title: HCT116 cells, shSMC4_2，CUT_Tag_H4K12la

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

data_processing:
Sequencing data were analyzed as follows. After trimming the adapters of reads and removing low-quality bases by Trim_Galore software in paired-end mode, clean reads were mapped to hg38 reference genome with Bowtie2 followed by removing PCR duplicates using Picard. The genome browser tracks in bigwig format were produced from merged replicates using samtools and peaks were called using MACS2 using parameters ‘-f BAMPE --broad -nomodel’. The bigwig data were visualized using the IGV software (Broad Institute).
Assembly: hg38
Library strategy: CUT&TAG

extract_protocol:
Magnetic beads purification
CUT&Tag libraries were generated following manufacturer’s protocol (Vazyme, TD903-01).

value: Colorectal cancer cell line

tag: antibody


title: OCI-Ly1, STAT6 N421K, 20min IL4, wash, 2h wait, biol rep 3

status: Public on Jul 17 2022

type: SRA

city: Munich

first: Michael

last: Mentz

state: Bavaria

address: Marchioninistrasse 15

department: 1Department of Internal Medicine III

country: Germany

institute: Ludwig-Maximilians University of Munich

library_source: transcriptomic

data_processing:
Raw sequence data was processed following the Drop-seq data pipeline as previously described (https://doi.org/10.1016/j.cell.2015.05.002)
Assembly: hg38, Ensemble release 84
Supplementary files format and content: Tab-delimited text file includes a gene expression matrix with UMI counts for 31835 unique ENSG IDs in 54 samples.

molecule: total RNA

organism: Homo sapiens

growth_protocol: OCI-Ly1 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Plus (Zymo Research, Irvine, California, USA) according to manufacturer's protocol.
RNA libraries for RNA-seq were prepared using the prime-seq protocol as previously described (dx.doi.org/10.17504/protocols.io.81wgb1pw3vpk/v2)

treatment_protocol: 1.0 x 10^6 viable cells were seeded in 1 ml growth medium. Cells were treated with IL-4 (10 ng/ml) for 20 min at 37C. After one wash in preheated PBS, cells were replated and incubated at 37C for 2 h, 4 h, and 8 h, respectively. After incubation, 10 µl cell suspension (or 10,000 cells) were transferred to a 96-well PCR tray, mixed with 100 µl Qiagen RLT buffer, and frozen at -80C.

tag: cell line

tag: cell type

value: B-NHL cell line carrying t(14;18)(q32;q21)

tag: genotype

value: STAT6 N421K

tag: treatment

value: 20min IL4, wash, 2h wait


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 2

value: STAT6 wild-type


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 9


title: OVA+DCs  3 weeks (s007)

city: Lyon

first: Marc

last: Vocanson

address: 21 avenue Tony Garnier

country: France

institute: CIRI - INSERM U1111

data_processing:
Data were demultiplexed, and transcript counts were adjusted to the expected number of molecules based on counts, 4096 possible UMI’s and Poissonian counting statistics as described in Grün et al. (Grün D, Nat. Methods, 2014)
The data was mapped with STAR 2.7.3a against the Human genome Hg38
After removing wells which include transcripts mapping to external ERCC, cells with less than 1300 UMIs/transcripts per cell, and keeping the top2000 highly variable genes, 1642 cells were left for further analysis.  (Seurat v3.2.2)
The top 2000 variable genes were selected with the VST method.
the first 11 PCA dimensions were selected to construct a k nearest neighbor graph (k=11 neighbors). Graph-based clustering (Louvain) with a resolution parameter of 0,8
Differential expression analyses between clusters or subsets of interest were performed using the Wilcoxon ranksum test using raw transcript counts and applying a threshold of 0.25 for log fold change and 0.05 for the adjusted P value.
Genome_build: Hg38
Supplementary_files_format_and_content: Count table with raw gene counts for every gene per single cell

molecule: polyA RNA

organism: Mus musculus

source_name: draining lymph node

extract_protocol:
Single-cell mRNA sequencing was performed according to a Robot-assisted Transcriptome SEQuencing (SORT-seq) protocol. Briefly, OVA+/- DC subsets were single-cell FACS sorted into 384-well hard shell plates (Biorad), with 5 µl of vapor-lock (Qiagen,) containing 100 nL of RT primers, dNTPs and synthetic mRNA Spike-Ins. After sorting, plates were snap-frozen on dry ice and stored at −80°C. Plates were designed to contain cells from different DC subsets. Further processing of cells, cDNA library generation, sequencing, and reads alignment were performed at Single Cell Discoveries (Utrecht, The Netherlands).
For amplification, cells were heat-lysed at 65° C followed by cDNA synthesis using steps based on the CEL-Seq2 protocol (Hashimshony et al. 2016) performed by robotic liquid handling platforms. After second strand cDNA synthesis, the barcoded material was pooled into libraries of 384 cells and amplified using IVT. Following amplification, library preparation was done according to the CEL-seq2 protocol to generate amplified cDNA libraries, which were barcoded using TruSeq small RNA primers (Illumina). The DNA library was paired-end sequenced on an Illumina Nextseq™ 500, high output, with a 1x75 bp Illumina kit (R1: 26 cycles, index read: 6 cycles, R2: 60 cycles)
UMI-based 3'scRNA-seq using CEL-seq2

treatment_protocol: Cells isolated from dLN were depleted of CD3+ and CD19+ cells using magnetics microbeads (Miltenyi Biotec, Paris, France). Live CD64- OVA+/- migratory DCs (MHC-IIhighCD11c+), migLCs (SIRPα+XCR1-Epcam+), migcDC2s (SIRPα+XCR1-Epcamlow), migcDC1 (SIRPα-XCR1+) were then sorted using FACS Aria II machine (Becton Dickinson).

tag: time

value: mixed sample (representing LC, cDC2, cDC1)


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 4h wait, biol rep 4

value: 20min IL4, wash, 4h wait


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 2h wait, biol rep 2

value: STAT6 D419N


title: OVA+DCs  8 weeks (s008)


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 2h wait, biol rep 1


title: HCT116 cells, shControl_2，CUT_Tag_H4K12la

country: China

library_source: genomic

molecule: genomic DNA

value: shControl


title: HCT116 cells, shSMC4_1，CUT_Tag_H4K12la


title: OCI-Ly1, STAT6 D419G, 20min IL4, wash, 2h wait, biol rep 3

value: STAT6 D419G


title: OCI-Ly1, STAT6 wild-type, 20min IL4, wash, 2h wait, biol rep 1


title: HCT116 cells, shSMC4，ATAC_seq

data_processing:
After trimming the adapters of reads and removing low-quality bases by Trim_Galore software in paired-end mode, clean reads were mapped to hg38 reference genome with Bowtie2 followed by removing PCR duplicates using Picard. The genome browser tracks in bigwig format were produced from merged replicates using samtools and peaks were called using MACS2 using parameters ‘-f BAMPE --nomodel --shift -100 --extsize 200 -nomodel’.
Assembly: hg38

extract_protocol:
Magnetic beads purification
ATAC-SEQ libraries were generated following manufacturer’s protocol (NOVOPROTEIN, N248).


title: WT-DMSO-Rep2

city: Iowa City

first: David

last: Price

state: IA

address: 500 Newton Road, 260 EMRB

department: Biochemistry

country: USA

institute: University of Iowa

data_processing:
Library strategy: PRO-Seq
Adapter trimming using trim_galore 0.6.
Alignment of trimmed reads to hg38 using bowtie 1.2.3 (PRO-Seq).
Deduplication of fragments based on their unique molecular index tags using the dedup program.
Conversion of deduped bed files into bedGraph and bigwig using bedtools genomecov and kentUtils bedGraphToBigWig programs.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing pileup of normalized PRO-Seq data.

source_name: HAP1 cells

growth_protocol: HAP1 cells were maintained in IMDM (Gibco 12440-053) supplemented with 10% FBS.

extract_protocol:
Rapid nuclei isolation steps for PRO-Seq were performed as previously described (Nilson et. al. 2017; Ball et. al. 2019).
Details of library construction for each type of assay are provided in the methods.

treatment_protocol: GTF-FKBP12-tagged HAP1 cells in a T-150 flask were treated with 400 nM dTAGV-1 or DMSO vehicle control for 2 h prior to harvesting nuclei for PRO-Seq.

value: 2 h DMSO


title: WT-dTAGV-1-Rep1

value: 2 h 400 nM dTAGV-1


title: HCT116 cells, shControl_1，CUT_Tag_H4K12la


title: OVA+DCs  1 week (s006)


title: TBP-FKBP12-DMSO-Rep1


title: OVA+DCs  1 week (s003)


title: OVA+DCs  3 weeks (s004)


title: E14.5_WT_7.2

city: Stanford

first: Devin

middle: Aalpoel

last: King

state: CA

address: 371 Serra Mall

department: Biology

institute: Stanford University

data_processing:
Alignment to GRCm38 using STAR v2.5.3a
Summarization of aligned reads into raw counts with Rsubread::featureCounts() function
Read count normalization using DESeq2::DESeq() function
Differential expression testing using DESeq2
Note, annotation file used is gencode.vM6.primary_assembly.annotation.gtf
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text file with raw counts per sample

source_name: Mouse embryonic whole hearts

growth_protocol: Standard M. musculus protocols

extract_protocol:
Whole heart mRNA extraction and purification
NEBNext Ultra RNA Library Prep Kit

treatment_protocol: Endothelial (Tie2) Ino80 disruption

tag: tissue

value: heart

tag: time point

tag: litter

value: WT


title: OCI-Ly1, STAT6 D419N, 20min IL4, wash, 2h wait, biol rep 3


title: TBP-FKBP12-DMSO-Rep2


title: OVA+DCs  8 weeks (s005)


title: HCT116 cells, shControl，ATAC_seq


title: TBP-FKBP12-dTAGV-1-Rep2


title: E14.5_Tie2_KO_1

value: KO


title: XPB-FKBP12-DMSO-Rep1


title: XPB-FKBP12-dTAGV-1-Rep2


title: E14.5_WT_7


title: XPB-FKBP12-DMSO-Rep2


title: TFIIB-FKBP12-dTAGV-1-Rep2


title: E14.5_Tie2_KO_4


title: WT-DMSO-Rep1


title: TFIIB-FKBP12-DMSO-Rep2


title: XPB-FKBP12-dTAGV-1-Rep1


title: TFIIB-FKBP12-DMSO-Rep1


title: TBP-FKBP12-dTAGV-1-Rep1


title: TAF1-FKBP12-DMSO-Rep2


title: E14.5_tie2_KO_2


title: E14.5_WT_8


title: OVA-DCs allergic mice (s009)


title: TFIIB-FKBP12-dTAGV-1-Rep1


title: E13.5_Tie2_KO_7


title: TAF1-FKBP12-DMSO-Rep1


title: TAF1-FKBP12-dTAGV-1-Rep2


title: D2582

first: Daniel

last: Bernstein

state: California

address: 450 Serra Mall

institute: Stanford

description: Cardiac Donor

data_processing:
Downstream analysis was performed using a combination of programs including STAR, HTseq, Cufflink and our wrapped scripts.
Alignments were parsed using Tophat and differential expressions were determined through DESeq2/edgeR (Wald test with FDR corrected p<0.05).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: Cardiac tissue

extract_protocol:
Cardiac tissues were flash frozen on dry ice, RNA was isolated from the frozen tissue using RNeasy Plus Micro kit (Qiagen, Valencia, CA)
RNA sequencing library was constructed using NEBNext® Ultra II RNA Library Prep Kit (New England Biolabs, Beverly, MA) according to manufacturer’s protocols.

