title: tumor-case-08


title: Liver tissue from ground-based control c57Bl6/j mice [Liv_C20]

status: Public on Feb 11 2024

type: SRA

city: Sharjah

first: Amir

middle: Ali

last: Khan

address: Emirates of Sharjah

department: Department of Applied Biology

country: United Arab Emirates

institute: University of Sharjah

description: mRNA sequencing

library_source: transcriptomic

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulat
Genome_build: mice
Supplementary_files_format_and_content: excel sheet of read counts

molecule: total RNA

organism: Mus musculus

growth_protocol: 18 weeks old, male c57BL/6j mice into ground-based controls (n = 3) and Hind limb uploaded (HU) mice. HU mice were further divided into two groups and treated with either PBS as the vehicle (HU-v; n = 3) or 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections) (n = 3).

extract_protocol:
Total mRNAs were extracted from liver tissues of the three groups of mice
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directiona

treatment_protocol: HU (n=3) mice were injected with 4-PBA (HU-t; 100mg/kg/d via intraperitoneal injections)

tag: tissue

value: Liver

tag: strain

tag: agent

tag: age

value: 18 weeks

tag: Sex

value: male


title: tumor-case-15

type: genomic

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

country: Germany

institute: University of Lübeck

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were hybridized, washed, and stained according to manufacturer's protocols.

data_processing: Data was imported into R, normalized (quantile normalization) and failed probes were removed; cross reactive probes and multi-mapped probes were removed as well.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Lymphnode

label_protocol: As per manufacturer

extract_protocol: As per manufacturer

tag: disease state

value: BPDCN

value: tumor

tag: gender

tag: primary location

value: Lymphnode


title: RNA-seq_data1_WT_rep1

city: Chongqing

first: Jie

last: Lan

state: Chongqing

address: No. 1 Yixueyuan Rd, Yuzhong District

department: Bioinformatics

country: China

institute: Chongqing medical university

data_processing:
ChIP-seq: The ChIP-seq data were mapped to the Mus musculus genome (mm9) and D. melanogaster genome assembly (dm6) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by Samtools and retained the uniquely mapped tags. Enriched peaks were called using MACS. Reads were normalized with fly reference as previous study.
RNA-seq: The RNA-seq data were mapped to the Mus musculus genome (mm9) using HISAT2 with the default parameters and gene counts were extracted by featureCounts. The normalization and differential expression between samples were performed with R package DEseq2.
ATAC-seq: The ATAC-seq data were mapped to the Mus musculus genome (mm9) using bowtie2 with the default parameters. Low quality reads and PCR duplicates were removed by SAMtools and retained the uniquely mapped tags. Enriched peaks were called using MACS.
Assembly: mm9, dm6
Supplementary files format and content: bedgraph, bigwig, txt files

source_name: mouse embryonic stem cells

growth_protocol: mES cells were cultured in medium in the presence of 1,000 U/ml LIF, with 90% DMEM, 10%FBS,1% nonessential amino acids,1% 2-mercaptoethanol, 1% L-glutamine,1% nucleosides, 1% Pen/Strep  in standard incubator with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions, and complementary DNA was reverse-transcribed using a Perfect Real Time kit (TaKaRa; RR047A).
Libraries were prepared according to the Illumina TruSeq protocol and sequenced using a HiSeq 2000 system at Berry Genomics.

tag: cell type

value: mouse embryonic stem cells

tag: genotype

value: Wild type


title: tumor-case-07

source_name: Skin

value: Skin


title: Liver tissue from ground-based control c57Bl6/j mice [Liv_C17]

description: mRNA sequencing


title: NIPBL dTAG treated +estradiol 72hrs replicate2 Hi-C

city: SAN DIEGO

first: Indumathi

last: Patta

state: CA

address: 9500 Gilman Drive, NSB5114A, LaJolla

department: Molecular Biology

country: USA

institute: UCSD

library_source: genomic

data_processing:
We used the runHiC pipeline (https://github.com/XiaoTaoWang/HiC_pipeline) to process Hi-C data. Specifically, we first used Chromap (PMID: 34772935) to map the fastq file from Hi-C experiment to the reference genome mm10. We then kept the uniquely mapped reads, removed PCR duplicates, and output the valid .pairs files defined by the 4DN consortium (https://github.com/4dn-dcic/pairix/blob/master/pairs_format_specification.md). In addition, we used Juicer (PMID: 27467249) to convert the processed Hi-C data into the .hic format, for visualization in the software Juicebox (https://www.aidenlab.org/juicebox/). We first performed such analysis for each biological replicate seperately, and applied HiCrep (PMID: 28855260) to evaluate the reproducibility of Hi-C contact frequency between two biological replicates. After confirming the high reproducibility, we pooled the two biological replicates from the same experimental condition, and used the pooled Hi-C data for all the downstream analysis.
Assembly: mm10
Supplementary files format and content: hic matrix containing chromatin interaction frequencies, .hic format

source_name: Ecomg myeloid progenitor cell line

growth_protocol: NIPBL-FKBP12F36V-EYFP progenitor cells were cultured in RPMI 1640 media supplemented with 10%FBS, glutamine, penicillin and streptomycin, GM-CSF, β-estradiol.

extract_protocol:
Approximately 5-10 million cells were crosslinked using formaldehyde to a final concentration of 2%. Crosslinked cells were processed for Hi-C using Arima-HiC Kit (A510008) according to the manufacturer’s instructions.
The library preparation of Hi-C DNA was performed using KAPA HyperPrep Kit (KK8502) according to the manufacturer’s instructions. .

treatment_protocol: dTAG-13 was added to the cells and cultured in opti-MEM media for 72hrs.

tag: cell line

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL

tag: treatment

value: dTAG treatment

tag: time


title: miRNAseq_C19KO_3

city: Edinburgh

first: Yuka

last: Kabayama

address: 5 Little France Drive

country: United Kingdom

institute: University of Edinburgh

description: Small RNA (15–40 nt)

data_processing:
For analysis of piRNA, adapter sequence 'AGATCGGAAGA' was removed from fastq file using cutadapt version 1.8.1 with option '-m 16 --trimmed-only'.
Processed reads were mapped with bowtie (1.2.1.1) to known miRNAs, non-coding RNAs, repeatmasker track (UCSC mm10), and mouse genome (UCSC mm10).
Up to 3 mismatches were allowed when reads are mapped to the mouse gneome.
For analysis of differentially expressed TEs, single-end reads were mapped to consensus sequences from Repbase (24.01) using bowtie2 (2.3.4.3).
Mapped reads per TE were counted by home made scripts.
Differentially expressed TEs were analysed using DESeq2 (1.30.0).
Assembly: UCSC mm10
Supplementary files format and content: The processed sRNA-seq data is the tab-delimited txt file that contains the sequence, length, count, and annotation of small RNAs as well as sample ID and condition.
Supplementary files format and content: The processed RNA-seq data is the raw count of TE species.

source_name: Foetal testes

extract_protocol:
Total RNA was extracted from 6 foetal testes using the QIAzol reagent following the manufacturer’s instructions.
Size selected (15–40 nt) total RNA was applied for library preparation using NEBnext Multiplex Small RNA Library Prep Set for Illumina (NEB).

value: mixed B6CBAF1/Crl; C57BL/6N

tag: developmental stage

value: testis


title: miRNAseq_C19KO_2

description: Small RNA (15–40 nt)


title: tumor-case-49


title: NIPBL dTAG treated +estradiol 72hrs replicate1 Hi-C


title: NIPBL Untreated +estradiol 72hrs replicate2 Hi-C


title: miRNAseq_C19KO_1

description: Small RNA (15–40 nt)


title: tumor-case-17


title: tumor-case-09

value: female


title: tumor-case-10


title: tumor-case-14


title: tumor-case-12

source_name: Bonemarrow

value: Bonemarrow


title: NIPBL Untreated +estradiol 72hrs replicate1 Hi-C


title: miRNAseq_control_3

description: Small RNA (15–40 nt)


title: RNA-seq_data1_WT_rep2


title: Liver tissue from ground-based control c57Bl6/j mice [Liv_C18]

description: mRNA sequencing

value: Liver


title: tumor-case-20


title: HSC,KO,rep3,RNA-seq

city: Tianjin

first: Jianwei

last: Wang

address: 10 Yuexin Street, Binhai New Area

institute: HAIHE LABORATORY OF CELL ECOSYSTEM

data_processing:
First,Trim_galore (version0.6.6 http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used for quality control and adaptor trimming.
Then, Processed reads were remove rRNA and then mapped to mm10 using Hisat2.
Finally,gene expressions were counted by featureCount and submitted to DEseq2 to different expression analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Reads count for each Sample

source_name: Bone marrow

growth_protocol: hematopoietic stem cells were sorted from bone marrow

extract_protocol:
Lysates were clarified from FACS-sorted  hematopoietic stem cells. 200 HSCs (Lineage- Sca-1+ c-kit+ CD34- CD150+) from WT or Mcph1-/- mice were sorted into lysis buffer directly.
RNA-seq:The transcriptome libraries were prepared using Smart-seq2 method. Then, Agilent Bioanalyzer 2100 system (Agilent Technologies) was used to assess the insertion size, and HiSeq PE Cluster Kit v4-cBot-HS (Illumina) was used to perform the clustering of the index-coded samples according the manufacturer’s instructions. Finally, the libraries were sequenced using an Illumina Hiseq platform with 150-bp paired-end.

value: Bone marrow

value: Hematopoietic stem cells


title: tumor-case-11

value: BPDCN

value: male


title: miRNAseq_control_2

description: Small RNA (15–40 nt)


title: tumor-case-50

value: tumor


title: HSC,KO,rep2,RNA-seq


title: HSC,KO,rep1,RNA-seq


title: HSC,WT,rep3,RNA-seq

value: WT


title: miRNAseq_control_1

description: Small RNA (15–40 nt)


title: tumor-case-01

value: Lymphnode


title: HSC,WT,rep2,RNA-seq


title: tumor-case-05


title: tumor-case-02

value: Skin


title: polyp_2_JQ1_2

city: Palo ALto

first: Yizhou

last: Zhu

address: 3165 Porter Dr, Rm 2260

department: Genetics

institute: Stanford University

data_processing:
RNA seq results were processed using Tomas Bencomo’s pipeline (https://github.com/tjbencomo/bulk-rnaseq),
Assembly: hg38
Supplementary files format and content: .sf (expression level per transcript), .csv (DESeq2 differential expression)

source_name: colon organoid

extract_protocol:
Total RNA was extracted from ~5mg frozen tissue using zymo extraction kit (R1054)
Assay was performed using NEB E7775S,E7490S following manufacturer's protocol. 1000 ng of DNase I-treated initial total RNA input was used

value: colon organoid

tag: Stage

value: Polyp

tag: donor


title: polyp_2_C1

value: DMSO


title: polyp_2_C2


title: HSC,WT,rep1,RNA-seq


title: Bonemarrow Progenitors ATTO High replicate2

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
CellRanger v6.1.2 was used for demultiplexing, alignment, filtering of cells, and generation of read count tables. Downstream analyses were performed using Seurat v 4.0.6.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Mouse bone marrow HSPs and precursor neutrophils were enriched by two step negative selection. Initially Ly6G+ cells were depleted, followed by further depletion with Ly6G, CD3, B220, Ter119, CD115, F4/80, Siglec-F, and CD11C.  Lineage depleted cells enriched for HSPs and neutrophil precursors were electroporated with Cas9-sgRNA RNP complexes against NIPBL using Lonza 4D-NucleofectorTM X unit (DN-107 program). Cells were cultured for 72hrs in opti-MEM medium supplemented with 10%FBS, glutamine, penicillin and streptomycin, β-mercapto ethanol, 25ng/mL mSCF, 25ng/mL mFLT3. ATTO high and ATTO lo/negative cells were FACS sorted and were used for single cell RNA sequencing.
Library was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell HT Training Reagent Kit, 10x Genomics).

value: Primary bone marrow progenitors

value: 6-10 weeks

tag: cell type (sorted)

value: ATTO high cells


title: polyp_1_JQ1_2

tag: tissue


title: polyp_2_JQ1_1


title: Bonemarrow Progenitors ATTO High replicate1

description: 10x Genomics

tag: strain

value: electroporated with Cas9-sgRNA RNP complexes against NIPBL


title: Bonemarrow Progenitors ATTO Lo/Negative replicate1

description: 10x Genomics

value: ATTO lo/negative cells


title: polyp_1_JQ1_1


title: Bonemarrow Progenitors ATTO Lo/Negative replicate2

description: 10x Genomics


title: polyp_1_C1


title: NIPBL dTAG treated -estradiol 72hrs replicate2

data_processing:
Quality control of the raw fastq files was performed using the software tool FastQC v0.11.9. Sequencing reads were aligned to the mouse genome (GRCm39.primary assembly.genome.fa) using the STAR v2.7.9a aligner. Read quantification was performed with RSEM v1.3.3 and Gencode annotation (gencode.vM27.primary_assembly.annotation.gtf). The R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential expression analysis.  Lowly expressed genes were filtered out (cpm > 1 in at least three samples). Trimmed mean of M-values (TMM) normalization was applied. The experimental design was modeled upon treatment type, treatment, condition and timepoint (~0 +TreatmentType_Treatment_Condition_Timepoint). Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing correction using a moderated t-statistic in Limma. Functional enrichment of the differentially expressed genes was performed using GProfiler.
Assembly: mm10
Supplementary files format and content: gene counts as TPM, FPKM in text format

growth_protocol: ECOMG progenitor cells were cultured in RPMI 1640 media supplemented with 10%FBS, glutamine, penicillin and streptomycin, β-mercapto ethanol, GM-CSF, β-estradiol. The differentiation of neutrophils was induced by withdrawal of β-estradiol from opti-MEM media supplemented with 10%FBS, glutamine, penicillin and streptomycin, β-mercapto ethanol, GM-CSF.

extract_protocol:
Total RNA was extracted using Rneasy mini plus kit (Qiagen), and was used for construction of sequencing libraries.
Libraries of RNAseq were constructed using standard Illumina protocols.

treatment_protocol: dTAG-13 was added to the cells and cultured in opti-MEM media for 24 and 72hrs.

