title: control_1

description:
US11263921_257403611528_S01_GE2_1200_Jun14_1_1.txt
Gene expression from the colon mucosa of a male rat fed a control diet (10% w/w cellulose)
PAm1

source_name: Colon mucosa of a rat fed a control diet, replicate 1

value: Wistar

value: male

tag: date

value: cellulose

tag: sample type

value: control

tag: tissue type

tag: cage

tag: slide

tag: slide position

tag: rin


title: Normal Lung_1

status: Public on Dec 01 2023

type: SRA

city: Hangzhou

first: Yao

last: Chen

state: Zhejiang

address: 866 Yuhangtang Rd

department: School of Medicine

country: China

institute: Zhejiang University

description: Microwell-seq analysis

library_source: transcriptomic

data_processing:
Data were aligned to the Homo sapiens GRCh38 genome using STAR 2.5.2a
The DGE data matrices were obtained using the Dropseq Core Computational Protocol  with default parameters
Downstream standard procedures for filtering, variable gene selection, dimensionality reduction and clustering were performed using the Seurat 2.4.3 in R3.5.0
Cellphonedb was to used to make ligand-receptor analysis
GRN analysis were performed using the CellRouter in R3.5.0
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

molecule: total RNA

organism: Homo sapiens

source_name: Normal Lung

growth_protocol: untached tissues

extract_protocol:
Cold lysis buffer (0.1 M Tris-HCl pH 7.5, 0.5 M LiCl, 1% SDS, 10 mM EDTA, and 5 mM dithiothreitol) was pipetted over the surface of the plate and removed after 12 min of incubation. The beads were then collected. After reverse transcription, exonuclease I treatment and cDNA amplification, the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparations were performed with the Microwell-seq protocol

treatment_protocol: Donated tissues were transported on ice, transferred to cold DPBS, and minced into ~1-mm pieces on ice using scissors. The samples were treated with various enzymes for different amounts of time.

tag: source id

value: embryo 2

tag: karyotype

value: diploidy

tag: age

value: 22 weeks

tag: tissue

value: Lung


title: plasma, subject 01c05642T8

type: protein

city: New York

first: Pushkala

last: Jayaraman

state: New York

address: 1 Gustave Levy Pl

department: Charles Bronfman Institute of Personalized Medicine

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: See https://www.synapse.org/#!Synapse:syn35874390/ for full clinical data and associated metadata including detailed description for process workflow.

hyb_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

data_processing:
As described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Preliminary normalization (no log2 transformation) procedure as per Somalogic guidelines. The code workflow creates the normalizations prior to running the linear model.  More details, see Data-Preprocessing section as described in Su, C.-Y. et al. Circulating proteins to predict adverse COVID-19 outcomes. medRxiv, 2021.2010.2004.21264015, doi:10.1101/2021.10.04.21264015 (2021).
Script used to analyze the data is available at:
https://github.com/Nadkarni-Lab/aki_covid_proteomics

molecule: protein

source_name: serum

extract_protocol: Blood samples were collected in Serum Separation Tubes (SST) with a polymer gel for serum separation as previously described in Del Valle DM, Kim-Schulze S, Huang HH, et al. An inflammatory cytokine signature predicts COVID-19 severity and survival. Nat Med. 2020. Samples were centrifuged at 1200 g for 10 minutes at 20°C. After centrifugation, serum was pipetted to a 15 mL conical tube. Serum was then aliquoted into cryovials and stored at -80°C.

tag: subject id

tag: blood sample id

tag: Sex

value: Male

tag: days since first sample

tag: patient classification at first sample

tag: covid-19 status

value: Positive

value: Yes

tag: instrument model

value: Somascan discovery platform v4


title: plasma, subject 01c05642T21

scan_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: No


title: zmuvr8-1_White_2

city: Shenzhen

first: Zhao

last: Zhiwei

state: Guangdong

address: 1066, Xueyuan Rd

department: College of Life Sciences and Oceanography

institute: Shenzhen univerisity

data_processing:
Illumina software used for basecalling.
Sequenced reads were processed using Trimmomatic(Version0.36), The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2(Version2.2.1.0).
Then quantified read counts per gene and normalized Fragments Per Kilobase exon per Million reads mapped (FPKM) values using Cufflinks TopHat（version:2.2.1）
FPKM and read counts valueof each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq(Version1.18.0)(2012) functions estimateSizeFactors and nbinomTest.
Assembly: B73_RefGen_v4_gramene_63
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Zea mays

source_name: leaf

growth_protocol: 7 days of B73 and zmuvr8-1 seedlings  grown in low white light

extract_protocol:
total RNA was isolated using RNAiso Plus kit (Takara Bio, Shiga, Japan)
The RNA library generation process followed the manufacturer’s protocol for the Illumina TruseqTM RNA sample prep Kit

treatment_protocol: treat with or without UVB treatment 1 hour

value: leaf

tag: developmental stage

value: 7 DAY OLD

tag: genotype

value: zmuvr8-1 mutant

tag: treatment

value: white light


title: A549 xenografts exposed to 7.5mg/kg dacomitinib,  replicate 1, scRNAseq

city: Shanghai

first: Yu

last: Yangziwei

state: Shanghai

address: 上海市浦东新区周祝公路279号

description: BD Rhapsody

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads of the cDNA library were processed through the BD Rhapsody Whole Transcriptome Assay Analysis Pipeline.
Assembly: hg18,mm9
Supplementary files format and content: Tab-separated values files and matrix files

organism:
Homo sapiens
Mus musculus

source_name: lung cancer

extract_protocol:
Mice were obtained from JiHui Laboratory Technology Co., Ltd. (China). All experimental protocols were approved by Shanghai University of Medicine and Health Sciences and mice were treated and sacrificed in accordance with the institutional guidelines for animal care. All mice were housed in a Specific Pathogen Free (SFP) environment at a suitable temperature (23±2 °C) and humidity (60±5 %) with a 12-h day/night cycle. 5 × 106 A549 cells were subcutaneously injected into the ventral flank of female nude mice (4 to 6 weeks old). After a few weeks，the tumors reached higher than 150 mm3 in volume calculated from the formula V = (length × width2)/2 using calipers, according to the report previously described(10). Mice were randomized into three groups gavaged through oral with vehicle (1% w/v CMC-Na, dissolved in sterile water), 7.5 mg/kg dacomitinib and 15 mg/kg dacomitinib, respectively. Mice were weighted and tumor sizes were measured every two or three days.
Single Cell preparation, library construction, sequencing and preliminary analysis were performed by Sinotech Genomics Co., Ltd. Shanghai, China. Each specimen was washed extensively in HyClone™ RPMI 1640 media, weighed, and enzymatically digested in 10 ml RPMI 1640 media supplemented with Collagenase type I (0.2 mg/mL，A004194, sangon, Shanghai, China), Collagenase type IV (0.2 mg/mL, A004186, sangon), Neutral Protease (0.1 mg/mL, A002100, sangon) and DNase I (0.01 mg/mL, B300065, sangon) for 1.5 h at 37°C with agitation. The mixture was strained consecutively through 70 μm and 40 μm cell strainers, washed twice in PBS, and centrifuged at 400 g for 5 minutes. After quenching digestion with excess RPMI-1640 medium, filtered single cell solutions were kept on ice until they were loaded into the BD Rhapsody system (BD, San Jose, CA) for single cell transcriptome isolation.   The final library was generated using microbead-captured single cell transcriptome as the manufacturer’s protocol. The final cDNA library was generated from double strand full length cDNA by random priming amplification with the BD Rhapsody cDNA Kit (633773, BD Biosciences) and the BD Rhapsody Targeted mRNA & AbSeq Amplification Kit (633774, BD Biosciences). All the libraries were sequenced in a PE150 mode (Pair-End for 150bp read) in the X Ten instrument (Illumina, San Diego, CA).

tag: cell type

value: lung cancer

value: 4-6 weeks old


title: wt-blood, scRNA-seq

city: nanjing

first: XU

last: Ying

state: jiangsu

address: xuanwu district

institute: Nanjing university

description: 10x Genomics

data_processing:
the demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files for scRNA-seq samples.

organism: Mus musculus

source_name: peripheral blood

extract_protocol:
21-week-old male db/db and wt mice (n = 3 each) were used for scRNA-seq analysis. Peripheral blood (200 μl /group) was collected by retro-orbital bleeding and collected in heparin tubes. Red blood cells were lysed by resuspension in 1 ml lysis buffer (BD Biosciences) for 15 min at RT, protected from light. 2 ml PBS containing 1% fetal bovine serum were added to stop lysis followed by centrifugation at 200 x g for 5 min, aspirating supernatant and repeating the lysis procedure once. Cells were washed twice with 2 ml PBS + 1% fetal bovine serum and re-suspended in 100 μl PBS + 1% fetal bovine serum.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cells 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.

value: peripheral blood

tag: strain

value: 21 weeks old

value: male

value: peripheral immune cells

value: wild-type


title: 10X_tdT_bleo_2w

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

data_processing:
Cell Ranger (v3.0.0) was used to process single cell 3' RNA-seq ouput. First, cell ranger mkfastq demultiplexed illumina BCLs into fastq files.
Then, using cell ranger count, reads were aligned to mm10 mouse reference genome.
Aligned reads were then read by Seurat (v4.0.4) and cell-gene raw expression matrices were made. Then, low quality cells (expressing less than 800 genes), potential doublets (expressing more than 6000 genes),potential dead cells (>10% mitochondrial gene percentage) and contaminating CD31- cells were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat to produce processed data files.
Dimensionality reduction, clustering and differential expression testing were performed using R package Seurat
Assembly: mm10
Supplementary files format and content: Cell-gene expression matrix of log normalized UMI counts for ECs following bleomycin administration (bleo_2w & bleo4w) or pneumonectomy (pnx_1w & pnx_4w) in WT(tdT mouse) or Kitl deleted mouse

source_name: Bleomycin 2 weeks lung EC

extract_protocol:
FACS sorted lung tdTomato+ cells and endothelial cells were processed on the 10X chromium system following the manufacturer's protocols
Using 10x single cell RNA sequencing 3' NEXT GEM v3.1 reagent Kit (10X genomics), cDNA libraries were constructed

treatment_protocol: Mice were pre-treated with tamoxifen to induced tdTomato expression in Apln expressing cells

tag: cell sorting

value: FACS sorted

value: lung EC

value: Adult

value: control

value: Bleomycin 2 weeks


title: B73_White+NUVB_3

value: Wild-type

value: 1 hour NUVB


title: plasma, subject 009619bdT4

label_protocol: As described in https://www.somalogic.com/wp-content/uploads/2016/08/SSM-002-Rev-3-SOMAscan-Technical-White-Paper.pdf

