 40B

value: Early group


title: MS patient 42D

value: 1-year group


title: MS patient 40D


title: MS patient 40C


title: TAA+SDX2


title: KGN/MLT (10-9M)

value: 1 nmol of melatonin L-1


title: MS patient 43D


title: MS patient 42A

value: Baseline group


title: TAA+SDX1


title: KGN/MLT (10-7M)

value: KGN cells

value: 1 umol of melatonin L-1


title: KGN/CTRL (no treatment)

value: Granulosa cells

value: no treatment


title: TAA3

value: vehicle-treated TAA


title: KGN/MLT (10-9M) + IIK7 (10-9M)

value: 1 nmol of melatonin L-1 + 1 nmol of IIK7 L-1


title: TU [chip1_1851035014_site_33]

value: Cancer cell


title: MS patient 40A

value: whole blood


title: TU-NK [chip1_1851035014_site_31]

value: Cancer-NK doublet


title: Unknown [chip1_1851035014_site_38]

value: Unknown


title: TAA1

value: liver


title: TAA2


title: MS patient 3D

value: female


title: MS patient 46A


title: TU-NK [chip1_1851035014_site_29]


title: NC3

value: control


title: MS patient 3B

value: Early group


title: Fadu_Fc 72h_4

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
trimming of adapter sequences using BBDUK k=13 ktrim=r useshortkmers=t mink=5 qtrim=r trimq=10 minlength=20
alignment of sequences using STAR against GRCh38.93 --runThreadN 8 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --readFilesCommand zcat --outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMattributes NH HI NM MD --outSAMtype BAM SortedByCoordinate --outFileNamePrefix
counting of reads at gene level using htseq -m intersection-nonempty -s yes -f bam -r pos using  Homo_sapiens.GRCh38.93.gtf
Assembly: hg38
Supplementary files format and content: raw gene counts for every gene and every sample

source_name: hypopharynx

growth_protocol: Kyse30 and FaDu (ATCC, Manassas, VA, USA) were passaged in DMEM or RPMI, 10% FCS, 1% penicillin/streptomycin, 5% CO2 atmosphere at 37°C. Treatment with EGF (PromoCell PromoKine, Heidelberg, Germany), EpEX-Fc (Pan et al. PMID: 30261040) were conducted under serum-free conditions for 6h and 72h.

extract_protocol:
total RNA was extracted from cell pellets using the Qiagen AllPrep DNA/RNA Micro Kit according to the kit manual.
RNA libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina kit following the manufacturer's instructions.

treatment_protocol: Treatements were all performed under serum-starvation conditions. Cells were plated in FCS-containing medium and were serum-starved 24h later for additional 24h before adding EGF or EpEX-Fc. EGF and EpEX-Fc treatment was performed for 6h and 72h before collecting samples.

value: Fadu

value: hypopharyngeal carcinoma

value: Fc


title: Fadu_EpEX 72h_4

value: EpEX


title: TU [chip1_1851035014_site_28]


title: NK [chip1_1851035014_site_27]

value: NK cell


title: MS patient 3A

value: Baseline group


title: Fadu_EGF 9nM 72h_4


title: MS patient 38D

value: 1-year group


title: MS patient 38B2


title: NC2


title: NC1


title: MS patient 38B1


title: Fadu_control 72h_4

value: Ctrl


title: Fadu_EGF_w_EpEX 72h_4


title: TU-NK [chip1_1851035014_site_32]


title: Fadu_EpEX 6h_4


title: TU [chip1_1851035014_site_30]


title: TU-NK [chip1_1851035014_site_26]


title: TU-NK [chip1_1851035014_site_25]


title: MS patient 38A


title: MS patient 37E

value: Long term group


title: Fadu_EGF 1_8nM 6h_4


title: Osteoclast mouse 3, infected, bio rep 2

city: Erlangen

first: Didier

last: Soulat

address: Wasserturm strasse 3/5

department: Institute of Clinical Microbiology, Immunology and Hygiene

institute: University Hospital of Erlangen and Friedrich-Alexander-University (FAU) Erlangen-Nürnberg

data_processing:
Data processing was performed by the Novogene company.
Sequence reads were trimmed for adaptor sequence/low-quality sequence
Trimmed sequence reads were mapped to the reference genome (mm10) using Hisat2 v2.0.5
Read count extraction and normalization were performed using Feature Counts v1.5.0-p3
Assembly: mm10
Supplementary files format and content: readcount_genename.xls files are Excel file presenting gene read counts of all samples as a matrix
Supplementary files format and content: infvsctrl_DEG_all.xls are Excel file presenting differentially expressed genes (DEG) of all samples as a matrix

source_name: osteoclasts

growth_protocol: Osteoclasts were differentiated from bone marrow progenitor cells in the presence of M-CSF and RANKL

extract_protocol:
Total RNA was extracted with RNA-Solv® Reagent (VWR).  5 μg RNA per sample was used as input material for the library preparation.
Library construction was performed by the Novogene company.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)

treatment_protocol: Cells were infected with L. infantum amastigotes at MOI=5 on day 2 of differentiation. RNA was prepared from mature osteoclasts 24 hpi.