tag: disease state

value: Donor


title: TAF1-FKBP12-dTAGV-1-Rep1


title: TAF4-FKBP12-dTAGV-1-Rep1


title: E13.5_Tie2_KO_3


title: D2552

description: Cardiac Donor


title: TAF4-FKBP12-DMSO-Rep1


title: ZC4H2_siRNA3

city: Shanghai

first: Jiajun

last: Qiu

address: West BeiJing Road

institute: Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine

data_processing:
The raw reads were first processed to remove any reads that contained adapter sequences and those containing poly-N and low-quality reads. After filtering of the reads, the index of the reference genome was built using Hisat2 v2.0.5, and paired-end clean reads were aligned to the reference genome.
FeatureCounts v1.5.0 p3 was used to count the read numbers mapped to each gene. Subsequently, the fragments per kilobase of transcript per million mapped reads of each gene were calculated based on the length of the gene in question and the reads count mapped to this gene.
Differential expression analysis of each group was performed using the R package DESeq2 (version 1.16.1). The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the false discovery rate. Genes with an adjusted P-value<0.05 identified by DESeq2 were assigned as differentially expressed genes (DEGs).
Supplementary files format and content: counts

source_name: neural stem cell

extract_protocol:
Total RNA was extracted from 293T cells using TRIzol™ (Tiangen Biotech Co., Ltd.) reagent, and RNA purity was checked using an Implen NanoPhotometer® spectrophotometer (Implen USA, Inc.). RNA integrity was assessed using the RNA Nano6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, Inc.).
A total of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep kit for Illumina® (New England BioLabs, Inc.) following the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. The library preparations were sequenced on a NovaSeq 6000 platform (Illumina, Inc.), and 125 bp/150 bp paired-end reads were generated.

value: neural stem cell

value: ZC4H2 were knockdown


title: E13.5_WT_4


title: E13.5_WT_2


title: D2507

description: Cardiac Donor


title: ZC4H2_siRNA1


title: D2540Red

description: Cardiac Donor


title: M2692

description: Cardiac HCM

value: HCM


title: E13.5_WT_1


title: N3

value: Control


title: WT-dTAGV-1-Rep2


title: M2860

description: Cardiac HCM


title: M2799_2

description: Cardiac HCM


title: Liver mitochondria, 65 week, bio rep 4

city: Göttingen

first: Abhishek

last: Aich

state: Please Select…

address: Humboldtallee 23,

institute: Universitätsmedizin Göttingen

data_processing:
EPI2ME Labs Differential gene expression Workflow
python was ued for statistical analysis and reporting,
minimap2 was used to align sequence reads in a splice-aware manner against a reference transcriptome,
samtools was used to process the aligned reads and prepares BAM files,
salmon was used for defining the expressed genes and quantifying aligned reads,
edgeR and StageR were used for differential expression analysis,
DEXSeq was used to quantify differential transcript usage.
Assembly: Mus_musculus GRCm38(mm10)
Supplementary files format and content: tab-delimited merged tsv file for differential counts from all samples

source_name: Liver

growth_protocol: Livers were excised from 12 and 65 week mice and mitochondria were isolated by homogenizaion using dounce homogenizers and differential centrifugations

extract_protocol:
The isolated and purified mitochondria were lysed in 1 ml TRIzol using the vendor’s protocol. The samples were then treated with DNase I (Thermo Scientific) following the manufacturer´s instructions. For purification of the sample, the RNA Clean and Concentrator Kit (R1013, Zymo Research) was used
Library was constructed using vendors protocol of PCR-cDNA Barcoding (SQK-PCB109)
PCR steps adds barcodes to each reverse transcribed RNA (cDNA) sample. The 8 barcodes provided in the kit were used to multiplex individual samples on a single flow cell

treatment_protocol: Mitochondria were further purified using sucrose gradient centifugation

value: Liver

value: Isolated Mitochondria

tag: strain

value: 65 week


title: Liver mitochondria, 65 week, bio rep 2


title: N1


title: E13.5_Tie2_KO_5


title: Liver mitochondria, 65 week, bio rep 1


title: M2673

description: Cardiac HCM


title: M433_2

description: Cardiac HCM


title: M2622

description: Cardiac HCM


title: ZC4H2_siRNA2


title: N2


title: M2803_2

description: Cardiac HCM


title: M2939Blu

description: Cardiac HCM


title: D1331_2

description: Cardiac Donor


title: M1385Red

description: Cardiac HCM


title: Liver mitochondria, 65 week, bio rep 3


title: D2254_2

description: Cardiac Donor


title: D1389_2

description: Cardiac Donor


title: hTS-siTEAD-rep3

type: RNA

city: Eiheiji

first: Tetsuya

last: Mizutani

state: Fukui

address: 4-1-1 Kenjojima

country: Japan

institute: Fukui Prefectural University

description: RMA expression value derived from Expression Console software

hyb_protocol: RNA samples were hybridized to Human Clariom S Gene Chip according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Raw gene expression data was normalized using RMA in Affymetrix Expression Console.

label: biotin

source_name: Human trophoblast stem cells

label_protocol: RNA samples were labeled to the Clariom S Human Array according to standardized protocols from Affymetrix..

growth_protocol: Human trophoblast stem cells were cultured in TS medium (DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.2% FBS, 1% penicillin/streptomycin, 0.3% bovine serum albumin, 1% ITS-X supplement , 1.5 μg/mL l-ascorbic acid, 50 ng/mL EGF, 2 μM CHIR99021, 0.5 μM A83–01, 1 μM SB431542, 0.8 mM valproic acid, and 5 μM Y27632) in a plate pre-coated with 1 μg/ml Col IV.

extract_protocol: The total RNA was isolated from the cells using the PureLink RNA Mini Kit (Thermo Fisher Scientific) with DNase I treatment, followed by RNA integrity number (RIN) measured using the Agilent 2100 Bioanalyzer.

treatment_protocol: Cells were transfected with YT- (10 nM ea), TEAD (20nM), or NC- (20 nM) siRNA, and cells were further incubated for 72 h in the TS medium.

tag: cell ytpe

value: Human trophoblast stem cells

tag: sirna

value: TEAD


title: M2856

description: Cardiac HCM


title: Liver mitochondria, 12 week, bio rep 1

value: 12 week


title: Thinning, May 2017, rep 1

city: Malaga

first: Rafael

middle: A

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

data_processing:
We removed the TrueSeq adaptors used in the library process with Trimmomatic software (Bolger et al., 2014, Bioinformatics, 30,2114). Once the sequences were cleaned, de novo assembly was performed with Trinity software (Haas et al., 2013, Nat Protoc. 8,1494) using the sequencing data from the 12 needle samples to construct a reference transcriptome.
For the transcript quantification, we used alignment-based methods by means of RSEM software (Li and Dewey, 2011, BMC Bioinformatics, 12,323). We normalized the number of reads that aligned to a transcript using the results of TPM (transcripts per million) divided by the transcript length. For the differential expression analysis of transcripts we used DESeq2 R package (Love et al., 2014, Genome Biology, 15,550).
Assembly: Pinsapo_Trinity_2.fasta
Supplementary files format and content: tab-delimited text file include RPKM values for each sample

organism: Abies pinsapo

source_name: Needles

growth_protocol: Field-grown adult trees from Sierra de las Nieves (Spain).

extract_protocol:
Total root RNA from maritime pine seedlings was isolated following the protocol described by Liao et al. (2004, Preparative Biochemistry & Biotechnology 34: 209–214) and modified by Canales et al. (2012, Frontiers in Plant Science 3: 100). The RNA concentration and purity were determined via spectrophotometry on a Nanodrop ND-1000 (Thermo Scientific, Waltham, MA, USA). Purity was determined through the 260/280 and 260/230 ratios. RNA quality was also determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA BR, Broad-Range, Assay Kit (Invitrogen, Paisley, UK). Samples with a RIN value > 7 were selected to mRNA isolation. The polyA-RNA isolation was performed using Dynabeads™ mRNA Purification Kit (Invitrogen, Paisley, UK) following the manufacturer’s instructions. This process was carried out twice per sample to avoid rRNA contamination. polyA-RNA quality was determined in a Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA). The concentration was verified with a Qubit 4 Fluorometer (Invitrogen, Paisley, UK) and Qubit RNA HS, High Sensitivity, Assay Kit (Invitrogen, Paisley, UK).
The sample sequencing was made by means of the company AscideaCro Genomics and Bioinformatics. The mRNA library preparation for sequencing were prepared using TruSeq RNA kits (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The samples were sequenced on an Illumina Hiseq 4000 sequnecer (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions obtaining paired-end reads of 150 bp length.

treatment_protocol: Trees were exposed to three field-treatments: (i) plots with reduced tree density and therefore decreased intra-specific competition for water and light: “Thinning” treatment; (ii) trees in adjacent forest stands where such adaptive management practices were not applied (high competition for both light and water; “Control” treatment), and (iii) trees in the thinned plot which were covered by a mesh to simulate a light environment similar to that in “Control” plots (high competition for light+low competition for water; “Thinning + Shading” treatment).

value: Needles

tag: provenance

value: Sierra de las Nieves, Spain

value: Thinning


title: M1455Red

description: Cardiac HCM


title: Liver mitochondria, 12 week, bio rep 3


title: IgG

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

description: CUT&Tag

data_processing:
After quality control, reads were aligned against hg38 by Bowtie2 (version 2.3.5.1) with the following parameters: --local --very-sensitive --no-mixed --no-discordant -I 10 -X 700.
Peak calling was performed by SEACR (version 1.3) for H3K4me3 and H3K27ac with relaxed mode or by SICER2 for H3K27me3  with following parameters; -w 1000 -g 3000
Genome_build: hg38

growth_protocol: 100,000 cells were prepared and binded to Concanavalin-coated magnetic beads (Bangs Laboratories Inc.).

extract_protocol:
The beads were washed and CUTANA pAG-Tn5 for CUT&Tag (EpiCypher Inc.) was binded to the secondary antibody. After incubated them with a solution containing Mg2+ to cleave the target DNA, the DNA was extracted and was amplified by 14 cycles of PCR.
The PCR product was purified using AMPureXP magnetic beads (Beckman Coulter).Sequence libraries were pooled at 5 nM, and if less than 5 nM (e.g. non-specific IgG), the entire library was pooled. The pooled library was sequenced on HiSeqX (Illumina) using 150bp paired end reads.
CUT&Tag

treatment_protocol: After permeabilizing with digitonin, cells were incubated with a primary antibody at room temperature for 2 hours and subsequently incubated with secondary antibody at room temperature for 1 hour. Rabbit polyclonal anti H3K4me3 antibody (ActiveMotif, 39159), Rabbit monoclonal anti H3K27ac antibody (Millipore, MABE647) and rabbit monoclonal anti H3K27me3 antibody (CST, #9733S) were used for primary antibody. Rabbit IgG (Merck Millipore, PP64) was used for IgG control. Guinea Pig anti-Rabbit IgG (antibodies-online) was used as secondary antibody.