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL

tag: differentiation

value: In vitro neutrophil differentiation

value: dTAG treated -estradiol


title: mucosa_1_JQ1_2

value: Mucosa


title: mucosa_1_JQ1_1


title: mucosa_1_C2


title: NIPBL dTAG treated -estradiol 72hrs replicate1


title: NIPBL Untreated -estradiol 72hrs replicate3

value: Untreated -estradiol


title: mucosa_1_C1


title: HT29_JQ1_1

value: colorectal cancer cell line


title: HT29_JQ1_2


title: HT29_C2


title: HT29_C1


title: HPCEC_JQ1_1

source_name: HPCEC

value: HPCEC

value: primary human colon epithelial


title: HPCEC_JQ1_2


title: NIPBL dTAG treated -estradiol 24hrs replicate2


title: NIPBL Untreated -estradiol 24hrs replicate3


title: polyp_1_C2

value: colon organoid

value: Polyp


title: NIPBL Untreated -estradiol 72hrs replicate2


title: NIPBL Untreated -estradiol 72hrs replicate1


title: HPCEC_C1

value: DMSO


title: MAU2 dTAG treated -estradiol 72hrs replicate3

value: human E2A_ER_Pbx1b, FKBP12F36V_MAU2


title: NIPBL dTAG treated -estradiol 24hrs replicate3


title: HPCEC_C2


title: NIPBL Untreated -estradiol 24hrs replicate1


title: HCT116_JQ1_2


title: Huh7_PC4-IP_eCLIP

first: Qimei

last: Pan

address: No.30, Gaotanyan Stright Street, ShaPingba District

institute: Army Medical University

data_processing:
Fastq files were processed through eCLIP pipeline version 0.2.1a (https://github.com/YeoLab/eclip/releases/tag/0.2.1a).
Adapter were removed by using cutadapter version 2.10. RNA adapter sequences:AUAUAGGNNNNNAGAUCGGAAGAGCGUCGUGUAG;DNA adapter sequences:NNNNNNNNNNAGATCGGAAGAGCACACGTCTG.
eCLIP-seq reads were aligned to the hg19 genome assembly using STAR version 3.2.
Assembly: hg19
Supplementary files format and content: BigWig files were generated using deeptools version 3.5.0

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were UV-crosslinked followed by lysed in lysis buffer and sonicated by BioRuptor.To fragment RNA, cell lysate was treated with RNaseI. IP samples were immunoprecipitated with anti-PC4 antibody conjugated with dynabeads protein A/G. IP sample were dephosphorylated, followed by on-bead ligation of barcoded RNA adapters. Then samples were run on NuPAGE Bis-Tris protein gels and transferred to nitrocellulose membranes where the RNA in the region 15kDa-90kDa was cut off the membrane. To digest the protein, proteinase K was added to the membrane until the RNA was released.
eCLIPseq libraries were generated with Q5 PCR Master mix (NEB, M0492L) according to the manufacturer’s instructions.
eCLIP-Seq

value: Hepatocellular carcinoma cells

tag: rip antibody


title: MAU2 dTAG treated -estradiol 72hrs replicate2


title: Liver tissue from hind-limb unloaded c57Bl6/j mice treated with PBS as vehicle [Liv_U19]

description: mRNA sequencing

value: Liver

tag: agent

value: PBS

tag: age

value: 18 weeks

tag: Sex

value: male


title: HCT116_JQ1_1


title: Huh7_Input_eCLIP


title: NIPBL dTAG treated -estradiol 72hrs replicate3

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL


title: Sample_11_11_E8

city: shanghai

first: zhicheng

last: shao

address: dongan road 130

institute: fudan

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: fibroblast

growth_protocol: Fibroblast was eltrotransfected with yamanaka factors and growth in E8 and E6（E8 without bFGF,TGFb） medium

extract_protocol:
Fibroblast was treat by ID-8 molecular and DMSO and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fibroblast was eltrotransfected with yamanaka factors and then treat with DMSO and ID-8 for 7 days in E6 medium

value: skin

value: DMSO treat 7 days in E8 medium

tag: disease state

value: normal


title: HCT116_C2

tag: cell type

value: colorectal cancer cell line


title: Sample_11_11_E6I250

value: ID-8 treat 7 days in E6 medium


title: MAU2 dTAG treated -estradiol 72hrs replicate1

tag: genotype

value: In vitro neutrophil differentiation

value: dTAG treated -estradiol


title: Sample_11_11_E6

value: DMSO treat 7 days in E6 medium


title: MAU2 Untreated -estradiol 72hrs replicate2

tag: cell line

value: human E2A_ER_Pbx1b, FKBP12F36V_MAU2

value: Untreated -estradiol


title: NIPBL dTAG treated -estradiol 24hrs replicate1

tag: treatment


title: Sample_10_24_E8


title: HCT116_C1

value: DMSO


title: Sample_10_24_E6I250


title: MAU2 Untreated -estradiol 72hrs replicate1

tag: time


title: Sample_10_24_E6


title: MAU2 dTAG treated -estradiol 24hrs replicate3


title: Sample_9_30_E8


title: NIPBL Untreated -estradiol 24hrs replicate2


title: Sample_9_30_E6I250


title: MAU2 dTAG treated -estradiol 24hrs replicate2


title: MAU2 dTAG treated -estradiol 24hrs replicate1


title: MAU2 Untreated -estradiol 24hrs replicate1


title: 24_MS_non-migrated (contact with BBB-EC)

city: Diepenbeek

first: Ibrahim

last: HAMAD

state: Yes

address: Agoralaan Building C

department: Hasselt University

country: Belgium

data_processing:
Quality of raw sequence reads was checked using FastQC version 0.11.8, and nucleotide calls with a quality score of 28 or higher were considered high quality. Adapters were removed using cutadapt v.2.4. Reads were aligned to the hg19 genome reference, using STAR (2.5.0e) and amaximum of five mismatches were allowed.
the raw counts were imported to R/Bioconductor package DESeq2 v.3.9 to identify differentially expressed genes among samples. The default DESeq2 options were used, including log fold change shrinkage.
Assembly: hg19
Supplementary files format and content: htseq-count

source_name: Blood

extract_protocol:
Tregs were added to insert with inflamed (24h) monolayer of BBB-EC to interact and migrate accross BBB-EC for 24h. Tregs were also cultured without BBB-EC but in same medium for 24h. Next, cells were collected and mRNA was isolated.
mRNA was harvested using Qiagen's RNeasy micro kit
RNA libraries for RNA-seq were prepared using SMART-Seq® Stranded Kit

value: Blood

value: primary

value: CD4+CD25highCD127low Tregs

value: Relapsing remitting MS (RRMS)

value: non-migrated (contact with BBB-EC)


title: 26_MS_untouched (BBB-EC medium only)

growth_protocol: Tregs were added to insert with inflamed (24h) monolayer of BBB-EC to interact and migrate accross BBB-EC for 24h. Tregs were also cultured without BBB-EC but in same medium for 24h. Next, cells were collected and mRNA was isolated.

value: untouched (BBB-EC medium only)


title: 23_MS_untouched (BBB-EC medium only)

treatment_protocol: Tregs were added to insert with inflamed (24h) monolayer of BBB-EC to interact and migrate accross BBB-EC for 24h. Tregs were also cultured without BBB-EC but in same medium for 24h. Next, cells were collected and mRNA was isolated.


title: MAU2 Untreated -estradiol 24hrs replicate2

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor


title: MAU2-NIPBL dTAG treated +estradiol 72hrs replicate3

value: no neutrophil differentiation

value: dTAG treated +estradiol


title: 22_MS_migrated (BBB-EC transmigrated)

value: migrated (BBB-EC transmigrated)


title: 21_MS_non-migrated (contact with BBB-EC)


title: CD34-KSL cells, Elovl6 KO, 4

city: Tsukuba

first: Yusuke

last: Kiyoki

state: Ibaraki

address: 1-1-1 Tennodai

department: Hematology

country: Japan

institute: University of Tsukuba

data_processing:
CLC Genomics Workbench v 10.1.1
Sequence reads were mapped using CLCGenomics Workbench
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: bone marrow cells

extract_protocol:
RNA was extracted by using Trizol reagent.
RNA-seq library was prepared using a NEBNext Ultra Directional RNA Library Prep Kit following manufacturer's instructions.

value: bone marrow cells

value: Elovl6 knock out


title: CD34-KSL cells, Elovl6 KO, 3


title: MAU2-NIPBL dTAG treated +estradiol 72hrs replicate1


title: CD34-KSL cells, WT, 2

value: WT


title: CD34-KSL cells, Elovl6 KO, 1


title: CD34-KSL cells, Elovl6 KO, 2


title: 27_MS_non-migrated (contact with BBB-EC)


title: 20_MS_untouched (BBB-EC medium only)


title: MAU2-NIPBL dTAG treated +estradiol 72hrs replicate2


title: 19_MS_migrated (BBB-EC transmigrated)


title: MAU2-NIPBL Untreated +estradiol 72hrs replicate3

value: Untreated +estradiol


title: 25_MS_migrated (BBB-EC transmigrated)


title: 18_MS_non-migrated (contact with BBB-EC)


title: MLL-AF9 transduces Lin-c-kit+ cells,Elovl6 KO, 2Week, 1


title: MLL-AF9 transduces Lin-c-kit+ cells,Elovl6 KO, 2Week, 2


title: Sample_9_30_E6

value: skin

value: DMSO treat 7 days in E6 medium

value: normal


title: MLL-AF9 transduces Lin-c-kit+ cells,WT, 2Week, 2


title: CD34-KSL cells, WT, 1


title: MLL-AF9 transduces Lin-c-kit+ cells,WT, 2Week, 1


title: MAU2-NIPBL Untreated +estradiol 72hrs replicate2


title: 17_MS_untouched (BBB-EC medium only)

value: Blood

value: primary


title: 16_MS_migrated (BBB-EC transmigrated)

value: CD4+CD25highCD127low Tregs

value: Relapsing remitting MS (RRMS)


title: NIPBL dTAG treated +estradiol 72hrs replicate3

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL


title: RNAseq_C19KO_3

description: rRNA depleted total RNA

source_name: P20 testis

extract_protocol:
Total RNA was extracted from 1 testis using QIAGEN RNeasy Mini kit and following manufacture’s protocol including on-column DNase treatment.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: mixed B6CBAF1/Crl; C57BL/6N

tag: developmental stage

value: testis


title: RNAseq_C19KO_2

description: rRNA depleted total RNA


title: 15_HC_non-migrated (contact with BBB-EC)

value: Healthy control

value: non-migrated (contact with BBB-EC)


title: NIPBL dTAG treated +estradiol 72hrs replicate2

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: no neutrophil differentiation

value: dTAG treated +estradiol


title: PEO1 WT conditioned medium from PEO4  rep 2

city: Chicago

first: Daniela

middle: Elena

last: Matei

state: IL

address: 303 E Superior St

department: Obstetrics and Gynecology

institute: Northwestern University

data_processing:
Fastq files were pre-analyzed using FastQC (0.11.5)
Fastq files were trimmed with low quality reads with TrimGalore (0.4.4)
Reads were aligned to the ENSEMBL human genome GRCh38 (release 91) using STAR (2.5.2)
BAM files from STAR alignment were sorted by name using Samtools (1.6)
HTSeq-count (anaconda 3.6) was used to generate raw counts for each BAM file
Assembly: GRCh38
Supplementary files format and content: counts

source_name: ascites

growth_protocol: Cells were growth in RPMI 1640 (Corning), 10% fetal bovine serum (FBS) (Corning), 1% penicillin/streptomycin (Sigma), and 1X GlutaMAX (Gibco), in a humidify atmosphere, 5% and 37°C.

extract_protocol:
RNA was isolated by using TRIzol (Invitrogen) according to the manufacturer’s instructions and quantified using a NanoDrop 3300 Fluorospectrometer.
The RNA sequencing (RNA-seq) libraries were prepared from 1 μg of total RNA of PEO1 WT or PEO1-RFP. Libraries were generated using the NEBNext Ultra II RNA library prep kit from Illumina (New England Biolabs, Inc.). Library preparation was perform accoding to manufacter's protocol.

treatment_protocol: PEO1 and PEO4 cells were co-cultured on a 1:7 proportion for 14 days and then FACS separated. Media was replaced every 3 days. For Conditioned media experiment, PEO4 media was collected, filtered and transferred to PEO1 cells over a period of 14 days.