value: Male

value: Positive

value: Yes

value: Somascan discovery platform v4


title: CKO-MII4

city: Nanjing

first: zhang

middle: hui

last: ru

address: 101 Longmian Avenue

institute: Nanjing Medical University

data_processing:
Samples were collected in tubes cointaining lysis component,and then amplified by Smart-Seq2 method.Single cell RNA was used as template,and primers containing Oligo(dT) were used as reverse transcription primers to bind mRNA with poly(A) tail to synthesize the first chain.In addition,several template-independent base C can be added to the end of the synthesized new strand,and a second strand can be synthezised using the newly sythesized strand as a Template by template-switching activity of reeverse transcriptase to obtain double-stranded cDNA.The same primer sequences were introduced at both ends of cDNA in reverse transcription process,which could achieve the unbiased amplification of cDNA ,and then the Tn5 transposable enzyme was used to construct the library for the second generation sequencing).
Supplementary files format and content: tab-delimited text files include reads numbers,Length, RPKM values for each Sample

source_name: ovary

extract_protocol:
Every fifteen oocytes were collected in tubes with  lysis component.
RNA libraries for sequencing  were prepared using standard Illumina protocols

value: MII oocyte

value: post natal day 35


title: plasma, subject 009619bdT1

value: No


title: 10X_scf_ct

source_name: scf-deleted Control lung EC

growth_protocol: 10x single cell RNA sequencing 3' NEXT GEM v3.1

value: scf-deleted


title: plasma, subject 009619bdT0


title: 10X_tdT_ct

source_name: Control lung EC


title: zmuvr8-1_White_3

value: leaf

value: 7 DAY OLD

value: zmuvr8-1 mutant

value: white light


title: B73_White_2


title: WT-MII2


title: WT-MII1


title: plasma, subject 005cd7b9T1


title: plasma, subject 0028c054T1

value: Female

value: Negative


title: db-blood, scRNA-seq

description: 10x Genomics

value: peripheral blood

value: 21 weeks old

value: male

value: peripheral immune cells

value: db/db


title: zmuvr8-1_White_1


title: B73_White_1

value: Wild-type


title: PDX_WGBS_tumor

city: Heidelberg

first: Leo

middle: Carl

last: Förster

state: Deutschland

address: Im Neuenheimer Feld 581

country: Germany

institute: DKFZ

library_source: genomic

data_processing:
We generated a combined human-mouse reference genome with bismark_genome_preparation to map reads using Bismark v0.20 with Bowtie2 v2.3.5.1. Paired reads were trimmed by trim_galore v0.5.0, and single-end reads individually mapped to the combined human-mouse reference with Bismark, setting "–q -N 1 -D 30 -R 3 -p 6 with --non_directional". PCR duplicates were removed using deduplicate_bismark, and mate-pairs recombined by merging deduplicated R1 and R2 BAMs with samtools merge. Finally, we ran the bismark_methylation_extractor tool with "--bedGraph" to quantify DNA methylation and counted CpG coverage using coverage2cytosine. The resulting CpG coverages were parsed and mouse and human methylation fractions per CpG determined separately.
hg38, mm10
comma separated matrix of detected CpGs (rows) average methylation and coverage (columns) per sample

molecule: genomic DNA

source_name: Brain tumor, brain

extract_protocol:
Genomic DNA from each coronal brain section was isolated using QiaAmp DNA microkit.
The protocol for bisulfite conversion and library preparation was adapted based on the genomic part of the scNMT-seq protocol (Cerrizuela, S. and Kaya, O. et al., STAR Protoc., 2022 based on Clark et al., 2018) with the following modifications: The gDNA input was adjusted to 100/20/4ng per sample. The number of first-strand purification cycles was decreased to 4 runs, and library amplification reaction was performed in 10 cycles.

value: Brain tumor, brain

value: TCF-Lef EGFP, TCF-Lef SFRP1, WT


title: Third instar CNS, gTET2

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

description:
TET_fusion_all.xlsx
Sample 5

data_processing:
Illumina Hiseq2500 reads were trimmed using Trimmomatic and checked  with FASTQC
Illumina reads were aligned to the Drosophila reference genome (dm6 Ensembl release 70) with Hisat2
Read counts were generated for each annotated gene using HTSeq-Count. RPKM (Reads Per Kilobase of exon per Megabase of library size) values were calculated using Cufflinks. Reads normalization, variance estimation and pair-wise differential expression analysis with multiple testing correction were conducted using the R Bioconductor DESeq2 package
SMRT-seq reads were aligned using pbmm2 tool (https://github.com/PacificBiosciences/pbmm2) on Drosophila genome (dm6 Ensembl realease 70)
6mA detection was performed on every samples and on merged ones with IpdSummary tool from KineticTools (http://github.com/PacificBiosciences/kineticsTools) applying following parameters: --identify m6A --numWorkers 16 --pvalue 0.01 --identifyMinCov 5 –methylFraction
Assembly: Drosophila genome (dm6 Ensembl release 70)
Supplementary files format and content: text file with RNA-seq expression
Supplementary files format and content: Excel file with 6mA detected localization and scores

organism: Drosophila melanogaster

source_name: central nervous system

extract_protocol:
Third instar CNS were dissected in ice cold PBS. Samples 1-6: Tissues were crushed in lysis buffer (100 mM Tris-HCl pH9, 1 mM EDTA, 1% SDS), digested with RNAse A for 15 min at room temperature and 30 min at 65°C, before being incubated with 4 volumes of 3.2 M LiCl, 0.9 M KAc for 30 min at 4°C. After centrifugation at 12000 g for 20 min at 4°C, the supernatant was extracted  with phenol-chloroform-isoamyl alcohol and DNA was precipitated with isopropanol. Samples 7-11:RNAs were extracted with Qiagen RNeasy Plus Micro kit and samples were converted to cDNA using Nugen’s Ovation RNA-Seq System.
Samples 1-6: libraries were prepared using a SMRTbell Express 2 Template prep kit. Samples 7-11: library preparation was performed using Kapa Biosystems library preparation kit.
Samples 1-6: SMRT-seq. Samples 7-11: RNA-seq

value: central nervous system

value: third instar larvae

value: tet null


title: CKO-MII3

value: MII oocyte

value: post natal day 35


title: CKO-MII2


title: Third instar CNS, gTET1

description:
TET_fusion_all.xlsx
Sample 4


title: B73_White+NUVB_2

value: leaf

value: 7 DAY OLD

value: 1 hour NUVB


title: WT-GV4

data_processing:
Samples were collected in tubes cointaining lysis component,and then amplified by Smart-Seq2 method.Single cell RNA was used as template,and primers containing Oligo(dT) were used as reverse transcription primers to bind mRNA with poly(A) tail to synthesize the first chain.In addition,several template-independent base C can be added to the end of the synthesized new strand,and a second strand can be synthezised using the newly sythesized strand as a Template by template-switching activity of reeverse transcriptase to obtain double-stranded cDNA.The same primer sequences were introduced at both ends of cDNA in reverse transcription process,which could achieve the unbiased amplification of cDNA ,and then the Tn5 transposable enzyme was used to construct the library for the second generation sequencing).
Supplementary files format and content: tab-delimited text files include reads numbers, length, RPKM values for each Sample

value: oocyte


title: SYSH-MPT-01 cells, CD146sh [M2]

city: Guangzhou

first: Nie

last: Yan

address: 107 Yangxi Road, Yuexiu District,

department: Sun Yat-sen Memorial Hospital,

institute: Sun Yat-sen University

data_processing:
The sequenced raw data is first filtered using SOAPnuke (v1.5.6) to filter out reads that containing the joint, with unknown base N content greater than 5% and low-quality reads. The clean data was aligned to the reference genome and quantitated gene expression was performed by using Salmon (v1.9.0) software.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: quant.txt for processed data

molecule: polyA RNA

extract_protocol:
350 ΜL Buffer TRIzol was added, the cells were lysed by vortex or mixed with pipette, and left at Ultra-low temperature refrigerator. The following cells' RNA extract was performed according to the protocol of Qiagen RNeasy Micro Kit.
Feature Extraction software

tag: cell line

value: breast phyllodes tumors

value: CD146 knockdown


title: B73_White+NUVB_1


title: SYSH-MPT-01 cells, Control [M1]

value: WT


title: WT2

first: sejie

last: yu

address: 1017 East Gate North Road

institute: The Second Clinical Medical College, Jinan University

data_processing:
Data filtering  The sequencing data was filtered with SOAPnuke [1] by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification  Bowtie2[2] was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) [3]. The heatmap was drawn by pheatmap (v1.0.8) [4] according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5) [5] (or DEGseq[6] or PoissonDis[7])with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) [8].
Assembly: GCF_000002035.6_GRCz11
Supplementary files format and content: text file includes raw counts for each Sample
Supplementary files format and content: text files include RPKM values for each Sample

organism: Danio rerio

source_name: genotype

extract_protocol:
The sample RNA was extracted and purified using the Qiagen kit
1Select the corresponding testing methods for quality inspection according to the requirements of samples and products.                                                                            2 mRNA Isolation 3 mRNA Fragmentation 4 cDNA Synthesis 5 End Repair, Add A and Adaptor Ligation 6 The PCR reaction system and program are configured and set up to amplify the product. 7 Library QC 8 Circularization Single-stranded PCR products are produced via denaturation. The reaction system and program for circularization are subsequently configured and set up. Single-stranded cyclized products are produced, while uncyclized linear DNA molecules are digested. 9 Sequencing

value: genotype

value: Wile Type


title: pikfyve3


title: AGS cells infected with shGABRD, biological rep2

type: RNA

city: Chengdu

first: Weibing

last: Leng

state: Sichuan

address: West China Hospital of Sichuan University, 37 Guoxue Xiang, Chenngdu, Sichuan Pr

department: West China Hospital

institute: Sichuan University

description: Gene expression from data AGS cells infected with shGABRD.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix human GeneChip Clariom S and the outcomes were scanned by Affymetrix Scanner 3000.

data_processing: The raw data about gene chips were normalized by using an RMA algorithm provided by Limma package. The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: 3’ IVT Biotin Label

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: AGS cells in logarithmic growth stage were prepared into cell suspension, and then 2 × 10^5 cells were added to the 6-well plate. After 24 h, lentivirus infection solution with shGABRD (GABRD knockdown) or shCtrl (negative control) was added to the 6-well plate at a virus titer of 1 × 10^8 TU/mL. After 20 h, the medium was changed once. The cells were continued to be cultured for 72 h.