value: osteoclasts

value: Infected with Leishmania infantum

tag: time

value: 24 hpi


title: Osteoclast mouse 3, infected, bio rep 1


title: Osteoclast mouse 2, infected, bio rep 1


title: TU-NK [chip1_1851035014_site_24]

city: New Delhi

value: Cancer-NK doublet


title: Osteoclast mouse 1, infected, bio rep 2


title: Fadu_EGF 9nM 6h_4


title: TU-NK [chip1_1851035014_site_23]


title: MS patient 37D

value: whole blood


title: Osteoclast mouse 1, infected, bio rep 1


title: Fadu_control 6h_4


title: TU-NK [chip1_1851035014_site_22]


title: NK [chip1_1851035014_site_21]


title: Fadu_Fc 6h_4


title: MS patient 37C

value: Intermediate group

value: female


title: Osteoclast mouse 3, not infected, bio rep 1

value: not infected


title: TU-NK [chip1_1851035014_site_20]


title: Fadu_EGF 1_8nM 72h_3

value: Fadu


title: Osteoclast mouse 3, not infected, bio rep 2


title: Fadu_EGF_w_EpEX 72h_3

value: hypopharyngeal carcinoma


title: MS patient 37B

value: Early group


title: TU-NK [chip1_1851035014_site_19]


title: Osteoclast mouse 2, not infected, bio rep 1


title: MS patient 37A


title: Fadu_Fc 72h_3

value: Fc


title: Osteoclast mouse 1, not infected, bio rep 2


title: MS patient 36D


title: TU [chip1_1851035014_site_18]

value: Cancer cell


title: MS patient 35E

value: male


title: TU [chip1_1851035014_site_16]


title: Osteoclast mouse 1, not infected, bio rep 1


title: MS patient 35B


title: Fadu_EGF 1_8nM 6h_3


title: TU-NK [chip1_1851035014_site_17]


title: TU-NK [chip1_1851035014_site_14]


title: MS patient 36A

value: Baseline group


title: Fadu_Fc 6h_3


title: Fadu_EGF 9nM 6h_3


title: TU-NK [chip1_1851035014_site_15]


title: TU-NK [chip1_1851035014_site_13]


title: Fadu_control 6h_3

value: Ctrl


title: NK [chip1_1851035014_site_12]

value: NK cell


title: MS patient 34E

value: Long term group


title: Fadu_control 0h_3


title: NK [chip1_1851035014_site_11]


title: MS patient 35A


title: Fadu_Fc 6h_2


title: NK [chip1_1851035014_site_10]


title: MS patient 34C2


title: MS patient 34C1


title: Fadu_EpEX 72h_2

value: EpEX


title: MS patient 33D

value: 1-year group


title: MS patient 34A


title: Unknown [chip1_1851035014_site_08]

value: Unknown


title: Fadu_EGF_w_EpEX 72h_2


title: MS patient 33B

value: whole blood


title: Fadu_EGF_w_EpEX 6h_2


title: MS patient 33A


title: NK [chip1_1851035014_site_07]


title: MS patient 32E


title: NK [chip1_1851035014_site_06]


title: NK [chip1_1851035014_site_09]


title: MS patient 32D


title: Fadu_EGF 9nM 72h_2


title: Fadu_EpEX 6h_2


title: NK [chip1_1851035014_site_05]


title: Fadu_EGF 9nM 6h_2


title: MS patient 34D


title: MS patient 32A


title: TU-NK [chip1_1851035014_site_04]

value: Cancer-NK doublet


title: MS patient 32B


title: Fadu_EGF 1_8nM 72h_2


title: NK [chip1_1851035014_site_03]


title: small RNA-seq for human iPS cells #1

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

data_processing:
Cutadapt (DOI:10.14806/ej.17.1.200) was used to remove the adapter sequences.
the retained reads of 24 to 35 bp in length (corresponding to small RNAs of 24 to 35 nucleotides, which is the range for typical piRNAs) were mapped to the respective reference genomes (hg38 or panTro5) by Hisat2 (Kim et al. 2019) allowing multiple hits.
Reads originated from TE regions in the repeatmasker track were counted and normalized as RPM.  If a read was mapped to multiple candidate regions, all regions were used for read counting, using a weighted number, 1/n, where n is the number of mapped regions.
Assembly: hg38/panTro5
Supplementary files format and content: tab-separated files with TE names and RPM values (total, sense hits, and antisense hits)

extract_protocol:
Total cellular RNAs were isolated from ~1×106 cells by using Isogen (TOYOBO) and Direct-ZolTM RNA (ZYMO RESEARCH) according to manufactures’ instructions.
After quality check by Agilent 2100 Bioanalyzer (Agilent Technologies), small RNA-seq libraries were prepared from approximately 0.5 μg of total RNA using NEBNext small RNA library kit (New England Biolabs).  After library amplification by PCR, products were run on 6% polyacrylamide gel electrophoresis, and a gel region corresponding to DNA sizes with 15 to 40 bp insertion were cut for DNA extraction.

value: iPS cells

value: female

tag: origin of_ipscs

value: nasal epithelial cells


title: MS patient 31D

tag: tissue


title: MS patient 31C

value: Intermediate group


title: NK [chip1_1851035014_site_02]

tag: cell type


title: Fadu_control 72h_2

value: Fadu

value: hypopharyngeal carcinoma


title: MSS_KD

city: Pittsburgh

first: Lin

last: Zhang

state: Pennsylvania

address: 5117 Centre Ave, Hillman Cancer Ctr Rm2.42a, 5117 Centre Ave

department: Pharmacology and Chemical Biology

institute: University of Pittsburgh

data_processing:
RNA-Seq and data analysis were performed by Novogene
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Data quality was ensured by the percentage of bases with a sequencing quality score above Q30.
Mapping was performed using hisat2 (2.0.5); quantification was analzyed by featureCounts (1.5.0-p3)
FPKM (fragments per kilobase of transcript per million mapped reads) of each gene was calculated based on the length of a gene and read counts mapped to this gene.
Differential expression analysis was performed using DESeq2 (1.20.0) and edgeR (3.22.5).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Cancer cells

growth_protocol: Parental HCT116 and CH3+5 HCT116 cells were growth in T75, plated at 20-30%, and left to grow 24 hours prior to transfection.

