title: TCR-2020-07-10-1-6

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-6_airr_rearrangement.tsv
2020-07-10-1-6_clonotypes.csv
2020-07-10-1-6_filtered_contig.fasta
2020-07-10-1-6_filtered_contig_annotations.csv

value: 17-2796 Baseline (hash6), 17-2796 Follow Up 1 (hash7), 17-2796 Follow Up 2 (hash8), 17-2796 Follow Up 3 (hash9), 17-2796 Follow Up 4 (hash10)


title: 12132022_W62004456-V1-2_S310_R2C2_2E_S218

status: Public on Jul 30 2024

type: SRA

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

description:
positive sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt

library_source: transcriptomic

data_processing:
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BC_count_table.txt; run31_R1BC_count_table.txt; run38_R1BC_count_table.txt; run46_R1BC_count_table.txt; run139_R1BC_count_table.txt; run141p3_R1BC_count_table.txt; run141p6_R1BC_count_table.txt
Supplementary files format and content: run27_R2BC_count_table.txt; run31_R2BC_count_table.txt; run38_R2BC_count_table.txt; run46_R2BC_count_table.txt; run139_R2BC_count_table.txt; run141p3_R2BC_count_table.txt; run141p6_R2BC_count_table.txt
Supplementary files format and content: run27_count_table.txt; run31_count_table.txt; run38_count_table.txt; run46_count_table.txt; run139_count_table.txt; run141p3_count_table.txt; run141p6_count_table.txt
Supplementary files format and content: run27_BC_pair_analysis_filenames.txt; run31_BC_pair_analysis_filenames.txt; run38_BC_pair_analysis_filenames.txt; run46_BC_pair_analysis_filenames.txt; run139_BC_pair_analysis_filenames.txt; run141p3_BC_pair_analysis_filenames.txt; run141p6_BC_pair_analysis_filenames.txt

molecule: total RNA

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: human nasopharyngeal swab

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
Other: RNAseq with limited amplicons.

tag: tissue

value: human nasopharyngeal swab

tag: bc run_id

tag: pipeline version

value: BC


title: ADPD_PTMN_PD_10x37xx_X015_S05_L034_B1_T2_P027.pe.q10.sort.rmdup.bam

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

country: USA

institute: Stanford University

description: Bulk ATAC-seq ADPD Putamen

library_source: genomic

data_processing:
The count normalized peak matrix was derived using featureCount.
Assembly: hg38
Supplementary files format and content: csv

molecule: genomic DNA

organism: Homo sapiens

source_name: brain

extract_protocol:
Nuclei were isolated from frozen tissue in accordance with protocol dx.doi.org/10.17504/protocols.io.6t8herw. After isolation, nuclei were cryopreserved in BAM Banker (Wako Chemicals) and stored at -80°C for use in other assays such as scATAC-seq and HiChIP.
Transposed fragments were purified and amplified as described previously (Buenrostro et al., Nature Methods 2015) with slight modification. Briefly, transposed fragments were pre-amplified for 3 cycles. Concentration of pre-amplified fragments was determined by qPCR and this concentration was used to estimate the total number of cycles required to obtain 160 femtomoles of fragments. A second PCR was performed to amplify the pre-amplified fragments for the desired number of cycles. Final libraries were again purified. Prior to sequencing, libraries were pooled and run on a 6% PAGE gel and excess primers and primer dimers below 125 bp were removed.

value: brain

tag: cell type

value: bulk


title: 12132022_W62004450-V1-2_S225_R2C2_20C_S192


title: GEX-2020-07-10-1-6

city: Philadelphia

first: Alexander

middle: C

last: Huang

state: PA

address: 421 Curie Boulevard

department: Department of Hematology/Oncology

institute: University of Pennsylvania

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-6_barcodes.tsv.gz
2020-07-10-1-6_features.tsv.gz
2020-07-10-1-6_matrix.mtx.gz

data_processing:
CellRanger v7.0.0 count was run on GEX and ADT fastqs together to generate a matrix containing both gene and protein counts, supplying a Feature Reference csv file containing the feature barcode library. CellRanger vdj was run on VDJ reads.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files containing both GEX and ADT data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz (linked to the corresponding GEX sample records)
Supplementary files format and content: CellRanger output files containing VDJ data: airr_rearrangement.tsv, clonotypes.csv, filtered_contig.fasta, filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: polyA RNA

source_name: peripheral blood

extract_protocol:
For PBMC samples, 300,000 cells from each sample were sorted on a DAPI negative gate for live cells. Pan T cell samples were additionally gated on CD3+. Non-naïve T cell sorted samples were additionally gated as cells that were not CD45RA+CCR7+. Non-naïve CD4 and CD8 sorted samples were additionally gated on CD4+ and CD8+, respectively.
Cells were with either a panel of 60 or 101 Total-Seq-C antibodies that also labeled samples individually through sample-specific barcodes. Cells were pooled and loaded on the 10x Chromium Next GEM Single Cell 5' Kit (v2) using a superloading strategy, mixing cells from different samples in each 10x lane. TCR sequences were enriched using the human V(D)J B/T cell enrichment. Libraries were prepared according to manufacturer’s protocol (10x Genomics).

value: peripheral blood

value: PBMC

tag: disease

value: melanoma

tag: treatment

value: immune checkpoint blockade

tag: isolate


title: Feature-2020-07-10-1-6

tag: feature panel


title: Feature-2020-07-10-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-5_barcodes.tsv.gz
2020-07-10-1-5_features.tsv.gz
2020-07-10-1-5_matrix.mtx.gz


title: TCR-2020-07-10-1-5

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-5_airr_rearrangement.tsv
2020-07-10-1-5_clonotypes.csv
2020-07-10-1-5_filtered_contig.fasta
2020-07-10-1-5_filtered_contig_annotations.csv


title: GEX-2020-07-10-1-5


title: 12132022_W62004428-V1-2_S366_R2C2_17E_S233


title: TCR-2020-07-10-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-4_airr_rearrangement.tsv
2020-07-10-1-4_clonotypes.csv
2020-07-10-1-4_filtered_contig.fasta
2020-07-10-1-4_filtered_contig_annotations.csv

value: non-naive T cells


title: Feature-2020-08-17-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-08-17-1-3_barcodes.tsv.gz
2020-08-17-1-3_features.tsv.gz
2020-08-17-1-3_matrix.mtx.gz

value: non-naive CD4 T cells

value: 15-1471 Follow Up 1 (hash7), 15-1471 Follow Up 2 (hash8), 15-1471 Follow Up 4 (hash10)


title: ADPD_PTMN_PD_04x37xx_X024_S09_L090_B1_T2_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004414-V1-2_S618_R2C2_4I_S308


title: Feature-2020-07-10-1-4

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-4_barcodes.tsv.gz
2020-07-10-1-4_features.tsv.gz
2020-07-10-1-4_matrix.mtx.gz


title: TCR-2020-07-10-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-3_airr_rearrangement.tsv
2020-07-10-1-3_clonotypes.csv
2020-07-10-1-3_filtered_contig.fasta
2020-07-10-1-3_filtered_contig_annotations.csv


title: 12132022_w62004410-V1-2_S662_R2C2_16I_S320


title: GEX-2020-07-10-1-4


title: 12132022_W62004491-V1-2_S824_R2C2_20K_S367


title: GEX-2020-07-10-1-3

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-3_barcodes.tsv.gz
2020-07-10-1-3_features.tsv.gz
2020-07-10-1-3_matrix.mtx.gz


title: 12132022_w62004409-V1-2_S957_R2C2_16M_S405


title: Feature-2020-07-10-1-3


title: ADPD_PTMN_PD_04x37xx_X024_S09_L089_B1_T1_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-2020-07-10-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-2_airr_rearrangement.tsv
2020-07-10-1-2_clonotypes.csv
2020-07-10-1-2_filtered_contig.fasta
2020-07-10-1-2_filtered_contig_annotations.csv


title: GEX-2020-07-10-1-2

description:
10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)
2020-07-10-1-2_barcodes.tsv.gz
2020-07-10-1-2_features.tsv.gz
2020-07-10-1-2_matrix.mtx.gz


title: ADPD_PTMN_PD_04x10xx_X026_S10_L042_B1_T2_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004403-V1-2_S1052_R2C2_2O_S433


title: ADPD_PTMN_PD_04x10xx_X026_S10_L041_B1_T1_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_10x37xx_X015_S05_L033_B1_T1_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004436-V1-2_S614_R2C2_3I_S307


title: 12132022_W62004397-V1-2_S345_R2C2_11E_S227


title: ADPD_PTMN_PD_07x41xx_X014_S02_L003_B1_T1_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_07x41xx_X014_S02_L004_B1_T2_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: ADPD_PTMN_PD_03x51xx_X029_S04_L032_B1_T2_P057.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: 12132022_W62004394-V1-2_S947_R2C2_13M_S402


title: 12132022_W62004387-V1-2_S495_R2C2_11G_S271


title: ADPD_PTMN_PD_03x43xx_X004_S01_L026_B1_T2_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: U937_rep3