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

treatment_protocol: AGS cells were collected after 48 h of infection with lentivirus, and the total RNA was extracted from them using Trizol (Sigma).

value: AGS

tag: shRNA

value: shGABRD


title: SYSH-BPT-01 cells, CD146OE [B2]

value: CD146 overexpression


title: Third instar CNS, gWT2

description:
WT_fusion_all.xlsx
Sample 2

value: central nervous system


title: SYSH-BPT-01 cells, Control [B1]


title: CKO-GV4

tag: age


title: Third instar CNS, gTET3

description:
TET_fusion_all.xlsx
Sample 6

tag: tissue

value: third instar larvae


title: WT-GV1


title: CKO-GV2


title: AGS cells infected with shCtrl, biological rep3

description: Gene expression from data AGS cells infected with shCtrl.

value: shCtrl


title: WT1


title: Third instar CNS, gWT1

description:
WT_fusion_all.xlsx
Sample 1


title: pikfyve2


title: BHLH156

status: Public on Nov 28 2023

city: Beijing

first: Qiang

last: Huo

address: Yuanmingyuan West Road

institute: China Agricultural University

data_processing:
Illumina software used for base calling
Trimmomatic (version 0.39) was used to trim the fastq files as follows: ILLUMINACLIP: TruSeq3-PE-2.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15, HEADCROP:0, MINLEN:75 and bowtie2 (version: 2.4.1)  was used to align them to the B73 v4 reference genome with the following parameters: -I 75 -X 1000 --no-discordant --no-mixed.
Peaks were called using GEM v3.4 with the following parameters: --d Read_Distribution_default.txt --k_min 4 --k_max 12 --outNP --q 3 --nrf --outNP --outHOMER –outMEME. Blacklisted peaks were subtracted to created to create final narrowPeak file.
Supplementary files format and content: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: DAP-seq

growth_protocol: B73 inbred line cultivated in the greenhouse of China Agricultural University (Beijing, China)

extract_protocol:
gDNA was extracted from maize B73 14 DAG leaf. gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (cat. no. NG101, TIANGEN) according to the manufacturer’s instructions.
gDNA libraries was prepared using TIANSeq DirectFast Library Kit (illumina) (cat. no. NG101, TIANGEN) according to the manufacturer’s instructions. Full length maize transcription factors’ coding sequences were cloned from maize 14 DAG leaf cDNA into the NotI and AscI sites of pUC57-Halo using MultlF Seamless Assembly Mix (cat. no. RM20523, ABclonal). Protein expression was using TNT SP6 High-YIELD Wheat Germ Master Protein Expression System (cat. no. L3260; Promega) according to the manufacturer’s instructions. Halo-fusion protein was bound to Magne HaloTag Beads (cat. no. G7281; Promega) and washed three times using TBSN buffer( 100 mM Tris buffer, pH 7.5, 50 mM NaCl, 0.005 % NP40). Then, 500 ng gDNA libraries was added and incubated at room temperature for 1.5 h. After incubation the beads was washed four times. Resuspended the beads in 30µl of EB buffer to recover DNA. The recovered DNA was were cleaned up with Silane magnetic beads, and amplified via PCR. The PCR products were cleaned up with Silane magnetic beads and sequenced using an NovaSeq platform (Illumina) by BerryGnomics.

tag: cultivar

tag: gene id

value: 14 DAG


title: WT-MII3

value: MII oocyte

value: post natal day 35


title: B73_White_3

value: leaf

value: 7 DAY OLD

value: Wild-type

value: white light


title: pikfyve1


title: CKO-GV1

value: oocyte


title: WT3


title: Third instar CNS, gWT3

description:
WT_fusion_all.xlsx
Sample 3


title: WT-GV2


title: ABI33


title: EREB18


title: MYB121


title: ZAG2


title: MYBR98


title: TCPTF40


title: EREB65


title: MYBR19


title: AGS cells infected with shGABRD, biological rep1


title: HSFTF17


title: AGS cells infected with shGABRD, biological rep3


title: WRKY123


title: WRKY102


title: NKD1


title: AGS cells infected with shCtrl, biological rep2


title: BZIP121


title: NACTF67


title: MYBR13


title: AGS cells infected with shCtrl, biological rep1


title: MYB155


title: MYB83


title: NACTF134


title: EREB211


title: PBF1


title: MYBR111


title: GATA25


title: WRKY71


title: WRKY79


title: MYBR86


title: EREB102


title: BZIP22


title: BZIP75


title: NACTF11


title: EREB2


title: BZIP23


title: NACTF2


title: ZmOrphan110


title: WRKY32


title: WRKY122


title: EREB150


title: HSFTF16


title: NKD2


title: NACTF29


title: BZIP111


title: NACTF65


title: EREB205


title: DBF1


title: MADS53


title: BZIP52


title: BZIP43


title: EREB97


title: NRP1


title: GBF1


title: WRKY72


title: SMH1


title: HB91


title: GLK44


title: OCL5A


title: AY110782


title: NACTF126


title: EREB196


title: THX47


title: BZIP78


title: 1d012968


title: BZIP54


title: 1d012427


title: WRKY1


title: 1d042933


title: MYB50


title: BZIP114


title: WRKY50


title: WRKY94


title: ZIM34


title: SFB1


title: WRKY47


title: CPP10


title: WRKY14


title: C3H11


title: WRKY37


title: WRKY67


title: MYBR29


title: WRKY105


title: HB96


title: HB118


title: NACTF61


title: HSFTF21


title: DOF36


title: BZR1


title: NACTF6


title: GATA24


title: WRKY93


title: EREB200


title: EREB118


title: BZIP60


title: WRKY8


title: MYBR33


title: BZIP104


title: ZIM10


title: EREB108


title: WRKY2


title: EREB79


title: MRP1


title: NACTF49


title: NACTF38


title: NACTF66


title: EREB147


title: EREB111


title: EREB54


title: WRKY92


title: NACTF77


title: CV8, HTO

status: Public on Nov 21 2023

first: Ellie

last: Ivanova

state: NY

address: 550 First Ave

department: Pathology

institute: NYU Langone

description:
Hashtag-derived oligonucleotide (HTO)
HTO: Read 1 contains cell barcode and UMI, Read 2 contains hashtag-derived tag

library_source: other

data_processing:
Cell Ranger software suite from 10x Genomics was used to demultiplex cellular barcodes, align reads to the human genome (GRCh38 ensemble, http://useast.ensembl.org/Homo_sapiens), and perform UMI counting.
ADT and HTO count matrices were generated using kallisto kb-count v0.24.1 and demultiplexed HTOs using HTODemux from Seurat v4.0.0.
Low quality cells were filtered out (< 200 genes/cell, > 15% mitochondrial genes).
Seurat was used to process the single-cell data, generate uniform manifold approximation and projection (UMAP) representation based on totalVI dimension reduction of RNA and ADT modalities.
R package scDblFinder was used to identify and filter out doublets.
RNA was normalized and batch-corrected by totalVI, while ADT values were corrected by the built-in integration function FindIntegrationAnchors in Seurat.
Clustering was performed by the Louvain algorithm and cell type identification was determined by clustering, SingleR annotations, corrected ADT levels and canonical markers for various immune cell subsets.
Further we performed sub-clustering on Myeloid, B, conventional T and innate-like T and NK cells to identify 32 individual populations.
BCR/TCR sequences were processed by Cell Ranger VDJ and added to the metadata of the combined Seurat object for each sample.
Assembly: GRCh38 ensemble
Supplementary files format and content: Seurat object: cv8_obj.rds. Contains processed data for experiment in SuperSeries
Library strategy: CITE-seq

source_name: PBMCs

extract_protocol:
PBMCs were isolated form whole blood using ficoll gradient. Cells were encapsulated in Gel-Beads-in emulsion (GEMs) using 10x Controller with a Chromium Next GEM Single Cell 5' Library & Gel Bead Kit v1.1
Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)
The CITE-seq and hashing protocol described by Stoeckius et. al. was used to generate an antibody-derived tag (ADT) sequencing library and hashtag oligo (HTO) library (Stoeckius et. al., 2017). Gene expression library and VDJ libraries were constructed according to the manufacturer’s protocol (10x Genomics)

value: PBMCs

tag: library type

value: HTO


title: CV8, TCRab

description:
Enriched TCRab fragment
TCRab: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (abT cell receptor)

value: TCRab


title: CV8, BCR

description:
Enriched BCR fragment
BCR: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment

value: BCR


title: CV8, GEX

description:
Gene expression (GEX)
GEX (5' mRNA): Read 1 contains cell barcode and UMI, Read 2 contains transcript, I1 contains library index

value: GEX


title: CV8, ADT

description:
Antibody-derived tags (ADT)
ADT: Read 1 contains cell barcode and UMI, Read 2 contains antibody-derived tag

value: ADT


title: OCL1


title: MYB73


title: BZIP8


title: 9_POST

city: Stockholm

first: Leonidas

middle: S

last: Lundell

state: Stockholm

address: Von Eulers Väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institute

description: RNAseq from adipose tissue biopsy obtained from participant 9, POST execise, with diagnosis of T2D

data_processing:
star/2.7.2b STAR --outReadsUnmapped Fastx --outSAMstrandField intronMotif--outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMtype BAM SortedByCoordinate
subread/2.0.2 featureCounts -p -B -C -T $threads -t exon -g gene_id
limma_3.48.3 filterByExpr.DGEList(dataDGE, design = model.matrix(~0 + group + sex), min.count = 15)
Assembly: hg 38, Ensembl 98
Supplementary files format and content: processed.data.csv contains cpm along with HUGO symbol, ensmbl, and entrezID

source_name: Adipose tissue biopsy

extract_protocol:
Approximately 30 mg of adipose tissue was used for RNA extraction. Tissues were homogenized using TissueLyser (Qiagen) in 1 mL TRIzol (Sigma-Aldrich). Chloroform was added, samples were mixed, subjected to centrifugation, and the aqueous phase was transferred to a new tube. Thereafter, 1:1 70% ethanol was added, and the total volume was loaded on silica-membrane columns. RNA extraction was performed using a commercially available kit (Rneasy lipid tissue kit, Qiagen). RNA concentration and purity were assessed by absorbance at 260 and 280 nm using NanoDrop One (Thermo Fisher Scientific, Waltham, MA).
Aliquots of RNA (300 ng) were analyzed using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina) as described (ref). Ribosomal RNA was removed from the sample using 35 μl of rRNA removal beads (Illumina) on a magnetic plate followed by cleanup of the ribosomal-depleted RNA with 193 μl of Agencourt RNAClean XP beads (Beckman Coulter), 70% ethanol wash, and elution into 10 μl elution buffer (Illumina). The RNA sample was fragmented for 4 min at 94°C in Elute, Prime, Fragment High Mix (Illumina) and then subjected to first-strand cDNA synthesis with 1 μl of Superscript III reverse transcriptase (Life Technologies) per sample using a thermocycler programmed to 25°C for 10 min, 50°C for 15 min, and 70°C for 15 min. Second-strand cDNA was synthesized by addition of Second-Strand Marking Master Mix, and samples were incubated at 16°C for 60 min. Samples were subjected to another bead cleanup before A-tailing and ligation of adapters as per kit instructions (Illumina). Following a third bead cleanup, samples were enriched for DNA fragments by amplification using the Illumina polymerase chain reaction (PCR) Primer Cocktail and PCR Master Mix, subjected to 98°C for 30 min, followed by a predefined cycle (98°C for 10 s, 60°C for 30 s, and 72°C for 30 s) that was repeated 3 to 15 times, on the basis of each individual sample, and finally incubated for 5 min at 72°C. Samples were cleaned and validated for DNA concentration using the Qubit dsDNA HS assay kit (Invitrogen) and for base pair size and purity using the Agilent High Sensitivity DNA chip and Bioanalyzer instrument.
38-bp paired-end sequencing on a NextSeq500

tag: Sex

value: M

tag: participant id

tag: diagnosis

tag: exercise

value: POST

value: Adipose tissue biopsy


title: 75_REC

description: RNAseq from adipose tissue biopsy obtained from participant 75, REC execise, with diagnosis of NGT