value: ascites

value: High grade serous ovarian cancer

value: PEO4 conditioned media treated

value: conditioned media treament


title: 14_HC_untouched (BBB-EC medium only)

value: Blood

value: untouched (BBB-EC medium only)


title: PEO1 WT rep 2

value: WT

value: Control


title: RNAseq_C19KO_1

description: rRNA depleted total RNA


title: NIPBL dTAG treated +estradiol 72hrs replicate1

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL


title: PEO1 WT rep 1


title: PEO1 WT conditioned medium from PEO4  rep 1


title: NIPBL Untreated +estradiol 72hrs replicate3

value: Untreated +estradiol


title: 13_HC_migrated (BBB-EC transmigrated)

value: primary

value: CD4+CD25highCD127low Tregs

value: migrated (BBB-EC transmigrated)


title: PEO1-RFP coculture rep 2

value: PEO4 co-culture

value: Co-culture


title: 12_HC_non-migrated (contact with BBB-EC)

value: Healthy control

value: non-migrated (contact with BBB-EC)


title: PEO1-RFP coculture rep 1

value: ascites


title: PEO1-RFP monoculture rep 2

value: High grade serous ovarian cancer

value: transfected with RFP


title: 11_HC_untouched (BBB-EC medium only)


title: NIPBL Untreated +estradiol 72hrs replicate2

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: no neutrophil differentiation


title: DN_23_005_RNP

city: San Francisco

first: Kristen

last: Seim

address: 201 Haskins Way

institute: GraphiteBio

description: 10X genomics

data_processing:
cellranger - alignemt
Seurat (v4.3.0) - Data processing and analysis
Seurat’s Read10X function was used to generate a count data matrix using the filtered count matrix genes and cells, gene names, and barcode files provided by 10X.
dittoSeq (v1.8.1) - Visualizations
Assembly: hg19
Supplementary files format and content: Robject
Supplementary files format and content: Robject with counts matrix and annotation

source_name: primary HSPC

extract_protocol:
Leuokopaks were purchased from AllCells LLC and these were collected from healthy donors per standard protocols using mobilization with G-CSF+ Plerixafor. CD34+ cells were isolated from the leukopaks within 24 h by first removing the platelets using the LOVO cell Processing System (Fresenius Kabi). GMP grade reagents, buffers and columns for CD34 immunomagnetic selection were purchased from Milteny Biotec and the platelet washed cells were incubated for 30-35 min using the CD34 Reagent following which a subsequent wash for excess antibodies was performed on the LOVO. The washed and labelled cells were subject to immunomagnetic selection using the CliniMACS Plus instrument (Miltenyi Biotec) following which the cells were cryopreserved at a concentration of 5x106-1x107 cells/mL in CryoMACS 50 or 250 Bags (Miltenyi Biotec) for the gene edited drug product generation step.
10X Genomics Chromium Next GEM Single Cell 3’ Gene Expression Reagent Kit

value: primary HSPC

value: RNP only (no AAV)


title: PEO1-RFP monoculture rep 1

value: Control


title: NIPBL Untreated +estradiol 72hrs replicate1

value: human E2A_ER_Pbx1b, FKBP12F36V_NIPBL

value: Untreated +estradiol


title: MAU2-NIPBL Untreated +estradiol 72hrs replicate1


title: 10_HC_migrated (BBB-EC transmigrated)

value: Blood

value: primary

value: CD4+CD25highCD127low Tregs


title: DN_23_005_CD34

description: 10X genomics

value: untreated


title: DN_23_005_625MOI_plusbooster

description: 10X genomics


title: 9_HC_non-migrated (contact with BBB-EC)

value: Healthy control


title: MAU2 dTAG treated +estradiol 72hrs replicate3

value: human E2A_ER_Pbx1b, FKBP12F36V_MAU2

value: dTAG treated +estradiol


title: DN_23_005_625MOI

description: 10X genomics

value: MOI 625


title: DN_23_004_RNP

description: 10X genomics


title: MAU2 dTAG treated +estradiol 72hrs replicate2


title: MAU2 dTAG treated +estradiol 72hrs replicate1


title: DN_23_004_CD34

description: 10X genomics


title: 8_HC_untouched (BBB-EC medium only)

value: untouched (BBB-EC medium only)


title: 7_HC_migrated (BBB-EC transmigrated)

value: migrated (BBB-EC transmigrated)


title: Huh7_Input-rep2

data_processing:
RIP-seq data were aligned and quantified using RSEM as well as STAR against the hg19 human reference genome and annotation (GTF format) downloaded from GENCODE official website. Gene counts were then used for downstreamed analysis.
Assembly: hg19
Supplementary files format and content: BigWig

extract_protocol:
Cells were crosslinked with formaldehyde and stopped with glycine.The cells were collected and incubated in cell lysis buffer. Then the RNA-protein complexes were enriched using anti-PC4 antibodies conjugated with protein A/G beads.The RNA immunocomplex was washed and incubated with proteinase K to release the RNAs from PC4-RNA immunocomplexes. RNA was isolated and extracted by using the phenol-chloroform method.
RIP-seq libraries were generated with TruSeq Stranded mRNA (Illumina) according to the manufacturer’s instructions.

value: Hepatocellular carcinoma cells


title: MAU2 Untreated +estradiol 72hrs replicate3

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: no neutrophil differentiation


title: MAU2 Untreated +estradiol 72hrs replicate2


title: DN_23_004_625MOI_plusbooster

description: 10X genomics

value: primary HSPC


title: DN_23_004_625MOI

description: 10X genomics


title: 5_HC_untouched (BBB-EC medium only)


title: Huh7_Input-rep1


title: 6_HC_non-migrated (contact with BBB-EC)

value: non-migrated (contact with BBB-EC)


title: DN_23_003_RNP

description: 10X genomics

value: RNP only (no AAV)


title: MAU2 Untreated +estradiol 72hrs replicate1

value: Untreated +estradiol


title: Huh7_siPC4-2

data_processing:
The fastq files were produced and the quality of the reads was assessed by FastQC software.
After reads alignment to human genome (ver. hg19) using Bowite-Tophat2 algorism, the BAM files were generated and quantified for differential transcript analysis using Cyfflinks.
The differentially expressed transcripts were defined as a statistical cut-off of p<0.001 and fold change (log2)>1 and <-1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen,15596018) according to the manufacturer’s instructions.
500ng of total RNA was taken out to generate the sequencing libraries by the Illumina’s TruSeq RNA Sample pre kit V2 (Illumina).

treatment_protocol: Cells were transfected with siRNAs targeting PC4(siNC,siPC4-1,siPC4-2) for 48 hours by using Lipofectamine RNAiMAX or 3000 (Thermo Fish Scientific, Waltham, MA) according to the manufacturer’s instructions.

value: PC4 knockdown

value: siPC4 transfection

value: 48hours after transfection


title: 4_HC_migrated (BBB-EC transmigrated)

value: Blood

value: primary

value: CD4+CD25highCD127low Tregs

value: Healthy control


title: Huh7_siPC4-1


title: NIPBL +estradiol 72hrs +dTAG

data_processing:
Raw ATACseq data was processed with the ATAC-seq pipeline implemented in bcbio-nextgen v1.2.8 that follows recommendations from the ENCODE ATAC-seq pipeline. Quality control of ATACseq data was performed using the software tool FastQC v0.11.8 , MultiQC v1.10.1 and ataqv v1.2.1. Raw reads were aligned to the mouse genome with BWA v0.7.17 and duplicates, multimappers and reads aligning to mitochondria were removed. BAM files are then split into separate BAM files for the nucleosome free (NF), mononucleosome (MN), dinucleosome (DN) and trinucleosome (TN) fractions. Peaks were called with MACS2 v2.2.7 separately on each fraction and on all combined fractions. Consensus peaks of the nucleosome free peaks were created by taking the peak with the highest score when peaks overlap with bedops v2.4.40. Peaks in Encode exclusion regions were removed (ENCFF547MET). We annotated peaks with the Bioconductor package ChIPseeker and TxDb.Mmusculus.UCSC.mm10.knownGene. We used R BioConductor packages edgeR and limma were used to implement the limma-voom method for differential chromatin accessibility analysis.  Peak counts were normalized with trimmed mean of M-values (TMM) normalization and the experimental design was modeled upon group (~0 +Group).  Significance was defined by using an adjusted p-value cut-off of 0.05 after multiple testing correction using a moderated t-statistic in Limma. Motif enrichment analysis was performed with Homer findMotifsGenome.pl -size given for all differentially accessible peaks. We integrated differentially expressed genes and differentially accessible peaks by merging the results of each significant comparison. Peaks and genes overlapping with RAD21 binding sites were identified by overlapping differentially accessible peaks with peaks obtained from GSE93127 using bedtools v2.30.0.
Assembly: mm10
Supplementary files format and content: narrowPeak, bedgraph

growth_protocol: ECOMG progenitor cells were cultured in RPMI media supplemented with 10%FBS, glutamine, penicillin and streptomycin, β-mercapto ethanol, GM-CSF, β-estradiol.

extract_protocol: 50,000 cells were used for library preparation according to the manufacturer’s protocol (ATAC-Seq kit, Active motif).

treatment_protocol: dTAG

value: +estradiol 72hrs +dTAG


title: 3_HC_non-migrated (contact with BBB-EC)


title: NIPBL +estradiol 6hrs +dTAG

value: +estradiol 6hrs +dTAG


title: Huh7_PC4-IP-rep2

value: Hepatocellular carcinoma cells


title: DN_23_003_625MOI_plusbooster

description: 10X genomics


title: Huh7_siNC-2

value: WT

value: siNC transfection


title: NIPBL +estradiol 0hr -dTAG

value: Ecomg myeloid progenitor cell line

value: Myeloid progenitor

value: +estradiol 0hr -dTAG


title: Huh7_PC4-IP-rep1


title: DN_23_003_625MOI

description: 10X genomics

value: primary HSPC

value: MOI 625


title: 2_HC_untouched (BBB-EC medium only)

value: untouched (BBB-EC medium only)


title: Huh7_siNC-1


title: 1_HC_migrated (BBB-EC transmigrated)

value: migrated (BBB-EC transmigrated)


title: Morphine, biol rep 2, snRNAseq

status: Public on Feb 10 2024

city: Stanford

first: Michelle

last: Monje

address: 265 Campus Drive, SIM1 G3035

department: Neurology

description: Sequenced on Illumina NextSeq 2000, 10X Chromium Next GEM Single Cell 3' HT Kit v3.1

data_processing:
The demultiplexing, barcoded processing, and alignment were performed using Cell Ranger v7.0.1 to generate filtered gene-barcode matrices (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Raw read (FASTQ) files were aligned to the mouse reference genome (mm10 - 2020-A).
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Brain (ventral tegmental area)

growth_protocol: Wild-type C57BL/6J (The Jackson Laboratory, 000664) mice were housed in a 12-hour light/dark cycle with unrestricted access to food and water.

extract_protocol:
Mice were transcardially perfused, brains were promptly harvested and flash frozen. Ventral tegmental area from both hemispheres were punched out. Tissues were dissociated using a Wheaton Dounce Homogenizer, stained with DAPI, and FACS sorted. RNA from sorted and 10X captured single-nuclei were extracted as a part of the 10X Chromium Next GEM Single Cell 3' HT Kit v3.1 process following the manufacturer's protocols.
Libraries for snRNA-seq were generated using 10X Chromium Next GEM Single Cell 3' HT Kit v3.1 following the manufacturer’s protocols.

treatment_protocol: Mice (saline control, n=3; 10 mg/kg morphine, n=3) were subjected to Conditioned Place Preference test.

value: Brain (ventral tegmental area)

value: Morphine (10 mg/kg)

value: Wild-type C57BL/6J

value: Female


title: Morphine, biol rep 1, snRNAseq

value: Male


title: Saline, biol rep 3, snRNAseq

value: Saline


title: Morphine, biol rep 3, snRNAseq


title: DN_23_003_CD34

description: 10X genomics

value: untreated


title: Saline, biol rep 2, snRNAseq


title: Saline, biol rep 1, snRNAseq


title: E17.5, Acta2-dsRed+, Pdgfra-GFP+, rep3

city: Philadelphia

first: Sylvia

middle: N

last: Michki

state: PA

address: 3615 Civic Center Blvd

department: Pulmonary & Sleep Medicine

institute: Children's Hospital of Philadelphia

data_processing:
Read alignment and quantification at gene-level using nf-core/rnaseq
Assembly: GRCm38
Supplementary files format and content: tab-separated file with scaled gene counts

source_name: lung

extract_protocol:
Whole mouse lung dissociated into single-cell suspension before FACS. dsRed+, GFP+ cells were sorted into FACS buffer, centrifuged, and resuspend in Trizol prior to total RNA extraction and library construction.
SMART-seq v4 Plus/ultra-low RNA input stranded total RNA-seq

value: lung

value: Acta2-dsRed+, Pdgfra-GFP+


title: P3, Acta2-dsRed+, Pdgfra-GFP+, rep3


title: P7, Acta2-dsRed+, Pdgfra-GFP+, rep3


title: P3, Acta2-dsRed+, Pdgfra-GFP+, rep2


title: P7, Acta2-dsRed+, Pdgfra-GFP+, rep1


title: P3, Acta2-dsRed+, Pdgfra-GFP+, rep1


title: P10, Acta2-dsRed+, Pdgfra-GFP+, rep1


title: E17.5, Acta2-dsRed+, Pdgfra-GFP+, rep2


title: P7, Acta2-dsRed+, Pdgfra-GFP+, rep2


title: P10, Acta2-dsRed+, Pdgfra-GFP+, rep3


title: E17.5, Acta2-dsRed+, Pdgfra-GFP+, rep1


title: ChIP_Input

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Aligned using bowtie with parameters: -v 2 -m 1 --best --strata
Assembly: mm10
Supplementary files format and content: bigWig: normalized read coverage

source_name: HT22 cells

extract_protocol:
DNA was extracted and sequencing libraries were prepared by Active Motif.
The ChIP DNA was used for qPCRs using indicated primers and data were plotted as the percentage of input. All experiments were performed three or more times, and representative results were shown in the figures. For ChIP-seq, 1 ng precipitated DNA or input was used to generate sequencing libraries using the Nextera XT DNA sample preparation Kit (Illumina). The resulting libraries were sequenced on Next-Seq (Illumina).