tag: type

value: SCLC (ASCL1 positive)

value: Merck Millipore, PP64


title: Control, May 2017, rep 1


title: H3K4me3

description: CUT&Tag

value: ActiveMotif, 39159


title: Liver mitochondria, 12 week, bio rep 4

value: WT


title: M476_2

description: Cardiac HCM


title: M2800_2

description: Cardiac HCM


title: Thinning, May 2017, rep 2


title: hTS-siYT-rep2

value: YAP/TAZ


title: hTS-siYT-rep3


title: Thinning and Shading, May 2017, rep 2

value: Thinning and Shading


title: Control, August 2016, rep 1


title: Thinning and Shading, August 2016, rep 1


title: Thinning, August 2016, rep 2


title: Control, May 2017, rep 2


title: H3K27ac

description: CUT&Tag

value: Millipore, MABE647


title: hTS-siTEAD-rep1


title: Oviduct_Cdc42KO_1

status: Public on Jul 16 2022

city: Nanjing

first: Ruiwei

last: Jiang

address: No.321 Zhongshan Road

department: Drum Tower Hospital Affiliated to Medical School

institute: Nanjing University

data_processing:
Zebra software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mm10 whole genome using HISAT2 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR package of R.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Oviduct_RNAseq_RPKM.xlsx: Excel file includes RPKM values for each Sample.

source_name: Oviduct

extract_protocol:
Total RNA was isolated from the mice oviducts following the standard TRIzol extraction protocol.
A total of 6 cDNA libraries (PgrCre/+Cdc42f/f and Cdc42f/f mice oviducts with three biological replicates) were sequenced using the BGISEQ-500 system by Huada Gene Technology Co., Ltd. (Shenzhen, China) to generate raw reads.

value: Oviduct

value: Day 2 of pregnancy


title: hTS-siNC-rep2

value: Control


title: hTS-siTEAD-rep2


title: Oviduct_FF_3


title: Oviduct_FF_1


title: Liver mitochondria, 12 week, bio rep 2

value: Liver

value: Isolated Mitochondria


title: Oviduct_FF_2


title: Thinning and Shading, May 2017, rep 1


title: Thinning and Shading, August 2016, rep 2


title: H3K27me3

description: CUT&Tag


title: Thinning, August 2016, rep 1


title: Gata4_KO_1, scRNAseq

city: Boston

first: Yan

last: Zhang

state: MASSACHUSETTS

address: 300 Longwood Ave.

institute: Boston Children's Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger was used to process the raw data and generate the gene expression matric using default parameters.
The merged matrix was transferred into the R statistical environment for further analysis using the Seurat package.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart ventricle

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: To prepare single cells for RNA-seq, Gata4fl/+;Rosa26mTmG/+;Cdh5(Pac)-CreER+ (Gata4_het) or Gata4fl/fl;Rosa26mTmG/+;Cdh5(Pac)-CreER+ (Gata4_KO) mouse embryos were induced with tamoxifen at E9.5 and the heart were collected at E12.5. Heart ventricles were dissociated to single cells with collagenase. scRNA-seq libraries were prepared from 10K of total ventricular cells according to the manufacturer's instructions (Chromium Next GEM, 10x Genomics). At least 20K paired-end 150bp reads were obtained for each cell.

value: all ventricular cells

value: heart ventricle

tag: age


title: Gata4_KO_2, scRNAseq

description: 10x Genomics


title: Control, August 2016, rep 2

value: Needles


title: Gata4_het_2, scRNAseq

description: 10x Genomics


title: Oviduct_Cdc42KO_3


title: scRNAseq_Lineage_Negative_Bone_Marrow_Wildtype_Rit1-M90I_Mx1Cre-

city: South San Francisco

first: Simon

middle: J

last: Hogg

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
FASTQ files for each sample were generated using the Cell Ranger (v6.1.1) mkfastq function.
Reads were aligned to the mouse Mm10 reference genome with the Cell Ranger (v6.1.1) count function using the pre-built Mm10 reference ('mm10-2020-A') provided by Cell Ranger.
Addition filtering, normalization, and dimensionality reduction was performed using the Seurat package (v4.1.0) using regularized negative binomial regression to normalize UMI count data (sctransform workflow).
Cells were filtered based on (i) percentage of mitochondrial reads being less than 15%, and (ii) 500< nCount_RNA < 25000. In addition, genes detected in <4 cells were removed, as well as cells that had fewer than 200 genes.
Applying these filters resulted in 7,528 cells for Wild-type bone-marrow, 10,610 cells for Lztr1 knock-out bone-marrow, and 2,398 cells for Rit1 mutant bone-marrow, that were used for all downstream analysis and visualization in Seurat, which was performed in Rstudio (v1.3.1073).
Assembly: Mm10
Supplementary files format and content: Filtered count matrix for each sample in gziped matrix file (matrix.mtx.gz) produced by Cell Ranger count (v6.1.1).
Supplementary files format and content: Filtered list of cell barcodes for each sample in gzipped tsv file (barcode.tsv.gz) produced by Cell Ranger count (v6.1.1).
Supplementary files format and content: Filtered list of gene features detected for each sample in gzipped tsv file (features.tsv.gz) produced by Cell Ranger count (v6.1.1).

source_name: Bone marrow

growth_protocol: 8-week-old Rit1M90I/+Mx1Cre-, Rit1M90I/+Mx1Cre+ and Lztr1fl/fl;Mx1Cre+ mice were treated with 3 doses of polyinosinic:polycytidylic acid (pIpC; 12 mg/kg) every other day.

extract_protocol:
Sorted cells were stained with Trypan blue and Countess II Automated Cell Counter (ThermoFisher) was used to assess both cell number and viability (90-91%). Following QC, the single cell suspension was loaded onto Chromium Chip B (10X Genomics PN 2000060) and GEM generation, cDNA synthesis, cDNA amplification, and library preparation of 3-6,700 cells proceeded using the Chromium Single Cell 3’ Reagent Kit v3 (10X Genomics PN 1000075) according to the manufacturer’s protocol.
cDNA amplification included 11 cycles and 240-370ng of the material was used to prepare sequencing libraries with 10 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/91 paired end run using the NovaSeq 6000 S1 Reagent Kit (100 cycles) (Illumina).  An average of 30 thousand reads was generated per cell.

treatment_protocol: Bone marrow cells were harvested from the mice 4-week following injection with pIpC and stained with the following flow cytometry antibodies: anti-CD3-APCcy7,  anti-CD11b-APCcy7, anti-Gr1-APCcy7, anti-B220-APCcy7 and anti-Ter119-APCcy7. Live lineage negative (APCcy7- and DAPI-) cells were sorted and suspended in PBS+0.04% BSA.

tag: mouse strain

tag: selection protocol

value: Live CD3-CD11b-Gr1-B220-Ter119- cells were sorted from bone marrow by flow cytometry


title: hTS-siNC-rep3

value: Human trophoblast stem cells


title: Oviduct_Cdc42KO_2


title: Etoh-fed NKO mouse liver rep1

city: Indianapolis

first: Zhihong

last: Yang

institute: Indiana University

data_processing:
Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system
HISAT2 was used to map reads to the mouse genome and StringTie was used to assemble the mapped reads
Genome_build: ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample ...

source_name: Etoh-fed mouse live

extract_protocol:
The total RNAs were extracted from ETOH-fed 5 WT and 4 Ncf1Lyz-/- mouse livers and submitted for a Poly(A) RNA sequencing.
The library was prepared following Illumina’s TruSeq-stranded mRNA sample preparation protocol and the RNA integrity was checked with Agilent Technologies 2100 bioanalyzer. Only the RNAs with RIN (RNA integrity) > 7 were used for the sequencing.

treatment_protocol: 10- to 12-week-old female mice were initially fed with Lieber-DeCarli liquid diet (catalog F1259SP, Bio-Serv) ad libitum for 5 days during acclimatization. Subsequently, the ethanol-fed groups were allowed free access to an ethanol diet (catalog F1258SP, Bio-Serv) containing 5% (v/v) ethanol for 10 days. On day 11, they received a single dose of ethanol (5 g/kg body weight) via oral gavage in the early morning and were sacrificed 9 hours later.

tag: stain

tag: disease

value: Etoh-binge model


title: Etoh-fed NKO mouse liver rep2

tag: genotype


title: Etoh-fed NKO mouse liver rep4


title: Etoh-fed WT mouse liver rep5


title: scRNAseq_Lineage_Negative_Bone_Marrow_Rit1-M90I_Mx1Cre+


title: Etoh-fed WT mouse liver rep4


title: Etoh-fed NKO mouse liver rep3


title: hTS-siYT-rep1


title: Etoh-fed WT mouse liver rep3


title: hTS-siNC-rep1


title: Etoh-fed WT mouse liver rep1


title: scRNAseq_Lineage_Negative_Bone_Marrow_Lztr1-floxed_Mx1Cre+


title: Etoh-fed WT mouse liver rep2


title: C1Q KO TauP301S Neg (SAM24386511)

first: Brad

last: Friedman

address: 1 DNA Way

department: Neuroinformatics

institute: Genentech, Inc.

data_processing:
Reads were aligned to the GRCm38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package. Gene models were from our internal database and available in the manuscript supplementary material. "nRPKM" normalization was performed. This is similar to "RPKM" normalization but includes an extra step for sizeFactor adjustment and is described in the Methods of the manuscript. Supplementary files use Entrez Gene IDs, counts and nRPKM statistics.
Genome_build: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized RPKM values for every gene and every sample

source_name: Brain (Hippocampus)

extract_protocol:
Tissue was rapidly frozen and stored until a full collection was obtained. RNA was extracted using the RNeasy Lipid Tissue extraction kit with on-column DNase digestion (Qiagen). Quality and quantity of total RNA samples were determined using ND-1000 spectrophotometer (Thermo Scientific) and Bioanalyzer 2100 (Agilent), respectively.
More details are provided in the manuscript

value: Brain (Hippocampus)

tag: diagnosis

value: Normal

tag: taup301s status

value: Negative

tag: c1q status

value: KO


title: C1Q WT TauP301S Neg (SAM24386516)

growth_protocol: More details are provided in the manuscript

tag: tissue

value: WT


title: C1Q WT TauP301S Pos (SAM24386519)

treatment_protocol: More details are provided in the manuscript

value: Positive


title: C1Q KO TauP301S Neg (SAM24386505)


title: C1Q WT TauP301S Neg (SAM24386514)


title: C1Q KO TauP301S Pos (SAM24386509)


title: C1Q WT TauP301S Pos (SAM24386510)


title: C1Q WT TauP301S Neg (SAM24386520)


title: C1Q WT TauP301S Pos (SAM24386515)


title: C1Q KO TauP301S Neg (SAM24386507)


title: C1Q WT TauP301S Pos (SAM24386517)


title: C1Q KO TauP301S Pos (SAM24386506)


title: C1Q WT TauP301S Neg (SAM24386518)


title: C1Q WT TauP301S Neg (SAM24386513)


title: C1Q KO TauP301S Pos (SAM24386508)


title: AdKO_Diff_1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Mm10 whole genome using HISAT2 with default parameters
Fragments Per Kilobase of exon model per Million mapped fragments  (FPKM) were calculated using EdgeR package of R.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: oviduct organoid_AdKO_Differentiation

growth_protocol: Oviducts were dissected from PgrCre/+Cdc42f/f and Cdc42f/f mice.Dispersed epithelia cells were mixed with Matrigel (BD Bioscience), seeded, and maintained in culture. Media were changed every 2-3 days, and organoids were passaged (~10,000 cells/well) every 8 days.