extract_protocol:
Parental HCT116 and CH3+5 HCT116 cells with transfection were collected, and RNA was harvested using Trizol.
RNA libraries were prepared for sequencing using the Illumina HiSeq platform.

treatment_protocol: Parental HCT116 and CH3+5 HCT116 cells were transfected with 0.2 μM control scrambled siRNA or siRNA against Werner helicase for 36 hours.

value: transfected with siRNA against Werner helicase


title: small RNA-seq for human iPS cells #2

value: dermal fibroblasts


title: MS patient 31B2

value: Early group

value: male


title: Fadu_control 6h_2

value: Ctrl


title: Fadu_Fc 72h_1

value: Fc


title: NK [chip1_1851035014_site_01]

value: NK cell


title: MS patient 31A

value: Baseline group


title: MSI

value: Parental HCT116

value: transfected with control scrambled siRNA


title: Fadu_Fc 6h_1


title: Fadu_EGF_w_EpEX 6h_1


title: Control

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

description:
10X Genomics 3' GEM Reagent Kit v3.1
1-E-ESCH1_S1

data_processing:
Base-calling was performed by Psomagen using Illumina software.
Fastq files were filtered, aligned with combined hg38 and mm10 reference index, and assigned to barcodes using 10X Genomics cellranger software v 4.0.0
Counts files (filtered_feature_bc_matrix.h5) were loaded into Seurat v 4.0.2 for sample merging, filtering, clustering and analysis of gene expression
Seurat clusters containing mouse glia (matching mm10 genome) were removed, leaving only human (matching hg38).
Genome_build: hg38
Supplementary_files_format_and_content: Output from combined Seurat data object with the GetAssay(slot="counts") command.  File is tab-delimited text file containing counts for sample-barcodes x genes.

source_name: Mixed inhibitory and excitatory neurons plated on primary mouse glia

growth_protocol: Excitatory (Ngn2) and inhibitory (Ascl1 and Dlx2) neurons were prepared by lentiviral induction of pluripotent stem cells and grown on mouse primary glia in Neurobasal medium. Cultures were harvested 6 weeks after induction.

extract_protocol:
For each cell line, two wells of a six well plate was plated with mixed cultures at 2x106 iNs and 2.5 x 105 glia/well.  On day 40, cells were dissociated with TrypLE (Thermo Fisher) for 5 min at 37°C, which preferentially releases neurons from glia. Cells were washed twice with 1X HBSS (Thermo Fisher), resuspended at 1200 cells/ml in 1% BSA/1X PBS and placed on ice.
Single-cell cDNA libraries were generated using the Chromium Next GEM Single Cell 3’ GEM Reagent Kits v3.1 (10X Genomics).  Approximately 2x104dissociated cells were loaded onto a cassette in the Chromium Controller with accompanying reagents to generate Gel Beads in Emulsions (GEMs). These were reverse transcribed to single-cell cDNA libraries before the oil emulsion was disrupted and cDNA purified using Dynabeads MyOne Silane (Thermo Fisher). cDNA was amplified by PCR for 11 cycles and purified using SPRIselect reagent (Beckman-Coulter).  cDNA fragmentation, A-tailing, and end repair was performed followed by adapter ligation for paired-end sequencing.  An additional 12 cycles of PCR were performed to incorporate the sample index sequences and to amplify the libraries before purification and sequencing.
scRNAseq

treatment_protocol: R451C mutations were generated from H1 hESC by CRISPR/Cas9 targeting.  Two isolates (A and B) were selected for this study.

tag: sample type

value: iPSC-derived neuron culture

tag: genotype

value: NLGN3 +/+


title: MSI_KD

tag: treatment

value: transfected with with siRNA against Werner helicase


title: NLGN3 R451C B

description:
10X Genomics 3' GEM Reagent Kit v3.1
3-RB-R451C-B_S3

value: NLGN3 R451C


title: MS patient 2B

value: whole blood

value: female


title: Fetal_Knee_6

city: Newcastle upon Tyne

first: Sarah

middle: J

last: Rice

state: Tyne and Wear

address: International Centre for Life, Central Parkway

country: United Kingdom

institute: Newcastle University

data_processing:
Pre-processing: Quality of FASTQ files was assessed with FastQC Version 11.8. Adapter sequences were removed using Trimmomatic Version 0.36. Paired-end reads were aligned to GRCh38 using Bowtie2 Version 2.3.4.2. Multi-mapped reads, duplicate reads, and reads aligning to the mitochondrial genome were removed using Picard Tools Version 2.2.4 and SAMtools Version 1.9. Peaks were called using MACS2 Version 2.1.1 and ENCODE blacklisted regions were removed from the peak calls using BEDTools Version 2.27.1.
Assembly: hg38
Supplementary files format and content: BigWig file of individual sample aligned to hg19