value: HT22 cells

value: Immortalized Hippocampal Neuronal Cell Line

value: WT

value: Input


title: ChIP_PRMT5

value: PRMT5 ChIP


title: TMG059_882_S46_L008_R1_001

city: Leicester

first: David

middle: John

last: Cousins

address: NIHR BRC Respiratory, Glenfield Hospital

department: Respiratory Sciences

institute: University of Leicester

data_processing:
To assess the differences between risankizumab and placebo, a pre-filtering step was performed to remove transcripts with low expression. The samples were normalized using the 'Trimmed Mean of M-values' method. The R-package limma in conjunction with voom transformation and observational weights was used to fit a standard linear regression model in a univariate fashion to the observed read counts
Genome_build: GRCh38

source_name: Sputum

extract_protocol:
Sputum cells were pelleted by centrifugation and total RNA was isolated
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient id

tag: visit


title: TMG059_883_S17_L003_R1_001

description:
TMG059_883
sample failed QC and was not included in the analysis


title: TMG059_881_S45_L008_R1_001


title: TMG059_880_S44_L008_R1_001


title: TMG059_879_S43_L008_R1_001


title: P10, Acta2-dsRed+, Pdgfra-GFP+, rep2


title: TMG059_878_S42_L008_R1_001


title: TMG059_877_S41_L008_R1_001


title: TMG059_876_S40_L007_R1_001


title: TMG059_875_S39_L007_R1_001


title: TMG059_874_S38_L007_R1_001


title: TMG059_873_S37_L007_R1_001


title: TMG059_870_S34_L006_R1_001


title: TMG059_872_S36_L007_R1_001


title: TMG059_868_S32_L006_R1_001


title: TMG059_871_S35_L007_R1_001


title: TMG059_866_S30_L006_R1_001


title: TMG059_865_S29_L006_R1_001


title: TMG059_867_S31_L006_R1_001


title: TMG059_861_S26_L005_R1_001


title: TMG059_860_S25_L005_R1_001


title: BM Mir21 KO-1

type: RNA

city: München

first: Maliheh

last: Nazari-Jahantigh

state: --Please select--

department: LMU

institute: IPEK

hyb_protocol: Following clean up and quantification, the cRNA (550 to 600 ng per sample) was fragmented and prepared for one-color-based hybridization (Gene Expression Hybridization Kit, Agilent Technologies). Labelled cRNA samples were hybridized at 65°C for 17 h on microarrays (Agilent SurePrint G3 Mouse Gene Expression 8x60K Microarrays).

scan_protocol: Microarrays were washed with increasing stringency (Gene Expression Wash Buffers, Agilent Technologies) and dried with acetonitrile (Sigma). Fluorescent signal intensities were detected with a microarray scanner (Agilent DNA Microarray Scanner) using Scan Control A.8.4.1 software (Agilent Technologies) and extracted from the images using Feature Extraction software (version 10.7.3.1, Agilent Technologies).

data_processing: Data were analyzed using GeneSpring GX 12.6 software (Agilent Technologies).

source_name: aortic arch-12wks high fat diet

label_protocol: Total RNA (RIN > 7.5, 100 ng per sample) was reverse transcribed into cDNA and then converted into cyanine-3 labeled cRNA (Low Input Quick-Amp Labeling Kit One-Color, Agilent Technologies).

extract_protocol: Total RNA was extracted using MirVana miRNA isolation kit

treatment_protocol: To generate bone marrow (BM) chimeric mice, female Mir21+/+ mice were subjected to whole-body X-ray irradiation (2 x 5 Gy within 4 hours, Faxitron CP-160), and BM cells from Mir21–/– and Mir21+/+ mice were injected into the tail vein one day later. Three weeks after the irradiation, mice were put on an HFD for 12 weeks. Next, aortic arch tissues were used for RNA isolation.