extract_protocol:
Total RNA was isolated from the mice oviducts and organoids following the standard TRIzol extraction protocol
A total of 10 cDNA libraries from organoids were generated using V8 RNA-seq Library Prep Kit (Vazyme, NR605) according to the manufacturer's instructions, then sequenced using Illumina Nova seq platform (PE150) by Novogene Bioinformatics Technology Co., Ltd (Beijing, China) to generate raw reads

treatment_protocol: To induce Cre mediated Cdc42 knockout in vitro, organoids from Cdc42f/f mice oviduct were digested as described above, then transfected with recombinant adenovirus Ad5-CMV-Cre (Ad-Cre). To induce multiciliated cell differentiation, the oviduct organoids were treated with 1×10^-8 M Estrogen (E2) and 1 μM Notch inhibitor DBZ for 6 days, purchased from Genechem (Shanghai, China).

value: Cdc42 f/f oviduct

value: Ad-Cre mediated Cdc42 knockout in vitro

tag: organoids status

value: differentiation


title: PgrKO_Con_2

source_name: oviduct organoid_PgrKO_Control

value: PgrCre/+Cdc42 f/f oviduct

value: Cdc42 knockout in vivo

value: control


title: PgrKO_Diff_1

source_name: oviduct organoid_PgrKO_Differentiation


title: C1Q KO TauP301S Pos (SAM24386521)


title: FF_Con_2

source_name: oviduct organoid_FF_Control

value: Cdc43 flox/flox in vivo


title: PgrKO_Diff_2


title: PgrKO_Con_1


title: FF_Diff_1

source_name: oviduct organoid_FF_Differentiation

value: Cdc44 flox/flox in vivo


title: KrasG12D/+Lkb1fl/fl

city: Guangzhou

first: Xue

last: Bai

address: No. 1023-1063, Shatai South Road, Baiyun District

institute: Southern Medical University

data_processing:
Real-Time Analysis (RTA) v3.4.4 and bcl2fastq (btq) v2.19 used for basecalling.
Libraries were sequenced on the Illumina Novaseq platform, paired-end mode.
For the raw fastq data, we first filtered low quality data with trimomatic software, followed by computational alignment using CellRanger (version 6.0, 10x Genomics) to map to the mm10 reference genome (GRCm38.91).
datasets were subjected to quality control steps using Seurat (R package, version 3.1.5) that included selecting cells with a library complexity of between 500 and 6000 features and selecting genes expressed by at least three cells, and filtering out cells with high percentages of mitochondrial genes (>20%).
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lung tumor section harboring KrasG12D/+Lkb1fl/f lmutation

growth_protocol: KrasG12D/+ mice were treated with nasal inhalation of lentiviruses targeting Lkb1 (KL) or Tomato (K, referred to as negative control)  to generate a mouse model with conditional knockout of Lkb1. The tumors were confirmed by microCT and harvested at twenty-week after lentiviruses infection. Conditional deletion of Lkb1 in the lung tumor sections was verified by  western blot.

extract_protocol:
Single-cell suspension were prepared after dissociation and digestion of the tumor tissue
Single-cell RNA-seq libraries were prepared with Chromium Next GEM Single cell 3’Reagent Kits V3.1 according to the manufacturer’s protocol. Single cells from two samples were mixed during the library construction process, and were seperated based on the labels after the sequencing.

value: lung

value: FVB


title: FF_Diff_2

value: Cdc45 flox/flox in vivo


title: C1Q KO TauP301S Neg (SAM24386512)

value: Brain (Hippocampus)


title: FF_Con_1

value: Cdc42 flox/flox in vivo


title: KrasG12D/+

source_name: lung tumor section harboring KrasG12D/+ mutation


title: SAM24378326

city: Mississauga

first: Alyaa

middle: M

last: Mohamed

state: Ontario

address: 7070 Mississauga Road Mississauga, ON L5N 5M8 Canada

country: Canada

institute: Hoffman La Roche

description: single cell RNA-Seq

data_processing:
Single-cell RNA sequencing data were processed with an in-house analysis pipeline as described (Seung-Hye et al., 2021) - details will be provided in the manuscript.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include UMI counts for each cell
Supplementary_files_format_and_content: tab-delimited text files include normalized UMI counts for each cell
Supplementary_files_format_and_content: tsne_coordinates_and_cluster_labels_all_cells.csv
Supplementary_files_format_and_content: tsne_coordinates_and_cluster_labels_microglia_cells.csv
Supplementary_files_format_and_content: tsne_coordinates_and_cluster_labels_immune_cells.csv

source_name: TPL2 WT TauP301S Pos

extract_protocol: Mice were perfused with PBS and mouse brain tissue were sub dissected and collected. Hippocampus tissues were directly dissociated into single cells and libraries were made from single cells.

value: 9-9.5 month old

value: brain

tag: tpl2 genotype


title: SAM24378324

description: single cell RNA-Seq

source_name: TPL2 KD TauP301S Pos

tag: strain

value: KD


title: SAM24378325

description: single cell RNA-Seq

value: Positive


title: SAM24378323

description: single cell RNA-Seq

value: WT


title: SAM24378320

description: single cell RNA-Seq


title: SAM24378321

description: single cell RNA-Seq

source_name: TPL2 KD TauP301S Neg

value: Negative


title: SAM24376447

description: single cell RNA-Seq


title: SAM24378319

description: single cell RNA-Seq

source_name: TPL2 WT TauP301S Neg


title: SAM24376445

description: single cell RNA-Seq


title: SAM24376446

description: single cell RNA-Seq


title: AdKO_Con_1

source_name: oviduct organoid_AdKO_Control

value: Cdc42 f/f oviduct

value: Ad-Cre mediated Cdc42 knockout in vitro


title: SAM24376443

description: single cell RNA-Seq


title: SAM24376442

description: single cell RNA-Seq


title: SAM24376441

description: single cell RNA-Seq


title: SAM24376440

description: single cell RNA-Seq


title: SAM24376444

description: single cell RNA-Seq


title: SAM24376438

description: single cell RNA-Seq


title: amniotic fluid fetal cells 32_10CMA

type: genomic

city: Fuzhou

first: Hailong

last: Huang

state: Fujian

address: No.18 Daoshan Road, Gulou District

institute: Fujian Maternity and Child Health Hospital

description: Hybridized to CytoScan 750K

hyb_protocol: DNA was processed as follows. Restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer`s instructions.

scan_protocol: The arrays were then washed using Affymetrix Fluidics Stations, and scanned using the GeneChip Scanner 750K

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console (AGCC version 4.0.0.1567). Data processing and analysis (CEL file generation, smoothing and segmentation) were used Chromosome Analysis Suite (version 3.3).
processed data includes: Copy number variation status (CNV)

label: Biotin

source_name: amniotic fluid fetal cells 32

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA of fetal cells in amniotic fluid or cord blood sampling was extracted with using the QIAamp DNA extraction kit (Qiagen, Dusseldorf, Germany)

tag: cell type

value: amniotic fluid fetal cells


title: WTCol0-0-S1

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

institute: Aix-Marseille Université

data_processing:
Checking quality with fastQC (0.11.5)
Trimming of library adapters and filtering on quality (reads with a Phred Quality score>20 and lenght > 30 bases were kept)
Alignement with Bowtie 2 (2.2.9) against TAIR10_cdna_20110103_representative_gene_model_updated
reads count with a command line derived from RNA-Seq : revelation of the messengers. Pieterse MJ, Verk MC Van, Hickman R, Wees SCM Van (2013). Trends Plant Sci 18:175–179
Quatification with SARTools 1.5.1 using edgeR (3.20.1)
Editing analysis with the protocole described in Bioinformatic Analysis of Chloroplast Gene Expression and RNA Posttranscriptional Maturations Using RNA Sequencing. Malbert et al. Methods Mol Biol. 2018;1829:279-294
Genome_build: TAIR10-31
Supplementary_files_format_and_content: Excel file containing transcript quantification in mutants and wt

organism: Arabidopsis thaliana

source_name: 6 day-old aerial parts

growth_protocol: Seeds are stratified for 3 days at 4°C in darkness before transfer to growth chamber for 6 days  (16hL/8hD: 8 am-12 pm, ~80 µE, ~65% humidity, ~21°C). Media: Murashige and Skoog (MS) 1/2, 1% sucrose, 0.4% phytagel

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen®, Hilden, Germany) according to the supplier’s instruction
TruSeq Stranded Total RNA with Ribo-Zero Plant, Illumina


title: WTCol0-0-S2


title: WTCol0-0-S3


title: tfIIfα2-0-S2


title: tfIIfα2-0-S3


title: cord blood sampling 3_8CMA

description: Hybridized to CytoScan 750K

source_name: cord blood sampling 3

value: cord blood sampling

value: microduplication of 15q13.3


title: tfIIfα2-0-S1


title: amniotic fluid fetal cells 14_4KP

description: Hybridized to CytoScan 750K

source_name: amniotic fluid fetal cells


title: SAM24378322

description: single cell RNA-Seq


title: amniotic fluid fetal cells_3KP

description: Hybridized to CytoScan 750K

value: Trisomy 21


title: cord blood sampling 3_1KP

description: Hybridized to CytoScan 750K

source_name: cord blood sampling


title: amniotic fluid fetal cells 16_1CMA

description: Hybridized to CytoScan 750K

value: microdeletion of 22q11.21


title: Cells_consiRNA_rep3

city: Umea

first: Jie

last: Song

state: AC

address: Medical Biosciences Department, Pathology, M21

department: Medical Bioscience

country: Sweden

institute: Umea University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with GenomeStudio

source_name: PC-3U cells, control siRNA

label_protocol: Biotinylated cRNA were prepared with the TargetAmp-Nano Labeling Kit for Illumina arrays.

extract_protocol: Total RNA was extracted from PC-3U cells using the RNeasy Mini Kit (Qiagen). RNA purity and integrity were evaluated with the Agilent RNA 6000 Nano Kit and Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: tumor stage

value: grade IV prostatic adenocarcinoma

tag: metastasis

value: bone

tag: treatement

value: control siRNA


title: Cells_APPL1/2siRNA_rep1

description: replicate 1

source_name: PC-3U cells, APPL1/2 siRNA

value: APPL1/2 siRNA


title: Cells_APPL1/2siRNA_rep3

description: replicate 3


title: Cells_consiRNA_rep2

description: replicate 2


title: Cells_APPL1/2siRNA_rep2

description: replicate 2


title: Patient 19 vaginal melanoma [19T]

city: Columbus

first: William

middle: E.

last: Carson III

state: OH

institute: The Ohio State University

hyb_protocol: RNA samples were hybridized overnight with nCounter reporter probes (8 μL) in hybridization buffer and in excess of nCounter capture probes (2 μL) at 65 °C for 18 h.  After overnight hybridization, excess probes were removed using two-step magnetic beads based purification on an automated fluidic handling system (nCounter Prep Station).  Biotinylated capture probe-bound samples were immobilized and recovered on a streptavidin-coated cartridge.

scan_protocol: The abundance of specific target molecules was then quantified using the nCounter digital analyzer.  Individual fluorescent barcodes and target molecules present in each sample were recorded with a CCD camera by performing a high-density scan (780 fields of view).  Images were processed internally into a digital format and exported as Reporter Code Count (RCC).

data_processing: All vaginal melanoma and adjacent healthy vaginal mucosa samples were included on a single cartridge.  6 positive, 8 negative and 20 housekeeping genes were included in the panel by the manufacturer. Negative controls were used to assess background hybridization and filter out target miRs with expression below the mean of the highest detected negative control sample. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between vaginal melanoma and vaginal mucosa while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.05 and a fold change of at least 2 used to identify differentially expressed mRNAs.