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

data_processing:
For the gene expression, we mapped the sequencing data to reference genome (hg38) using STAR, and defined transcript coordinates according to the gene annotation format file (GTF file) from GENCODE (Release 27, GRCh38).
The Gene abundances are given as Reads Per Kilobase per Million mapped reads (RPKM) with “cuffnorm” command using the Cufflinks package.
Assembly: hg38
Supplementary files format and content: Excel file include RPKM values for each Sample …

extract_protocol:
Total RNA of the wild type and shENO1 U937cells were extracted using the QIAamp AllPrep RNA Mini Kit (Cat# 80204, QIAGEN), according to the manufacturer's specifications.
Libraries were constructed using the TruSeq RNA Sample Preparation Kits (Illumina), and the quality of the library was assessed using Bioanalyzer 2100 (Agilent Technologies).

tag: cell line

value: AML

value: wild type


title: U937_rep2


title: 12132022_W62004380-V1-2_S145_R2C2_20B_S171


title: TCR-HD-P6-wk3

description: 10x Genomics Chromium Next GEM Single Cell 5' Kit (v2)

library_source: transcriptomic single cell

data_processing:
CellRanger v7.0.1 count was run on RNA fastqs. CellRanger vdj was run on TCR fastqs.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files containing RNA data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files containing vdj data: airr_rearrangement.tsv, clonotypes.csv, filtered_contig.fasta, filtered_contig_annotations.csv

extract_protocol:
PBMCs were sorted on Live CD3+CD8+ T cells.
Library was performed according to the manufacturer's instructions (Chromium Next GEM Single Cell 5’, 10x Genomics).

value: CD8 T cells

value: healthy

tag: subject id

tag: timepoint

tag: type

value: TCR


title: ADPD_PTMN_PD_03x43xx_X004_S01_L025_B1_T1_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: U937_rep1


title: U937_shENO1_rep2


title: TCR-HD-P6-wk0


title: TCR-HD-P5-wk3


title: 12132022_W62004359-V1-2_S197_R2C2_12C_S184


title: TCR-HD-P5-wk0


title: ADPD_PTMN_PD_01x39xx_X025_S12_L022_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: GEX-HD-P6-wk3

value: GEX


title: U937_shENO1_rep3


title: 12132022_W62004348-V1-2_S1068_R2C2_6O_S437

value: human nasopharyngeal swab


title: ADPD_PTMN_PD_00x45xx_X012_S06_L011_B1_T1_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: GEX-HD-P5-wk3


title: 12132022_W62004314-V1-2_S978_R2C2_22M_S411

value: BC


title: U937_shENO1_rep1


title: ADPD_PTMN_PD_00x45xx_X012_S06_L012_B1_T2_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen

value: brain


title: ADPD_PTMN_PD_03x51xx_X029_S04_L031_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen

value: bulk


title: GEX-HD-P5-wk0

value: peripheral blood


title: TCR-18-3282-wk12

data_processing:
CellRanger v7.0.1 count was run on GEX fastqs. CellRanger vdj was run on TCR fastqs.
Assembly: GRCh38-2020-A
Supplementary files format and content: CellRanger output files containing GEX data: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: CellRanger output files containing VDJ data: airr_rearrangement.tsv, clonotypes.csv, filtered_contig.fasta, filtered_contig_annotations.csv

tag: patient

value: aPD-1 immune checkpoint blockade


title: ADPD_PTMN_PD_00x26xx_X031_S03_L078_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-18-3282-wk9

value: melanoma


title: ADPD_PTMN_PD_00x26xx_X031_S03_L077_B1_T1_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-18-3282-wk3


title: 12132022_W62004287-V1-2_S460_R2C2_2G_S262


title: TCR-18-3282-wk0


title: ADPD_PTMN_PD_00x09xx_X002_S01_L026_B1_T2_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-17-3017-wk12


title: TCR-17-3017-wk9


title: 12132022_W62004286-V1-2_S509_R2C2_15G_S275


title: 12132022_W62004258-V1-2_S954_R2C2_15M_S404


title: 12132022_W62004226-V1-2_S1048_R2C2_1O_S432


title: 12132022_W62004356-V1-2_S341_R2C2_10E_S226


title: TCR-17-3017-wk3


title: TCR-17-3017-wk6


title: GEX-HD-P6-wk0


title: ADPD_PTMN_PD_00x09xx_X002_S01_L025_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Putamen


title: TCR-17-3017-wk0


title: ADPD_SMTG_PD_97x52xx_X011_S12_L071_B1_T1_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004193-V1-2_S1090_R2C2_12O_S443


title: TCR-16-2006-wk12


title: ADPD_SMTG_PD_94x31xx_X006_S12_L048_B1_T2_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: Feature-2020-07-10-1-2

value: immune checkpoint blockade

value: 17-2796 Baseline (hash6), 17-2796 Follow Up 1 (hash7), 17-2796 Follow Up 2 (hash8), 17-2796 Follow Up 3 (hash9), 17-2796 Follow Up 4 (hash10)


title: 12132022_W62004181-V1-2_S789_R2C2_10K_S357


title: TCR-16-2006-wk9


title: ADPD_SMTG_PD_94x31xx_X006_S12_L047_B1_T1_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: TCR-16-2006-wk3


title: TCR-16-2006-wk6


title: 12132022_W62004171-V1-2_S348_R2C2_12E_S228


title: TCR-16-2006-wk0


title: ADPD_SMTG_PD_93x19xx_X009_S02_L004_B1_T2_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004147-V1-2_S178_R2C2_7C_S179


title: TCR-13-689-wk12


title: TCR-13-689-wk9


title: ADPD_SMTG_PD_93x19xx_X009_S02_L003_B1_T1_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: TCR-13-689-wk3


title: GEX-18-3282-wk9


title: ADPD_SMTG_PD_13x60xx_X016_S06_L060_B1_T2_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004127-V1-2_S1072_R2C2_7O_S438


title: 12132022_W62004123-V1-2_S929_R2C2_8M_S397


title: TCR-13-689-wk0


title: GEX-18-3282-wk6


title: ADPD_SMTG_PD_13x22xx_X030_S03_L053_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: GEX-18-3282-wk3


title: ADPD_SMTG_PD_13x60xx_X016_S06_L059_B1_T1_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004115-V1-2_S34_R2C2_9A_S137


title: GEX-18-3282-wk0


title: GEX-17-3017-wk9


title: ADPD_SMTG_PD_12x65xx_X027_S08_L062_B1_T2_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004112-V1-2_S488_R2C2_9G_S269


title: ADPD_SMTG_PD_12x69xx_X024_S04_L079_B1_T1_P045.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: GEX-17-3017-wk6


title: 12132022_W62004111-V1-2_S936_R2C2_10M_S399


title: GEX-17-3017-wk3


title: ADPD_SMTG_PD_12x65xx_X027_S08_L061_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: GEX-16-2006-wk12


title: GEX-17-3017-wk0


title: 12132022_W62004106-V1-2_S626_R2C2_6I_S310


title: GEX-17-3017-wk12


title: GEX-18-3282-wk12


title: 12132022_W62004116-V1-2_S925_R2C2_7M_S396


title: GEX-16-2006-wk9


title: 12132022_W62004104-V1-2_S186_R2C2_9C_S181


title: GEX-16-2006-wk6


title: ADPD_SMTG_PD_12x50xx_X013_S09_L041_B1_T1_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: GEX-16-2006-wk3