value: F

value: NGT

value: REC


title: 71_POST

description: RNAseq from adipose tissue biopsy obtained from participant 71, POST execise, with diagnosis of T2D


title: 75_POST

description: RNAseq from adipose tissue biopsy obtained from participant 75, POST execise, with diagnosis of NGT


title: 75_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 75, PRE execise, with diagnosis of NGT

value: PRE


title: 7_POST

description: RNAseq from adipose tissue biopsy obtained from participant 7, POST execise, with diagnosis of T2D


title: 7_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 7, PRE execise, with diagnosis of T2D


title: CV8, TCRgd

description:
Enriched TCRgd fragment
TCRgd: Read 1 contains cell barcode and UMI, Read 2 contains enriched VDJ fragment (gdT cell receptor)

value: TCRgd


title: NACTF109

value: 14 DAG

value: leaf


title: WRKY48


title: 68_REC

description: RNAseq from adipose tissue biopsy obtained from participant 68, REC execise, with diagnosis of T2D


title: MYBR81


title: EREB209


title: 68_POST

description: RNAseq from adipose tissue biopsy obtained from participant 68, POST execise, with diagnosis of T2D


title: 66_REC

description: RNAseq from adipose tissue biopsy obtained from participant 66, REC execise, with diagnosis of NGT


title: 67_POST

description: RNAseq from adipose tissue biopsy obtained from participant 67, POST execise, with diagnosis of T2D


title: 67_REC

description: RNAseq from adipose tissue biopsy obtained from participant 67, REC execise, with diagnosis of T2D


title: 66_POST

description: RNAseq from adipose tissue biopsy obtained from participant 66, POST execise, with diagnosis of NGT


title: NACTF5


title: 9_REC

description: RNAseq from adipose tissue biopsy obtained from participant 9, REC execise, with diagnosis of T2D


title: 64_REC

description: RNAseq from adipose tissue biopsy obtained from participant 64, REC execise, with diagnosis of T2D


title: 9_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 9, PRE execise, with diagnosis of T2D


title: 63_REC

description: RNAseq from adipose tissue biopsy obtained from participant 63, REC execise, with diagnosis of T2D


title: 71_REC

description: RNAseq from adipose tissue biopsy obtained from participant 71, REC execise, with diagnosis of T2D


title: 62_REC

description: RNAseq from adipose tissue biopsy obtained from participant 62, REC execise, with diagnosis of NGT


title: 60_REC

description: RNAseq from adipose tissue biopsy obtained from participant 60, REC execise, with diagnosis of NGT


title: 62_POST

description: RNAseq from adipose tissue biopsy obtained from participant 62, POST execise, with diagnosis of NGT


title: 60_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 60, PRE execise, with diagnosis of NGT


title: 71_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 71, PRE execise, with diagnosis of T2D


title: 7_REC

description: RNAseq from adipose tissue biopsy obtained from participant 7, REC execise, with diagnosis of T2D


title: 68_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 68, PRE execise, with diagnosis of T2D


title: 67_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 67, PRE execise, with diagnosis of T2D


title: 66_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 66, PRE execise, with diagnosis of NGT


title: 58_POST

description: RNAseq from adipose tissue biopsy obtained from participant 58, POST execise, with diagnosis of T2D


title: 57_REC

description: RNAseq from adipose tissue biopsy obtained from participant 57, REC execise, with diagnosis of NGT


title: 6_REC

description: RNAseq from adipose tissue biopsy obtained from participant 6, REC execise, with diagnosis of T2D


title: 65_REC

description: RNAseq from adipose tissue biopsy obtained from participant 65, REC execise, with diagnosis of T2D


title: 65_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 65, PRE execise, with diagnosis of T2D


title: 56_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 56, PRE execise, with diagnosis of T2D


title: 53_REC

description: RNAseq from adipose tissue biopsy obtained from participant 53, REC execise, with diagnosis of T2D


title: 65_POST

description: RNAseq from adipose tissue biopsy obtained from participant 65, POST execise, with diagnosis of T2D


title: 53_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 53, PRE execise, with diagnosis of T2D


title: 64_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 64, PRE execise, with diagnosis of T2D


title: 64_POST

description: RNAseq from adipose tissue biopsy obtained from participant 64, POST execise, with diagnosis of T2D


title: 49_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 49, PRE execise, with diagnosis of NGT


title: 56_POST

description: RNAseq from adipose tissue biopsy obtained from participant 56, POST execise, with diagnosis of T2D


title: 62_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 62, PRE execise, with diagnosis of NGT


title: 63_POST

description: RNAseq from adipose tissue biopsy obtained from participant 63, POST execise, with diagnosis of T2D


title: 46_POST

description: RNAseq from adipose tissue biopsy obtained from participant 46, POST execise, with diagnosis of T2D


title: 44_REC

description: RNAseq from adipose tissue biopsy obtained from participant 44, REC execise, with diagnosis of T2D


title: 46_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 46, PRE execise, with diagnosis of T2D


title: 6_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 6, PRE execise, with diagnosis of T2D


title: 6_POST

description: RNAseq from adipose tissue biopsy obtained from participant 6, POST execise, with diagnosis of T2D


title: 49_REC

description: RNAseq from adipose tissue biopsy obtained from participant 49, REC execise, with diagnosis of NGT


title: 59_REC

description: RNAseq from adipose tissue biopsy obtained from participant 59, REC execise, with diagnosis of NGT


title: 59_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 59, PRE execise, with diagnosis of NGT


title: 58_REC

description: RNAseq from adipose tissue biopsy obtained from participant 58, REC execise, with diagnosis of T2D


title: 63_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 63, PRE execise, with diagnosis of T2D


title: 58_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 58, PRE execise, with diagnosis of T2D


title: 57_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 57, PRE execise, with diagnosis of NGT


title: 4_REC

description: RNAseq from adipose tissue biopsy obtained from participant 4, REC execise, with diagnosis of T2D


title: 60_POST

description: RNAseq from adipose tissue biopsy obtained from participant 60, POST execise, with diagnosis of NGT


title: 57_POST

description: RNAseq from adipose tissue biopsy obtained from participant 57, POST execise, with diagnosis of NGT


title: 4_POST

description: RNAseq from adipose tissue biopsy obtained from participant 4, POST execise, with diagnosis of T2D


title: 38_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 38, PRE execise, with diagnosis of T2D


title: 56_REC

description: RNAseq from adipose tissue biopsy obtained from participant 56, REC execise, with diagnosis of T2D


title: 38_POST

description: RNAseq from adipose tissue biopsy obtained from participant 38, POST execise, with diagnosis of T2D


title: 50_REC

description: RNAseq from adipose tissue biopsy obtained from participant 50, REC execise, with diagnosis of NGT


title: 53_POST

description: RNAseq from adipose tissue biopsy obtained from participant 53, POST execise, with diagnosis of T2D


title: 50_POST

description: RNAseq from adipose tissue biopsy obtained from participant 50, POST execise, with diagnosis of NGT


title: 59_POST

description: RNAseq from adipose tissue biopsy obtained from participant 59, POST execise, with diagnosis of NGT


title: 50_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 50, PRE execise, with diagnosis of NGT


title: 37_REC

description: RNAseq from adipose tissue biopsy obtained from participant 37, REC execise, with diagnosis of T2D


title: 37_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 37, PRE execise, with diagnosis of T2D


title: 49_POST

description: RNAseq from adipose tissue biopsy obtained from participant 49, POST execise, with diagnosis of NGT


title: 37_POST

description: RNAseq from adipose tissue biopsy obtained from participant 37, POST execise, with diagnosis of T2D


title: 46_REC

description: RNAseq from adipose tissue biopsy obtained from participant 46, REC execise, with diagnosis of T2D


title: 44_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 44, PRE execise, with diagnosis of T2D


title: 34_POST

description: RNAseq from adipose tissue biopsy obtained from participant 34, POST execise, with diagnosis of T2D


title: 44_POST

description: RNAseq from adipose tissue biopsy obtained from participant 44, POST execise, with diagnosis of T2D


title: 34_REC

description: RNAseq from adipose tissue biopsy obtained from participant 34, REC execise, with diagnosis of T2D


title: 42_REC

description: RNAseq from adipose tissue biopsy obtained from participant 42, REC execise, with diagnosis of NGT


title: 33_REC

description: RNAseq from adipose tissue biopsy obtained from participant 33, REC execise, with diagnosis of NGT


title: 42_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 42, PRE execise, with diagnosis of NGT


title: 33_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 33, PRE execise, with diagnosis of NGT


title: 42_POST

description: RNAseq from adipose tissue biopsy obtained from participant 42, POST execise, with diagnosis of NGT


title: 4_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 4, PRE execise, with diagnosis of T2D


title: 38_REC

description: RNAseq from adipose tissue biopsy obtained from participant 38, REC execise, with diagnosis of T2D


title: 35_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 35, PRE execise, with diagnosis of T2D


title: 35_REC

description: RNAseq from adipose tissue biopsy obtained from participant 35, REC execise, with diagnosis of T2D


title: 35_POST

description: RNAseq from adipose tissue biopsy obtained from participant 35, POST execise, with diagnosis of T2D


title: 32_POST

description: RNAseq from adipose tissue biopsy obtained from participant 32, POST execise, with diagnosis of NGT


title: 34_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 34, PRE execise, with diagnosis of T2D


title: 31_REC

description: RNAseq from adipose tissue biopsy obtained from participant 31, REC execise, with diagnosis of T2D


title: 31_POST

description: RNAseq from adipose tissue biopsy obtained from participant 31, POST execise, with diagnosis of T2D


title: 32_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 32, PRE execise, with diagnosis of NGT


title: 32_REC

description: RNAseq from adipose tissue biopsy obtained from participant 32, REC execise, with diagnosis of NGT


title: 30_REC

description: RNAseq from adipose tissue biopsy obtained from participant 30, REC execise, with diagnosis of T2D


title: 30_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 30, PRE execise, with diagnosis of T2D


title: 3_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 3, PRE execise, with diagnosis of NGT


title: 3_REC

description: RNAseq from adipose tissue biopsy obtained from participant 3, REC execise, with diagnosis of NGT


title: 27_REC

description: RNAseq from adipose tissue biopsy obtained from participant 27, REC execise, with diagnosis of NGT


title: 31_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 31, PRE execise, with diagnosis of T2D


title: 26_REC

description: RNAseq from adipose tissue biopsy obtained from participant 26, REC execise, with diagnosis of T2D


title: 26_POST

description: RNAseq from adipose tissue biopsy obtained from participant 26, POST execise, with diagnosis of T2D


title: 23_REC

description: RNAseq from adipose tissue biopsy obtained from participant 23, REC execise, with diagnosis of NGT


title: 22_POST

description: RNAseq from adipose tissue biopsy obtained from participant 22, POST execise, with diagnosis of NGT


title: 30_POST

description: RNAseq from adipose tissue biopsy obtained from participant 30, POST execise, with diagnosis of T2D