source_name: Cartilage

extract_protocol:
Fresh cartilage tissue from proximal (hip, n=6) and distal (knee, n=6) human fetal femurs at 12 post conception weeks, was dissected and provided by the HDBR. Adult articular cartilage was dissected from hip (n=5) and knee (n=5) joint arthroplasty obtained as described above. For chondrocyte isolation, the cartilage was digested in 1% collagenase solution (Sigma Aldrich) for 3h (fetal) or 16h (arthroplasty) at 37˚C. Cells were washed with 1xPBS, re-suspended in 5%FBS-DMEM and counted. Nuclei were isolated from 50,000 cells by 3min incubation on ice in lysis buffer (5M NaCl, 1M MgCl2, 1M Tris-HCl (pH 7.5), 10% w/v NP-40 (Roche), 10% w/v Tween 20 (Roche) and 1% w/v Digitonin (Promega). Isolated nuclei were re-suspended in a transposase mix (25μl 2xTD Buffer, 2.5μl TDE1 enzyme (Nextera Tn5 transposase, Illumina), 0.5μl 1% w/v Digitonin, 0.5μl 10% w/v Tween 20, 16.5μl 1xPBS and 5μl nuclease-free H2O) and incubated for 30min at 37˚C, 1000rpm.
DNA was purified using MinElute PCR Purification kit (Qiagen) according to manufacturer’s instructions and eluted in 10μl H2O. The purified DNA was partially amplified by PCR in a 50μl reaction using the NEB Next High-Fidelity PCR Master Mix (New England Biolabs, Hitchin, UK) and primer Ad1_noMX in combination with barcoded primers (Supplementary Material, Table S15). A 5μl aliquot of the reaction was amplified by qPCR and the remaining 45μl was amplified by PCR for an additional number of cycles, calculated for each sample based on the qPCR readings, to avoid amplification to saturation. The libraries were purified using AMPure XP magnetic beads (Beckman Coulter).

value: Cartilage

tag: tissue source

value: Knee

value: primary chondrocyte

value: WT

tag: disease state

value: control


title: Fetal_Knee_4


title: MS patient 2A

tag: age

tag: Sex


title: NLGN3 R451C A

description:
10X Genomics 3' GEM Reagent Kit v3.1
2-RA-R451CA_S2


title: MS patient 2D

value: 1-year group


title: Hut78-1uMRomidepsin72hrs-replicate4

city: TAmpa

first: Yonghong

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

data_processing:
Illumina BaseSpace software (bcl2fastq v2.20.0.422) used for basecalling.
Sequenced reads were trimmed for adaptor sequence with cutadapt (https://doi.org/10.14806/ej.17.1.200) (version 1.8.1), and mapped to hg19 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by htseq-count (version 0.6.1) using Gencodev30 transcript annotations for human
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene count for each sample

source_name: HuT78 (ATCC TIB-161) cell line

extract_protocol:
Cells were washed, trypsinized,follwed by total RNA was extraction using RNeasy Plus micro kit. Genomic DNA was removed by DNase treatment.
RNA libraries were prepared for sequencing using Ovation® Human FFPE RNA-Seq kit

tag: cell line

value: sezary syndrome

value: romidepsin


title: Fetal_Knee_5


title: Fadu_EGF 9nM 72h_1

value: Fadu

value: hypopharyngeal carcinoma


title: MS patient 29D

value: male


title: Hypoxia_NEN_2

type: genomic

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

description: genomic DNA from SK-N-BE(2) NEN under hypoxia replicate 2

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IInfinium Human MethylationEPIC BeadChip v1.0 B5 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using iScan™ System

data_processing: Standard Illumina Processing Protocol

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: SK-N-BE(2)l cells were maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), extra 1mM and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: DNA extraction was carried out with samples were extracted by using PureLink™ Genomic DNA Mini Kit (Gibco, K182001), according to the protocol provided by the supplier.

treatment_protocol: Neuroblastoma cell SK-N-BE(2) treated by 1µM NEN under normoxia and hypoxia (0.5%) for 24hrs