title: 12132022_W62004103-V1-2_S26_R2C2_7A_S135


title: ADPD_SMTG_PD_11x90xx_X021_S08_L016_B1_T2_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004102-V1-2_S330_R2C2_7E_S223


title: GEX-13-689-wk9


title: GEX-13-689-wk12


title: GEX-13-689-wk6


title: GEX-13-689-wk3


title: ADPD_SMTG_PD_11x90xx_X021_S08_L015_B1_T1_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004097-V1-2_S338_R2C2_9E_S225


title: ADPD_SMTG_PD_10x37xx_X008_S05_L082_B1_T2_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: GEX-13-689-wk0


title: 12132022_W62004094-V1-2_S6_R2C2_2A_S130


title: ADPD_SMTG_PD_10x37xx_X008_S05_L081_B1_T1_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004092-V1-2_S778_R2C2_7K_S354


title: ADPD_SMTG_PD_04x37xx_X026_S12_L046_B1_T2_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004086-V1-2_S630_R2C2_7I_S311


title: ADPD_SMTG_PD_04x37xx_X026_S12_L045_B1_T1_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: ADPD_SMTG_PD_12x50xx_X013_S09_L042_B1_T2_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004084-V1-2_S194_R2C2_11C_S183


title: ADPD_SMTG_PD_04x10xx_X014_S04_L008_B1_T2_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: ADPD_SMTG_PD_03x51xx_X012_S12_L023_B1_T1_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: ADPD_SMTG_PD_03x51xx_X012_S12_L024_B1_T2_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: ADPD_SMTG_PD_04x10xx_X014_S04_L007_B1_T1_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004068-V1-2_S498_R2C2_12G_S272


title: 12132022_W62004076-V1-2_S634_R2C2_8I_S312


title: 12132022_W62004075-V1-2_S480_R2C2_7G_S267


title: ADPD_SMTG_PD_03x43xx_X002_S04_L032_B1_T2_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004045-V1-2_S1080_R2C2_9O_S440


title: ADPD_SMTG_PD_03x43xx_X002_S04_L031_B1_T1_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: TCR-13-689-wk6


title: 12132022_W62004022-V1-2_S42_R2C2_11A_S139


title: ADPD_SMTG_PD_00x45xx_X019_S05_L034_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: BMDM, STAT3

city: Nanjing

first: Yuxin

last: Wang

address: 163 Xianlin Road

institute: Nanjing University

data_processing:
Read quality was assessed with FastQC (v0.12.1) and adapters trimmed using Cutadapt (v4.4)
Reads were aligned to reference mouse genome (mm10 assembly, UCSC) using Bowtie2 (v2.5.1)
Assembly: mm10 (UCSC)
Supplementary files format and content: bed file
Library strategy: CUT&RUN

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
CUT&RUN assays were carried out using the Hyperactive pG-MNase CUT&RUN Assay Kit (HD101-01, Vazyme) according to the manufacturer’s instructions.
CUT&RUN library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: BMDMs were isolated from the femurs and tibiase of C57BL/6J or PPARg T166A mice. Bone marrow cells were differentiated for 7 days in the presence of M-CSF (50 ng/ml). On day 7, macrophage purity of the culture was routinely tested by the expression of F4/80 and CD11b by flow cytometry. Around 95-99% of the cells expressed high levels of F4/80 and CD11b after differentiation.

value: Bone marrow

tag: antibody

value: anti-STAT3 (BS1336, Bioworld)

value: Bone marrow-derived macrophages


title: ADPD_SMTG_PD_00x45xx_X019_S05_L033_B1_T1_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62004002-V1-2_S215_R2C2_17C_S189


title: ADPD_SMTG_PD_01x39xx_X015_S03_L030_B1_T2_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: rfISCs,H3K4me3,CUT&Tag

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output
CUT&Tag-Seq reads were trimmed by fastp v0.19.11,and discarding reads left with < 50 bp
Peaks were called using MACS2 v2.1.2 with significance cut-off q-value <=0.05
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
The cells were digested into single cells by the TrypLE and resuspended with precooled PBS. CUT&Tag experiments were carried out using High-Sensitivity Kit (for Illumina)(N259-YH01-01S, Novoprotein)
CUT&Tag libraries were prepared for sequencing using standard Illumina protocols from Novogene

value: Intermediate stem cells between rosette and formative stem cells

value: H3K4me3 (Active Motif, 39060)


title: Skin Macrophages 6 dpi, TA, rep5

data_processing:
Read quality was assessed with FastQC (v0.12.1) and adapters trimmed using Cutadapt (v4.4)
Reads were then aligned to the mm10 genome (UCSC) using HISAT2 (v2.2.1), and counted using featureCounts
Assembly: mm10 (UCSC)
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: skin

extract_protocol:
Total RNA was extracted from differentiated adipocytes in vitro, using the TRIzol reagent (Invitrogen).
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

treatment_protocol: Mice were anesthetized with ketamine and killed. The dorsal skin was removed and cut into tiny pieces, followed by incubation with complete medium (RPMI 1640 and 10% FBS) containing 0.1 mg/ml DNase I, 0.5 mg/ml hyaluronidase and 2 mg/ml collagenase IV in a shaking water bath (37 °C) for 2 h. The cell suspension was filtered with a 40-μm cell nylon mesh to obtain a single-cell suspension. The remaining red blood cells were lysed using RBC lysis buffer. The skin digest was resuspended in MACS buffer and incubated with anti-F4/80 microbeads (Miltenyi Biotech, 130-110-443) for 15 min at 4 °C. Then, the F4/80+ fraction was isolated using MACS MS columns according to the manufacturer’s instructions.

value: skin

value: skin wound macrophages

tag: genotype

value: PPARg T166A

value: Skin injury, 6 dpi


title: 12132022_W62004085-V1-2_S56_R2C2_15A_S143

value: human nasopharyngeal swab

value: BC


title: TCR-18-3282-wk6

value: CD8 T cells

value: TCR


title: Skin Macrophages 6 dpi, TA, rep4


title: GEX-16-2006-wk0

value: peripheral blood

value: aPD-1 immune checkpoint blockade

value: GEX


title: 12132022_W62004004-V1-2_S638_R2C2_9I_S313


title: rfISCs,H3K27me3,CUT&Tag

value: H3K27me3 (Active Motif, 39055)


title: ADPD_SMTG_PD_00x27xx_X025_S10_L018_B1_T2_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri

value: brain

value: bulk


title: Skin Macrophages 6 dpi, TA, rep3


title: Skin Macrophages 6 dpi, TA, rep1


title: ADPD_SMTG_PD_00x27xx_X025_S10_L017_B1_T1_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: 12132022_W62003869-V1-2_S1101_R2C2_15O_S446


title: 12132022_W62003994-V1-2_S652_R2C2_13I_S317


title: ADPD_SMTG_PD_00x26xx_X031_S12_L096_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: Skin Macrophages 6 dpi, TA, rep2


title: 12132022_W62003998-V1-2_S786_R2C2_9K_S356


title: 12132022_W62003965-V1-2_S933_R2C2_9M_S398


title: ADPD_SMTG_PD_00x09xx_X010_S08_L040_B1_T2_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: Skin Macrophages 6 dpi, WT, rep6

value: WT


title: ADPD_SMTG_PD_00x09xx_X010_S08_L039_B1_T1_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: Skin Macrophages 6 dpi, TA, rep6


title: Skin Macrophages 6 dpi, WT, rep4


title: 12132022_W62003676-V1-2_S1118_R2C2_20O_S451


title: 12132022_W62003619-V1-2_S597_R2C2_20H_S303


title: 12132022_W62003865-V1-2_S63_R2C2_17A_S145


title: ADPD_CAUD_PD_97x52xx_X022_S12_L047_B1_T1_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_97x52xx_X022_S12_L048_B1_T2_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Skin Macrophages 6 dpi, WT, rep3