tag: gender

value: female


title: BM Mir21 KO-2


title: BM Mir21 KO-3


title: BM Mir21 WT-1


title: BM Mir21 WT-2


title: BM Mir21 WT-3


title: TMG059_859_S24_L005_R1_001


title: TMG059_858_S23_L004_R1_001


title: TMG059_855_S20_L004_R1_001


title: TMG059_853_S18_L004_R1_001


title: TMG059_856_S21_L004_R1_001


title: TMG059_852_S25_L005_R1_001


title: TMG059_854_S19_L004_R1_001


title: TMG059_849_S22_L004_R1_001


title: TMG059_850_S23_L004_R1_001


title: TMG059_864_S28_L005_R1_001


title: TMG059_851_S24_L004_R1_001

description:
TMG059_851
sample failed QC and was not included in the analysis


title: TMG059_848_S21_L004_R1_001


title: TMG059_847_S20_L004_R1_001


title: TMG059_869_S33_L006_R1_001


title: TMG059_863_S27_L005_R1_001


title: TMG059_845_S18_L003_R1_001


title: TMG059_844_S17_L003_R1_001


title: TMG059_843_S16_L003_R1_001


title: TMG059_840_S13_L003_R1_001


title: TMG059_835_S8_L002_R1_001


title: TMG059_838_S11_L002_R1_001


title: TMG059_841_S14_L003_R1_001


title: TMG059_839_S12_L002_R1_001


title: TMG059_836_S9_L002_R1_001


title: TMG059_834_S7_L002_R1_001


title: TMG059_833_S6_L001_R1_001


title: TMG059_857_S22_L004_R1_001


title: TMG059_832_S5_L001_R1_001


title: TMG059_831_S4_L001_R1_001


title: TMG059_814_S22_L004_R1_001


title: TMG059_828_S1_L001_R1_001


title: TMG059_829_S2_L001_R1_001


title: TMG059_811_S2_L001_R1_001


title: TMG059_804_S14_L004_R1_001


title: TMG059_800_S26_L005_R1_001


title: TMG059_846_S19_L004_R1_001


title: TMG059_842_S15_L003_R1_001


title: TMG059_797_S35_L006_R1_001


title: TMG059_806_S45_L008_R1_001


title: TMG059_809_S15_L004_R1_001


title: TMG059_790_S8_L003_R1_001


title: TMG059_785_S6_L001_R1_001


title: TMG059_764_S6_L002_R1_001


title: TMG059_767_S16_L003_R1_001


title: TMG059_761_S16_L003_R1_001


title: TMG059_780_S45_L008_R1_001


title: TMG059_837_S10_L002_R1_001


title: TMG059_753_S46_L008_R1_001


title: TMG059_749_S28_L005_R1_001


title: TMG059_751_S48_L008_R1_001


title: TMG059_745_S33_L006_R1_001


title: TMG059_752_S13_L004_R1_001


title: TMG059_747_S20_L005_R1_001


title: TMG059_830_S3_L001_R1_001


title: TMG059_740_S10_L002_R1_001


title: TMG059_738_S27_L005_R1_001


title: TMG059_746_S11_L003_R1_001


title: TMG059_737_S21_L006_R1_001

description:
TMG059_737
sample failed QC and was not included in the analysis


title: TMG059_736_S17_L005_R1_001


title: TMG059_734_S13_L004_R1_001


title: TMG059_733_S37_L008_R1_001


title: TMG059_731_S13_L004_R1_001


title: TMG059_727_S15_L003_R1_001


title: TMG059_728_S9_L003_R1_001


title: TMG059_723_S10_L002_R1_001


title: TMG059_722_S19_L004_R1_001


title: TMG059_726_S9_L002_R1_001


title: TMG059_729_S21_L004_R1_001


title: TMG059_770_S3_L001_R1_001


title: TMG059_720_S23_L005_R1_001


title: TMG059_719_S10_L002_R1_001


title: TMG059_716_S7_L002_R1_001


title: TMG059_713_S74_L007_R1_001

description:
TMG059_713
sample failed QC and was not included in the analysis


title: TMG059_706_S21_L004_R1_001


title: TMG059_711_S24_L007_R1_001


title: TMG059_693_S3_L001_R1_001


title: TMG059_692_S5_L001_R1_001


title: TMG059_735_S5_L002_R1_001


title: TMG059_739_S25_L007_R1_001


title: TMG059_701_S17_L003_R1_001


title: TMG059_705_S27_L006_R1_001


title: TMG059_704_S2_L001_R1_001


title: TMG059_691_S23_L004_R1_001


title: TMG059_689_S32_L007_R1_001


title: TMG059_687_S13_L003_R1_001


title: TMG059_702_S39_L007_R1_001


title: TMG059_688_S15_L003_R1_001


title: TMG059_685_S35_L008_R1_001


title: TMG059_683_S97_L007_R1_001


title: TMG059_686_S25_L007_R1_001

description:
TMG059_686
sample failed QC and was not included in the analysis


title: TMG059_677_S29_L007_R1_001


title: TMG059_678_S31_L007_R1_001


title: TMG059_681_S6_L001_R1_001


title: TMG059_673_S14_L003_R1_001


title: TMG059_680_S8_L002_R1_001


title: TMG059_672_S23_L004_R1_001

description:
TMG059_672
sample failed QC and was not included in the analysis


title: TMG059_670_S43_L008_R1_001


title: TMG059_718_S19_L004_R1_001


title: TMG059_709_S7_L002_R1_001

description:
TMG059_709
sample failed QC and was not included in the analysis


title: TMG059_669_S21_L006_R1_001


title: TMG059_667_S40_L008_R1_001


title: TMG059_665_S36_L007_R1_001


title: TMG059_663_S33_L008_R1_001


title: TMG059_660_S26_L005_R1_001


title: TMG059_658_S11_L002_R1_001


title: TMG059_655_S20_L004_R1_001


title: TMG059_657_S29_L005_R1_001


title: TMG059_652_S35_L007_R1_001


title: TMG059_650_S30_L006_R1_001


title: TMG059_647_S12_L004_R1_001


title: TMG059_638_S26_L005_R1_001


title: TMG059_636_S20_L006_R1_001


title: TMG059_632_S20_L004_R1_001


title: TMG059_675_S16_L003_R1_001


title: TMG059_627_S19_L006_R1_001


title: TMG059_625_S8_L003_R1_001


title: TMG059_621_S15_L003_R1_001


title: TMG059_629_S22_L007_R1_001


title: TMG059_622_S8_L002_R1_001


title: TMG059_624_S8_L002_R1_001


title: TMG059_619_S15_L005_R1_001


title: TMG059_617_S3_L001_R1_001


title: TMG059_615_S32_L006_R1_001


title: TMG059_614_S20_L004_R1_001


title: TMG059_616_S8_L002_R1_001


title: TMG059_613_S23_L005_R1_001


title: TMG059_611_S24_L004_R1_001


title: TMG059_605_S12_L004_R1_001


title: TMG059_608_S2_L001_R1_001


title: TMG059_607_S38_L007_R1_001


title: TMG059_612_S100_L008_R1_001


title: TMG059_639_S4_L001_R1_001


title: TMG059_644_S31_L007_R1_001


title: TMG059_603_S9_L003_R1_001


title: TMG059_598_S3_L001_R1_001


title: TMG059_593_S44_L008_R1_001


title: TMG059_587_S21_L005_R1_001


title: TMG059_604_S31_L006_R1_001


title: TMG059_633_S17_L005_R1_001


title: TMG059_590_S12_L004_R1_001


title: TMG059_574_S43_L008_R1_001


title: TMG059_568_S22_L007_R1_001


title: TMG059_566_S5_L002_R1_001


title: TMG059_570_S72_L007_R1_001


title: TMG059_564_S12_L003_R1_001


title: TMG059_559_S36_L007_R1_001


title: TMG059_555_S21_L004_R1_001


title: TMG059_550_S16_L003_R1_001


title: TMG059_547_S25_L006_R1_001


title: TMG059_541_S3_L001_R1_001


title: TMG059_558_S26_L005_R1_001


title: TMG059_539_S1_L001_R1_001


title: TMG059_537_S1_L001_R1_001


title: TMG059_543_S23_L004_R1_001


title: TMG059_529_S15_L003_R1_001


title: TMG059_588_S34_L007_R1_001


title: TMG059_526_S37_L007_R1_001


title: TMG059_522_S10_L004_R1_001


title: TMG059_578_S98_L008_R1_001


title: TMG059_520_S8_L003_R1_001


title: TMG059_516_S4_L002_R1_001


title: TMG059_512_S27_L008_R1_001


title: TMG059_518_S7_L003_R1_001


title: TMG059_524_S7_L002_R1_001


title: TMG059_515_S33_L006_R1_001


title: TMG059_535_S1_L001_R1_001


title: TMG059_509_S1_L001_R1_001


title: TMG059_576_S24_L004_R1_001


title: TMG059_561_S32_L007_R1_001


title: TMG059_505_S11_L002_R1_001


title: TMG059_496_S14_L003_R1_001


title: TMG059_492_S31_L008_R1_001


title: TMG059_491_S3_L001_R1_001


title: TMG059_488_S5_L001_R1_001


title: TMG059_477_S1_L001_R1_001


title: TMG059_479_S27_L008_R1_001


title: TMG059_533_S7_L002_R1_001


title: TMG059_473_S11_L003_R1_001


title: TMG059_471_S9_L003_R1_001


title: TMG059_469_S39_L007_R1_001


title: TMG059_459_S13_L004_R1_001


title: TMG059_467_S36_L007_R1_001


title: TMG059_465_S35_L006_R1_001


title: TMG059_449_S27_L007_R1_001


title: TMG059_450_S15_L005_R1_001


title: TMG059_448_S43_L008_R1_001


title: TMG059_446_S3_L001_R1_001


title: TMG059_439_S95_L007_R1_001


title: TMG059_441_S47_L008_R1_001


title: TMG059_445_S16_L003_R1_001


title: TMG059_438_S42_L008_R1_001


title: TMG059_436_S30_L006_R1_001


title: TMG059_435_S20_L006_R1_001


title: TMG059_434_S10_L002_R1_001

description:
TMG059_434
sample failed QC and was not included in the analysis


title: TMG059_432_S8_L002_R1_001


title: TMG059_431_S3_L001_R1_001


title: TMG059_493_S32_L008_R1_001


title: TMG059_489_S23_L006_R1_001


title: TMG059_430_S39_L008_R1_001


title: TMG059_426_S31_L006_R1_001


title: TMG059_422_S35_L008_R1_001


title: TMG059_418_S13_L003_R1_001


title: TMG059_427_S22_L006_R1_001


title: TMG059_417_S36_L007_R1_001


title: TMG059_420_S2_L001_R1_001


title: TMG059_411_S24_L005_R1_001


title: TMG059_414_S15_L004_R1_001


title: TMG059_463_S33_L008_R1_001


title: TMG059_410_S42_L007_R1_001

description:
TMG059_410
sample failed QC and was not included in the analysis


title: TMG059_406_S18_L004_R1_001


title: TMG059_401_S18_L005_R1_001


title: TMG059_398_S33_L007_R1_001


title: TMG059_396_S25_L005_R1_001


title: TMG059_397_S28_L006_R1_001


title: TMG059_399_S77_L008_R1_001


title: TMG059_393_S20_L004_R1_001


title: TMG059_385_S28_L008_R1_001


title: TMG059_395_S21_L005_R1_001


title: TMG059_388_S31_L006_R1_001


title: TMG059_391_S19_L005_R1_001


title: TMG059_383_S26_L008_R1_001


title: TMG059_382_S24_L005_R1_001


title: TMG059_386_S29_L006_R1_001


title: TMG059_374_S31_L006_R1_001


title: TMG059_366_S25_L005_R1_001


title: TMG059_380_S39_L007_R1_001


title: TMG059_378_S37_L007_R1_001


title: TMG059_363_S26_L008_R1_001


title: TMG059_354_S11_L002_R1_001


title: TMG059_355_S25_L005_R1_001


title: TMG059_376_S7_L002_R1_001


title: TMG059_408_S28_L005_R1_001


title: TMG059_359_S15_L005_R1_001


title: TMG059_364_S19_L006_R1_001


title: TMG059_350_S19_L006_R1_001


title: TMG059_357_S23_L007_R1_001


title: TMG059_361_S24_L008_R1_001


title: TMG059_346_S15_L005_R1_001


title: TMG059_344_S4_L002_R1_001

description:
TMG059_344
sample failed QC and was not included in the analysis


title: TMG059_342_S11_L004_R1_001


title: TMG059_352_S5_L001_R1_001


title: TMG059_340_S7_L002_R1_001


title: TMG059_348_S7_L003_R1_001


title: TMG059_339_S36_L008_R1_001


title: TMG059_337_S21_L007_R1_001


title: TMG059_336_S40_L008_R1_001


title: TMG059_333_S15_L003_R1_001


title: TMG059_334_S38_L008_R1_001


title: TMG059_332_S35_L007_R1_001


title: TMG059_330_S25_L005_R1_001


title: TMG059_331_S30_L006_R1_001


title: TMG059_328_S11_L004_R1_001


title: TMG059_326_S17_L006_R1_001


title: TMG059_323_S18_L004_R1_001


title: TMG059_300_S46_L008_R1_001


title: TMG059_303_S5_L001_R1_001

description:
TMG059_303
sample failed QC and was not included in the analysis


title: TMG059_325_S20_L004_R1_001


title: TMG059_301_S3_L001_R1_001


title: TMG059_291_S19_L004_R1_001


title: TMG059_297_S21_L004_R1_001


title: TMG059_309_S31_L006_R1_001


title: TMG059_320_S13_L003_R1_001


title: TMG059_299_S41_L007_R1_001


title: TMG059_311_S6_L002_R1_001


title: TMG059_294_S35_L006_R1_001


title: TMG059_318_S19_L004_R1_001


title: TMG059_288_S18_L003_R1_001


title: TMG059_292_S29_L005_R1_001


title: TMG059_282_S17_L004_R1_001


title: TMG059_284_S27_L007_R1_001

description:
TMG059_284
sample failed QC and was not included in the analysis


title: TMG059_278_S4_L002_R1_001


title: TMG059_277_S3_L002_R1_001


title: TMG059_322_S15_L003_R1_001


title: TMG059_315_S13_L003_R1_001


title: TMG059_268_S33_L006_R1_001


title: TMG059_307_S13_L005_R1_001


title: TMG059_310_S10_L002_R1_001


title: TMG059_287_S12_L002_R1_001


title: TMG059_281_S30_L007_R1_001


title: TMG059_289_S21_L005_R1_001


title: TMG059_305_S4_L001_R1_001


title: TMG059_265_S22_L007_R1_001


title: TMG059_252_S1_L001_R1_001


title: TMG059_266_S23_L007_R1_001


title: TMG059_263_S6_L002_R1_001


title: TMG059_243_S18_L006_R1_001


title: TMG059_279_S5_L002_R1_001


title: TMG059_247_S12_L003_R1_001


title: TMG059_270_S11_L003_R1_001


title: TMG059_240_S19_L004_R1_001


title: TMG059_251_S14_L003_R1_001


title: TMG059_245_S11_L003_R1_001


title: TMG059_249_S12_L003_R1_001


title: TMG059_230_S41_L008_R1_001


title: TMG059_231_S1_L001_R1_001


title: TMG059_224_S1_L001_R1_001

description:
TMG059_224
sample failed QC and was not included in the analysis


title: TMG059_242_S6_L001_R1_001


title: TMG059_238_S17_L004_R1_001


title: TMG059_236_S7_L002_R1_001


title: TMG059_218_S16_L005_R1_001


title: TMG059_214_S31_L007_R1_001

description:
TMG059_214
sample failed QC and was not included in the analysis


title: TMG059_227_S37_L008_R1_001


title: TMG059_223_S34_L007_R1_001


title: TMG059_219_S13_L004_R1_001


title: TMG059_212_S26_L006_R1_001


title: TMG059_206_S10_L004_R1_001


title: TMG059_208_S1_L001_R1_001


title: TMG059_234_S11_L002_R1_001


title: TMG059_205_S23_L005_R1_001


title: TMG059_221_S32_L007_R1_001


title: TMG059_200_S18_L004_R1_001


title: TMG059_201_S27_L006_R1_001


title: TMG059_198_S16_L004_R1_001


title: TMG059_203_S16_L004_R1_001


title: TMG059_193_S28_L007_R1_001


title: TMG059_197_S17_L005_R1_001


title: TMG059_189_S1_L001_R1_001


title: TMG059_186_S9_L002_R1_001


title: TMG059_217_S76_L008_R1_001


title: TMG059_191_S27_L006_R1_001

description:
TMG059_191
sample failed QC and was not included in the analysis


title: TMG059_176_S36_L008_R1_001


title: TMG059_182_S3_L001_R1_001


title: TMG059_180_S1_L001_R1_001


title: TMG059_172_S12_L003_R1_001


title: TMG059_166_S28_L006_R1_001


title: TMG059_160_S21_L005_R1_001


title: TMG059_162_S23_L005_R1_001

description:
TMG059_162
sample failed QC and was not included in the analysis


title: TMG059_150_S6_L002_R1_001


title: TMG059_146_S29_L006_R1_001


title: TMG059_158_S16_L004_R1_001


title: TMG059_155_S11_L003_R1_001


title: TMG059_164_S26_L006_R1_001


title: TMG059_152_S8_L002_R1_001


title: TMG059_144_S22_L005_R1_001


title: TMG059_140_S11_L003_R1_001


title: TMG059_139_S14_L003_R1_001

description:
TMG059_139
sample failed QC and was not included in the analysis


title: TMG059_136_S1_L001_R1_001


title: TMG059_133_S44_L008_R1_001


title: TMG059_184_S7_L002_R1_001


title: TMG059_170_S33_L007_R1_001


title: TMG059_178_S5_L002_R1_001


title: TMG059_168_S31_L007_R1_001


title: TMG059_131_S42_L008_R1_001

description:
TMG059_131
sample failed QC and was not included in the analysis


title: TMG059_142_S13_L003_R1_001


title: TMG059_127_S37_L007_R1_001


title: TMG059_129_S39_L007_R1_001


title: TMG059_174_S14_L003_R1_001


title: TMG059_124_S101_L008_R1_001


title: TMG059_121_S24_L005_R1_001


title: TMG059_120_S23_L005_R1_001


title: TMG059_119_S1_L001_R1_001


title: TMG059_118_S6_L002_R1_001


title: TMG059_110_S27_L005_R1_001


title: TMG059_115_S31_L006_R1_001


title: TMG059_117_S33_L006_R1_001


title: TMG059_104_S18_L005_R1_001


title: TMG059_106_S11_L003_R1_001


title: TMG059_103_S23_L004_R1_001


title: TMG059_101_S21_L004_R1_001


title: TMG059_98_S17_L003_R1_001


title: TMG059_96_S15_L003_R1_001


title: TMG059_87_S10_L002_R1_001


title: TMG059_92_S20_L005_R1_001


title: TMG059_94_S13_L003_R1_001


title: TMG059_91_S17_L003_R1_001


title: TMG059_84_S16_L004_R1_001


title: TMG059_125_S102_L008_R1_001


title: TMG059_123_S33_L006_R1_001


title: TMG059_85_S25_L007_R1_001


title: TMG059_75_S21_L005_R1_001


title: TMG059_72_S24_L005_R1_001


title: TMG059_82_S24_L006_R1_001

description:
TMG059_82
sample failed QC and was not included in the analysis


title: TMG059_77_S34_L008_R1_001


title: TMG059_73_S34_L007_R1_001


title: TMG059_62_S13_L003_R1_001


title: TMG059_63_S24_L006_R1_001


title: TMG059_70_S19_L004_R1_001


title: TMG059_108_S25_L005_R1_001


title: TMG059_59_S26_L008_R1_001


title: TMG059_68_S23_L004_R1_001


title: TMG059_56_S92_L007_R1_001


title: TMG059_50_S1_L001_R1_001


title: TMG059_99_S19_L004_R1_001

description:
TMG059_99
sample failed QC and was not included in the analysis


title: TMG059_44_S22_L005_R1_001


title: TMG059_80_S28_L007_R1_001


title: TMG059_52_S1_L001_R1_001


title: TMG059_41_S16_L003_R1_001


title: TMG059_36_S21_L004_R1_001


title: TMG059_34_S26_L005_R1_001


title: TMG059_38_S17_L004_R1_001


title: TMG059_28_S14_L003_R1_001


title: TMG059_21_S26_L005_R1_001


title: TMG059_18_S5_L001_R1_001


title: TMG059_15_S47_L008_R1_001


title: TMG059_8_S29_L008_R1_001


title: TMG059_60_S5_L002_R1_001


title: TMG059_7_S41_L007_R1_001


title: TMG059_10_S42_L008_R1_001


title: TMG059_11_S43_L008_R1_001


title: TMG059_48_S21_L006_R1_001

description:
TMG059_48
sample failed QC and was not included in the analysis


title: TMG059_5_S39_L007_R1_001


title: TMG059_815_S28_L008_R1_001.fastq.gz

value: 8 (EOT)