value: neuroblastoma


title: Hut78-DMSO72hrs-replicate4

value: DMSO


title: Hut78-DMSO72hrs-replicate1


title: Hypoxia_NEN_3

description: genomic DNA from SK-N-BE(2) NEN under hypoxia replicate 3


title: Hut78-1uMRomidepsin72hrs-replicate3


title: MS patient 31B1

value: Early group


title: Hypoxia_CTRL_2

description: genomic DNA from SK-N-BE(2) control under hypoxia replicate 2


title: Fetal_Knee_3


title: Hypoxia_CTRL_3

description: genomic DNA from SK-N-BE(2) control under hypoxia replicate 3


title: Fadu_EGF 1_8nM 72h_1


title: Fadu_EGF 9nM 6h_1


title: Fetal_Knee_1


title: Fetal_Knee_2


title: Fadu_control 72h_1

value: Ctrl


title: Normoxia_NEN_1

description: genomic DNA from SK-N-BE(2) NEN under normoxia replicate 1


title: Fetal_Hip_6

value: Hip


title: Hut78-1uMRomidepsin72hrs-replicate2


title: Hypoxia_NEN_1

description: genomic DNA from SK-N-BE(2) NEN under hypoxia replicate 1


title: MS patient 29A

value: whole blood

value: Baseline group


title: Fadu_EGF 1_8nM 6h_1


title: Normoxia_NEN_2

description: genomic DNA from SK-N-BE(2) NEN under normoxia replicate 2


title: Normoxia_NEN_3

description: genomic DNA from SK-N-BE(2) NEN under normoxia replicate 3


title: Hut78-1uMRomidepsin72hrs-replicate1


title: MS patient 29C

value: Intermediate group


title: Fadu_control 6h_1


title: Hypoxia_CTRL_1

description: genomic DNA from SK-N-BE(2) control under hypoxia replicate 1


title: MS patient 28D

value: female


title: Fetal_Hip_5

value: Cartilage

value: primary chondrocyte

value: WT


title: Fadu_control 0h_1


title: Hut78-10nMF5446-72hrs-replicate4

value: sezary syndrome


title: MSS

value: transfected with control scrambled siRNA


title: Fetal_Hip_4

value: control


title: Normoxia_CTRL_2

description: genomic DNA from SK-N-BE(2) control under normoxia replicate 2


title: Hut78-10nMF5446-72hrs-replicate2


title: Fetal_Hip_3


title: Kyse_EpEX 72h_4

source_name: esophagus

value: Kyse

value: esophageal squamous cell carcinoma

value: EpEX


title: Kyse_EGF 1_8nM 72h_4


title: Hut78-10nMChaetocin72hrs-replicate4

value: Chaetocin


title: Kyse_EGF 9nM 72h_4


title: Fetal_Hip_2


title: Fadu_EpEX 72h_1

value: Fadu

value: hypopharyngeal carcinoma


title: Hut78-10nMChaetocin72hrs-replicate3


title: Normoxia_CTRL_3

description: genomic DNA from SK-N-BE(2) control under normoxia replicate 3

value: neuroblastoma


title: MS patient 28B2

value: whole blood

value: Early group


title: MS patient 28B1


title: MS patient 27E

value: Long term group

value: male


title: MS patient 28A

value: Baseline group

value: female


title: OA_Knee_4

value: Cartilage

value: Knee

value: primary chondrocyte

value: WT

value: OA


title: MS patient 27D

value: 1-year group


title: Normoxia_CTRL_1

description: genomic DNA from SK-N-BE(2) control under normoxia replicate 1


title: Hut78-10nMChaetocin72hrs-replicate2

value: sezary syndrome


title: MS patient 27A


title: Hut78-10nMF5446-72hrs-replicate3


title: Fetal_Hip_1

value: Hip

value: control


title: OA_Knee_5


title: Kyse_EGF 1_8nM 6h_4

value: Kyse

value: esophageal squamous cell carcinoma


title: RAJI-input

data_processing:
Sequencing adaptors and low-quality bases were trimmed off from the raw sequencing reads using cutadapt
Processed reads were aligned to human reference genome GRCh38 using Bowtie2 and further filtered to remove discordant read pairs and reads with low alignment scores.
Strand cross-correlation (SCC) analysis and calculation of NSC (normalized strand coefficient) and RSC (relative strand coefficient) values were performed using phantompeakqualtools.
Narrow peaks were called by MACS2  for histone marker H3K27ac with a minimal cutoff at narrow peak q-value (nq) <0.05. Broad peaks were called by MACAS2 for histone markers H3K27m3 and H2K9m3 with a minimal cutoff at nq<0.05 and broad peak q-value (bp) <0.05.
Genome_build: hg19
Supplementary_files_format_and_content: peak bed files
Supplementary_files_format_and_content: Bigwig files were generated using deeptools bamCoverage function with  parameter --normalizeUsing RPGC

source_name: RAJI (ATCC CCL-86) cell line

growth_protocol: HuT78 and K562 were grown in IMDM 10% FBS and Penicillin/Streptomycin. Jurkat and RAJI were grown in RPMI 10% FBS with Penicillin/Streptomycin.

extract_protocol:
DNA was purified using QiAquick PCR Purification Kit (28106) after immunoprecipitation
Ten nanograms of immunoprecipitated DNA was fragmented to 300 base pairs using a Covaris M220 Focused-ultrasonicator (Covaris, Inc., Woburn, MA) and then used to generate sequencing libraries using the Kapa HyperPrep Kit (Roche Sequencing and Life Science, Wilmington, MA). The size and quality of the library was evaluated using the Agilent BioAnalyzer, and the library was quantitated with the Kapa Library Quantification Kit. Each enriched DNA library was then sequenced on an Illumina NextSeq 500 sequencer to generate 50 million 75-base paired-end reads

value: RAJI

value: Burkitt's lymphoma

tag: chip antibody

value: untreated


title: MS patient 26E

value: whole blood

value: Long term group

value: male


title: Hut78-10nMChaetocin72hrs-replicate1

value: Chaetocin


title: Kyse_EGF 9nM 6h_4


title: OA_Knee_3

value: Cartilage

value: Knee


title: Kyse_Fc 6h_4

value: Fc


title: MS patient 26D


title: Kyse_control 6h_4

value: Ctrl


title: RAJI-H3K9m3

value: H3K9me3 (Abcam; rabbit clone# ab8898)


title: OA_Knee_1

value: primary chondrocyte

value: WT

value: OA


title: RAJI-H3K27m3

value: Anti-H3K27Me3 (Cell Signaling; rabbit clone# C36B11)


title: MS patient 25E

value: female


title: Kyse_EGF_w_EpEX 72h_3

value: Kyse

value: esophageal squamous cell carcinoma


title: RAJI-H3K27ac

value: RAJI

value: Burkitt's lymphoma

value: H3K27ac (Abcam; rabbit clone# ab4729),

value: untreated


title: OA_Knee_2


title: Kyse_control 0h_4


title: K562-input

source_name: K562 (ATCC CCL-243) cell line

value: chronic myelogenous


title: OA_Hip_4

value: Cartilage

value: Hip


title: K562-H3K9m3


title: MS patient 25D

value: whole blood

value: 1-year group


title: MS patient 25B

value: Early group


title: MS patient 25A

value: Baseline group


title: MS patient 26A

value: male


title: OA_Hip_3

value: primary chondrocyte

value: WT

value: OA


title: K562-H3K27m3

value: Anti-H3K27Me3 (Cell Signaling; rabbit clone# C36B11)