title: 12132022_W62003514-V1-2_S807_R2C2_15K_S362


title: Skin Macrophages 6 dpi, WT, rep2


title: Skin Macrophages 6 dpi, WT, rep1


title: ADPD_CAUD_PD_94x31xx_X010_S02_L027_B1_T1_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_94x31xx_X010_S02_L028_B1_T2_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003474-V1-2_S22_R2C2_6A_S134


title: 12132022_W62003502-V1-2_S484_R2C2_8G_S268


title: 12132022_W62003909-V1-2_S1034_R2C2_18N_S429


title: Ac, N, Ribo-seq-N2

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

description:
Ribo-Seq-Differential_translation efficiency.txt
Ribo-Seq-gene_count_matrix.csv

library_source: other

data_processing:
Pre-processed reads of RNA-seq, Ribo-seq and MeRIP-seq were then subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches.
The sorted mapping files of Ribo-seq and RNA-seq were used for quantification with StringTie (v2.1.7) (Pertea, Pertea et al., 2015). Note that Ribo-Seq reads were mapped with additional parameters: --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33. Next, the obtained read counts were converted to TPM (transcripts per million).
Genes with cutoff values of TPM > 5 for RNA-Seq were used for downstream analysis. The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets. Next, translational efficiency (TE) analysis was calculated by dividing the ribosome footprint density by the Ribo-seq TPM value when it's larger than 0 with mRNA abundance (RNAseq TPM).
The differential translation efficiency gene (DTEG) was analyzed by RiboDiff (v0.2.2). After alignment, m1A peaks enriched via IP over input control were detected based on a combination of corresponding biological replicates using MACS2 (v2.2.7.1) algorithm with -q 0.05. Minimum free energy (MFE) calculation of m1A methylated genes was performed by using the ViennaRNA package.
Assembly: Acart.genome.v1.fa.gz
Supplementary files format and content: Differential_peaks_by_edgeR.txt
Supplementary files format and content: RNA-Seq_gene_count_matrix.csv
Supplementary files format and content: Ribo-Seq-Differential_translation efficiency.txt
Supplementary files format and content: Ribo-Seq-gene_count_matrix.csv
Library strategy: Ribo-seq

molecule: other

organism: Amphidinium carterae

source_name: exponentially grown cells

growth_protocol: Dinoflagellate Amphidinium carterae was cultured in f/2 medium at a constant temperature of 23°C. The lighting conditions were maintained under a 12:12 hour light-dark cycle with a photon flux density of 50µmol·m-2·s-1.

extract_protocol:
Total RNA was extracted from A. carterae using RNAzol®RT (MRC) according to the manufacturer’s protocol.  Polyadenylated RNA (polyA+ RNA) was enriched from the total RNA samples by using two successive rounds of purification with VAHTS mRNA Capture Beads (Vazyme Biotech, Nanjing, China).
m1A-RIP RNA library was prepared by VAHTS Universal V8 RNA-seq Library Prep Kit. For RNA-seq, the isolated total RNA from A. carterae cells (three biological replicates for all treatments) was sent to the Beijing Genomics Institute (BGI, Shenzhen, China) for strand specific mRNA library construction. For Ribo-seq, library was prepared using VAHTSTM Small RNA Library Prep Kit for Illumina.

treatment_protocol: For nitrogen depletion experiment in A. carterae, the exponentially grown cells were washed once with sterile sea water and then cultured in normal and nitrogen-depletion f/2 medium respectively at an initial concentration of 2.5 × 10^4 cells/ml. For Ribo-seq, A. carterae cells (~40 million cells, two biological samples for each treatment) collected in the morning were treated with 100 µg/ml Cycloheximide (CHX) for 8 minutes.

value: exponentially grown cells

value: nitrogen-depletion f/2 medium


title: 12132022_W62003465-V1-2_S204_R2C2_14C_S186


title: ADPD_CAUD_PD_13x60xx_X027_S10_L066_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_93x19xx_X012_S09_L017_B1_T1_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_93x19xx_X012_S09_L018_B1_T2_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003435-V1-2_S526_R2C2_20G_S280


title: Ac, F2, Ribo-seq-F2

data_processing:
Pre-processed reads of RNA-seq, Ribo-seq and MeRIP-seq were then subjected to alignment against Acart.genome.v1 using software STAR (version 2.7.10a), allowing for no more than 2 mismatches.
The sorted mapping files of Ribo-seq and RNA-seq were used for quantification with StringTie (v2.1.7) (Pertea, Pertea et al., 2015). Note that Ribo-Seq reads were mapped with additional parameters: --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33. Next, the obtained read counts were converted to TPM (transcripts per million).
Genes with cutoff values of TPM > 5 for RNA-Seq were used for downstream analysis. The R package DESeq2 was used to perform differential gene expression of RNA-seq datasets. Next, translational efficiency (TE) analysis was calculated by dividing the ribosome footprint density by the Ribo-seq TPM value when it's larger than 0 with mRNA abundance (RNAseq TPM).
The differential translation efficiency gene (DTEG) was analyzed by RiboDiff (v0.2.2). After alignment, m1A peaks enriched via IP over input control were detected based on a combination of corresponding biological replicates using MACS2 (v2.2.7.1) algorithm with -q 0.05. Minimum free energy (MFE) calculation of m1A methylated genes was performed by using the ViennaRNA package.
Assembly: Acart.genome.v1.fa.gz
Supplementary files format and content: Differential_peaks_by_edgeR.txt
Supplementary files format and content: RNA-Seq_gene_count_matrix.csv
Supplementary files format and content: Ribo-Seq-Differential_translation efficiency.txt
Supplementary files format and content: Ribo-Seq-gene_count_matrix.csv

value: normal


title: ADPD_CAUD_PD_13x60xx_X027_S10_L065_B1_T1_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003449-V1-2_S909_R2C2_3M_S392


title: Ac, N, Ribo-seq-N1


title: Ac, F2, Ribo-seq-F1


title: Skin Macrophages 6 dpi, WT, rep5

value: skin

value: skin wound macrophages


title: ADPD_SMTG_PD_00x26xx_X031_S12_L095_B1_T1_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Middle Temporal Gyri


title: ADPD_CAUD_PD_12x69xx_X011_S06_L060_B1_T2_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003431-V1-2_S322_R2C2_5E_S221


title: 12132022_W62003429-V1-2_S291_R2C2_18D_S213


title: 12132022_W62003430-V1-2_S18_R2C2_5A_S133


title: ADPD_CAUD_PD_12x69xx_X011_S06_L059_B1_T1_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_12x65xx_X028_S08_L016_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Control_03

city: Houston

first: Sung Wook

last: Kang

state: TX

address: one plaza

department: Surgery

institute: Baylor college of medicine

data_processing:
The raw sequence reads were mapped to GRCm38 using STAR (V2.5.3a).
The alignmented bam file were performed using markduplicated.
The FPRM value extract were performed using cufflinks.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file FPKM counts for each samples
Supplementary files format and content: tab-delimited text file Cufflinks counts for each samples

source_name: Tumor

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.
The clean RNA samples were used for library preparation in the Genomic and RNA Profling Core, Baylor College of Medicine. Libraries were constructed using a Truseq library preparation kit (Illumina, USA) following the manufacturer’s instructions.

value: Tumor


title: Ac, nanopore-S1

data_processing:
The raw sequencing data quality values were screened using a default threshold of 7. Only reads surpassing this threshold were retained. The raw fastq data were then filtered using NanoFilt (version 2.8.0) with parameters -q 7 and -l 50. To further improve data quality, the filtered Direct RNA data were corrected using fmlrc2 (version 0.1.4) based on the Illumina sequencing data.
The corrected transcript sequences were aligned to the reference genome (Acart.genome.v1) using minimap2 (version 2.17-r941) and subsequent statistics on this alignment were performed using samtools (version 1.11).
After alignment, the Flair software (version 1.5.0) generated a consensus sequence. This sequence was aligned to the reference genome, and redundancies were efficiently removed using StringTie (version 2.1.4). To further refine the results, transcripts were compared with the genome's known transcripts using gffcompare (version 0.12.1), which facilitated the discovery of novel transcripts.
NanoPolish (version 0.13.2) was used to calculate the polyA tail lengths of the original data, resulting in a summary table regarding polyA length and transcript expression level.
Assembly: Acart.genome.v1.fa.gz
Supplementary files format and content: S1.polyA_expression.txt

source_name: Microalgal cells

growth_protocol: Dinoflagellate Amphidinium carterae was cultured in f/2 medium at a constant temperature of 23°C under a 12:12 hour light-dark cycle with a photon flux density of 50µmol·m-2·s-1.