title: TMG059_827_S46_L008_R1_001.fastq.gz


title: TMG059_812_S3_L001_R1_001.fastq.gz


title: TMG059_807_S10_L003_R1_001.fastq.gz


title: TMG059_798_S9_L002_R1_001.fastq.gz


title: TMG059_792_S22_L006_R1_001.fastq.gz


title: TMG059_805_S29_L005_R1_001.fastq.gz


title: TMG059_794_S26_L007_R1_001.fastq.gz


title: TMG059_810_S41_L007_R1_001.fastq.gz


title: TMG059_796_S34_L006_R1_001.fastq.gz


title: TMG059_793_S28_L005_R1_001.fastq.gz


title: TMG059_26_S12_L003_R1_001


title: TMG059_13_S7_L002_R1_001


title: TMG059_781_S10_L002_R1_001.fastq.gz


title: TMG059_773_S3_L001_R1_001.fastq.gz


title: TMG059_783_S10_L003_R1_001.fastq.gz


title: TMG059_788_S6_L002_R1_001.fastq.gz


title: TMG059_789_S18_L005_R1_001.fastq.gz


title: TMG059_787_S14_L004_R1_001.fastq.gz


title: TMG059_771_S4_L001_R1_001.fastq.gz


title: TMG059_769_S9_L002_R1_001.fastq.gz


title: TMG059_766_S40_L007_R1_001.fastq.gz


title: TMG059_765_S34_L006_R1_001.fastq.gz


title: TMG059_758_S38_L007_R1_001.fastq.gz


title: TMG059_755_S17_L005_R1_001.fastq.gz


title: TMG059_754_S30_L007_R1_001.fastq.gz


title: TMG059_750_S32_L006_R1_001.fastq.gz


title: TMG059_741_S27_L005_R1_001.fastq.gz


title: TMG059_791_S9_L003_R1_001.fastq.gz


title: TMG059_730_S20_L006_R1_001.fastq.gz


title: TMG059_717_S30_L006_R1_001.fastq.gz


title: TMG059_696_S3_L001_R1_001.fastq.gz


title: TMG059_674_S4_L001_R1_001.fastq.gz


title: TMG059_676_S45_L008_R1_001.fastq.gz


title: TMG059_700_S35_L007_R1_001.fastq.gz


title: TMG059_699_S32_L006_R1_001.fastq.gz


title: TMG059_784_S22_L004_R1_001.fastq.gz


title: TMG059_698_S41_L008_R1_001.fastq.gz


title: TMG059_666_S37_L007_R1_001.fastq.gz


title: TMG059_668_S41_L008_R1_001.fastq.gz


title: TMG059_664_S33_L006_R1_001.fastq.gz


title: TMG059_661_S27_L005_R1_001.fastq.gz


title: TMG059_671_S44_L008_R1_001.fastq.gz


title: TMG059_656_S21_L004_R1_001.fastq.gz


title: TMG059_654_S19_L005_R1_001.fastq.gz


title: TMG059_651_S47_L008_R1_001.fastq.gz


title: TMG059_648_S3_L001_R1_001.fastq.gz


title: TMG059_646_S24_L005_R1_001.fastq.gz


title: TMG059_645_S19_L004_R1_001.fastq.gz


title: TMG059_643_S41_L007_R1_001.fastq.gz


title: TMG059_649_S29_L006_R1_001.fastq.gz


title: TMG059_642_S40_L007_R1_001.fastq.gz


title: TMG059_635_S27_L008_R1_001.fastq.gz


title: TMG059_628_S16_L003_R1_001.fastq.gz


title: TMG059_715_S4_L001_R1_001.fastq.gz


title: TMG059_710_S8_L002_R1_001.fastq.gz


title: TMG059_620_S16_L005_R1_001.fastq.gz


title: TMG059_684_S14_L004_R1_001.fastq.gz


title: TMG059_565_S36_L008_R1_001.fastq.gz


title: TMG059_618_S4_L001_R1_001.fastq.gz


title: TMG059_560_S37_L007_R1_001.fastq.gz


title: TMG059_554_S20_L004_R1_001.fastq.gz


title: TMG059_562_S33_L007_R1_001.fastq.gz


title: TMG059_609_S24_L005_R1_001.fastq.gz


title: TMG059_557_S25_L005_R1_001.fastq.gz


title: TMG059_513_S28_L008_R1_001.fastq.gz


title: TMG059_546_S26_L006_R1_001.fastq.gz


title: TMG059_490_S24_L006_R1_001.fastq.gz


title: TMG059_506_S94_L007_R1_001.fastq.gz


title: TMG059_525_S8_L002_R1_001.fastq.gz


title: TMG059_542_S4_L001_R1_001.fastq.gz


title: TMG059_474_S12_L003_R1_001.fastq.gz


title: TMG059_455_S5_L001_R1_001.fastq.gz


title: TMG059_444_S15_L003_R1_001.fastq.gz


title: TMG059_466_S14_L003_R1_001.fastq.gz


title: TMG059_419_S10_L002_R1_001.fastq.gz


title: TMG059_630_S23_L007_R1_001.fastq.gz


title: TMG059_623_S9_L002_R1_001.fastq.gz


title: TMG059_416_S35_L007_R1_001.fastq.gz


title: TMG059_421_S34_L008_R1_001.fastq.gz


title: TMG059_433_S9_L002_R1_001.fastq.gz


title: TMG059_394_S17_L004_R1_001.fastq.gz


title: TMG059_392_S20_L005_R1_001.fastq.gz


title: TMG059_387_S30_L006_R1_001.fastq.gz


title: TMG059_369_S3_L001_R1_001.fastq.gz


title: TMG059_335_S39_L008_R1_001.fastq.gz


title: TMG059_389_S30_L007_R1_001.fastq.gz


title: TMG059_353_S10_L002_R1_001.fastq.gz


title: VSMCs of Cmklr1 knockout mice, rep2

city: north york

first: michael

last: dong

state: ON

address: 114-38 hollywood ave

country: Canada

institute: Shenzhen Children's Hospital

data_processing:
The clean data was obtained by removing adapters and low-quality reads. All downstream analyses were based on clean, high-quality data. The RPKM (reads per kilobase per million reads) of each gene was calculated based on the read counts mapped to this gene and the length of the gene. Differential expression analysis between the two groups was performed using the DESeq R package (1.16.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing raw counts data for each sample

source_name: Thoracic aorta

extract_protocol:
Total RNA was extracted from the VSMCs of Cmklr1-/- and Cmklr1+/+ mice following standard protocols of RNA isolation. Quantification and quality of RNA was assessed.
The library preparation and sequencing were performed by Wenzheng Biotechnology Co., Ltd. on an Illumina NovaSeq platform following the manufacturer’s instructions, and the paired-end reads were generated. The raw data were stored as FASTQ files.

tag: tissue

value: Thoracic aorta

value: Vascular Smooth Muscle Cells

value: Cmklr1 knockout

value: gene knockout


title: TMG059_324_S19_L004_R1_001.fastq.gz


title: TMG059_341_S8_L002_R1_001.fastq.gz


title: VSMCs of Cmklr1 knockout mice, rep1


title: TMG059_321_S14_L003_R1_001.fastq.gz


title: TMG059_306_S9_L002_R1_001.fastq.gz


title: VSMCs of wild type mice, rep3

value: control for gene knockout


title: VSMCs of wild type mice, rep2


title: VSMCs of wild type mice, rep1


title: P7-P132 Acta2-CreERT2, R26R-LSL-EYFP

data_processing:
Read alignment using STAR-solo
Ambient RNA correction using scvi-tools scAR model
QC, filtering, normalization using scanpy
Batch-correction using harmony-pytorch
Projections and clustering using scanpy
Assembly: GRCm39
Supplementary files format and content: anndata hdf5 (h5ad) gzipped Yap/Taz KO scRNA-seq dataset, processed using scanpy, containing cell barcodes, annotations, and gene expression values (raw and normalized).
Supplementary files format and content: compressed zip file of STAR-solo gene expression matrices for lineage trace experiments.

extract_protocol:
Whole mouse lung dissociated into single-cell suspension before FACS.
10X genomics GEXv3 3’-scRNA-seq

value: Acta2-CreERT2, R26R-LSL-EYFP

value: P7 tamoxifen


title: TMG059_415_S16_L004_R1_001.fastq.gz


title: TMG059_285_S28_L007_R1_001.fastq.gz


title: P1-P23 Acta2-CreERT2, Yap/Taz fl/fl KO, rep1, CD45+ spike-in

value: Acta2-CreERT2, R26R-LSL-EYFP, Yap/Taz fl/fl KO

value: P1 tamoxifen


title: P83-P90 Acta2-CreERT2, R26R-LSL-EYFP

value: lung

value: P83 tamoxifen


title: P1-P23 Acta2-CreERT2, Yap/Taz fl/fl KO, rep2, CD45-


title: TMG059_267_S9_L002_R1_001.fastq.gz


title: TMG059_283_S18_L004_R1_001.fastq.gz


title: P1-P23 Acta2-CreERT2, Yap/Taz fl/fl HET, rep2, CD45-

value: Acta2-CreERT2, R26R-LSL-EYFP, Yap/Taz fl/fl HET


title: P1-P23 Acta2-CreERT2, Yap/Taz fl/fl HET, rep1, CD45+ spike-in


title: TMG059_248_S13_L003_R1_001.fastq.gz


title: TMG059_241_S20_L004_R1_001.fastq.gz


title: VSMCs of Cmklr1 knockout mice, rep3


title: TMG059_233_S4_L001_R1_001.fastq.gz


title: P1-P7 Acta2-CreERT2, Yap/Taz fl/fl HET, rep1, CD45+ spike-in


title: TMG059_293_S34_L006_R1_001.fastq.gz


title: TMG059_183_S4_L001_R1_001.fastq.gz


title: TMG059_295_S9_L002_R1_001.fastq.gz


title: Rep2-SOX2

city: Hong Kong

first: Sik Yin

last: Ho

address: Laboratory Block, 21 Sassoon Block

country: Hong Kong

institute: The University of Hong Kong

data_processing:
The raw 150 bp paired-end RNA-seq reads obtained were aligned to the mm10 reference transcriptome using RSEM and bowtie 2.0.
Gene level alignment results for each sample were then merged and annotated with glbase3.
RSEM was used to calculate the read counts per gene (Li and Dewey, 2011); and EDAseq (Risso et al., 2011) was used to normalize said read counts for GC content.
The final read count table was generated by filtering for genes with read counts with at least 20 counts in at least two samples.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file contains normalized RNA expression gene counts. The first column denotes the Ensembl gene ID (ensg); the second column denotes the official gene name (name); and the third column onwards denotes the normalized RNA expression gene counts for each RNA sample.

source_name: Tet-Off Sox2 mESCs

extract_protocol:
Total RNA was extracted using TRIzol® reagent according to the manufacturer's protocol. 2µg total RNA was used for library construction.
RNA libraries were constructed by GENEWIZ. Briefly, libraries were enriched for mRNA via poly(A) selection. Then, cDNA was generated from the RNA and adapters ligated to the cDNA.

value: Tet-Off Sox2 mESCs

value: (1) transduced with SOX2-encoding lentiviruses; (2) silenced expression of endogenous SOX2

value: DOX


title: TMG059_290_S22_L005_R1_001.fastq.gz


title: Rep2-E57D

value: (1) transduced with SOX17E57D-encoding lentiviruses; (2) silenced expression of endogenous SOX2


title: TMG059_163_S24_L005_R1_001.fastq.gz

value: 8 (EOT)


title: Rep2-2TS22C

value: wild-type


title: TMG059_147_S30_L006_R1_001.fastq.gz


title: P1-P7 Acta2-CreERT2, Yap/Taz fl/fl KO, rep1, CD45+ spike-in


title: Rep2-mESC

source_name: mESC was derived from wild-type ICR mice


title: TMG059_143_S14_L003_R1_001.fastq.gz


title: TMG059_153_S9_L002_R1_001.fastq.gz


title: Rep1-E57D


title: TMG059_134_S45_L008_R1_001.fastq.gz


title: Rep1-SOX2


title: TMG059_126_S103_L008_R1_001.fastq.gz


title: TMG059_229_S40_L008_R1_001.fastq.gz


title: TMG059_130_S40_L007_R1_001.fastq.gz


title: TMG059_66_S31_L007_R1_001


title: TMG059_111_S28_L005_R1_001.fastq.gz


title: Rep1-2TS22C


title: TMG059_122_S32_L006_R1_001.fastq.gz


title: TMG059_107_S20_L005_R1_001.fastq.gz


title: Zc3h14_WT_testis

city: Hefei

first: Xiaolin

address: Huangshan Road

institute: USTC

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the reference genome with Bowtie2. For linear RNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels. For circRNA annotation, CIRI2 and Find_circ were used, and backspliced read per million (BRPM) was used to calculate circRNA levels.
Assembly: hg19 (human), mm10 (mouse) and ASM294v2 (yeast)
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: Testis

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) followed by RNase R treatment or not according to the manufacturer’s instructions.

value: Testis

value: WT


title: Zc3h14_KO_pachy

source_name: Pachytene spermatocytes

value: Pachytene spermatocytes

value: Zc3h14 knockout


title: Zc3h14_KO_testis


title: Zc3h14_WT_pachy


title: TMG059_102_S22_L004_R1_001.fastq.gz


title: TMG059_97_S16_L003_R1_001.fastq.gz


title: ZNHIT1_Vector_DMSO_rep2

city: Shanghai

first: Fengrui

last: Sui

address: Dong'an Road

institute: Fudan University

data_processing:
The raw paired-end ChIP-Rx reads were trimmed by Trim Galore v0.6.7 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapters and low-quality sequences (-q 25 -e 0.1 --stringency 4) and then aligned to the human genome hg19 and mouse genome mm10 assembly using Bowtie v2.5.0 with default parameters. Unmapped reads, low mapping quality reads (MAPQ < 30), and PCR duplicates were filtered out by using SAMtools v1.16.1 (parameters: -F 3844 -f 2 -q 30) and Picard v2.27.5 with default parameters (https://broadinstitute.github.io/Picard/). Reads mapping to mm10 were computed using SAMtools flagstat, and the normalization factor was determined as 1e6/mm10_count. Normalized bigwig files were generated by deeptools v3.5.1. Any reads mapping to ENCODE blacklist regions were excluded using bedtools v2.30.0. Peaks were called using macs2 v2.2.7.1 with q-value threshold of 0.05. Transcription Start Sites (TSS) in DLD-1 cells were determined using previously published PRO-cap data. Genome annotation and reference genome sequences were downloaded from the UCSC Genome Browser. RefSeq-validated transcripts with PRO-cap signal at the region between TSS-10bp and TSS+300bp were selected. For protein-coding transcripts with multiple isoforms, the transcript with the most significant PRO-cap signal was selected as the representative gene and then TSS was defined by the position of the maximum PRO-cap signal. Finally, Transcripts within ±1kb of the nearest gene were removed.
Assembly: hg19
Supplementary files format and content: BW

growth_protocol: DLD-1, and mouse embryonic fibroblast (MEF) cells were grown in Dulbecco’s mini- mum essential medium (DMEM) (Gibco) supplemented with 10% fetal bovine serum (FBS) (Yeasen)

extract_protocol:
Cells were disrupted using lysis buffer containing 50 mM HEPES pH 8.0, 300 mM NaCl, 5% (v/v) Glycerol, 0.2% (w/v) chaps, 2 mM MgCl2, 0.5 mM EDTA (Ethylenediaminetetraacetic Acid), 2 mM DTT (Dithiothreitol), 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 μg/mL Aprotinin, 1 μg/mL Pepstatin, 1 μg/mL Leupeptin for 30 min. After centrifuging at 17,000 x g for 15 min, supernatant was collected to incubate with Flag-M2 beads (Sigma) for 4 hours. After immunoprecipitation, protein was washed for three times with wash buffer mentioned above then eluted using wash buffer containing 400 ng/μl Flag peptide (Meilunbio) additionally. All the steps were performed at 4°C.
For each ChIP assay, 1 x 107 DLD-1 cells were used, as described, and 1 x 106 MEF cells were mixed with DLD-1 cells as the spike-in. The mixed supernatant was incubated with 3ug antibody overnight. The libraries were prepared with the VAHTS Universal Plus DNA Library Prep Kit for Illumina (Vazyme). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the DNBSEQ-T7.