title: 21_REC

description: RNAseq from adipose tissue biopsy obtained from participant 21, REC execise, with diagnosis of NGT


title: 33_POST

description: RNAseq from adipose tissue biopsy obtained from participant 33, POST execise, with diagnosis of NGT


title: 3_POST

description: RNAseq from adipose tissue biopsy obtained from participant 3, POST execise, with diagnosis of NGT


title: 23_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 23, PRE execise, with diagnosis of NGT


title: 23_POST

description: RNAseq from adipose tissue biopsy obtained from participant 23, POST execise, with diagnosis of NGT


title: 2_REC

description: RNAseq from adipose tissue biopsy obtained from participant 2, REC execise, with diagnosis of T2D


title: 22_REC

description: RNAseq from adipose tissue biopsy obtained from participant 22, REC execise, with diagnosis of NGT


title: 2_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 2, PRE execise, with diagnosis of T2D


title: 2_POST

description: RNAseq from adipose tissue biopsy obtained from participant 2, POST execise, with diagnosis of T2D


title: 26_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 26, PRE execise, with diagnosis of T2D


title: 19_REC

description: RNAseq from adipose tissue biopsy obtained from participant 19, REC execise, with diagnosis of T2D


title: 22_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 22, PRE execise, with diagnosis of NGT


title: 21_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 21, PRE execise, with diagnosis of NGT


title: 21_POST

description: RNAseq from adipose tissue biopsy obtained from participant 21, POST execise, with diagnosis of NGT


title: 20_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 20, PRE execise, with diagnosis of NGT


title: 20_REC

description: RNAseq from adipose tissue biopsy obtained from participant 20, REC execise, with diagnosis of NGT


title: 16_POST

description: RNAseq from adipose tissue biopsy obtained from participant 16, POST execise, with diagnosis of NGT


title: 27_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 27, PRE execise, with diagnosis of NGT


title: 15_REC

description: RNAseq from adipose tissue biopsy obtained from participant 15, REC execise, with diagnosis of NGT


title: 15_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 15, PRE execise, with diagnosis of NGT


title: 20_POST

description: RNAseq from adipose tissue biopsy obtained from participant 20, POST execise, with diagnosis of NGT


title: 12_POST

description: RNAseq from adipose tissue biopsy obtained from participant 12, POST execise, with diagnosis of T2D


title: 27_POST

description: RNAseq from adipose tissue biopsy obtained from participant 27, POST execise, with diagnosis of NGT


title: 11_REC

description: RNAseq from adipose tissue biopsy obtained from participant 11, REC execise, with diagnosis of T2D


title: 11_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 11, PRE execise, with diagnosis of T2D


title: 1_REC

description: RNAseq from adipose tissue biopsy obtained from participant 1, REC execise, with diagnosis of T2D


title: 19_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 19, PRE execise, with diagnosis of T2D


title: 1_POST

description: RNAseq from adipose tissue biopsy obtained from participant 1, POST execise, with diagnosis of T2D


title: 19_POST

description: RNAseq from adipose tissue biopsy obtained from participant 19, POST execise, with diagnosis of T2D


title: 18_REC

description: RNAseq from adipose tissue biopsy obtained from participant 18, REC execise, with diagnosis of NGT


title: 18_POST

description: RNAseq from adipose tissue biopsy obtained from participant 18, POST execise, with diagnosis of NGT


title: hESC H9, 24hr of convex curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 2

status: Public on Nov 19 2023

city: Seoul

first: Hyung-Min

last: Ahn

address: 145, Anam-ro, Seongbuk-gu

institute: Korea University

data_processing:
HISAT2
FeatureCounts
Read counts were extracted and normalized by a custom Python script.
Assembly: GRCh38.109
Supplementary files format and content: tab-delimited text file of raw read counts for each sample
Supplementary files format and content: tab-delimited text file of transcript-per-million values for each sample

growth_protocol: Pluripotent H9 cells were subcultured using ReLeSR (Stem Cell Technologies) at a Matrigel (Corning)-coated polydimethylsiloxane (PDMS) plate and maintained in mTeSR1 (Stem Cell Technologies) for 72 hours in humidified atmosphere with 5% CO2 at 37C. Then they were treated with N2B27 media containing 10 µSB431542 and 0.1 µLDN for 48 hours in humidified atmosphere with 5% CO2 at 37C for neuroepithelial differentiation before experimental treatment.

extract_protocol:
RNA was extracted using mirVana™ miRNA Isolation Kit (ThermoFisher). After total RNA purification, the sample was treated with DNase using DNA-Free kit (Ambion). RNA purity was determined by assaying 1 µl of total RNA extract on a NanoDrop8000 spectrophotometer. Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer with an RNA Integrity Number (RIN) value.
mRNA sequencing libraries were prepared according to the manufacturer’s instructions (Illumina Truseq stranded mRNA library prep kit). mRNA was purified and fragmented from total RNA (1ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Cleaved RNA fragments primed with random hexamers were reverse transcribed into first strand cDNA using reverse transcriptase, random primers, dUTP in place of dTTP. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR to create the final strand specific cDNA library.

treatment_protocol: For external curvature groups, plate curving of either concave or convex curvature was applied for 24 hours with the continued induction through dual SMAD inhibition in N2B27 media. For the control group, only 24 hours of dual SMAD inhibition in N2B27 media was treated without the application of external curvature, culturing them in a flat conformation.

value: embryonic stem cell

value: WT

value: convex curvature and neuroepithelial differentiation


title: 17_REC

description: RNAseq from adipose tissue biopsy obtained from participant 17, REC execise, with diagnosis of T2D


title: 17_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 17, PRE execise, with diagnosis of T2D


title: 17_POST

description: RNAseq from adipose tissue biopsy obtained from participant 17, POST execise, with diagnosis of T2D


title: GIST-R1-3

status: Public on Nov 09 2023

city: Tokyo

first: Ruslan

last: Deviatiiarov

address: Hongo 2-1-1, Bunkyo-ku

department: Intractable Disease Research Center

country: Japan

institute: Juntendo University

data_processing:
Quality of sequenced reads was accessed through FastQC v0.11.5.
Unwanted adapter and rRNA matching reads were filtered out with Trimmomatic = 0.38.
Trimmed reads were aligned to human genome assembly hg38 (UCSC primary chromo-somes) with Hisat2 v2.1.0
Then counted with HTSeq v2.0.1 against Gencode v43 basic annotation
Further analyses, including FPKM normalization, were conducted in R environment.
Assembly: Hg38 UCSC
Supplementary files format and content: Tables with raw and FPKM normalized counts per transcript.

growth_protocol: GIST cells were grown in a humidified atmosphere of 5% CO2 at 37 °C (LamSystems, Miass, Russia).

extract_protocol:
Total RNA was isolated from the GIST cell lines using the TRIzol reagent (RNAiso, Invitrogen, Carlsbad, CA, USA).
The quantity and purity of RNA was estimated on a NanoPhotometer (Implen), and 800 ng of RIN ≥7 of total RNA was used for library construction using NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA) according to the manu-facturer’s instruction.


title: GIST-T1-2


title: 16_REC

description: RNAseq from adipose tissue biopsy obtained from participant 16, REC execise, with diagnosis of NGT


title: GIST-R2-3


title: GIST-R1-1


title: 16_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 16, PRE execise, with diagnosis of NGT


title: GIST-R2-2


title: 15_POST

description: RNAseq from adipose tissue biopsy obtained from participant 15, POST execise, with diagnosis of NGT


title: ChIP_WT_H3K4me1_rep2

status: Public on Oct 31 2023

first: Xiao

last: Ge

address: No. 800 Dongchuan Road

institute: Shanghai JiaoTong University

data_processing:
Paired-end reads were aligned to the mouse genome (M. musculus, UCSC mm9) or human genome(GRCh37/hg19) using Bowtie (version 1.2.3).
Sam files were then converted into Bam files and indexed. BedGraph files were generated using bigWigToBedGraph software with Bam file as input.
Assembly: M. musculus, UCSC mm9 or H.Sapiens UCSC hg19
Supplementary files format and content: bigwig and bedGraph files suitable for viewing on UCSC

source_name: cortex

extract_protocol:
2 × 106 of cortex neurons or cultured cell were used for one experiment. Neuron cells were first dissected and digested using 0.00625% collagenase.
The neuron suspension or cultured cell were cross-linked using 1% formaldehyde in 10% FBS/PBS for 10 min at room temperature followed by washing twice with PBS solution containing proteinase inhibitors (Roche). Cells were then resuspended and lysed twice with 1ml prechilled lysis buffer containing proteinase inhibitors (Roche) for 10 min with slow rotations. For neuron sample, additional SDS was then added to the lysis solution to adjust final SDS concentration to 0.4% to help sonication. Cells were then sonicated to break DNA fragments to about 100-10000 bp using the Bioruptor system (25% energy, with working time 15s and resting time of 45s, 20cycles). After sonication, lysis buffer not containing SDS was added to adjust final SDS concentration to 0.1% to allow binding of antibodies to proteins while cultured cell move directly to the antibody binding step. After removing the insoluble debris by centrifuging at 14000g for 10 min, the lysate was precleaned with protein-A agarose beads (16-157; Millipore) for 1hr with slow rotation to remove non-specificity binding and incubated with specific antibodies overnight with slow rotation at 4°C. The next day the antibody-protein-DNA complex was purified by adding protein A-agarose beads and incubate for 4hr with slow rotation, followed by washing with low salt buffer, high salt buffer, no salt buffer, LiCl buffer and TE buffer and finally eluted into elution buffer (0.1M NaHCO3, 1% SDS). Reverse cross-link and DNA purification was performed and the sample were prepared into libraries using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme) following the manufacturer’s instruction. The ChIP-seq libraries were sequenced using an Illumina Novaseq6000 platform.