extract_protocol:
Total RNA was extracted from A. carterae using RNAzol®RT (MRC) according to the manufacturer’s protocol.
The total RNA isolated from A. carterae cells was sent to Wuhan Benagen Technology Co., Ltd. for library construction using standard protocols. In brief, polyA+ RNA was reverse transcribed to produce the first strand of cDNA, creating a hybrid RNA-cDNA molecule. This product was then purified using Agencourt RNAClean XP beads. Sequencing adapters were subsequently added to the purified molecules, and the ligation products underwent another round of purification with the same beads. A motor protein was added to prepare the sample for sequencing.
Nanopore direct RNA-sequencing

value: Microalgal cells


title: Control_02


title: Control_01


title: 12132022_W62003413-V1-2_S359_R2C2_15E_S231

value: human nasopharyngeal swab

value: BC


title: ADPD_CAUD_PD_11x90xx_X018_S05_L010_B1_T2_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003415-V1-2_S1094_R2C2_13O_S444


title: DKK3_03


title: ADPD_CAUD_PD_12x65xx_X028_S08_L015_B1_T1_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_11x90xx_X018_S05_L009_B1_T1_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003401-V1-2_S232_R2C2_22C_S194


title: DKK3_02


title: ADPD_CAUD_PD_10x37xx_X030_S11_L070_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003393-V1-2_S1056_R2C2_3O_S434


title: DKK3_01


title: 12132022_W62003391-V1-2_S669_R2C2_18I_S322


title: 12132022_W62003390-V1-2_S666_R2C2_17I_S321


title: ADPD_CAUD_PD_07x41xx_X006_S09_L042_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003387-V1-2_S516_R2C2_17G_S277


title: CD45+ cells from resting neonate and adult skin HTO library

city: New York

first: Dr. Shruti

last: Naik

state: NY

address: 1425 Madison Ave

department: Immunology and Immunotherapy

institute: Icahn School of Medicine at Mount Sinai

description: hashtag derived oligonucleotide

data_processing:
Hashed samples were pooled for library preparation (Chromium Single Cell 3′ Library, 10x Genomics) and sequenced on an Illumina HiSeq 4000 as 150 bp paired-end reads. Non-Hashed samples were processed independently for the library preperation and were also sequenced using the same platform (Illumina HiSeq 4000 as 150 bp paired-end reads)
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The Cell Ranger Single-Cell Software Suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform sample demultiplexing, barcode processing, and single-cell 3’ gene counting
The cDNA insert was aligned to the mm10/GRCm38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene-barcode matrix
Assembly: (mm10/GRCm38)
Supplementary files format and content: Raw feature-barcode matrix (raw_feature_bc_matrix) and Filtered feature-barcode matrices (filtered_feature_bc_matrix) containing only cell barcodes in H5 format for each sample.

molecule: protein

source_name: dorsal skin

extract_protocol:
Skins from neonate mice or female adult mice were cut and weighted, around 1.5X2cm sized skin were minced in 2ml PBS with 55um b-mercaptoethanol, 10mM HEPES, 250ug/ml liberase TL and incubated with shaking for 2.5 hours in 37C. Digestions were stopped with adding EDTA to 12.5mM, and rinsed with PBS containing 4% FBS and 10mM HEPES (FACS buffer) through 70um strainers. After washing, single-cell suspensions were preincubated with anti-CD16/32 prior staining with surface fluorescent conjugated antibodies and/or oligo-tagged antibodies at predetermined concentrations. Stained cells were resuspended in 4′,6-diamidino-2-phenylindole (DAPI) in FACS buffer prior to FACS sorting. For resting condition hashtag labeled CD45+ cells were sorted from neonate and adult mice fo library preparation. For PBS or HDM inoculated neonate mice, CD301b+cDC2 cells were enriched from each group to mix with other cell types to get enough representations. Final ratio of different cell types is CD301b+cDC2: Other CD45+ cells: Epidermal cells: Lineage negative cells=1:2:2:2. Cells from each treatment were sequenced independently.
Library construction were performed according to manufacter's  instruction  for single cell 3' 10x genomic

treatment_protocol: Untreated neonate and adult dorsal skin were used to analyze baseline antigen presenting cells. PBS and HDM inoculated neonate dorsal skin were collected 9 hours after treatment for characterize dendritic cell activtion by HDM .

value: dorsal skin


title: ADPD_CAUD_PD_07x41xx_X006_S09_L041_B1_T1_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: PBS treated neonate skin

description: polyA RNA

value: wild type

value: PBS injection


title: HDM treated neoante skin

description: polyA RNA

value: HDM injection


title: 12132022_w62003382-V1-2_S383_R2C2_22E_S238


title: ADPD_CAUD_PD_04x37xx_X020_S01_L050_B1_T2_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: CD45+ cells from resting neonate and adult skin mRNA library

description: polyA RNA


title: 12132022_W62003378-V1-2_S645_R2C2_11I_S315


title: ADPD_CAUD_PD_04x37xx_X020_S01_L049_B1_T1_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_04x10xx_X001_S08_L016_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Liver,PAE+HMD,Male,Dam 26

city: Perth

first: Nikki

last: Schultz

state: WA

address: 15 Hospital Ave Nedlands

country: Australia

institute: Telethon Kids Institute

data_processing:
Fastq files mapped to mm10 with BS-Seeker2 and CG-maptools.  CGmap output files were combined as a bsseq object in an R environment.
Sex chromosome reads were filtered out, and reads from mice in same treatment groups were combined using collapseBSseq function.
CpGs with an aggregated coverage below 10X in each tissue type were removed.  94.9% of CpGs in the brain and 93.8% in the liver were retained.
Assembly: mm10
Supplementary files format and content: bigwig, bsseq object as .rds file

source_name: Liver

growth_protocol: C57BL/6J female mice were mated with males of equivalent type.

extract_protocol:
RNA was harvested from frozen tissues using Chemagic 360 instrument (PerkinElmer) and quantified
Libraries were prepared using Lucigen NxSeq AmpFREE Low DNA Library Kit (Lucigen) and bisulfite-converted using Zymo EZ DNA-Methylation Gold Kit (Zymo Research), and PCR amplified using KAPA HiFi Uracil PCR Kit (Kapa Biosystems).

treatment_protocol:
Pregnant mice were treated with either 10% (v/v) ethanol from 10 days prior to mating until 10 days post-conception, or non-acidified water.
Mice were fed with either normal chow or folate and choline-enriched (high methyl donor) chow throughout pregnancy.

value: Liver

value: Prenatal alcohol exposure + high methyl donor diet


title: 12132022_W62003334-V1-2_S1187_R2C2_18P_S473


title: Liver,PAE+Normal,Male,Dam 2

value: Prenatal alcohol exposure + normal diet


title: 12132022_W62003319-V1-2_S774_R2C2_6K_S353


title: Liver,H2O+HMD,Female,Dam 6

value: Water + high methyl donor diet


title: ADPD_CAUD_PD_04x10xx_X001_S08_L015_B1_T1_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate

value: brain

value: bulk


title: 12132022_W62003368-V1-2_S502_R2C2_13G_S273


title: ADPD_CAUD_PD_03x51xx_X024_S06_L083_B1_T1_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_03x51xx_X024_S06_L084_B1_T2_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003314-V1-2_S782_R2C2_8K_S355


title: ADPD_CAUD_PD_03x43xx_X017_S03_L006_B1_T2_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003143-V1-2_S796_R2C2_12K_S359


title: Liver,H2O+HMD,Female,Dam 11


title: Liver,H2O+Normal,Female,Dam 13

value: Water + normal diet


title: ADPD_CAUD_PD_00x45xx_X002_S02_L028_B1_T2_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Brain,PAE+HMD,Female,Dam 26