title: OA_Hip_2


title: Kyse_EGF 9nM 72h_3

value: Kyse

value: esophageal squamous cell carcinoma


title: K562-H3K27ac


title: MS patient 24E

value: Long term group

value: female


title: MS patient 24D


title: OA_Hip_1


title: OA_Hip_5


title: Kyse_Fc 72h_3

value: Fc


title: Jurkat-input

source_name: Jurkat E6 (ATCC TIB-152) cell line

value: Jurkat

value: acute T cell leukemia

value: untreated


title: MS patient 24C

value: whole blood

value: Intermediate group


title: SK-N-BE(2) cell, NEN, 24h, Replicate3

data_processing:
kallisto
slueth
Supplementary files format and content: Hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow

extract_protocol:
The total RNA from treatment groups (Ctrl and NEN treated, n = 3) were extracted using Trizol reagent (#15596026) according to the manufacturer’s instructions
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA

treatment_protocol: Proper number of cells were plate in 10cm dishes before  treatment by DMSO or 1µM NEN for 24h.  Each group contain 3 biological replicates.

value: bone marrow

value: neuroblastoma cell

value: NEN


title: Kyse_EGF_w_EpEX 6h_3


title: Kyse_EpEX 6h_3

value: EpEX


title: Kyse_EGF 1_8nM 72h_3


title: Jurkat-H3K9m3

value: H3K9me3 (Abcam; rabbit clone# ab8898)


title: Jurkat-H3K27m3


title: SK-N-BE(2) cell, NEN, 24h, Replicate1


title: Jurkat-H3K27ac

value: H3K27ac (Abcam; rabbit clone# ab4729),


title: SK-N-BE(2) cell, NEN, 24h, Replicate2


title: MS patient 24B

source_name: PAXgene Blood miRNA

value: Early group


title: Kyse_control 72h_3

value: Kyse

value: Ctrl


title: Hut78-input

value: sezary syndrome


title: Kyse_EGF 9nM 6h_3

value: esophageal squamous cell carcinoma


title: SK-N-BE(2) cell, CTRL, 24h, Replicate2

value: DMSO


title: MS patient 23E

value: Long term group

value: female


title: Hut78-H3K9m3

value: untreated


title: Kyse_Fc 6h_3

value: Fc


title: MS patient 23C

value: whole blood

value: Intermediate group


title: MS patient 23A

value: Baseline group


title: MS patient 22E

value: male


title: Hut78-H3K27m3

value: Anti-H3K27Me3 (Cell Signaling; rabbit clone# C36B11)


title: Hut78-H3K27ac


title: P2-42-32-A3

city: Guangzhou

first: Gong

address: 601,Huangpu Avenue West,Tianhe District

department: College of Life Science and Technology

institute: Jinan University

data_processing:
Sequenced reads were trimmed for adaptor sequence by cutadapt, low-complexity or low-quality sequence were discard.
mapped to reference using fanse3 with parameters -E5% --indel -S14
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated in . 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.
Genome_build: hg19 mRNA from UCSC

source_name: Tumor

extract_protocol:
Tissues were flash frozen on dry ice. RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the library construction for sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: lung

tag: t stage

tag: n stage

tag: m stage

tag: tumor stage

value: IB

tag: smoking

value: lung adenocarcinoma


title: Kyse_control 6h_3

value: Kyse

tag: tissue

tag: timepoint


title: Kyse_control 0h_3

value: Ctrl


title: MS patient 24A


title: MS patient 22D

value: 1-year group


title: P2-42-32-A6

source_name: Adjacent normal


title: P2-42-31-K5


title: P2-42-31-K4

value: IIIa


title: Antibody-5

city: Hangzhou

first: Jianing

last: Chen

address: Qingchun Road 79#

institute: Zhejiang university

description:
otu_table.relative for antibody.xls
reletive abundance of OTUs

library_source: other

data_processing:
library strategy: 16S rDNA seq
Sequencing libraries were prepared and the library quality was evaluated
the library was sequenced and the paired-end reads were generated
The gene sequence data were processed with default parameters
Sequences with ≥97% similarity were assigned to the same operational taxonomic units
The representative sequence for each OTU was screened for further annotation. The output data was further analyzed using Statistical Analysis
Assembly: Not applicatable
Supplementary files format and content: Matrix table with relative abundance for every gene and every sample
Supplementary files format and content: RELATIVE-genome.xls: reletive abundance in kingdom, class, family, genus and species
Supplementary files format and content: otu-FMT.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for in vivo.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative. in vitro.xls: reletive abundance of OTUs
Supplementary files format and content: otu_table.relative for antibody.xls: reletive abundance of OTUs
Supplementary files format and content: gene.description-TRANS.xls: gene information of transcriptome

molecule: other

source_name: Intestine

extract_protocol:
Total genome DNA from murine luminal samples from ileocecus was extracted for amplification
Sequencing libraries were prepared and the library quality was evaluated
DNA V3-V4 region or genome