treatment_protocol: One replicate was DMSO or dTAG-13 treated for 3 hours.

value: colorectal adenocarcinoma cells

tag: chip antibody

value: untreated


title: TMG059_71_S18_L003_R1_001.fastq.gz


title: TMG059_69_S15_L003_R1_001.fastq.gz


title: ZNHIT1_Vector_dTAG_rep2

value: treated with dTAG13


title: Rep1-mESC

value: mESC was derived from wild-type ICR mice


title: ZNHIT1_Mut_dTAG_rep2


title: ZNHIT1_WT_dTAG_rep2


title: TMG059_58_S28_L005_R1_001.fastq.gz


title: ZNHIT1_Vector_DMSO_input_rep2


title: TMG059_55_S10_L002_R1_001.fastq.gz


title: ZNHIT1_Vector_dTAG_input_rep2


title: TMG059_35_S27_L005_R1_001.fastq.gz


title: TMG059_47_S4_L001_R1_001.fastq.gz


title: ZNHIT1_WT_dTAG_input_rep2


title: ZNHIT1_Mut_dTAG_input_rep2


title: TMG059_19_S6_L001_R1_001.fastq.gz


title: DLD1_ZNHIT1_24h_rep2

value: treated with dTAG13 for 24 hours


title: TMG059_12_S44_L008_R1_001.fastq.gz


title: TMG059_813_S21_L004_R1_001.fastq.gz


title: TMG059_606_S36_L006_R1_001.fastq.gz


title: DLD1_ZNHIT1_12h_rep2

value: treated with dTAG13 for 12 hours


title: DLD1_ZNHIT1_0h_rep2

value: treated with dTAG13 for 0 hours


title: TMG059_596_S22_L004_R1_001.fastq.gz


title: DLD1_ZNHIT1_6h_rep2

value: treated with dTAG13 for 6 hours


title: DLD1_ZNHIT1_6h_input_rep2


title: DLD1_ZNHIT1_12h_input_rep2


title: DLD1_ZNHIT1_24h_input_rep2


title: TMG059_589_S35_L007_R1_001.fastq.gz


title: TMG059_594_S28_L007_R1_001.fastq.gz


title: DLD1_ZNHIT1_0h_input_rep2


title: ZNHIT1_Vector_dTAG_rep1


title: TMG059_584_S25_L005_R1_001.fastq.gz


title: TMG059_582_S8_L002_R1_001.fastq.gz


title: ZNHIT1_Mut_dTAG_rep1


title: TMG059_585_S78_L008_R1_001.fastq.gz


title: ZNHIT1_Vector_DMSO_rep1


title: ZNHIT1_WT_dTAG_rep1


title: TMG059_580_S10_L002_R1_001.fastq.gz


title: TMG059_581_S7_L002_R1_001.fastq.gz


title: TMG059_579_S99_L008_R1_001.fastq.gz


title: ZNHIT1_Vector_DMSO_input_rep1


title: TMG059_577_S5_L002_R1_001.fastq.gz


title: ZNHIT1_Vector_dTAG_input_rep1


title: TMG059_567_S6_L002_R1_001.fastq.gz


title: TMG059_569_S23_L007_R1_001.fastq.gz


title: TMG059_571_S73_L007_R1_001.fastq.gz


title: DLD1_ZNHIT1_24h_rep1


title: DLD1_ZNHIT1_12h_rep1


title: DLD1_ZNHIT1_6h_rep1


title: TMG059_575_S44_L008_R1_001.fastq.gz


title: TMG059_563_S35_L008_R1_001.fastq.gz


title: DLD1_ZNHIT1_0h_rep1


title: DLD1_ZNHIT1_24h_input_rep1


title: TMG059_540_S2_L001_R1_001.fastq.gz


title: DLD1_ZNHIT1_12h_input_rep1


title: TMG059_536_S2_L001_R1_001.fastq.gz


title: TMG059_534_S8_L002_R1_001.fastq.gz


title: DLD1_ZNHIT1_6h_input_rep1


title: TMG059_528_S14_L003_R1_001.fastq.gz


title: DLD1_ZNHIT1_0h_input_rep1


title: TMG059_527_S38_L007_R1_001.fastq.gz


title: TMG059_521_S9_L003_R1_001.fastq.gz


title: Nab2_KO

organism: Schizosaccharomyces pombe

source_name: Yeast

value: Yeast

value: Nab2 knockout


title: ZNHIT1_WT_dTAG_input_rep1


title: TMG059_519_S8_L003_R1_001.fastq.gz


title: LD330


title: ZNHIT1_Mut_dTAG_input_rep1


title: TMG059_517_S5_L002_R1_001.fastq.gz


title: TMG059_510_S2_L001_R1_001.fastq.gz


title: TMG059_495_S29_L006_R1_001.fastq.gz


title: TMG059_494_S2_L001_R1_001.fastq.gz


title: MU07CELL002

city: Bunkyo-ku

first: Naoaki

last: Mizuno

state: Tokyo

address: 1-5-45 Yushima

institute: Tokyo Medical and Dental University

description: keratinocyte

data_processing:
Reads were adpter-trimmed by Trimmomatic and aligned onto mm10 by HISAT2 on a local Galaxy server.
Mapped reads are counted by featureCounbts on the Galaxy server based on the GTF file of Ensemble36 version-release.97.
Transcript integrity number (TIN) and Gene Body Coverage were analyzed by RSeQC to exclude low-quality samples.
The count was normalized by DESeq2 (version 1.36.0) and analyzed for differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: The  processed data file, raw_counts_B6N_E14.5_skin_PRJNA1056324.tsv, is a raw count matrix in tabuler/tsv format.

source_name: skin

growth_protocol: C57BL/6N wild type or Trp63 mutant embryos at E14.5 in surrogate ICR mothers.

extract_protocol:
The single cells were sorted by flowcytometry onto CDS Sorting Solution of SMART-Seq HT Kit (Takara Bio Inc., Shiga, Japan. Catalog No. Z4436N). The crude lysate were subjected to reverse transcriptions and cDNA amplifications.
cDNA library was constructed by SMART-Seq HT following the FACSAria sorting. cDNA library of Trp63 mutant embryos was screened by qPCR for enrichment of the target cell lineage. Illumina library was prepared by NexteraXT.

treatment_protocol: The skin of WT (C57BL/6N background) fetuses at E14.5 was soaked in dispase and separated into the epidermis and dermis. The single cells of the WT epidermis by treated with trypsin. The p63 knockout fetuses (C57BL/6N background) were directly digested with trypsin. Samples were stained with following antibodies: anti-mouse CD45 (clone 30-F11, eBioscience), TER119 (clone TER-119, eBioscience), anti-CD140a (clone APA5, Biolegend). The single cell of the PI-/CD45- /TER119-/CD140a- population was sorted by FACS aria II or III (BD).