source_name: Brain

value: Brain


title: ADPD_CAUD_PD_00x45xx_X002_S02_L027_B1_T1_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003094-V1-2_S766_R2C2_4K_S351


title: Brain,H2O+HMD,Male,Dam 6


title: 12132022_W62003379-V1-2_S1097_R2C2_14O_S445


title: 12132022_W62003077-V1-2_S913_R2C2_4M_S393


title: ADPD_CAUD_PD_10x37xx_X030_S11_L069_B1_T1_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Brain,PAE+Normal,Female, Dam 2


title: ADPD_CAUD_PD_00x27xx_X023_S12_L072_B1_T2_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_00x27xx_X023_S12_L071_B1_T1_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_CAUD_PD_00x26xx_X016_S03_L054_B1_T2_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: 12132022_W62003058-V1-2_S905_R2C2_2M_S391


title: Brain,H2O+Normal,Male,Dam 3


title: Liver,PAE+Normal,Male,Dam 4


title: Liver,PAE+HMD,Female,Dam 26


title: Liver,H2O+Normal,Male,Dam 13


title: 12132022_W61907609-V1-2_S447_R2C2_20F_S259


title: 12132022_w62000383-V1-2_S1175_R2C2_14P_S469


title: ADPD_CAUD_PD_03x43xx_X017_S03_L005_B1_T1_P037.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: Brain,H2O+HMD,Female,Dam 6


title: 12132022_W61907604-V1-2_S297_R2C2_20D_S215


title: ADPD_CAUD_PD_00x26xx_X016_S03_L053_B1_T1_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Caudate


title: ADPD_HIPP_PD_97x52xx_X026_S09_L039_B1_T1_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: Brain,H2O+Normal,Male,Dam 13


title: 12132022_W62003117-V1-2_S1076_R2C2_8O_S439


title: Brain,PAE+HMD,Female,Dam 25


title: 12132022_W61907603-V1-2_S758_R2C2_2K_S349


title: ADPD_HIPP_PD_94x31xx_X001_S12_L023_B1_T1_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W62003073-V1-2_S1060_R2C2_4O_S435


title: Liver,H2O+HMD,Male,Dam 6


title: 12132022_W61907597-V1-2_S610_R2C2_2I_S306


title: ADPD_HIPP_PD_93x19xx_X027_S07_L060_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: Liver,H2O+Normal,Male,Dam 3


title: Liver,PAE+Normal,Female,Dam 2


title: ADPD_HIPP_PD_94x31xx_X001_S12_L024_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W62203034-V1-2_S1203_R2C2_24P_S477

description:
negative sample
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_W62203031-V1-2_S1200_R2C2_23P_S476


title: Liver,PAE+HMD,Female,Dam 25


title: ADPD_HIPP_PD_97x52xx_X026_S09_L040_B1_T2_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: ADPD_HIPP_PD_12x65xx_X003_S12_L024_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: ADPD_HIPP_PD_93x19xx_X027_S07_L059_B1_T1_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W62102692-V1-2_S1129_R2C2_23O_S454


title: Liver,H2O+Normal,Female,Dam 3


title: ADPD_HIPP_PD_11x90xx_X011_S05_L058_B1_T2_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W62102671-V1-2_S1133_R2C2_24O_S455


title: Liver,H2O+HMD,Male,Dam 11


title: Liver,PAE+Normal,Female,Dam 4


title: ADPD_HIPP_PD_11x90xx_X011_S05_L057_B1_T1_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: Brain,H2O+HMD,Male,Dam 11


title: ADPD_HIPP_PD_04x10xx_X010_S07_L038_B1_T2_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W60702257-V1-2_S765_R1C3_4K_S85

description:
positive sample
run27_R1BC_count_table.txt
run27_R2BC_count_table.txt
run27_count_table.txt
run27_BC_pair_analysis_filenames.txt


title: Brain,H2O+Normal,Female,Dam 13


title: ADPD_HIPP_PD_04x10xx_X010_S07_L037_B1_T1_P017.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W60702276-V1-2_S467_R1C3_4G_S54


title: 12132022_W60702256-V1-2_S1100_R1C3_15O_S123


title: ADPD_HIPP_PD_03x43xx_X001_S11_L022_B1_T2_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: ADPD_HIPP_PD_03x43xx_X001_S11_L021_B1_T1_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq ADPD Hippocampus


title: 12132022_W60702253-V1-2_S912_R1C3_4M_S100


title: Brain,H2O+HMD,Female,Dam 11


title: 12132022_W60701910-V1-2_S365_R1C3_17E_S47


title: A2_P30_2

city: Montreal

first: Gilbert

last: Bernier

state: Quebec

address: 5690 rosemont boulevard

institute: HMR

description: readcount P60.txt

data_processing:
Base-calling and feature count were done using Illumina software. For differential expression analysis, Dseq2 was used on the R program.
Assembly: HG38
Supplementary files format and content: countmatrix

source_name: Neurons J60

growth_protocol: the iPSC were differentiated into adult neurons using the method desribed in Flamier at al 2018

extract_protocol:
the RNA was extracted using Quiagen RNA kits according to the manufacturer instructions.
cDNA was prepared according to the manufacturer’s instructions (NEB library).

value: Neurons J60

value: AD


title: A2_P30_1

description: readcount P60.txt


title: Brain,PAE+Normal,Male,Dam 2


title: AD2_2

description: readcount P60.txt


title: Liver,PAE+HMD,Male,Dam 25


title: Brain,H2O+Normal,Female,Dam 3


title: Brain,PAE+Normal,Female,Dam 4


title: 12132022_W60701890-V1-2_S960_R1C3_17M_S109


title: 12132022_W60701870-V1-2_S214_R1C3_17C_S31


title: G2_P30_2

description: readcount P60.txt

value: CTL


title: 12132022_W60701879-V1-2_S21_R1C3_6A_S6

value: human nasopharyngeal swab


title: 12132022_W60702260-V1-2_S617_R1C3_4I_S70

value: BC


title: Brain, PAE+HMD,Male,Dam 25


title: GB2_1

description: readcount P60.txt


title: primary white adipocyte,siNfe2l1+siAtf3, 400 µM cholesterol, biol rep 4

city: Munich

first: Carolin

last: Jethwa

address: Max-Lebsche-Platz 30

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

data_processing:
Removing of reads containing adapter, reads containing ploy-N and low quality reads from raw data by fastp software to obtain clean data. Calculation of  Q20, Q30 and GC content.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: Mus Musculus(GRCm39/mm39)
Supplementary files format and content: xls file containing raw counts for each sample

source_name: primary white adipocyte

growth_protocol: Primary white adipocytes were maintained in DMEM F-12 supplemented with 10% FBS and 1%antibiotics in a humidifed atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was harvest using NucleoSpin® RNA Kit (Macherey Nagel).
mRNA library preparation (poly A enrichment)

value: primary white adipocyte

value: Nfe2l1 + Atf3 knockdown

value: cholesterol


title: primary white adipocyte,siNfe2l1+siAtf3, 400 µM cholesterol, biol rep 3


title: G1_P30_1

description: readcount P60.txt


title: 12132022_W60701865-V1-2_S173_R1C3_6C_S23

data_processing:
Samples sequenced using Illumina NextSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie to standard amplicons from original screens, as well as two rounds of trimming and mapping to forward and reverse 5 bp barcode references.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were used to aggregate the forward and reverse barcodes.
Final analysis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1) as well as customized sequences for our forward and reverse 5 bp barcode sequences
Supplementary files format and content: run27_R1BC_count_table.txt; run31_R1BC_count_table.txt; run38_R1BC_count_table.txt; run46_R1BC_count_table.txt; run139_R1BC_count_table.txt; run141p3_R1BC_count_table.txt; run141p6_R1BC_count_table.txt
Supplementary files format and content: run27_R2BC_count_table.txt; run31_R2BC_count_table.txt; run38_R2BC_count_table.txt; run46_R2BC_count_table.txt; run139_R2BC_count_table.txt; run141p3_R2BC_count_table.txt; run141p6_R2BC_count_table.txt
Supplementary files format and content: run27_count_table.txt; run31_count_table.txt; run38_count_table.txt; run46_count_table.txt; run139_count_table.txt; run141p3_count_table.txt; run141p6_count_table.txt
Supplementary files format and content: run27_BC_pair_analysis_filenames.txt; run31_BC_pair_analysis_filenames.txt; run38_BC_pair_analysis_filenames.txt; run46_BC_pair_analysis_filenames.txt; run139_BC_pair_analysis_filenames.txt; run141p3_BC_pair_analysis_filenames.txt; run141p6_BC_pair_analysis_filenames.txt