source_name: Vaginal melanoma

label_protocol: Normalized quantitation of RNA for loading into the Nanostring nCounter was determined using the percentage of RNA fragments that are larger than 200 nucleotides (DV200), using a 2200 Tapestation (Agilent) with an RNA Screentape kit. For DV200 > 65% 100 ng of RNA was used; for DV200 between 25% and 65%, 200 ng of RNA was used; for DV200 < 25%, 300 ng of RNA was used. Individual mRNAs were ligated to DNA tags provided by the manufacturer. Excess tags were washed away.

extract_protocol: RNA isolated from 2 mm diameter cylindrical punch samples of formalin fixed, paraffin embedded (FFPE) human biopsy tissue using a modified Qiagen miRNeasy FFPE kit protocol. RNA concentration was determined using a Nanodrop spectrophotometer and Qubit analysis.

tag: subject id

value: Patient 19

value: vaginal melanoma


title: Patient 23 healthy vaginal mucosa [23N]

source_name: Vaginal mucosa

value: Patient 23

value: healthy vaginal mucosa


title: Patient 20 vaginal melanoma [20T]

value: Patient 20


title: Patient 23 vaginal melanoma [23T]


title: Cells_consiRNA_rep1

description: replicate 1


title: Patient 20 healthy vaginal mucosa [20N]


title: Vulvar melanoma patient V14 cartridge 3 [V14]

data_processing: Both vulvar melanoma and primary cutaneous melanoma was included on each cartridge, distributed across three cartridges.  6 positive, 8 negative and 20 housekeeping genes were included in the panel by the manufacturer. Negative controls were used to assess background hybridization and filter out target miRs with expression below the mean of the highest detected negative control sample. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between vulvar melanoma and primary cutaneous melanoma while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.05 and a fold change of at least 2 used to identify differentially expressed miRs.

source_name: Vulvar melanoma

extract_protocol: RNA isolated from four 20 um thick scrolls of formalin fixed, paraffin embedded human biopsy tissue using the Invitrogen RecoverAll total nucleic acid isolation kit for FFPE. RNA concentration was determined using a Nanodrop spectrophotometer and Qubit analysis.

tag: subject status/id

value: Vulvar melanoma patient V14


title: Vulvar melanoma patient V17 cartridge 2 [V17]

value: Vulvar melanoma patient V17


title: Vulvar melanoma patient V18 cartridge 2 [V18]

value: Vulvar melanoma patient V18


title: Vulvar melanoma patient V12 cartridge 2 [V12]

value: Vulvar melanoma patient V12


title: Vulvar melanoma patient V3 cartridge 2 [V3]

value: Vulvar melanoma patient V3


title: Vulvar melanoma patient V13 cartridge 2 [V13]

value: Vulvar melanoma patient V13


title: Vulvar melanoma patient gyn 12 cartridge 2 [Gyn12T]

value: Vulvar melanoma patient gyn 12


title: Vulvar melanoma patient V4 cartridge 1 [V4]

value: Vulvar melanoma patient V4


title: Vulvar melanoma patient V10 cartridge 1 [V10]

value: Vulvar melanoma patient V10


title: Vulvar melanoma patient V1 cartridge 1 [V1]

value: Vulvar melanoma patient V1


title: Patient 19 healthy vaginal mucosa [19N]


title: Vulvar melanoma patient V15 cartridge 3 [V15]

value: Vulvar melanoma patient V15


title: Vulvar melanoma patient gyn 14 cartridge 2 [Gyn14T]

value: Vulvar melanoma patient gyn 14


title: Vulvar melanoma patient gyn 27 cartridge 1 [Gyn27T]

value: Vulvar melanoma patient gyn 27


title: Vulvar melanoma patient gyn 24 cartridge 1 [Gyn24T]

value: Vulvar melanoma patient gyn 24


title: Primary cutaneous melanoma patient 41 cartridge 3 [NU41]

source_name: Primary cutaneous melanoma

value: Primary cutaneous melanoma patient 41


title: SAM24376439

description: single cell RNA-Seq

tag: age

value: 9-9.5 month old

value: brain

value: KD

value: Positive


title: Primary cutaneous melanoma patient 6 cartridge 3 [NU6]

value: Primary cutaneous melanoma patient 6


title: Vulvar melanoma patient gyn 22 cartridge 1 [Gyn22T]

value: Vulvar melanoma patient gyn 22


title: Primary cutaneous melanoma patient 11 cartridge 2 [NU11]

value: Primary cutaneous melanoma patient 11


title: Primary cutaneous melanoma patient 9 cartridge 2 [NU9]

value: Primary cutaneous melanoma patient 9


title: Primary cutaneous melanoma patient 12 cartridge 1 [NU12]

value: Primary cutaneous melanoma patient 12


title: Vulvar melanoma patient V2 cartridge 2 [V2]

value: Vulvar melanoma patient V2


title: Primary cutaneous melanoma patient 40 cartridge 1 [NU40]

value: Primary cutaneous melanoma patient 40


title: Vulvar melanoma patient V5 cartridge 1 [V5]

value: Vulvar melanoma patient V5


title: Primary cutaneous melanoma patient 3 cartridge 1 [NU3]

value: Primary cutaneous melanoma patient 3


title: Primary cutaneous melanoma patient 2 cartridge 1 [NU2]

value: Primary cutaneous melanoma patient 2


title: Patient 25 vaginal melanoma [25T]

hyb_protocol: Tagged microRNAs were hybridized to capture and reporter probes at 64°C for 18 hours. Hybridized probes were immobilized onto a streptavidin-coated cartridge via nCounter Prep Station (Nanostring).

scan_protocol: Fluorescence of each hybridized miR-probe complex was analyzed by an nCounter Digital analyzer (Nanostring Technologies, Seattle, WA) via high density scan with 600 fields of view.

data_processing: All vaginal melanoma and adjacent healthy vaginal mucosa samples were included on a single cartridge.  5 positive, 5 negative and 5 housekeeping genes were included in the panel by the manufacturer. Negative controls were used to assess background hybridization and filter out target miRs with expression below the mean of the highest detected negative control sample. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between vaginal melanoma and vaginal mucosa while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.05 and a fold change of at least 2 used to identify differentially expressed miRs.

label_protocol: 100 ng of RNA per sample was loaded onto a Nanostring nCounter cartridge. Individual miRs were ligated to DNA tags provided by the manufacturer. Excess tags were washed away.

value: Patient 25

value: vaginal melanoma


title: Patient 25 healthy vaginal mucosa [25N]

value: healthy vaginal mucosa


title: Patient 29 vaginal melanoma [29T]

value: Patient 29


title: Patient 29 healthy vaginal mucosa [29N]


title: Primary cutaneous melanoma patient 43 cartridge 2 [NU43]

value: Primary cutaneous melanoma patient 43


title: Patient 19 healthy vaginal mucosa [19N]

value: Patient 19


title: Patient 23 vaginal melanoma [23T]

value: Patient 23


title: Patient 20 vaginal melanoma [20T]

value: Patient 20


title: Patient 19 vaginal melanoma [19T]


title: Patient 7 healthy vaginal mucosa [7N]

value: Patient 7


title: Primary cutaneous melanoma patient 40 cartridge 3 [NU40_3]

data_processing: Both vulvar melanoma and primary cutaneous melanoma was included on each cartridge, distributed across three cartridges.  5 positive, 5 negative and 5 housekeeping genes were included in the panel by the manufacturer. Negative controls were used to assess background hybridization and filter out target miRs with expression below the mean of the highest detected negative control sample. The upper quartile normalization method was then used to normalize across biological samples. Linear models and a moderated t-test were employed to detect differential expression between vulvar melanoma and primary cutaneous melanoma while considering cartridge effect. Significance was adjusted using a Bonferroni procedure to control the mean number of false positives.  Statistical software SAS 9.4 and R 3.6 were used for analysis with an α of 0.05 and a fold change of at least 2 used to identify differentially expressed miRs.


title: Vulvar melanoma patient gyn 22 cartridge 3 [Gyn22T_3]

value: Vulvar melanoma patient gyn 22


title: Patient 7 vaginal melanoma [7T]


title: Vulvar melanoma patient V14 cartridge 3 [V14_3]

value: Vulvar melanoma patient V14


title: Vulvar melanoma patient V13 cartridge 3 [V13_3]

value: Vulvar melanoma patient V13


title: Primary cutaneous melanoma patient 43 cartridge 3 [NU43_3]


title: Vulvar melanoma patient V15 cartridge 3 [V15_3]

value: Vulvar melanoma patient V15


title: Primary cutaneous melanoma patient 2 cartridge 3 [NU2_3]


title: Vulvar melanoma patient V6 cartridge 3 [V6_3]

value: Vulvar melanoma patient V6


title: Vulvar melanoma patient V5 cartridge 3 [V5_3]

value: Vulvar melanoma patient V5


title: Patient 23 healthy vaginal mucosa [23N]


title: Vulvar melanoma patient V2 cartridge 3 [V2_3]

value: Vulvar melanoma patient V2


title: Vulvar melanoma patient V3 cartridge 3 [V3_3]

value: Vulvar melanoma patient V3


title: Gata4_het_1, scRNAseq

description: 10x Genomics

source_name: heart ventricle

value: all ventricular cells

value: heart ventricle


title: Patient 20 healthy vaginal mucosa [20N]

value: healthy vaginal mucosa


title: Primary cutaneous melanoma patient 3 cartridge 2 [NU40_2]

value: Primary cutaneous melanoma patient 3


title: amniotic fluid fetal cells_2KP

description: Hybridized to CytoScan 750K

value: amniotic fluid fetal cells

value: Trisomy 21


title: Vulvar melanoma patient gyn 2 cartridge 3 [Gyn2T]

value: Vulvar melanoma patient gyn 2


title: Vulvar melanoma patient V14 cartridge 2 [V14_2]


title: Vulvar melanoma patient gyn 22 cartridge 2 [Gyn22T_2]


title: Primary cutaneous melanoma patient 9 cartridge 2 [NU9_2]

value: Primary cutaneous melanoma patient 9


title: Primary cutaneous melanoma patient 41 cartridge 2 [NU41_2]

value: Primary cutaneous melanoma patient 41


title: Vulvar melanoma patient V18 cartridge 2 [V18_2]

value: Vulvar melanoma patient V18


title: Vulvar melanoma patient V17 cartridge 2 [V17_2]

value: Vulvar melanoma patient V17


title: Vulvar melanoma patient gyn 12 cartridge 2 [V12_2]

value: Vulvar melanoma patient gyn 12


title: Vulvar melanoma patient V4 cartridge 2 [V4_2]

value: Vulvar melanoma patient V4


title: Primary cutaneous melanoma patient 3 cartridge 2 [NU3_2]


title: Vulvar melanoma patient V8 cartridge 3 [V8_3]

value: Vulvar melanoma patient V8


title: Primary tumor_13

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

data_processing:
raw fastq files were examined for quality using FastQC (v0.11.9) and MultiQC (v1.10)
paired fastq files were aligned to human genome hg38 using HISAT2(v2.2.1).
count were quantified from BAM files using featureCounts(v2.0.2)
Genome_build: Genome_build: hg38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: TPM normalized gene count in csv format

source_name: Mammary

extract_protocol:
Tumor pieces snapped frozen on dry ice, and RNA was harvested using Trizol reagents and Direct-zol™ RNA  MiniPrep kit (ZymoResearch; Cat. No. R2052). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary tumor

tag: cancer type

value: HER2+ breast cancer


title: Vulvar melanoma patient gyn 4 cartridge 1 [Gyn4T_1]

value: Vulvar melanoma patient gyn 4


title: Vulvar melanoma patient gyn 14 cartridge 1 [Gyn14T_1]