value: skin

value: surface ectoderm remnant

value: Trp63 mutant


title: MU06CELL010

description: keratinocyte


title: MU06CELL007

description: keratinocyte


title: MU06CELL006

description: keratinocyte


title: MU06CELL008

description: keratinocyte

value: K5 K14high


title: MU07CELL001

description: keratinocyte


title: TMG059_497_S15_L003_R1_001.fastq.gz


title: MU06CELL004

description: omitted

value: omit


title: TMG059_470_S40_L007_R1_001.fastq.gz


title: MU06CELL005

description: keratinocyte


title: TMG059_523_S11_L004_R1_001.fastq.gz


title: MU06CELL003

description: keratinocyte


title: TMG059_468_S37_L007_R1_001.fastq.gz


title: MU06CELL002

description: keratinocyte


title: TMG059_478_S20_L004_R1_001.fastq.gz


title: MU06CELL009

description: keratinocyte


title: TMG059_464_S34_L008_R1_001.fastq.gz


title: MU05CELL006

description: keratinocyte


title: MU06CELL001

description: keratinocyte


title: TMG059_460_S96_L007_R1_001.fastq.gz


title: MU05CELL004

description: keratinocyte


title: TMG059_447_S42_L008_R1_001.fastq.gz


title: TMG059_451_S16_L005_R1_001.fastq.gz


title: TMG059_440_S22_L004_R1_001.fastq.gz


title: TMG059_472_S10_L003_R1_001.fastq.gz


title: MU05CELL002

description: omitted


title: TMG059_428_S23_L006_R1_001.fastq.gz


title: MU04CELL010

description: keratinocyte


title: TMG059_429_S27_L005_R1_001.fastq.gz


title: MU04CELL009

description: keratinocyte


title: TMG059_425_S30_L006_R1_001.fastq.gz


title: MU05CELL001

description: omitted


title: TMG059_407_S19_L004_R1_001.fastq.gz


title: TMG059_400_S17_L005_R1_001.fastq.gz


title: MU04CELL006

description: keratinocyte


title: MU04CELL004

description: omitted


title: TMG059_390_S18_L005_R1_001.fastq.gz


title: MU04CELL008

description: keratinocyte


title: MU04CELL005

description: keratinocyte


title: MU04CELL007

description: keratinocyte


title: TMG059_384_S27_L008_R1_001.fastq.gz


title: TMG059_379_S38_L007_R1_001.fastq.gz


title: TMG059_375_S32_L006_R1_001.fastq.gz


title: MU04CELL002

description: omitted


title: TMG059_368_S2_L001_R1_001.fastq.gz


title: TMG059_591_S26_L006_R1_001.fastq.gz


title: MU04CELL001

description: omitted


title: MU05CELL003

description: keratinocyte


title: MU04CELL003

description: keratinocyte


title: TMG059_442_S9_L003_R1_001.fastq.gz


title: TMG059_365_S29_L005_R1_001.fastq.gz


title: TMG059_437_S31_L006_R1_001.fastq.gz


title: MU03CELL022

description: keratinocyte


title: MU05CELL005

description: keratinocyte


title: TMG059_367_S30_L005_R1_001.fastq.gz


title: TMG059_362_S25_L008_R1_001.fastq.gz


title: TMG059_360_S16_L005_R1_001.fastq.gz


title: MU03CELL021

description: omitted


title: MU03CELL019

description: keratinocyte


title: TMG059_358_S24_L007_R1_001.fastq.gz


title: MU03CELL018

description: keratinocyte


title: TMG059_356_S26_L005_R1_001.fastq.gz


title: TMG059_351_S20_L006_R1_001.fastq.gz


title: MU03CELL016

description: keratinocyte


title: TMG059_347_S16_L005_R1_001.fastq.gz


title: TMG059_349_S12_L002_R1_001.fastq.gz


title: MU03CELL015

description: keratinocyte


title: TMG059_345_S11_L002_R1_001.fastq.gz


title: TMG059_343_S12_L004_R1_001.fastq.gz


title: MU03CELL010

description: keratinocyte


title: TMG059_329_S12_L004_R1_001.fastq.gz


title: TMG059_338_S5_L001_R1_001.fastq.gz


title: MU03CELL012

description: keratinocyte


title: MU03CELL008

description: keratinocyte


title: MU03CELL023

description: keratinocyte


title: MU03CELL009

description: keratinocyte


title: MU03CELL006

description: keratinocyte


title: TMG059_319_S20_L004_R1_001.fastq.gz


title: TMG059_317_S7_L003_R1_001.fastq.gz


title: MU03CELL005

description: keratinocyte


title: MU03CELL004

description: keratinocyte


title: MU03CELL020

description: keratinocyte


title: TMG059_316_S14_L003_R1_001.fastq.gz


title: TMG059_314_S7_L002_R1_001.fastq.gz


title: MU03CELL001

description: keratinocyte


title: TMG059_304_S3_L001_R1_001.fastq.gz


title: MU03CELL002

description: keratinocyte


title: MU03CELL013

description: keratinocyte


title: TMG059_298_S22_L004_R1_001.fastq.gz


title: TMG059_296_S2_L001_R1_001.fastq.gz


title: MU02CELL045

description: keratinocyte


title: MU02CELL044

description: keratinocyte


title: TMG059_280_S6_L002_R1_001.fastq.gz


title: MU02CELL042

description: omitted

value: neural progenitor


title: MU02CELL043

description: keratinocyte


title: TMG059_275_S1_L001_R1_001.fastq.gz


title: TMG059_269_S34_L006_R1_001.fastq.gz


title: MU02CELL040

description: keratinocyte


title: TMG059_327_S18_L006_R1_001.fastq.gz


title: MU02CELL041

description: keratinocyte


title: TMG059_264_S7_L002_R1_001.fastq.gz


title: MU02CELL039

description: keratinocyte


title: TMG059_246_S37_L008_R1_001.fastq.gz


title: TMG059_250_S13_L003_R1_001.fastq.gz


title: TMG059_253_S2_L001_R1_001.fastq.gz


title: MU02CELL038

description: keratinocyte


title: MU02CELL037

description: omitted


title: TMG059_308_S14_L005_R1_001.fastq.gz


title: TMG059_244_S19_L006_R1_001.fastq.gz


title: MU03CELL003

description: omitted


title: MU02CELL036

description: keratinocyte


title: MU02CELL047

description: keratinocyte


title: TMG059_239_S18_L004_R1_001.fastq.gz


title: MU02CELL034

description: omitted


title: MU02CELL046

description: keratinocyte


title: TMG059_232_S2_L001_R1_001.fastq.gz


title: MU02CELL033

description: keratinocyte


title: TMG059_271_S12_L003_R1_001.fastq.gz


title: MU02CELL032

description: keratinocyte


title: TMG059_228_S38_L008_R1_001.fastq.gz


title: TMG059_222_S33_L007_R1_001.fastq.gz


title: TMG059_226_S32_L008_R1_001.fastq.gz


title: TMG059_220_S14_L004_R1_001.fastq.gz


title: MU02CELL030

description: keratinocyte


title: MU02CELL031

description: keratinocyte


title: MU02CELL028

description: keratinocyte


title: TMG059_215_S32_L007_R1_001.fastq.gz


title: MU02CELL027

description: keratinocyte


title: MU02CELL026

description: keratinocyte


title: MU02CELL023

description: keratinocyte


title: TMG059_209_S2_L001_R1_001.fastq.gz


title: MU02CELL022

description: keratinocyte


title: TMG059_207_S11_L004_R1_001.fastq.gz


title: TMG059_202_S15_L004_R1_001.fastq.gz


title: TMG059_199_S17_L004_R1_001.fastq.gz


title: MU02CELL016

description: keratinocyte


title: TMG059_194_S29_L007_R1_001.fastq.gz


title: TMG059_185_S8_L002_R1_001.fastq.gz


title: TMG059_237_S5_L001_R1_001.fastq.gz


title: MU02CELL015

description: keratinocyte


title: TMG059_192_S28_L006_R1_001.fastq.gz


title: MU02CELL020

description: keratinocyte


title: MU02CELL018

description: keratinocyte


title: MU02CELL013

description: keratinocyte


title: MU02CELL029

description: keratinocyte


title: TMG059_179_S6_L002_R1_001.fastq.gz


title: MU02CELL012

description: keratinocyte


title: TMG059_173_S13_L003_R1_001.fastq.gz


title: TMG059_181_S2_L001_R1_001.fastq.gz


title: MU02CELL011

description: keratinocyte


title: MU02CELL009

description: keratinocyte


title: MU02CELL008

description: keratinocyte


title: MU02CELL007

description: keratinocyte


title: TMG059_165_S27_L006_R1_001.fastq.gz


title: TMG059_159_S17_L004_R1_001.fastq.gz


title: MU02CELL006

description: keratinocyte


title: TMG059_156_S12_L003_R1_001.fastq.gz


title: MU02CELL005

description: keratinocyte


title: TMG059_151_S7_L002_R1_001.fastq.gz


title: TMG059_145_S28_L006_R1_001.fastq.gz


title: MU02CELL004

description: keratinocyte


title: TMG059_141_S12_L003_R1_001.fastq.gz


title: MU02CELL003

description: keratinocyte


title: MU02CELL002

description: keratinocyte


title: TMG059_137_S2_L001_R1_001.fastq.gz


title: WT02CELL024

description: keratinocyte

value: basal layer

value: wild type


title: TMG059_100_S20_L004_R1_001.fastq.gz


title: MU02CELL001

description: keratinocyte


title: TMG059_109_S26_L005_R1_001.fastq.gz


title: TMG059_116_S32_L006_R1_001.fastq.gz


title: WT02CELL023

description: omitted

value: Vim high


title: WT02CELL022

description: keratinocyte


title: TMG059_128_S38_L007_R1_001.fastq.gz


title: TMG059_169_S32_L007_R1_001.fastq.gz


title: TMG059_161_S22_L005_R1_001.fastq.gz


title: TMG059_105_S19_L005_R1_001.fastq.gz


title: TMG059_95_S14_L003_R1_001.fastq.gz


title: WT02CELL021

description: keratinocyte

value: intermediate layer


title: TMG059_81_S29_L007_R1_001.fastq.gz


title: WT02CELL018

description: omitted


title: WT02CELL020

description: keratinocyte


title: TMG059_86_S26_L007_R1_001.fastq.gz


title: WT02CELL017

description: keratinocyte


title: WT02CELL015

description: keratinocyte


title: TMG059_76_S26_L006_R1_001.fastq.gz


title: TMG059_64_S25_L006_R1_001.fastq.gz


title: WT02CELL013

description: keratinocyte


title: TMG059_74_S35_L007_R1_001.fastq.gz


title: WT02CELL012

description: keratinocyte


title: TMG059_61_S6_L002_R1_001.fastq.gz


title: WT02CELL011

description: keratinocyte


title: TMG059_57_S93_L007_R1_001.fastq.gz


title: WT02CELL010

description: keratinocyte


title: WT02CELL019

description: omitted


title: TMG059_88_S11_L002_R1_001.fastq.gz


title: WT02CELL008

description: keratinocyte


title: TMG059_51_S1_L001_R1_001.fastq.gz


title: TMG059_49_S22_L006_R1_001.fastq.gz


title: TMG059_39_S18_L004_R1_001.fastq.gz


title: TMG059_42_S17_L003_R1_001.fastq.gz


title: TMG059_33_S25_L005_R1_001.fastq.gz


title: TMG059_17_S4_L001_R1_001.fastq.gz


title: TMG059_27_S13_L003_R1_001.fastq.gz


title: WT02CELL014

description: keratinocyte


title: WT02CELL003

description: keratinocyte


title: WT02CELL002

description: keratinocyte


title: WT02CELL004

description: keratinocyte

value: K17 high


title: WT02CELL005

description: keratinocyte


title: WT03CELL024

description: keratinocyte


title: TMG059_6_S40_L007_R1_001.fastq.gz


title: WT03CELL021

description: keratinocyte


title: WT03CELL020

description: keratinocyte


title: shAnxa2-OGDR-3

city: Changsha

first: Xibin

last: Tian

address: Tianma Road

institute: Hunan University

data_processing:
 The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
 the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads
Index of the reference genome was built using Hisat2 v2.0.4 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.4.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: BV2 microglia cell

growth_protocol: BV2 microglia cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Oxygen-glucose deprivation and reoxygenation (OGD/R) was induced by treatment of 94%N2/5%CO2/1%O2 with no glucose DMEM for 4h and  reoxygenation was achieved by replacing  with normal culture medium

value: BV2 microglia cell

value: microglia cell

value: Anxa2 knockdown

value: OGD4h R12h


title: WT03CELL018

description: keratinocyte


title: WT03CELL019

description: keratinocyte


title: WT02CELL007

description: keratinocyte


title: WT03CELL017

description: keratinocyte


title: WT02CELL006

description: keratinocyte


title: shAnxa2-CTRL-3

value: WT

value: Control

value: non-Treat


title: WT03CELL016

description: keratinocyte

value: skin


title: shAnxa2-CTRL-1


title: shAnxa2-OGDR-2

value: Oxygen-glucose deprivation and reoxygenation (OGD/R)


title: shAnxa2-OGDR-1


title: shCtrl-OGDR-3


title: TMG059_14_S46_L008_R1_001.fastq.gz


title: TMG059_9_S30_L008_R1_001.fastq.gz


title: shCtrl-OGDR-2


title: shAnxa2-CTRL-2


title: WT03CELL013

description: keratinocyte


title: WT03CELL014

description: omitted

value: unknown cell


title: shCtrl-OGDR-1


title: shCtrl-CTRL-2


title: WT03CELL011

description: keratinocyte


title: WT03CELL010

description: keratinocyte


title: shCtrl-CTRL-3


title: WT03CELL006

description: keratinocyte


title: WT03CELL008

description: keratinocyte


title: WT03CELL009

description: keratinocyte


title: CGD_Ly6C+_MHC2+_72h_rep3_L005

city: Denver

first: Donna

middle: Leslie

last: Bratton

state: CO

address: 1400 Jackson St. Rm A540

department: Pediatrics

institute: National Jewish Health

data_processing:
FASTQ files were generated using the Illumina bcl2fastq converter (version 2.17).
Nextera TruSight adapters were trimmed with skewer (version 0.2.2), which by default removes reads with a remaining length of less than 18 nt.
Trimmed reads were mapped with the STAR aligner (version 2.4.1d) to the GRCm38 assembly of the mouse genome using gene using gene annotations from Ensembl version 84.
Reads mapping to each gene of the Ensembl 84 annotation were counted with the featureCounts program from the Subread software package (v1.5.1).
Transcripts per million aligned fragments (TPM) were calculated from the gene counts using the sum of all bases covered by any transcript of a gene as its transcript length.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts and transcripts per million (TPM) assigned to each gene of the mouse Ensembl 84 annotation and sample, as tab-separated text tables: 1) output from subread featureCounts (2 subread_genecounts.txt* files), separated by sequencing run, 2) aggregated by adding different sequencing runs for each sample (counts and TPM)

source_name: CGD 72h LyC6+ MHC2+ rep3

growth_protocol: Parent animals were obtained from Jackson laboratories. Experimental mice were bred and housed in a specific pathogen free facility at National Jewish Health, Denver, CO, USA.

extract_protocol:
Peritoneal lavage was collected using 8mL buffer (HBSS w/o Ca2+ Mg2+,  20mM HEPES, 1mM EDTA). Total lavage cells were stained with antibodies for FACS and sorted to purify monocytes/macrophages of the indicated phenotype. Total RNA was extracted using the Qiagen RNeasy micro kit according to manufacturer's instructions.
A Clontech SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Mountain View, CA, USA) and Nextera XT (San Diego, CA, USA) kit were used. Briefly, library construction started from isolation of total RNA species, followed by SMARTer 1st strand cDNA synthesis, full length dscDNA amplification by LD-PCR, followed by purification and validation. After that, the samples were taken to the Nextera XT protocol where the sample is simultaneously fragmented and tagged with adapters followed by a limited-cycle PCR that adds indexes. Once validated, the barcoded-pooled libraries were sequenced using 1×50bp chemistry on the HiSeq 2500 as routinely performed by the NJH Genomics Facility.

treatment_protocol: Mice were treated with intraperitoneal injection of 200ug Zymosan A (Sigma)

tag: strain

value: Peritoneal Lavage

value: Male

value: 8-12 weeks

value: i.p. Zymosan

tag: time point

value: 72 hours

value: MoMac Ly6C+ MHCII+


title: CGD_Ly6C+_MHC2+_72h_rep3_L004


title: CGD_Ly6C+_MHC2+_72h_rep3_L003


title: WT03CELL004

description: keratinocyte

value: basal layer

value: wild type


title: WT03CELL003

description: keratinocyte


title: WT03CELL007

description: keratinocyte


title: WT03CELL005

description: keratinocyte


title: WT03CELL015

description: keratinocyte


title: CGD_Ly6C+_MHC2+_72h_rep3_L002


title: WT03CELL002

description: keratinocyte


title: CGD_Ly6C+_MHC2+_72h_rep2_L005

source_name: CGD 72h LyC6+ MHC2+ rep2


title: CGD_Ly6C+_MHC2+_72h_rep3_L001


title: shCtrl-CTRL-1

value: BV2 microglia cell

value: microglia cell


title: WT03CELL001

description: keratinocyte


title: MU01CELL082

description: omitted

value: Trp63 mutant


title: CGD_Ly6C+_MHC2+_72h_rep2_L004


title: CGD_Ly6C+_MHC2+_72h_rep2_L003


title: MU01CELL084

description: omitted

value: mutant fibroblast


title: CGD_Ly6C+_MHC2+_72h_rep2_L002


title: MU01CELL083

description: omitted


title: MU01CELL085

description: omitted


title: CGD_Ly6C+_MHC2+_72h_rep1_L004

source_name: CGD 72h LyC6+ MHC2+ rep1


title: CGD_Ly6C+_MHC2+_72h_rep2_L001


title: MU01CELL080

description: keratinocyte

value: surface ectoderm remnant


title: CGD_Ly6C+_MHC2+_72h_rep1_L005


title: MU01CELL081

description: omitted


title: CGD_Ly6C+_MHC2+_72h_rep1_L003


title: MU01CELL078

description: omitted


title: MU01CELL079

description: omitted


title: CGD_Ly6C+_MHC2+_72h_rep1_L002


title: CGD_Ly6C+_MHC2+_72h_rep1_L001


title: MU01CELL074

description: omitted


title: MU01CELL073

description: omitted


title: MU01CELL077

description: omitted


title: Ly6C+_MHC2+_72h_rep3_L005

source_name: WT 72h LyC6+ MHC2+ rep3

value: wildtype


title: MU01CELL075

description: omitted

value: skin


title: MU01CELL072

description: omitted


title: Ly6C+_MHC2+_72h_rep3_L007


title: Ly6C+_MHC2+_72h_rep2_L006

source_name: WT 72h LyC6+ MHC2+ rep2


title: Ly6C+_MHC2+_72h_rep3_L006


title: MU01CELL076

description: omitted


title: Ly6C+_MHC2+_72h_rep2_L005


title: MU01CELL071

description: omitted


title: MU01CELL070

description: omitted


title: Ly6C+_MHC2+_72h_rep1_L007

source_name: WT 72h LyC6+ MHC2+ rep1


title: MU01CELL069

description: omitted


title: Ly6C+_MHC2+_72h_rep1_L005


title: MU01CELL068

description: omitted