title: 12132022_W60701868-V1-2_S463_R1C3_3G_S53


title: Brain,PAE+Normal,Male,Dam 26


title: 12132022_W60701847-V1-2_S325_R1C3_6E_S40


title: Brain,PAE+HMD,Male,Dam 26


title: G1_P30_2

description: readcount P60.txt


title: 12132022_W60702245-V1-2_S1059_R1C3_4O_S115


title: 12132022_W60701808-V1-2_S475_R1C3_6G_S56


title: primary white adipocyte,siNfe2l1+siAtf3, 400 µM cholesterol, biol rep 2


title: 12132022_W60701895-V1-2_S1_R1C3_1A_S1


title: A11_P5_1

description: readcount P30.txt

source_name: Neurons J30

value: Neurons J30


title: AD2_1

description: readcount P60.txt


title: primary white adipocyte,siNfe2l1+siAtf3, 400 µM cholesterol, biol rep 1


title: 12132022_W60701806-V1-2_S625_R1C3_6I_S72


title: A11_P5_2

description: readcount P30.txt


title: primary white adipocyte,siAtf3, 400 µM cholesterol, biol rep 4

value: Atf3 knockdown


title: A12_P5_1

description: readcount P30.txt


title: GB2_2

description: readcount P60.txt


title: 12132022_W60701801-V1-2_S773_R1C3_6K_S87


title: 12132022_W60701784-V1-2_S920_R1C3_6M_S102


title: LGNJ302

description: readcount P30.txt


title: primary white adipocyte,siAtf3, 400 µM cholesterol, biol rep 2


title: A12_P5_2

description: readcount P30.txt


title: LGNJ303

description: readcount P30.txt


title: A22_P5_1

description: readcount P30.txt


title: primary white adipocyte,siNfe2l1, 400 µM cholesterol, biol rep 3

value: Nfe2l1 knockdown


title: 12132022_W60701397-V1-2_S613_R1C3_3I_S69


title: 12132022_W60701394-V1-2_S29_R1C3_8A_S8


title: 12132022_W60701359-V1-2_S459_R1C3_2G_S52


title: A22_P5_2

description: readcount P30.txt


title: 12132022_W60701350-V1-2_S5_R1C3_2A_S2


title: G2_P5_2

description: readcount P30.txt


title: primary white adipocyte,siNfe2l1, 400 µM cholesterol, biol rep 2


title: primary white adipocyte,siNfe2l1, 400 µM cholesterol, biol rep 1


title: primary white adipocyte,siNfe2l1, 400 µM cholesterol, biol rep 4


title: 12132022_W60701345-V1-2_S455_R1C3_1G_S51


title: G2_P5_1

description: readcount P30.txt


title: primary white adipocyte,scramble, 400 µM cholesterol, biol rep 4

value: WT


title: primary white adipocyte,scramble, 400 µM cholesterol, biol rep 3


title: 12132022_W60701344-V1-2_S177_R1C3_7C_S24


title: 12132022_W60701343-V1-2_S153_R1C3_1C_S18


title: G1_P5

description: readcount P30.txt


title: primary white adipocyte,siAtf3, 400 µM cholesterol, biol rep 3


title: 12132022_W60701409-V1-2_S1067_R1C3_6O_S117


title: primary white adipocyte,siAtf3, 400 µM cholesterol, biol rep 1


title: GB14NJ302

description: readcount P30.txt


title: 12132022_W60701336-V1-2_S329_R1C3_7E_S41


title: primary white adipocyte,scramble, 400 µM cholesterol, biol rep 2


title: GB14NJ303

description: readcount P30.txt


title: GB14NJ301

description: readcount P30.txt


title: 12132022_W60701242-V1-2_S305_R1C3_1E_S35


title: primary white adipocyte,siNfe2l1+siAtf3, control treatment, biol rep 4

value: control


title: LG1

description: readcount iPSC.xls

source_name: iPSc

value: iPSc


title: 12132022_W60700964-V1-2_S644_R1C3_11I_S76


title: 12132022_W60701024-V1-2_S792_R1C3_11K_S91


title: LG2

description: readcount iPSC.xls


title: 12132022_W60701023-V1-2_S351_R1C3_13E_S45


title: primary white adipocyte,siAtf3, control treatment, biol rep 4


title: primary white adipocyte,siNfe2l1+siAtf3, control treatment, biol rep 1


title: primary white adipocyte,siNfe2l1+siAtf3, control treatment, biol rep 2


title: primary white adipocyte,siNfe2l1+siAtf3, control treatment, biol rep 3


title: AD18_1_1

description: readcount iPSC.xls


title: primary white adipocyte,siAtf3, control treatment, biol rep 2


title: 12132022_W60700870-V1-2_S317_R1C3_4E_S38


title: 12132022_W60701230-V1-2_S761_R1C3_3K_S84


title: primary white adipocyte,siAtf3, control treatment, biol rep 3


title: AD18_1_2

description: readcount iPSC.xls


title: AD2_2_1

description: readcount iPSC.xls


title: 12132022_W60700443-V1-2_S932_R1C3_9M_S105


title: 12132022_W60700432-V1-2_S522_R1C3_19G_S64


title: primary white adipocyte,siNfe2l1, control treatment, biol rep 4


title: 12132022_W60700271-V1-2_S358_R1C3_15E_S46


title: primary white adipocyte,scramble, 400 µM cholesterol, biol rep 1


title: AD17_1_1

description: readcount iPSC.xls


title: 12132022_W60604928-V1-2_S157_R1C3_2C_S19


title: 12132022_W60604925-V1-2_S665_R1C3_17I_S79


title: AD2_2_2

description: readcount iPSC.xls


title: AD1_1_2

description: readcount iPSC.xls


title: primary white adipocyte,siAtf3, control treatment, biol rep 1


title: AD1_1_1

description: readcount iPSC.xls


title: primary white adipocyte,siNfe2l1, control treatment, biol rep 3


title: AD17_1_2

description: readcount iPSC.xls


title: primary white adipocyte,siNfe2l1, control treatment, biol rep 2


title: primary white adipocyte,scramble, control treatment, biol rep 3


title: 12132022_W60604316-V1-2_S185_R1C3_9C_S26


title: primary white adipocyte,scramble, control treatment, biol rep 4


title: GB2_1_1

description: readcount iPSC.xls


title: 12132022_W60604356-V1-2_S777_R1C3_7K_S88


title: GB1_4_1

description: readcount iPSC.xls


title: 12132022_W60604310-V1-2_S785_R1C3_9K_S90


title: primary white adipocyte,scramble, control treatment, biol rep 2


title: 12132022_W60604670-V1-2_S1121_R1C3_21O_S126


title: Muscle, Zfp697 mKO, reloading 3 days, rep3

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using STAR 2.7.3a with extra arguments --outFilterScoreMinOverLread 0   --outFilterMatchNmin 0   --outFilterMatchNminOverLread 0   --outFilterMismatchNmax 33   --seedSearchStartLmax 12   --alignSJoverhangMin 8   --alignEndsType Local
Reads aligning to gene exons (Mus_musculus.GRCm38.94.gtf) were counted using featureCounts v2.0.3 program from Subread package, summarized at gene level.
Differential gene expression at FDR level 0.05 was obtained using DESeq2 R package, genes with total raw counts less then 1 across all samples were excluded from analysis
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text file includes raw read counts for all samples
Supplementary files format and content: tab-delimited text files includes differetial gene expression analysis output from DESeq2

source_name: gastrocnemius skeletal muscle

extract_protocol:
Total RNA was extracted from mice gastrocnemius muscles using Trizol reagent
Samples were purified by poly-A enrichment before library creation using Illumina TruSeq Stranded mRNA,