value: cortex

value: cortex-neuron

value: neuron

value: wildtype

tag: antibody

value: Abcam ab8895


title: 18_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 18, PRE execise, with diagnosis of NGT

value: M


title: 12_REC

description: RNAseq from adipose tissue biopsy obtained from participant 12, REC execise, with diagnosis of T2D

value: Adipose tissue biopsy


title: native tissue mix, true barnyard, 100k nuclei, standard txci-ATAC-seq

status: Public on Oct 25 2023

city: Tucson

first: Hao

last: Zhang

state: AZ

address: 1230 N Cherry Ave

department: CMM

institute: The University of Arizona

description:
10X Genomics
standard_txci.native_tissue_mixed_species_mapping_report_100k.txt.gz
standard_txci.native_mm10_liver_fragments.tsv.gz
standard_txci.native_mm10_liver_metadata.txt.gz
standard_txci.native_mm10_liver_readcount_matrix.rds.gz
standard_txci.native_mm10_lung_fragments.tsv.gz
standard_txci.native_mm10_lung_metadata.txt.gz
standard_txci.native_mm10_lung_readcount_matrix.rds.gz
standard_txci.native_hg38_lung_fragments.tsv.gz
standard_txci.native_hg38_lung_metadata.txt.gz
standard_txci.native_hg38_lung_readcount_matrix.rds.gz

library_source: genomic single cell

data_processing:
Fastq files were generated using bcl2fastq with the following options: “--ignore-missing-bcls”, “--no-lane-splitting”, and “--create-fastq-for-index-reads”. Then, we modified the fastq files by attaching the first 8 bp (Tn5 barcodes) of Read 2 to the header and removing the first 27 bp (8 bp of Tn5 barcodes + 19 bp of Tn5 mosaic end) from Read 2 with a custom python script. Barcodes that did not perfectly match any of the expected barcodes were converted to the closest matching barcode if the edit distance was no greater than 2. Barcodes matching more than 1 expected barcode after correction were removed. After barcode correction, we demultiplexed samples based on a combination of Tn5 barcodes and i7 sample indices and generated a combined barcode for each read by concatenating the i7 sample index, 10X bead barcode, and Tn5 barcode. Next, we removed the sequence adaptors and low-quality reads using trimmomatic with following parameters: “LEADING:3; TRAILING:3; SLIDINGWINDOW:4:10; MINLEN:20” and then mapped the trimmed reads to a hybrid hg38/mm10 reference genome using Bowtie2 with a maximum fragment length of 2000 pb (-X 2000) and 1 base trimmed from the 3’ end of each read (-3 1). Following mapping, only the reads confidently (MAPQ ≥ 10) aligned to the assembled nuclear chromosomes and in proper pairs (determined by “-f3” and “-F12” options in SAMtools) were preserved for downstream analysis. To eliminate PCR duplicates, we removed all fragments that possessed the same combined barcode and identical start and end coordinates, keeping a random representative read for each end of the molecule using a custom script. For each combined barcode, we quantified the number of deduplicated reads mapping to the human and mouse genome and filtered out the combined barcodes with fewer than 1,000 total reads. The cell barcodes that had at least 90% of reads aligned to either the human or mouse genome were assigned to the major species. The barcodes with more than 10% of reads aligned to the minor genome were determined as collision barcodes. For human and mouse barcodes, only the reads mapping to the corresponding genome were used for the downstream analysis.
The deduplicated bed files were used to call peaks with MACS2, considering a 200 bp window centered on the read start using the parameters ‘--nomodel --keep-dup all --extsize 200 --shift -100’. Because each peak may have multiple summits and will therefore be listed multiple times in the resulting peak bed file, the peaks output from MACS2 were then merged into a single peak set for each sample using bedtools “merge”. The consolidated peaks were then intersected with the ENCODE blacklist to remove signal-artifact regions using bedtools “intersect” with “-v” option.
Assembly: mm10 and hg38
Supplementary files format and content: Tab-separated values files and R data serialization files

source_name: lung and liver

growth_protocol: The GM12878 and CH12.LX cells were cultured at 37°C with 5% CO2 in RPMI 1640 medium containing 15% FBS, 100 U/ml Penicillin Streptomycin. Cells were counted and split to either 300,000 or 100,000 cells/ml three times a week.  For mouse lung and liver samples, the dissected samples were flash-frozen in liquid nitrogen and then transferred to -80°C for long-term storage.

extract_protocol:
For cell lines, the cells were collected and washed with 1x PBS containing 0.1% BSA, and then resuspended in 200 μl of ATAC-seq resuspension buffer (RSB;10 mM Tris-HCl pH 7.5, 10 mM NaCl, and 3 mM MgCl2 in nuclease-free water) supplemented with 0.1% IGEPAL, 0.01% digitonin, and 0.1% Tween-20 to lyse cells. The cell lysis reaction was incubated on ice for 3 min, and then stopped by adding 1 ml RSB containing 0.1% Tween-20. After centrifugation of the resulting nuclei at 500 r.c.f for 10 min at 4°C and removal of the supernatant, the nuclei were either resuspended in 100 μl of PBS containing 0.04% BSA (PBSB) to proceed with barcoded transposition or resuspended in a nuclei-freezing buffer (NFB) for storage in liquid nitrogen. The NFB was prepared with 50 mM Tris-HCI pH 8.0, 5 mM Magnesium Acetate, 25% glycerol, 0.1 mM EDTA, 5 mM DTT, and 2% (v/v) protease inhibitor. To isolate nuclei from mouse tissues, we cut a ~0.1-0.2 g piece from each sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution) in Nuclei EZ prep buffer, into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube. An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with a hemocytometer, and centrifuged at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei in the NFB to make a concentration of 4 to 5 million nuclei/ml. 1 ml aliquots of the nuclei were flash-frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
A 96-well plate pre-loaded with 5 μl of 500 nM pre-indexed Tn5 transposase per well (iTSM plate) was used to multiplex samples and perform barcoded transposition. The isolated nuclei were diluted in PBSB to a concentration of 2,857 per μl. Then, we mixed 7 μl of nuclei solution (20,000 nuclei) with 13 μl of of TBS (12.5 μl of Illumina Tagment DNA Buffer, 0.25 μl of 1% Digitonin in DMSO, and 0.25 μl of 10% Tween-20 in nuclease-free water) for each well. This 20 μl nuclei/transposition mixture (containing 20,000 nuclei) was then added to each well of the iTSM plate to make a total volume of 25 μl reaction per well. After loading nuclei, the iTSM plate was sealed and briefly shaken at 1000 rpm for 1 min on a pre-chilled thermomixer. The barcoded transposition was performed at 37°C for 1 hour on a thermocycler with a heated lid at 47°C. At the end of incubation, the plate was briefly centrifuged at 500 r.c.f for 10 seconds and then chilled on ice for 5 min to stop the transposition reaction. After quenching enzyme activity, the nuclei were pooled and diluted with 1 ml tagmentation washing buffer (TMG, which contains 10mM Tris Acetate pH 7.8, 5mM Magnesium acetate and 10% glycerol in nuclease-free water), and then centrifuged at 500 r.c.f for 10 min in a pre-chilled swinging-bucket centrifuge at 4°C. After aspirating the supernatant, the nuclei were resuspended in 500 μl TMG and then transferred to a 1.5 ml LoBind tube through a 40 um Flowmi Cell strainer. The nuclei suspension was then centrifuged at 500 r.c.f for 5 min in a pre-chilled fixed-angle centrifuge at 4°C. After centrifugation, 400 μl of supernatant was removed. The 100 μl of supernatant left from the first aspiration was then carefully removed by pipetting with a P200 pipette tip to avoid disturbing the nuclei pellet. The nuclei were resuspended with 30 μl of loading buffer containing 1x TB1, 1x standard storage buffer, and 5 μM short SBS oligo, and then counted with a hemocytometer. After counting, the volume of solution containing the appropriate number of nuclei was taken and diluted with the loading buffer to make a total volume of 15 μl, which was used as an input into the 10x Chromium Controller. The GEM generation, Barcoding, and Post GEM Incubation Cleanup were performed following Steps 2 and 3 described in the 10X Chromium Next GEM Single Cell ATAC protocol (v1.1, Document No. CG000209 Rev D) except for Step 2.5, in which 8 cycles were used for GEM incubation. For Sample Index PCR (step 4.1), we substituted the Single Index N Set A (10X Genomics) with 25 uM i7 TruSeq primer containing an 8 bp custom barcode and added 2.5 μl of customized i7 primer to each 10X library. The PCR was performed following the 10X protocol shown in Step 4.1 but with 5 total cycles. The Double Sided Size Selection was then conducted as described in Step 4.2 shown in the 10X protocol. Following the size selection, the txci-ATAC-seq libraries were quantified by Qubit 1X dsDNA HS Assay Kit and run on a 6% PAGE gel to check the library quality.

value: lung and liver

tag: nuclei input


title: 11_POST

description: RNAseq from adipose tissue biopsy obtained from participant 11, POST execise, with diagnosis of T2D

value: POST


title: 1_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 1, PRE execise, with diagnosis of T2D


title: 12_PRE

description: RNAseq from adipose tissue biopsy obtained from participant 12, PRE execise, with diagnosis of T2D


title: hESC H9, 24hr of convex curvature and dual SMAD inhibition after 48hr of dual SMAD inhibitionno, replicate 3

tag: genotype

tag: treatment


title: lung mix, decoy DNA, true barnyard

description:
10X Genomics
blocking_condition_species_mapping_report.txt.gz

source_name: lung

value: lung


title: hESC H9, 24hr of no curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 2

tag: cell type

value: neuroepithelial differentiation


title: hESC H9, 24hr of convex curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 1


title: hESC H9, 24hr of no curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 3


title: lung mix, block oligo, pseudo-barnyard


title: cell line mix,SBS primer, true barnyard

source_name: GM12878 and CH12.LX

growth_protocol: The GM12878 and CH12.LX cells were cultured at 37°C with 5% CO2 in RPMI 1640 medium containing 15% FBS, 100 U/ml Penicillin Streptomycin. Cells were counted and split to either 300,000 or 100,000 cells/ml three times a week.   For mouse lung and liver samples, the dissected samples were flash-frozen in liquid nitrogen and then transferred to -80°C for long-term storage.