value: Vulvar melanoma patient gyn 14


title: Vulvar melanoma patient gyn 12 cartridge 1 [Gyn12T_1]


title: Vulvar melanoma patient V1 cartridge 2 [V1_2]

value: Vulvar melanoma patient V1


title: Vulvar melanoma patient gyn 22 cartridge 1 [Gyn22T_1]

value: Vulvar melanoma patient gyn 22


title: Vulvar melanoma patient gyn 24 cartridge 1 [Gyn24T_1]

value: Vulvar melanoma patient gyn 24


title: Primary tumor_12


title: Vulvar melanoma patient gyn 27 cartridge 1 [Gyn27T_1]

value: Vulvar melanoma patient gyn 27


title: Vulvar melanoma patient gyn 2 cartridge 1 [Gyn2T_1]


title: Primary cutaneous melanoma patient 3 cartridge 1 [NU3_1]

value: Primary cutaneous melanoma patient 3


title: Primary cutaneous melanoma patient 6 cartridge 1 [NU6_1]

value: Primary cutaneous melanoma patient 6


title: Primary cutaneous melanoma patient 12 cartridge 1 [NU12_1]

value: Primary cutaneous melanoma patient 12


title: Primary cutaneous melanoma patient 11 cartridge 1 [NU11_1]

value: Primary cutaneous melanoma patient 11


title: BS558_DP47_96_ADT

city: Basel

first: Marina

last: Natoli

state: Basel city

address: Hebelstrasse 20

department: DBM

country: Switzerland

institute: University Hospital Basel

description:
Antibody-derived oligonucleotide library matched to mRNA samples
Antibody-derived oligonucleotide (ADT)

library_source: other

data_processing:
Cell Ranger v5.0 was used for demultiplexing, alignment, filtering, barcode counting and UMI counting
Assembly: hg18
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: protein

source_name: Ovarian tumour

extract_protocol:
10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A)
3' paired end scRNAseq with CITE-seq

treatment_protocol: Libraires were prepared following the 10x Genomics protocol for 3′ gene expression profiling with feature barcoding (CG000206, Rev A) and cDNA or library quality was assessed using a 4200 TapeStation System (Agilent).

tag: patient id

value: Ovarian tumour

tag: treatment

tag: treatment time

tag: library type

value: ADT

tag: antibodies/tags

value: TotalSeqB TBNK cocktail BioLegend cat. 399902


title: BS558_PD1LAG3_96_ADT

tag: tissue


title: BS558_PD1TIM3_96_ADT


title: BS558_PD1_96_ADT


title: Primary tumor_11


title: BS1036_DP47_96_ADT

source_name: Melanoma metastasis

value: Melanoma metastasis


title: Vulvar melanoma patient V10 cartridge 2 [V10_2]

value: Vulvar melanoma patient V10


title: Primary tumor_10

value: Primary tumor


title: BS1036_PD1LAG3_96_ADT


title: Primary tumor_9

value: HER2+ breast cancer


title: Vulvar melanoma patient gyn 3 cartridge 1 [Gyn3T_1]

value: Vulvar melanoma patient gyn 3


title: Primary tumor_8


title: BS1036_PD1_96_ADT


title: Primary tumor_7


title: BS558_DP47_48_ADT


title: Primary tumor_5


title: BS558_PD1_48_ADT


title: Primary tumor_4


title: BS1036_PD1LAG3_48_ADT


title: Primary tumor_6


title: BS1036_DP47_48_ADT


title: BS1036_PD1TIM3_48_ADT


title: Primary tumor_2


title: Primary tumor_1


title: BS1030_DP47_96_ADT

source_name: Lung Tumour

value: Lung Tumour


title: BS1030_PD1TIM3_96_ADT


title: Metastatic tumor_6

source_name: Brain

value: Breast Cancer Metastasis to Brain


title: BS1030_PD1LAG3_96_ADT


title: Metastatic tumor_7


title: BS1036_PD1_48_ADT


title: BS1030_PD1_96_ADT


title: BS1030_DP47_48_ADT


title: Metastatic tumor_3

source_name: Lung

value: Breast Cancer Metastasis to Lung


title: Genome_Wide_CRISPR_Screen_TF1_LZTR1-KO_Day0_Replicate2

data_processing:
Library strategy: CRISPR screen
FASTQ files were trimmed using cutadapt (version 2.5) to remove sequences dervied from the sgRNA expression vector to yield the 20 b.p. sgRNA sequence only.
sgRNA counts were generated using MaGeCk (version 0.5.9.4) count command using options for read-depth normalization (--norm-method total).
Statistical comparisons between days 0 and 14 for each genotype were computed using MaGeCK test command using default parameters.
Genome_build: HG19
Supplementary_files_format_and_content: Counts matrix of non-normalized sgRNA counts

source_name: Erythroleukemia

growth_protocol: TF1 RIT1 mutant cells expressing Cas9-RFP or TF1 LZTR1 KO cells were transduced with lentivirus expressing human CRIPSR Brunello sgRNA library and puromycin selection (2 µg/ml) was performed in human GM-CSF containing media for 7 days.

extract_protocol:
Cell pellets were lysed and genomic DNA was extracted (NucleoSpin Blood XL, Takara) and quantified by Qubit (ThermoScientific). A quantity of gDNA covering 1,000X representation of gRNAs was PCR amplified using TaKaRa Ex Taq® DNA Polymerase (Takara) to add Illumina adapters and multiplexing barcodes.
Amplicons were quantified by Qubit and Bioanalyzer (Agilent), multiplexed, and sequenced on an Illumina HiSeq 2500 to obtain approximately 25e6 75b.p. single-end reads per sample.

treatment_protocol: Then, GM-CSF (Day 0) was washed out and surviving cells were harvested at 14 days after cytokine depletion (Day 14).

tag: cell line

tag: genetic perturbation

value: LZTR1 depletion by CRISPR/Cas9

tag: crispr sgrna library

value: Human sgRNA library Brunello in lentiCRISPRv2

tag: day of selection


title: BS1036_PD1TIM3_96_ADT

tag: cell type


title: Metastatic tumor_2


title: BS1030_PD1LAG3_48_ADT


title: Genome_Wide_CRISPR_Screen_TF1_LZTR1-KO_Day0_Replicate1


title: Metastatic tumor_4


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-M90I_Day14_Replicate2

value: RIT1-M90I expression by cDNA


title: BS558_PD1LAG3_48_ADT


title: Metastatic tumor_1


title: Primary tumor_3


title: Metastatic tumor_5


title: BS1030_PD1_48_ADT


title: Genome_Wide_CRISPR_Screen_TF1_LZTR1-KO_Day14_Replicate1


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-M90I_Day14_Replicate1


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-M90I_Day0_Replicate1


title: Ub-KO1-CHIP-seq-1

city: Wuhan

first: Chun

middle: Xian

last: Lan

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

data_processing:
For ChIP-seq ,Illumina Casava1.7 software used for basecalling, the adapter was trimmed by Trim galore(v0.6.2). Then these reads were aligned to the human reference genome GRCh38 using Bowtie2 (v2.3.4.2) with the default parameters.The uniquely mapped reads were sorted by Samtools (v1.9) and then performed peak calling by MACS2(v2.1.2) with the callpeak module (the parameter --call-summits --nomodel --extsize 150 -p 0.005). The bam files were converted to the bigWig signal files by DeepTools(v3.3.0) with the bamCoverage module ,Homer was used to annotated nearby genes from the peaks obtained from MACS2 and to find motif that enrich in the binding sequence.
Genome_build: GRCh38
Supplementary_files_format_and_content: bw

growth_protocol: PGP1 cells were maintained in mTeSR1 (StemCell Technologies) on Matrigel-coated cell culture plate at 37℃ with 5% CO2.

extract_protocol:
For ChIP-seq, the PGP1 cells (~5x10^6 cells/repeat)  were crosslinked in 1% formaldehyde for 10 min at room temperature with rotation. Cross-linking was stopped by incubating with 0.125M glycine for 5 min at room temperature with rotation.Then cells were collected and treated in  cell lysis buffer (10mM Tris-HCl (pH 8.0), 140 mM NaCl, 0.2% NP-40) plus1x cOmplete Protease Inhibitor (Roche) and incubated on ice for 10 min to isolate nuclei. After washed once with cold DBPS, isolated nuclei were sonicated in Nuclear lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) with 1x cOmplete Protease Inhibitor (Roche) in Diagenode Bioruptor Pico to obtain 200-500bp chromatin fragments. The sonication condition was 10 cycles of 20s/on and 30s/off.  After centrifuging, the soluble sonicated fragments were incubated with 5ug antibody and Protein A/G Dynabeads with rotating overnight at 4 °C to enrich fragmented chormatin.Then the DNA fragments were eluted with the elution buffer (100mM NaHCO3 and 1%SDS) and reverse crosslinked at 67 °C over night. Finally, the immunoprecipitation DNA were purified with Phenol-chloroform Protocol for chip-seq. The DNA were sent to Geekgene (Beijing, China) for ChIP-seq library construction and sequencing.
libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/variation

tag: chip antibody

value: H2AK119Ub (cell signaling technology, #8240)


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-M90I_Day0_Replicate2


title: BS1030_PD1TIM3_48_ADT


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-F82C_Day14_Replicate2

value: RIT1-F82C expression by cDNA


title: BS1014_PD1LAG3_96_ADT


title: BS1014_PD1TIM3_96_ADT


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-F82C_Day14_Replicate1


title: P5, NFPA tumor, scRNAseq

city: Bethesda

first: Prashant

last: Chittiboina

state: MD

address: 3D20, 10 Center Drive

department: NINDS

institute: NIH

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Adenoma

extract_protocol:
Fresh tumor samples were stored and transported in 0.9% NaCl or RPMI 1640 on ice. Samples were chopped into ~2-4mm3 sized pieces and dissociated using the Human Tumor Dissociation Kit in gentleMACS C tubes using the gentleMACS dissociator (Bergisch Gladbach, North Rhine-Westphalia, Germany). Samples were briefly centrifuged at 300 rpm for 30 seconds and filtered through a 70-nm strainer. The single cell suspensions were washed with 10 mL of RPMI 1640 and re-centrifuged at 2100 rpm for 5 minutes at 4 Celsius. Single-cell suspensions then underwent red blood cell (RBC) lysis using the RBC Lysis Solution 10X (Bergisch Gladbach, North Rhine-Westphalia, Germany). Following RBC lysis, non-viable cells were removed using the Dead Cell Removal Kit (Bergisch Gladbach, North Rhine-Westphalia, Germany). Single cell suspension quality, number and viability were assessed with a dual fluorescence cell counter Luna-FL (Logos Biosystems, Gyeonggi-do, South Korea).
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).

value: pituitary cells

value: Adenoma


title: BS1014_DP47_96_ADT

value: ADT


title: P4, GH normal, scRNAseq

description: 10x Genomics

source_name: Normal gland

value: Normal gland


title: BS1014_PD1_96_ADT

value: TotalSeqB TBNK cocktail BioLegend cat. 399902


title: P3, CD3 normal, scRNAseq

description: 10x Genomics


title: BS1014_DP47_48_ADT


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-F82C_Day0_Replicate1


title: Genome_Wide_CRISPR_Screen_TF1_RIT1-F82C_Day0_Replicate2


title: BS1014_PD1LAG3_48_ADT


title: P3, CD3 tumor, scRNAseq

description: 10x Genomics


title: BS1014_PD1TIM3_48_ADT


title: P4, GH tumor, scRNAseq

description: 10x Genomics


title: P2, CD2 normal, scRNAseq

description: 10x Genomics


title: 1171tfIIfa1-0-2

source_name: 6 day-old aerial parts

extract_protocol:
Total RNA was extracted using RNeasy kit (Qiagen®, Hilden, Germany) according to the supplier’s instruction
TruSeq_Stranded_mRNA_SamplePrep_Guide_15031047_D protocol (Illumina®, California, U.S.A.)