value: Intestine

tag: cell type

value: bacteria

value: wild type

value: high fat

tag: molecule type

value: rDNA


title: SK-N-BE(2) cell, CTRL, 24h, Replicate3

value: bone marrow

value: neuroblastoma cell

tag: treatment

value: DMSO

tag: time


title: MS patient 22B2

data_processing: Data from the Microarray Scanner C was extracted using Agilent Feature Extraction Software v. 12.03.1 (Agilent Technologies) and a Quality Control report for each microarray slide was provided after the data extraction

extract_protocol: 210 full blood samples were collected in PAXgene tubes during the TREMEND (Tecfidera in Relapsing-Remitting Multiple Sclerosis: Endothelial Dysfunction) phase IV clinical trial from 52 RRMS patients and 22 controls from March 2014 to August 2016 and kept in 80oC. In 2020, the microRNA was extracted with Blood miRNA Kit from Qiagen. Quality and quantity assessment of extracted RNA on NanoDrop 2000c spectrophotometer (ThermoFischer) and 2100 bioanalyzer (Agilent).

value: whole blood

value: Intermediate group

value: male


title: Kyse_EGF 1_8nM 6h_3

value: esophageal squamous cell carcinoma


title: Kyse_EGF_w_EpEX 72h_2


title: Antibody-4

tag: genotype


title: Kyse_EpEX 72h_2

value: EpEX


title: MS patient 22B1

value: Early group

tag: age


title: P2-42-31-H7

value: lung

tag: disease state

value: lung adenocarcinoma


title: Antibody-3


title: MS patient 22A

value: Baseline group

tag: Sex


title: SK-N-BE(2) cell, CTRL, 24h, Replicate1

tag: cell line


title: P2-42-31-H6

tag: gender

value: IB


title: Kyse_EGF 1_8nM 72h_2

value: Kyse


title: Antibody-2

value: Intestine

value: bacteria

value: wild type


title: P2-42-31-E7

tag: t stage


title: Antibody-1

value: high fat

value: rDNA


title: MS patient 21E

value: Long term group

value: female


title: Kyse_control 72h_2

value: Ctrl


title: P2-42-31-E10

value: male


title: P2-42-31-E1


title: MS patient 21D

value: whole blood

value: 1-year group


title: Kyse_EGF_w_EpEX 6h_2

value: esophageal squamous cell carcinoma


title: GATA3KO_EBL_rep2

first: Kun

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Reads were trimmed by Trimmomatic to remove the bases with low quality and adapter sequences
The trimmed reads were align to ARS-UCD1.2  by Hisat2
The raw reads counts of all expressed genes were quatified by FeatureCounts
The abundance of all expressed genes were normalized  by DESeq2
Differentially expressed genes were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >2 or <0.5
Assembly: ARS-UCD1.2
Supplementary files format and content: text files include normalized counts calculated by DESeq2 for each sample

organism: Bos taurus

source_name: embryo

extract_protocol:
Polyadenylated RNAs were captured and reverse transcribed with an Oligo(dT) primer
The RNA-seq libraries were constructed according to a Smart-seq2 procedures. Briefly, mRNA was fragmented and reverse transcribed. The cDNA library was subject to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.

tag: developmental stage

value: early blastocyst

value: 7.0 day after fertilization

value: embryos were injected with BE3 mRNA and GATA3 sgRNAs mix at zygote stage


title: GATA3KO_EBL_rep3


title: MS patient 21C

value: Intermediate group


title: P2-42-31-D8

value: lung

tag: n stage

tag: m stage

value: I

value: lung adenocarcinoma


title: Kyse_EGF 1_8nM 6h_2

value: Kyse


title: GATA3KO_EBL_rep1


title: MS patient 21A

value: Baseline group


title: Kyse_EGF_w_EpEX 72h_1


title: GATA3KO_EBL_rep4


title: P2-41-33-D7

tag: tumor stage

tag: smoking


title: MS patient 20E

tag: tissue

tag: timepoint


title: MS patient 21B

value: Early group


title: CDX2KO_EBL_rep4

value: embryos were injected with BE3 mRNA and CDX2 sgRNAs mix at zygote stage


title: MS patient 20D

value: female


title: Kyse_Fc 72h_2

value: Fc


title: P2-41-33-D10


title: CDX2KO_EBL_rep2


title: P2-41-33-C8

value: male

value: IIB


title: CDX2KO_EBL_rep3


title: P2-41-33-D1


title: Kyse_EpEX 72h_1

value: EpEX


title: CDX2KO_EBL_rep1


title: MS patient 20B

value: whole blood


title: NC_EBL_rep3 (control)

value: early blastocyst

value: embryos were injected with BE3 mRNA at zygote stage


title: P2-41-33-C2


title: Kyse_EGF 9nM 72h_1

value: esophageal squamous cell carcinoma


title: Kyse_control 72h_1

value: Ctrl


title: Kyse_EGF 9nM 6h_2


title: NC_EBL_rep2 (control)

value: 7.0 day after fertilization


title: Kyse_EpEX 6h_1


title: MS patient 20A


title: P2-41-32-K4

value: lung


title: NC_EBL_rep1 (control)