extract_protocol:
For cell lines, the cells were collected and washed with 1x PBS containing 0.1% BSA, and then resuspended in 200 μl of ATAC-seq resuspension buffer (RSB;10 mM Tris-HCl pH 7.5, 10 mM NaCl, and 3 mM MgCl2 in nuclease-free water) supplemented with 0.1% IGEPAL, 0.01% digitonin, and 0.1% Tween-20 to lyse cells. The cell lysis reaction was incubated on ice for 3 min, and then stopped by adding 1 ml RSB containing 0.1% Tween-20. After centrifugation of the resulting nuclei at 500 r.c.f for 10 min at 4°C and removal of the supernatant, the nuclei were either resuspended in 100 μl of PBS containing 0.04% BSA (PBSB) to proceed with barcoded transposition or resuspended in a nuclei-freezing buffer (NFB) for storage in liquid nitrogen. The NFB was prepared with 50 mM Tris-HCI pH 8.0, 5 mM Magnesium Acetate, 25% glycerol, 0.1 mM EDTA, 5 mM DTT, and 2% (v/v) protease inhibitor.  To isolate nuclei from mouse tissues, we cut a ~0.1-0.2 g piece from each sample removed from -80°C and kept it on dry ice until use. The tissue block was thawed almost completely on ice for 1 min and then injected with 1 ml of cell lysis buffer, which was made of 1x cOmplete protease inhibitor cocktail (1 tablet per 10 ml solution) in Nuclei EZ prep buffer, into the center of the tissue with a 30G needle and syringe. Following lysis buffer injection, the tissue was chopped into small pieces with scissors and then transferred along with the lysing buffer into a gentleMACS C tube. An additional 1 ml of lysing buffer was added into the C tube to make a final volume of 2 ml. The minced tissue was then homogenized using a gentleMACS tissue dissociator by running the ‘m_lung_01’ program followed by the first 20 sec of the ‘m_lung_02’ program. After homogenization, tissue lysate was briefly centrifuged to reduce foam and then passed through a 40 μm cell strainer in a 50ml tube. After passing the sample through, the strainer was rinsed with 4 ml of washing buffer (PBS with 1% BSA). The nuclei were counted with a hemocytometer, and centrifuged at 500 r.c.f for 5 min at 4°C. Then, we removed the supernatant and resuspended the nuclei in the NFB to make a concentration of 4 to 5 million nuclei/ml. 1 ml aliquots of the nuclei were flash-frozen in liquid nitrogen and then transferred to a liquid nitrogen dewar for long-term storage.
A 96-well plate pre-loaded with 5 μl of 500 nM pre-indexed Tn5 transposase per well (iTSM plate) was used to multiplex samples and perform barcoded transposition. The isolated nuclei were diluted in PBSB to a concentration of 2,857 per μl. Then, we mixed 7 μl of nuclei solution (20,000 nuclei) with 13 μl of of TBS (12.5 μl of Illumina Tagment DNA Buffer, 0.25 μl of 1% Digitonin in DMSO, and 0.25 μl of 10% Tween-20 in nuclease-free water) for each well. This 20 μl nuclei/transposition mixture (containing 20,000 nuclei) was then added to each well of the iTSM plate to make a total volume of 25 μl reaction per well. After loading nuclei, the iTSM plate was sealed and briefly shaken at 1000 rpm for 1 min on a pre-chilled thermomixer. The barcoded transposition was performed at 37°C for 1 hour on a thermocycler with a heated lid at 47°C. At the end of incubation, the plate was briefly centrifuged at 500 r.c.f for 10 seconds and then chilled on ice for 5 min to stop the transposition reaction. After quenching enzyme activity, the nuclei were pooled and diluted with 1 ml tagmentation washing buffer (TMG, which contains 10mM Tris Acetate pH 7.8, 5mM Magnesium acetate and 10% glycerol in nuclease-free water), and then centrifuged at 500 r.c.f for 10 min in a pre-chilled swinging-bucket centrifuge at 4°C. After aspirating the supernatant, the nuclei were resuspended in 500 μl TMG and then transferred to a 1.5 ml LoBind tube through a 40 um Flowmi Cell strainer. The nuclei suspension was then centrifuged at 500 r.c.f for 5 min in a pre-chilled fixed-angle centrifuge at 4°C. After centrifugation, 400 μl of supernatant was removed. The 100 μl of supernatant left from the first aspiration was then carefully removed by pipetting with a P200 pipette tip to avoid disturbing the nuclei pellet. The nuclei were resuspended with 30 μl of loading buffer containing 1x TB1, 1x standard storage buffer, and 5 μM short SBS oligo, and then counted with a hemocytometer. After counting, the volume of solution containing the appropriate number of nuclei was taken and diluted with the loading buffer to make a total volume of 15 μl, which was used as an input into the 10x Chromium Controller. The GEM generation, Barcoding, and Post GEM Incubation Cleanup were performed following Steps 2 and 3 described in the 10X Chromium Next GEM Single Cell ATAC protocol (v1.1, Document No. CG000209 Rev D) except for Step 2.5, in which 8 cycles were used for GEM incubation. For Sample Index PCR (step 4.1), we substituted the Single Index N Set A (10X Genomics) with 25 uM i7 TruSeq primer containing an 8 bp custom barcode and added 2.5 μl of customized i7 primer to each 10X library. The PCR was performed following the 10X protocol shown in Step 4.1 but with 5 total cycles. The Double Sided Size Selection was then conducted as described in Step 4.2 shown in the 10X protocol. Following the size selection, the txci-ATAC-seq libraries were quantified by Qubit 1X dsDNA HS Assay Kit and run on a 6% PAGE gel to check the library quality.

value: GM12878 and CH12.LX


title: hESC H9, 24hr of no curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 1


title: cell line mix,SBS primer, pseudo-barnyard


title: cell line mix,decoy DNA, true barnyard


title: lung mix, SBS primer, true barnyard


title: cell line mix,decoy DNA, pseudo-barnyard


title: hESC H9, 24hr of concave curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 2

value: concave curvature and neuroepithelial differentiation


title: cell line mix,block oligo, pseudo-barnyard


title: mouse lung, wild-type, replicate 3, 200k nuclei, standard txci-ATAC-seq

description:
10X Genomics
standard_txci.cc16ko_wt_mm10_lung_fragments.tsv.gz
standard_txci.cc16ko_wt_mm10_lung_metadata.txt.gz
standard_txci.cc16ko_wt_mm10_lung_readcount_matrix.rds.gz

tag: strain

value: wild-type

value: 8 weeks

tag: replicate

value: replicate 3


title: hESC H9, 24hr of concave curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 1

tag: cell line

value: embryonic stem cell

value: WT


title: GIST-T1-1


title: GIST-T1-3


title: mouse lung, wild-type, replicate 2, 200k nuclei, standard txci-ATAC-seq

tag: age

value: replicate 2


title: GIST-R1-2


title: mouse lung, wild-type, replicate 2, 100k nuclei, standard txci-ATAC-seq

tag: tissue


title: mouse lung, native, replicate 2, 200k nuclei, standard txci-ATAC-seq

description:
10X Genomics
standard_txci.native_mm10_lung_fragments.tsv.gz
standard_txci.native_mm10_lung_metadata.txt.gz
standard_txci.native_mm10_lung_readcount_matrix.rds.gz

value: 24 weeks


title: mouse lung, wild-type, replicate 1, 100k nuclei, standard txci-ATAC-seq

value: replicate 1


title: mouse lung, CC16 deficient, replicate 1, 100k nuclei, standard txci-ATAC-seq

value: CC16 deficient


title: mouse lung, CC16 deficient, replicate 2, 100k nuclei, standard txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 3, 100k nuclei, standard txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 3, 200k nuclei, standard txci-ATAC-seq


title: native tissue mix, true barnyard, 200k nuclei, standard txci-ATAC-seq

description:
10X Genomics
standard_txci.native_tissue_mixed_species_mapping_report_200k.txt.gz
standard_txci.native_mm10_liver_fragments.tsv.gz
standard_txci.native_mm10_liver_metadata.txt.gz
standard_txci.native_mm10_liver_readcount_matrix.rds.gz
standard_txci.native_mm10_lung_fragments.tsv.gz
standard_txci.native_mm10_lung_metadata.txt.gz
standard_txci.native_mm10_lung_readcount_matrix.rds.gz
standard_txci.native_hg38_lung_fragments.tsv.gz
standard_txci.native_hg38_lung_metadata.txt.gz
standard_txci.native_hg38_lung_readcount_matrix.rds.gz


title: mouse lung, native, replicate 2, 100k nuclei, standard txci-ATAC-seq


title: lung mix, SBS primer, pseudo-barnyard


title: mouse liver, native, replicate 2, 100k nuclei, standard txci-ATAC-seq

description:
10X Genomics
standard_txci.native_mm10_liver_fragments.tsv.gz
standard_txci.native_mm10_liver_metadata.txt.gz
standard_txci.native_mm10_liver_readcount_matrix.rds.gz

source_name: liver

value: liver


title: mouse lung, native, replicate 1, 200k nuclei, standard txci-ATAC-seq


title: lung mix, decoy DNA, pseudo-barnyard


title: lung mix, block oligo, true barnyard


title: GIST-R2-1


title: cell line mix,block oligo, true barnyard


title: mouse liver, native, replicate 1, 200k nuclei, standard txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 1, 200k nuclei, standard txci-ATAC-seq


title: mouse lung, wild-type, replicate 3, 100k nuclei, standard txci-ATAC-seq


title: mouse lung, wild-type, replicate 3, 50k nuclei, phased-txci-ATAC-seq

description:
10X Genomics
phased_txci.cc16ko_wt_mm10_lung_fragments.tsv.gz
phased_txci.cc16ko_wt_mm10_lung_readcount_matrix.rds.gz
phased_txci.cc16ko_wt_mm10_lung_metadata.txt.gz


title: mouse lung, CC16 deficient, replicate 2, 200k nuclei, standard txci-ATAC-seq


title: mouse lung, wild-type, replicate 2, 50k nuclei, phased-txci-ATAC-seq


title: mouse lung, wild-type, replicate 1, 200k nuclei, standard txci-ATAC-seq


title: mouse lung, native, replicate 1, 100k nuclei, standard txci-ATAC-seq


title: mouse liver, native, replicate 2, 200k nuclei, standard txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 2, 50k nuclei, phased-txci-ATAC-seq


title: mouse liver, native, replicate 1, 100k nuclei, standard txci-ATAC-seq


title: Adu003

status: Public on Oct 17 2023

city: St Louis

first: Jichang

last: Han

state: MO

address: 4905 Children's PI

institute: Washington University in St Louis

description: 10x Genomics

data_processing:
Illumina base call (BCL) files converted to FASTQ using "cellranger mkfastq"
Expression data processed with "cellranger count"
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peritoneal cavity

extract_protocol:
Peritoneal wash was collected at the beginning of the procedure before it was affected by the surgical process. Briefly, about 1 L (for adults) or 200 mL (for children) of sterile saline was flushed into the human peritoneal cavity and the abdomen was massaged for 2 minutes for a thorough wash before the saline containing peritoneal cells were vacuumed out. Live CD45+ immune cells were then FACS sorted for library preparation.
10X Genomics Chromium Single Cell 5' Library and Gel Bead Kit

value: peritoneal cavity

value: CD45+ immune cell

tag: surgical procedure

value: Laparoscopic  sleeve gastrectomy

tag: age range

tag: gender

value: Female


title: mouse lung, wild-type, replicate 2, 100k nuclei, phased-txci-ATAC-seq

value: lung


title: mouse lung, wild-type, replicate 3, 100k nuclei, phased-txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 2, 100k nuclei, phased-txci-ATAC-seq


title: Adu001

description: 10x Genomics

value: Laparoscopic RYGB


title: hESC H9, 24hr of concave curvature and dual SMAD inhibition after 48hr of dual SMAD inhibition, replicate 3

value: concave curvature and neuroepithelial differentiation


title: mouse lung, CC16 deficient, replicate 3, 50k nuclei, phased-txci-ATAC-seq


title: mouse lung, CC16 deficient, replicate 1, 50k nuclei, phased-txci-ATAC-seq


title: NC-PKU-13-PBMC

status: Public on Sep 28 2023

first: Zhi

middle: John

last: Lu

address: Shuangqing Road

department: School of Life Sciences

institute: Tsinghua University

data_processing:
Adaptors and low-quality sequences in the raw sequencing data were trimmed using cutadapt version 2.3. Remeined reads were mapped to ERCC's spike-in sequences, NCBI's UniVec sequences and human rRNA sequences sequentially. GC oligos introduced in reverse transcription were trimmed off, after which reads shorter than 30 nt were discarded.
STAR (version 2.5.3a_modified) was used to map clean reads to the hg38 genome index built with the GENCODE v27 annotation
Duplicates in the aligned reads were removed using Picard Tools MarkDuplicates (version 2.20.0)
The count matrix was constructed using featureCounts11 v1.6.2 with the GENCODE v27 annotation, transcripts with uncertain coding potential annotation extracted from mitranscriptome, circular RNA annotation from circBase, Promoter, enhancer and repeat regions frm UCSC Genome Browser. Reads mapped to mitochondrial RNAs were excluded.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: PBMC

extract_protocol:
RNA was extracted from individuals' PBMC samples using Trizol.
RNA library is prepared using SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian kit.