tag: genotype


title: Ub-CHIP-seq-1

source_name: iPSC

value: WT


title: P2, CD2 tumor, scRNAseq

description: 10x Genomics


title: 1171tfIIfa1-0-3


title: 1171tfIIfa1-0-1


title: P1, CD1, scRNAseq

description: 10x Genomics

source_name: Normal gland plus adenoma

value: Normal gland plus adenoma


title: 1171WTCol3-0-2


title: 1171WTCol3-0-3


title: BS558_DP47_96h

description:
3' mRNA library
poly A RNA

value: Ovarian tumour

value: mRNA


title: BS558_PD1TIM3_96h

description:
3' mRNA library
poly A RNA


title: BS558_PD1LAG3_96h

description:
3' mRNA library
poly A RNA


title: JB7_CD_Normal

data_processing:
Paired-end sequence files (.fastq) per sample were quality inspected using the FastQC tool 0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) then adaptor clipped (TruSeq3-PE-2.fa:2:30:10) and trimmed to remove 5' nucleotide bias (HEADCROP:12) and low quality calls (TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:15) using the Trimmomatic tool 0.39
Surviving intact pairs of reads per sample were then imported into the CLCbio Genomics Workbench v11 (https://www.qiagenbioinformatics.com/) and reference mapped by sample in stranded fashion against the current instance of the human genome (GRCh38) using the "RNA-Seq Analysis" tool supported therein under default parameters.
Expression in counts per known annotated gene (Homo_sapiens.GRCh38.96.chr.gff3) were then exported from the tool.
Analysis of bulk RNA sequencing data for paired core-margin samples was performed using the edgeR package on total exon counts per gene.
A paired analysis was performed with GLM-based approach was used with design matrix including patient and sample type. Genes were filtered by expression with filterByExpr, dispersion estimated with estimateDisp, and the GLM fit with glmFit. The log ratio test was used to detect differences between core vs margin or CD vs nonCD samples using glmLRT, and significant genes were recorded at FDR<0.01 and log fold-change > 1.5.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include nrmalized values for each Sample

source_name: Pituitary cells

extract_protocol:
Paired human adenoma and normal pituitary gland were procured from surgery and immediately flash frozen in 1 mL of Qiazol (Qiagen, Germany) within Lysing Matrix E tubes (MP Biomedicals, Santa Ana, CA) in dry ice. We thawed the contents and homogenized the tissues using a Fast Prep-24 Homogenizer, (MP Biomedicals) for 20 seconds at 4.5 m/s. Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Germany). RNA quantity and quality were measured by NanoDrop ND-1000, and integrity assessed by agarose gel electrophoresis. PolyA+ mRNA isolation, size fragmentation, cDNA synthesis, size selection, and next gen sequencing were performed at the National Intramural Sequencing Center, Bethesda, MD
RNA-Seq libraries were constructed from 1 μg total RNA after rRNA depletion using Ribo-Zero GOLD (Illumina). The Illumina TruSeq RNA Sample Prep V2 Kit was used according to manufacturer’s instructions.

value: Pituitary cells

tag: group

value: Normal


title: JB2_CD_Adenoma


title: BS1036_DP47_96h

description:
3' mRNA library
poly A RNA

value: Melanoma metastasis


title: BS558_PD1_96h

description:
3' mRNA library
poly A RNA


title: JB1_CD_Normal


title: dsGSK3beta3

city: Xinxiang

first: Libo

last: Hou

state: Henan

address: 110 Room, College of Fisheries, 46 Jianshe East Road

institute: Henan normal university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample ...

organism: Eriocheir sinensis

source_name: hemolymph

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hemolymph

value: hemocytes

tag: time point

value: EsGSK3β knockdown


title: dsGFP5

value: GFP knockdown


title: BS1036_PD1_96h

description:
3' mRNA library
poly A RNA


title: BS1036_PD1TIM3_96h

description:
3' mRNA library
poly A RNA


title: dsGSK3beta2


title: dsGFP6


title: Prl2-/- fetal liver cells [PRL2KO2_S36]

city: Chicago

last: Liu

state: Illinois

address: Northwestern University, 303 East Superior Street, Lurie 5-107

institute: Department of Medicine

data_processing:
Illumina NovaSeq 6000 sequencing.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Illumina NovaSeq 6000 sequencing.
Raw reads as mapped by STAR RNA-seq aligner.Unique reads as mapped by STAR.High quality reads from bamutils stats. Reads mapped to each different region from bamutils stats. Reads mapped on gene from featureCounts.
Supplementary files format and content: Raw reads as mapped by STAR RNA-seq.

source_name: fetal liver

growth_protocol: Prl2+/+ and Prl2-/- fetal liver cells were harvested from E14.5 day of fetal livers.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Clontech SMART-Seq v4 Ultra Low Input RNA Kit (Cat# ), 96 rxns; Illumina Nextera XT DNA Lib Kit.

treatment_protocol: Genotyping of each fetal were comfirmd by using DNeasy Blood & Tissue Kit (Qiagen, 69504)

value: fetal liver

tag: age

value: hematopoietic stem and progenitor cells


title: Prl2-/- fetal liver cells [PRL2KO1_S35]


title: BS558_DP47_48h

description:
3' mRNA library
poly A RNA

tag: patient id


title: dsGSK3beta1

tag: treatment


title: 1171WTCol3-0-1


title: JB8_CD_Normal

value: Adenoma


title: dsGFP3


title: BS558_PD1LAG3_48h

description:
3' mRNA library
poly A RNA

tag: treatment time


title: JB3_CD_Normal

value: Normal (adjacent)


title: BS558_PD1_48h

description:
3' mRNA library
poly A RNA

tag: library type


title: dsGFP2


title: BS1036_DP47_48h

description:
3' mRNA library
poly A RNA

tag: antibodies/tags


title: BS1036_PD1LAG3_96h

description:
3' mRNA library
poly A RNA

tag: tissue


title: Prl2+/+ fetal liver cells [WT2_S32]


title: dsGFP1


title: Prl2+/+ fetal liver cells [WT3_S33]


title: Prl2+/+ fetal liver cells [WT1_S31]


title: Prl2-/- fetal liver cells [PRL2KO3_S37]


title: dsCatenin3

value: Esβ-catenin knockdown


title: dsCatenin2


title: dPFC, tunnel4

city: Hangzhou

first: Chenlu

last: Xu

address: Xihu street

institute: Zhejiang university

data_processing:
FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast tool, which was used to merge paired-end reads (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3198573/).
Fastq to fasta format step was then processed using the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). Reads with fasta format were mapped to targeted Bisulfite Genome (hg19) by Blast (https://www.ncbi.nlm.nih.gov/pubmed/20003500). Unmapped reads were filtered and mapped reads with coverage greater than 90% and identity greater than 95% were kept as effective reads and were used for following statistics. Sequencing depth for each amplicon per sample was calculated by blasting the effective reads against the targeted genome region. Reads less than 10-fold were removed and overall sequencing depth for each sample were evaluated. Methylation and haplotype were analyzed using Perl script. Statistics were performed by t-test and ANOVA.
Assembly: mm10
Supplementary files format and content: Excel files include methylation level value of each sample
Library strategy: MethylTarget

source_name: dPFC

extract_protocol:
Genomic DNA was extracted with Animal Genomic DNA Rapid Extraction Kit. The integrity and quality of genomic DNA were detected by agarose gel electrophoresis and Nanodrop 2000, respectively.
The index PCR amplification products of all samples were mixed in equal quantities, and the final methyltarget sequencing library was obtained by tapping and recycling. The fragment length distribution of the library was verified by Agilent 2100 Bioanalyzer.

value: dPFC

tag: cultivar

value: ICR mice

value: tunnel (air pollution)


title: dPFC, tunnel2

value: WT


title: BS1036_PD1_48h

description:
3' mRNA library
poly A RNA

value: mRNA


title: dsCatenin1


title: dPFC, tunnel3


title: BS1030_DP47_96h

description:
3' mRNA library
poly A RNA

value: Lung Tumour


title: dPFC, tunnel1


title: BS1030_PD1LAG3_96h

description:
3' mRNA library
poly A RNA


title: dPFC, campus4

value: campus (control)


title: BS1030_PD1TIM3_96h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_2_RNA-seq]

city: Tianjin

first: Tong

last: Hao

state: China

department: College of Life Sciences

institute: College of Life Sciences, Tianjin Normal University

data_processing:
For RNA-seq, The original image data were transferred into sequencing data by base calling, which were defined as raw reads. Clean data (clean reads) were obtained by removing reads containing an adapter, reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30, and GC contents of the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Then, E. sinensis genome was downloaded from NCBI BioProject database (accession number PRJNA555707) and used as reference genome. 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. 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.
Assembly: accession number reference genome is PRJNA555707
Supplementary files format and content: narrowPeak files of peak information
Supplementary files format and content: excel files of differential genes from RNA_seq

growth_protocol: The healthy river crabs obtained from aquatic farm were cultured in a plastic incubator (70×40×50 cm) at 20±1◦C with natural light.

extract_protocol:
total RNA was extracted using the TRIzol method (Invitrogen) for RNA-seq analysis.
For RNA-seq analysis, RNA integrity was assessed using the RNA Nano 6000 Assay Kit of a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using a NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's recommendations. Library quality was assessed on the Agilent Bioanalyzer 2100 system and 150 bp paired-end reads were generated.

treatment_protocol: During collection of the samples, crabs with average weight of 8.41±1.47 g were put on the ice plate for low-temperature anesthesia. Muscle of each crab were quickly collected and put in liquid nitrogen immediately, and then transferred to −80◦C refrigerator for preservation.

value: muscle

tag: weight

tag: Stage

value: post-molt stage


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_3_RNA-seq]


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_1_RNA-seq]


title: dPFC, campus3


title: BS1030_PD1_96h

description:
3' mRNA library
poly A RNA


title: dPFC, campus2


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_3_RNA-seq]

value: pre-molt stage


title: BS1036_PD1LAG3_48h

description:
3' mRNA library
poly A RNA

value: Melanoma metastasis


title: PCGF6_ChIP-seq_rep2

data_processing:
For RNA-seq, Illumina Casava1.7 software used for basecalling,Sequenced reads were trimmed for adaptor sequence, the clean data were mapped to GRC38 whole genome using HISAT2 version 2.1.0 with parameters -p 64 --dta --rna-strandness RF -x.Raw reads were performed with FeatureCounts using gencode.v29.annotation.gtf.Raw counts were normalized to Transcripts Per Million (TPM).Gene expression difference was analyzed by Bioconductor R package DESeq2.
For ChIP-seq ,Illumina Casava1.7 software used for basecalling, the adapter was trimmed by Trim galore(v0.6.2). Then these reads were aligned to the human reference genome GRCh38 using Bowtie2 (v2.3.4.2) with the default parameters.The uniquely mapped reads were sorted by Samtools (v1.9) and then performed peak calling by MACS2(v2.1.2) with the callpeak module (the parameter --call-summits --nomodel --extsize 150 -p 0.005). The bam files were converted to the bigWig signal files by DeepTools(v3.3.0) with the bamCoverage module ,Homer was used to annotated nearby genes from the peaks obtained from MACS2 and to find motif that enrich in the binding sequence.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include the TPM values for each sample

growth_protocol: For RNA-seq and ChIP-seq  ,PGP1 cells were maintained in mTeSR1 (StemCell Technologies) on Matrigel-coated cell culture plate at 37℃ with 5% CO2.