title: P2-41-32-K1

value: lung adenocarcinoma


title: MS patient 1D

value: 1-year group


title: P2-41-33-B9

value: IIIa


title: Kyse_EGF 1_8nM 72h_1

value: Kyse


title: Kyse_EGF_w_EpEX 6h_1


title: MS patient 1B

value: Early group


title: MS patient 1C

value: Intermediate group

value: female


title: zf 7dpf gneKO biol rep 3

city: Jerusalem

first: Stella

last: Mitrani-Rosenbaum

address: Ein Karem

country: Israel

institute: Hadassah -The Hebrew University Medical Center

data_processing:
NextSeq basecall files were converted to fastq using the bcl2fastq program with default parameters .   Quality-trimming was done using in-house Perl scripts, with a quality threshold of 32. In short, the scripts use a sliding window of 5 bases from the read's end and trim one base at a time until the average quality of the window passes the given threshold. Poly-G, adapter sequences, and poly-T were removed with cutadapt (v1.18), using a minimal overlap of 1 (-O parameter), allowing for read wildcards, and filtering out reads that became shorter than 15 nt (-m parameter). Filtering the remaining reads was done with the fastq_quality_filter (v0.0.14) program, with a quality threshold of 20 at 90 percent or more of the read's positions.
The processed fastq files were aligned to the zebrafish transcriptome and genome using TopHat (v2.1.1). The genome version was GRCz11, with annotations from Ensembl release 95. Alignment allowed up to 6 mismatches per read, a maximum gap of 5 bases, and a total edit distance of 11.
Quantification was done using htseq-count (v0.6.0). Strand information was set to 'reverse', and an annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
Normalization and differential expression analysis were done in R with the DESeq2 (v1.22.1) package. Genes with a sum of counts less than 20 over all samples were filtered out. Significance threshold was taken as padj < 0.1 .
Assembly: GRCz11
Supplementary files format and content: An excel file with raw counts, normalized counts and differential expression results. 'raw.' columns are raw counts, 'norm.' columns are the values after DESeq2 normalization. 'baseMean, log2FoldChange, lfcSE, stat, pvalue, padj' are corresponding result of DESeq2 analysis. 'sig' indicates significance according to threshold (padj<0.1).
Supplementary files format and content: Missing values are denoted by '?'.  A value can be missing because it did not appear in the annotation file used for quantification of reads, or because it was filtered by DESeq2.

organism: Danio rerio

source_name: whole embryo

extract_protocol:
Total RNA samples were extracted either from a pool of > 10 embryos/larvae
Library preparation was done using KAPA Stranded mRNA Sequencing Kit

value: whole embryo

value: KO


title: P2-41-32-J2


title: P2-41-32-J5


title: MS patient 1A

first: Atul

address: Ole Maaløes Vej 5, building 2, 3 floor

institute: Rigshospitalet

value: Baseline group


title: zf 7dpf gneKO biol rep 2


title: MS patient 19D

value: whole blood

value: male


title: zf 7dpf gneKO biol rep 1


title: MS patient 19E

value: Long term group


title: Kyse_Fc 72h_1

value: esophageal squamous cell carcinoma

value: Fc


title: P2-41-32-J1


title: Kyse_Fc 6h_1


title: zf 7dpf gnehet biol rep 3

value: HT


title: Kyse_EGF 9nM 6h_1


title: Kyse_EGF 1_8nM 6h_1


title: MS patient 19B


title: P2-41-32-B2

value: lung


title: Kyse_control 6h_1

value: Ctrl


title: Kyse_control 0h_1


title: P2-41-32-H8

description: breast cancer lung metastasis

value: lung adenocarcinoma


title: MS patient 19A


title: P2-41-32-A10

value: Tis


title: DH16044_3

first: Enrique

last: Vazquez de Luis

address: Melchor Fernandez Almagro, 3

institute: CNIC

data_processing:
Illumina Casava software used for basecalling and bcl2fastq for demultiplexing.
Sequenced reads quality was evaluated from FastQC.
Reads were trimmed for Illumina adaptors with cutadapt.
Reference Genome was indexed from RSem (Li B et al. 2011) and sequence reads were aligned using RSem.
RNA-Seq data were normalized using Transcripts Per Million (TPM) Trimmed Mean of M values (Robinson MD and A Oshlack 2010).
Assembly: Human sequenced genome GRCh38 v91
Supplementary files format and content: Tab-delimited text files include raw, TPM and RPKM (Reads Per Kilobase Million) values for each sample.

source_name: Blood

extract_protocol:
Total RNA was isolated using RNeasy Micro Kit (Qiagen) and was quantified and purity checked using a NanoDrop ND-1000 (Thermo Scientific, Waltham, MA, USA). RNA integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
Low Input RNAs were used to amplify the cDNA using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara). 1 ng of amplified cDNA was used to generate barcoded libraries using the Nextera XT DNA library preparation kit (Illumina). Libraries were quantified using a Qubit™ dsDNA HS assay with the Qubit fluorometer (Life Technologies, Carlsbad, California). Average library size and the size distribution were determined using a DNA 1000 assay in an Agilent 2100 Bioanalyzer. Libraries were normalized to 10nM using Tris-Cl 10mM, pH8.5 with 0.1% Tween 20.
Libraries were applied to an Illumina flow cell for cluster generation (SR Cluster Kit cBot) and sequence-by-synthesis single reads of 49 or 60 base length using the SBS Kit (Illumina) were generated on the HiSeq 2500 or the HiSeq 4000 following the standard sequencing protocol. Reads were further processed using the bcl2fastq package (Illumina) to split reads according to adapter indexes and produce fastq files. RNA-Seq was performed at the Genomics Unit of the Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid.

value: Blood

tag: time point

tag: library type

value: Low Input

tag: cell type

value: NK cells


title: MS patient 18D

value: 1-year group

value: female


title: MS patient 18C

value: Intermediate group


title: zf 7dpf gnehet biol rep 1

value: whole embryo

tag: genotype


title: P2-41-31-G5

tag: age


title: DH16044_1