value: PBMC

tag: Stage


title: NC-PKU-12-PBMC


title: mouse lung, CC16 deficient, replicate 1, 100k nuclei, phased-txci-ATAC-seq

value: 8 weeks


title: NC-PKU-11-PBMC


title: mouse lung, CC16 deficient, replicate 3, 100k nuclei, phased-txci-ATAC-seq

value: replicate 3


title: CRC-PKU-31-PBMC

value: Male


title: M1_CL-like3

status: Public on Oct 16 2023

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

institute: Cancer Research Centre of Lyon

description: 10x Genomics 3' standard v1 Visium Spatial Gene Expression; spaceranger-1.2.2

data_processing:
spaceranger-1.2.2 for samples M1 to M11
spaceranger-1.3.0 for samples M13 to M16
Pathological annotations by V Cockenpot, breast pathologist at Centre Léon Bérard, Lyon (FR)
Assembly: GRCh38
Supplementary files format and content: per-sample matrix of counts per spot in hierarchical data format
Supplementary files format and content: pathological annotations, as annotated and exported via Loupe Browser
Library strategy: Spatial transcriptomics: single-spot UMI-based RNA-seq

source_name: Breast

extract_protocol:
After optimisation, RNA permeabilisation on the Visium slide was set to 12 minutes and processed according to the manufacturer's protocol (10X Genomics)
Visium 3' V1 protocol (10X Genomics)

value: Breast

value: Normal

tag: cell subtype

value: CL-like


title: Breast Cancer, Xenium In Situ Spatial Gene Expression Rep 2

status: Public on Oct 09 2023

city: Pleasanton

first: Stephen

middle: Richardson

last: Williams

state: CA

address: 6230 Stoneridge Mall Rd

department: Computational Biology

institute: 10x Genomics

hyb_protocol: The Xenium samples underwent 15 rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section. Decoding of transcripts was performed using a Xenium codebook ? a collection of codewords that were assigned to genes in the gene panel. In order to assign mRNAs to cells, the spatial boundaries of cells were defined by nuclear expansion. Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/assay/xenium-in-situ-gene-expression-probe-hybridization-ligation-amplification. Xenium was run on a prototype instrument.

scan_protocol: Xenium In Situ Analyzer

data_processing:
Data processed using Xenium Ranger software.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep2.ome.tif: Post-Xenium hematoxylin and eosin stained tissue image which can be registered to Replicate #2 Xenium data.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep2_homography.csv: Alignment file to be used in conjunction with Post-Xenium_HE_Rep2.ome.tif for H&E registration in Xenium Explorer.

label: Xenium Human Probe Set

source_name: 5 µm section Breast Cancer

label_protocol: Xenium Human Probe Set

extract_protocol: Two replicate 5 μm sections were taken each for Xenium. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy.  A 5 μm section was also taken from Sample #2 for Xenium.

tag: disease state

value: Breast Cancer


title: NC-PKU-9-PBMC


title: CRC-PKU-29-PBMC


title: Breast Cancer, Xenium In Situ Spatial Gene Expression Rep 1

data_processing:
Data processed using Xenium Ranger software.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep1.ome.tif: Post-Xenium hematoxylin and eosin stained tissue image which can be registered to Replicate #1 Xenium data.
Supplementary_files_format_and_content: Post-Xenium_IF_Rep1.ome.tif: Post-Xenium immunofluorescence tissue image which can be registered to Replicate #1 Xenium data.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep1_homography.csv: Alignment file to be used in conjunction with Post-Xenium_HE_Rep1.ome.tif for H&E registration in Xenium Explorer.
Supplementary_files_format_and_content: Post-Xenium_IF_Rep1_homography.csv: Alignment file to be used in conjunction with Post-Xenium_IF_Rep1.ome.tif for IF registration in Xenium Explorer.


title: CRC-PKU-32-PBMC


title: mouse lung, wild-type, replicate 1, 50k nuclei, phased-txci-ATAC-seq

value: wild-type

value: replicate 1


title: CRC-2415350-PBMC

value: missing


title: Wild-type-TOL 1

status: Public on Sep 13 2023

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

data_processing:
RNA-seq reads were mapped against Mus musculus reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with DESeq2
GO/KEGG enrichment analysis was performed with G:profiler
Assembly: GRCm38
Supplementary files format and content: txt file containing RSEM expected counts

source_name: Zeb1f/f Peritoneal Macrophages-Set 1

growth_protocol: Freshly isolated peritoneal macrophages

extract_protocol:
Total RNA was isolated using Trizol
TruSeq® Stranded mRNA LT Sample Prep Kit

treatment_protocol: LPS treated peritoneal macrophages

value: Peritoneal lavage macrophages sorted by flow cytometry using CD11b and F4/80 markers

value: LPS two doses


title: NC-PKU-10-PBMC

value: Female


title: NC-PKU-14-PBMC


title: LHS1, MeDIP, 2hr, 256X, rep2

status: Public on Sep 05 2023

city: UNIVERSITY PARK

first: Lu

last: Bai

state: PENNSYLVANIA

address: 406 SOUTH FREAR, UNIVERSITY PARK

department: BMB

institute: Penn State University

data_processing:
Paired-end reads of 50 bp or 150 bp were processed with fastp (version 0.23.2) to remove low quality reads. Processed reads were aligned to S. cerevisiae genome (sacCer3) with BWA (version 0.7.17). Aligned bam files were deduplicated with Picard MarkDuplicates (version 3.0.0). bigwig files were generated by deeptools bamCoverage (version 3.5.1) for visualization purposes. To detect differentially methylated NDRs, aligned reads on each NDR were counted by Subread featureCounts (version 2.0.3) using a list of NDR coordinates generated from a previous study, with the following parameters “-p -O”. Fold change and P-value were generated by DEseq2 (1.38.0) without outliers filtering. log2 (Fold Change) > 0.7 and the adjusted P-value < 0.05 were used as the cutoff for identifying differentially methylated regions.
Assembly: sacCer3
Supplementary files format and content: table generated by DEseq2
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown in 50 mL synthetic media with/without methionine at 30°C to OD660 = 0.3.

extract_protocol:
Standard MeDIP protocol for preparation of methylated genomic DNA
MeDIP-Seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L). Next generation sequencing was performed on NextSeq 2000 (Illumina).

treatment_protocol: β-estradiol (Sigma, 50-28-2) was added to a final concentration of 2 nM for 1/2 hrs, allowing the LacI-NLS-M.CviPI fusion protein to express. For MATa and MATalpha viewpoint, glucose (D) or galactose(G) was added according to the experimental conditions.

tag: chip antibody

tag: condition

value: 2hr, 2nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, LHS1::256XLacO::HIS3


title: mouse lung, wild-type, replicate 1, 100k nuclei, phased-txci-ATAC-seq

value: lung

tag: nuclei input


title: CRC-PKU-30-PBMC

value: PBMC


title: CRC-PKU-27-PBMC


title: MNR2, MeDIP, 2hr, 256X, rep1

tag: genotype

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, MNR2::256XLacO::HIS3


title: CRC-2415420-PBMC


title: CRC-PKU-28-PBMC


title: LHS1, MeDIP, 2hr, 256X, rep1


title: MNR2, MeDIP, 2hr, 256X, rep2


title: MBR1, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, MBR1::256XLacO::HIS3


title: LSM4, MeDIP, 2hr, 256X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, LSM4::256XLacO::HIS3


title: MBR1, MeDIP, 2hr, 256X, rep2


title: LSM4, MeDIP, 2hr, 256X, rep1


title: SHC1, MeDIP, 2hr, 256X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, SHC1::256XLacO::HIS3


title: CDC43, MeDIP, 2hr, 256X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, CDC43::256XLacO::HIS3


title: OLE1, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, OLE1::256XLacO::HIS3


title: VHR1, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, VHR1::256XLacO::HIS3


title: CDC43, MeDIP, 2hr, 256X, rep1


title: SHC1, MeDIP, 2hr, 256X, rep1


title: YBP2, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, YBP2::256XLacO::HIS3


title: Ctrl, MeDIP, 2hr, 0X, rep2

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2


title: PUS2, MeDIP, 2hr, 256X, rep1

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, PUS2::256XLacO::HIS3


title: OLE1, MeDIP, 2hr, 256X, rep2


title: PUS2, MeDIP, 2hr, 256X, rep2


title: VHR1, MeDIP, 2hr, 256X, rep2


title: YBP2, MeDIP, 2hr, 256X, rep2


title: Ctrl, MeDIP, 2hr, 0X, rep1


title: BLCA_Trp_290

status: Public on Aug 24 2023

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

institute: Lund Univeristy

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials. Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). Transfer 200ul of hyb solution to each array, then tape holes and parafilm. â€¢ Hybridize 16 hours at 45° at 60rpm Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Raw data was RNA normalized, adjusted for labeling batch using ComBat and merged by median probe set values per gene symbol.
probe group file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1
meta-probeset file: Platform design info was retrieved via bioconductor: pd.hugene.1.0.st.v1

label: biotin

source_name: FFPE tissue specimen

label_protocol: SensationPlus FFPE Amplification and WT labeling kit or GeneChip WT Pico kit.

extract_protocol: Total RNA was extracted using the HighPure FFPET kit (Roche)

tag: labeling kit

value: GeneChip WT Pico kit

tag: labeling batch

tag: clinical tnm staging

tag: chemotherapy type

value: palliative

tag: lundtax rna-subtype

value: BASQ

tag: lundtax ihc-subtype

tag: consensus classifier subtype

tag: rm-lymphnode

value: yes

tag: rm-local

value: no

tag: rm-lung

tag: rm-liver

tag: rm-bone

tag: rm-other


title: BLCA_Trp_240

value: GU

value: LumU


title: PCL10, MeDIP, 2hr, 256X, rep1

tag: strain

tag: chip antibody

value: 2hr, 2nM Beta-estradiol

value: MATa, his3-11,15, leu2-3,112, trp1-1, ura3-1, can1-100, ade2-1, ADH1::2xlexO-GAL1corepr-LacI-SV40NLS-M.CviPI:ADH1pr-LexA-ERHBD-VP16AD::LEU2, PCL10::256XLacO::HIS3


title: PCL10, MeDIP, 2hr, 256X, rep2

tag: condition


title: BLCA_Trp_238

value: Uro

value: StromaRich


title: BLCA_Trp_237


title: BLCA_Trp_244


title: BLCA_Trp_268

value: UroA


title: BLCA_Trp_245

value: LumNS


title: BLCA_Trp_229


title: BLCA_Trp_277


title: BLCA_Trp_242

value: Mes


title: BLCA_Trp_233


title: BLCA_Trp_230


title: BLCA_Trp_235

value: UroC


title: BLCA_Trp_225


title: BLCA_Trp_227

value: LumP


title: BLCA_Trp_226

value: UroB


title: BLCA_Trp_221

value: GeneChip WT Pico kit


title: BLCA_Trp_220

value: palliative