extract_protocol:
For RNA-seq, the RNA was extracted with HiPure Total RNA Mini Kit (Magen, Cat#R4111-03).For ChIP-seq, the PGP1 cells (~5x106 cells/repeat)  were crosslinked in 1% formaldehyde for 10 min at room temperature with rotation. Cross-linking was stopped by incubating with 0.125M glycine for 5 min at room temperature with rotation.Then cells were collected and treated in  cell lysis buffer (10mM Tris-HCl (pH 8.0), 140 mM NaCl, 0.2% NP-40) plus1x cOmplete Protease Inhibitor (Roche) and incubated on ice for 10 min to isolate nuclei. After washed once with cold DBPS, isolated nuclei were sonicated in Nuclear lysis buffer (50 mM Tris-HCl (pH 8.0), 10 mM EDTA (pH 8.0), 1% SDS) with 1x cOmplete Protease Inhibitor (Roche) in Diagenode Bioruptor Pico to obtain 200-500bp chromatin fragments. The sonication condition was 10 cycles of 20s/on and 30s/off.  After centrifuging, the soluble sonicated fragments were incubated with 5ug antibody and Protein A/G Dynabeads with rotating overnight at 4 °C to enrich fragmented chormatin.Then the DNA fragments were eluted with the elution buffer (100mM NaHCO3 and 1%SDS) and reverse crosslinked at 67 °C over night. Finally, the immunoprecipitation DNA were purified with Phenol-chloroform Protocol for chip-seq. The DNA were sent to Geekgene (Beijing, China) for ChIP-seq library construction and sequencing.
For RNA-seq and ChIP-seq , the libraries were prepared for sequencing using standard Illumina protocols.

tag: cell line

value: PCGF6 (proteintech, 24103-1-AP)


title: BS1030_DP47_48h

description:
3' mRNA library
poly A RNA

tag: cell type


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_1_RNA-seq]


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_2_RNA-seq]


title: BS1030_PD1LAG3_48h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_3_ATAC-seq]

data_processing:
For ATAC-seq, Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). Q20 and Q30 of the raw data and clean data were calculated. These reads were aligned to a reference genome downloaded from NCBI BioProject database (accession number PRJNA555707) using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with MACS2 using ‘MACS2 call-peak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
Assembly: accession number reference genome is PRJNA555707
Supplementary files format and content: narrowPeak files of peak information
Supplementary files format and content: excel files of differential peaks from ATAC_seq

extract_protocol:
nuclei were extracted from muscle samples for ATAC-seq anlysis.
For ATAC-seq analysis, the nuclei pellet was re-suspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min. Equimolar Adapter1 and Adatper 2 were added after transposition. PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated.

tag: molecule type

value: nuclei pellet


title: BS1036_PD1TIM3_48h

description:
3' mRNA library
poly A RNA


title: BS1030_PD1TIM3_48h

description:
3' mRNA library
poly A RNA


title: BS1030_PD1_48h

description:
3' mRNA library
poly A RNA


title: PCGF6_ChIP-seq_rep1

tag: genotype/variation

tag: chip antibody


title: BS1014_DP47_96h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_2_ATAC-seq]


title: muscle sample of Eriocheir sinensis in post-molt stage [Emu_A_1_ATAC-seq]


title: Input_rep1


title: BS1014_PD1LAG3_96h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_3_ATAC-seq]


title: PCGF6KO2_rep1


title: BS1014_PD1TIM3_96h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_1_ATAC-seq]


title: dPFC, campus1

tag: genotype


title: PCGF6KO1_rep2


title: BS1014_PD1_96h

description:
3' mRNA library
poly A RNA


title: muscle sample of Eriocheir sinensis in pre-molt stage [Emu_D_2_ATAC-seq]


title: PCGF6KO2_rep2


title: BS1014_PD1LAG3_48h

description:
3' mRNA library
poly A RNA


title: PCGF6KO1_rep1


title: BS1014_DP47_48h

description:
3' mRNA library
poly A RNA


title: Input_rep2


title: BS1014_PD1TIM3_48h

description:
3' mRNA library
poly A RNA


title: CD4 T cells, Control Day 0 rep 4

status: Public on Jul 15 2022

city: Tampa

first: Rebecca

last: Hesterberg

address: 12902 Magnolia Dr.

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 mm10 reference genome using star v2.5.3a with default settings.
Uniquely mapped reads were counted at gene-level by HTSeq (version 0.6.1) using Gencode vM21 annotations for mouse
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes normalized gene count for each sample

source_name: Spleen

extract_protocol:
CD4 T cells were isolated using immunomagnetic negative selection. T cells were then pelleted and RNA was extracted using a commercial kit (Macherey-Nagel)
100ng RNA was used to prepare libraries for sequencing using Nugen Mouse RNA-seq kit

tag: strain

value: control

tag: time point

value: Day 0

value: spleen

value: CD4 T cell


title: CD4 T cells, Control Day 0 rep 1


title: CD4 T cells, Control Day 0 rep 5


title: WT_rep1


title: CD4 T cells, Control Day 0 rep 2


title: CD4 T cells, Late Day 14 rep 3

value: C57Bl/6 mice transplanted with Eu-Myc lymphoma cells

value: Day 14


title: CD4 T cells, Late Day 14 rep 2


title: CD4 T cells, Control Day 0 rep 3


title: WT_rep2


title: CD4 T cells, Early Day 7 rep 5

value: Day 7


title: CD4 T cells, Late Day 14 rep 4


title: CD4 T cells, Early Day 7 rep 2


title: CD4 T cells, Early Day 7 rep 6


title: CD4 T cells, Late Day 14 rep 1


title: Hetero_1.5years

city: Tokyo

first: Tomoko

last: Tanaka

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in the hippocampus of the Rp58 hetero-KO mice at 12-18 months

hyb_protocol: 0.6 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (G4852B) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 3µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: Hetero, Hippocampus, 18 months

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng of total RNA using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: All mice were maintained under a 12:12 h light/dark cycle (lights on at 8:00 AM).

extract_protocol: Three independent total RNA samples from each group were mixed and purified using a RNeasy Plus Universal Kit (Qiagen, Hilden, Germany).

tag: age

value: 18 months

value: Hippocampus

value: Rp58 hetero-KO


title: CD4 T cells, Early Day 7 rep 4

tag: treatment


title: Hetero_4months

description: Gene expression in the hippocampus of the Rp58 hetero-KO mice at 4 months

source_name: Hetero, Hippocampus, 4 months

value: 4 months


title: CD4 T cells, Early Day 7 rep 1


title: CD4 T cells, Early Day 7 rep 3


title: HeLa parental cell line rep 2

city: Rome

first: Grazia Daniela

last: Raffa

address: P.le Aldo Moro 5

country: Italy

institute: Sapienza Università di Roma

data_processing:
Primary data acquisition was performed by MinKNOW.
Basecalling and demultiplexing of Fast5 files obtained by sequencing were performed using Guppy v4.2.2.
Reads with Q-score >7 were mapped to hg38 genome using Minimap2 v2.17 with parameters -ax splice.
To assemble and quantify transcripts from Nanopore reads we used FLAIR v1.4. BAM files obtained with Minimap2 were converted into BED12 files using the bam2Bed12.py utility included in FLAIR. After this, splice junctions of reads were corrected using FLAIR correct module using both the GENCODE v33 GTF file and short Illumina reads of the  corresponding samples. BED12 files were then filtered to maintain only reads with at least one splice junction.
Filtered BED12 files from all samples were used to assemble the transcriptome using the FLAIR collapse module, providing the GENCODE GTF file to annotate the results and requiring at least 10 supporting reads to identify novel transcripts. Transcripts from both the GENCODE and FLAIR GTF files were quantified using the FLAIR quantify module.
Genome_build: hg38
Supplementary_files_format_and_content: GTF file describing the transcriptome assembled by FLAIR.
Supplementary_files_format_and_content: Tab-delimited text file including TPM values in each sample calculated for each transcript assembled by FLAIR.

source_name: HeLa

growth_protocol: HeLa S3 cells were cultured in DMEM supplemted with 10% Fetal Bovine Serum and Penicillin-Streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted with Trizol reagent (Ambion), treated with Ambion™ DNase I (RNase-free) extracted with phenol/chloroform. RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA).
RNA libraries were prepared for Oxford Nanopore MinION  sequencing using PCR-cDNA Barcoding (SQK-PCB109) protocol.

value: Cervical adenocarcinoma

value: wild type


title: HeLa TGS1 CRISPR mutant clone 2


title: BS1014_PD1_48h

description:
3' mRNA library
poly A RNA

source_name: Lung Tumour

tag: patient id

value: Lung Tumour

tag: treatment time

value: mRNA


title: HeLa SMN CRISPR mutant clone 2

value: SMN -/-


title: WT_4months

description: Gene expression in the hippocampus of the wild-type mice at 4 months

source_name: WT, Hippocampus, 4 months

value: WT


title: CD4 T cells, Early Day 7 rep 7


title: HeLa SMN CRISPR mutant clone 1


title: WT_1.5years

description: Gene expression in the hippocampus of the wild-type mice at 12-18 months

source_name: WT, Hippocampus, 18 months


title: HeLa parental cell line rep 1


title: HepG2 cell, mock sample for ATF4 overexpression condition

first: Sihui

last: Ma

address: Yayoi 1-1-1

institute: The university of Tokyo

description: Gene expression data of HepG2 cell under ATF4 overexpression condition, mock

hyb_protocol: After washing and staining, array scanning was performed using GeneChip Hybridization and Affymetrix Gene Array Scanner 3000

data_processing: The data were analyzed with Transcriptome Analysis Console using Affymetrix default analysis settings and global scaling as normalization method.

source_name: HepG2 cell, ATF4 overexpression condition, mock

label_protocol: For global miRNA expression profiling, total RNA (1000 ng) was labeled using the FlashtagTM RNA Labeling Kit.

growth_protocol: Human hepatocellular carcinoma cells (HepG2) were obtained from the American Type Culture Collection (Rockville, MD, USA) and cultured in Dulbecco's modified Eagle's medium (DMEM; Sigma-Aldrich, St. Louis, MO, USA) containing 10% (v/v) fetal bovine serum (Sigma-Aldrich) and 1% (v/v) penicillin-streptomycin (Sigma-Aldrich) at 37 °C and 5% (v/v) CO2 atmosphere.

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

treatment_protocol: HepG2 cells were seeded on 6-well plates at 70–80% confluent density and cultured for 24 h in antibiotic-free DMEM.  For leucine starvation, the cells were grown in minimum essential medium (Sigma-Aldrich) lacking leucine but supplemented with 10% (v/v) fetal bovine serum. Before starvation, the cells were rinsed twice with phosphate-buffered saline (Gibco, Waltham, MA, USA).For overexpression experiments, ATF4-overexpressing plasmid and pcDNA3.1 empty vector were transfected into HepG2 cells using Invitrogen Lipofectamine 2000 (Thermo Fisher Scientific) following the manufacturer's instructions. After 6 h, the culture medium was replaced with a complete medium and incubated for further 24 h.

value: ATF4 overexpression, mock