tag: strain

tag: Sex

value: female

value: gastrocnemius skeletal muscle

value: mKO

tag: intervention


title: GB1410_2

description: readcount iPSC.xls


title: primary white adipocyte,scramble, control treatment, biol rep 1


title: 12132022_W60604304-V1-2_S337_R1C3_9E_S43

tag: tissue

tag: bc run_id


title: GB2_1_2

description: readcount iPSC.xls

tag: cell type


title: 12132022_W60604292-V1-2_S487_R1C3_9G_S59

tag: pipeline version


title: 12132022_W60604268-V1-2_S967_R1C3_19M_S110


title: Muscle, Zfp697 mKO, reloading 3 days, rep2


title: 12132022_W60604192-V1-2_S629_R1C3_7I_S73


title: GB1410_1

description: readcount iPSC.xls


title: LGJ10_b

source_name: Neurons J10

value: Neurons J10


title: Muscle, Zfp697 mKO, reloading 3 days, rep1


title: LGJ10_a

value: AD


title: Muscle, flox/flox, reloading 3 days, rep3

value: flox


title: 12132022_W60604198-V1-2_S924_R1C3_7M_S103

source_name: human nasopharyngeal swab

value: human nasopharyngeal swab


title: 12132022_W60604131-V1-2_S1079_R1C3_9O_S120

value: BC


title: GB19J10_b

value: CTL


title: GB16_1_1

description: readcount iPSC.xls


title: primary white adipocyte,siNfe2l1, control treatment, biol rep 1

value: primary white adipocyte

tag: treatment


title: GB1_4_2

description: readcount iPSC.xls


title: Muscle, flox/flox, reloading 3 days, rep2


title: 12132022_W60604075-V1-2_S76_R1C3_21A_S16


title: Muscle, flox/flox, reloading 3 days, rep1


title: GB17J10_b


title: GB19J10_a


title: Muscle, Zfp697 mKO, unloading 10 days, rep3


title: GB17J10_a


title: 12132022_W60604090-V1-2_S753_R1C3_1K_S82


title: AD2_1J10_b


title: Muscle, Zfp697 mKO, unloading 10 days, rep1


title: Muscle, flox/flox, unloading 10 days, rep3


title: 12132022_W60604069-V1-2_S904_R1C3_2M_S98


title: 12132022_W60604061-V1-2_S769_R1C3_5K_S86


title: Muscle, flox/flox, unloading 10 days, rep2


title: 12132022_W60604009-V1-2_S193_R1C3_11C_S28


title: Muscle, Zfp697 mKO, unloading 10 days, rep2


title: AD1_1J10_b


title: 12132022_W60604039-V1-2_S169_R1C3_5C_S22


title: AD1_1J10_a


title: 12132022_W60604006-V1-2_S799_R1C3_13K_S92


title: GB21J10_b


title: Muscle, flox/flox, unloading 10 days, rep1


title: 12132022_W60604003-V1-2_S494_R1C3_11G_S60


title: Muscle, Zfp697 mKO, control, rep2

value: ctrl


title: GB21J10_a


title: 12132022_W60604002-V1-2_S946_R1C3_13M_S107


title: 12132022_W60604074-V1-2_S379_R1C3_21E_S49


title: Muscle, Zfp697 mKO, control, rep1


title: AD2_1J10_a


title: Muscle, flox/flox, control, rep3


title: 12132022_W60604000-V1-2_S344_R1C3_11E_S44


title: Muscle, flox/flox, control, rep2


title: PANC-1_KHSRP_PARCLIP-seq_rep1

city: Guangzhou

first: Zhou

last: yifan

state: 周一帆

address: 74 Zhongshan Second Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Sequenced reads were cleaned for adaptor and low-quality sequence, then CLIP-seq reads were mapped to hg19 using Bowtie2, RNA-seq reads using STAR.
Piranha was used for CLIP-seq peak calling,  RSEM was used for quantification.
Bam file were transform into bigwig format using deepTools.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: txt

source_name: PANC-1 cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
RNA libraries for miCLIP-seq and PARCLIP-seq were prepared using the NEBNext small RNA library prep kit. RNA-seq libraries were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina.
miCLIP-seq, PARCLIP-seq, RNA-seq

value: PANC-1 cells

value: pancreatic cancer cell line


title: 12132022_W60603992-V1-2_S55_R1C3_15A_S13

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)
Other: RNAseq with limited amplicons.


title: Muscle, flox/flox, control, rep1


title: PANC-1_miCLIP-seq_rep2


title: 12132022_W60603976-V1-2_S309_R1C3_2E_S36


title: PANC-1_KHSRP_PARCLIP-seq_rep2


title: PANC-1_miCLIP-seq_rep1


title: Muscle, Zfp697 mKO, control, rep3


title: SIG-9206

city: Münster

first: Klaus

last: Schughart

address: Von-Esmarch-Str 56

department: Virology

institute: University Münster

data_processing:
Reads were quality checked with package FastQC (version 0.11.9), then trimmed using Trimgalore (version 0.6.7) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.7.9a) with default settings.
Mapped reads were counted using RsubRead (version 2.8.1). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.26.0).
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample.

source_name: blood

extract_protocol:
Whole blood RNA was extracted from PAX gene tubes as described in the manufacturer’s protocol (QIAGEN PreAnalytiX)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). Library construction: Globin mRNA was depleted from total RNA using GLOBINclear Kit, human (ThermoFisher, Invitrogen). Subsequently, a strand-specific RNA sequencing library was generated using NEBNext® Ultra  II Directional RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols.
The library was sequenced on Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit (300 cycles) with an average of 40 million reads per RNA sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes.

value: blood

value: m

tag: disease state

value: infected


title: SIG-9909

value: f


title: 12132022_W60603941-V1-2_S62_R1C3_17A_S14


title: 12132022_W60603948-V1-2_S651_R1C3_13I_S77


title: SIG-9203


title: SIG-9201


title: 12132022_W60603936-V1-2_S17_R1C3_5A_S5


title: PPKO_Mybl2KO_D21_Rep1

city: Rockville

first: Kun-Lin

last: Ho

state: MD

address: 10322 Strathmore Hall St Apt 405

institute: HJF

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/lox-quality using CLC genomic benchwork (parameter-quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost:3 deletion cost 3: length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: raw counts for each sample

source_name: PPKO

growth_protocol: DKO and PPKO spheroids were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C in a low attachement plate

extract_protocol:
RNA was harvested using Rnesay mini plus kit (Qiagen). 1.3ug of total RNA was used for the ocnstruction or sequencing libraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq library prep kit following manufacture's protocols

treatment_protocol: cell were fed with DMEM supplemented with 10% FBS every other day

value: PPKO

value: prostate cancer

value: Pten:Trp53:Mybl2 KO


title: PPKO_WT_D21_Rep1

value: Pten:Trp53 KO


title: PPKO_Mybl2KO_D21_Rep2


title: PPKO_WT_D21_Rep2


title: DKO_Mybl2KO_D21_Rep2

source_name: DKO

value: DKO

value: Pten:Rb1:Mybl2 KO


title: 12132022_W60603935-V1-2_S1086_R1C3_11O_S121

value: human nasopharyngeal swab


title: SIG-9199


title: DKO_Mybl2KO_D21_Rep1


title: PANC-1_miCLIP-seq_rep3

value: WT


title: DKO_WT_D21_Rep2

value: Pten:Rb1 KO


title: 12132022_W60603923-V1-2_S1047_R1C3_1O_S112

value: BC


title: 12132022_W60603964-V1-2_S207_R1C3_15C_S30


title: DKO_WT_D21_Rep1


title: 12132022_W60603928-V1-2_S633_R1C3_8I_S74


title: SIG-9197


title: 12132022_W60603952-V1-2_S501_R1C3_13G_S61


title: 12132022_W60603914-V1-2_S781_R1C3_8K_S89


title: SIG-9191


title: 12132022_W60603921-V1-2_S161_R1C3_3C_S20


title: SIG-9183


title: 12132022_W60603904-V1-2_S13_R1C3_4A_S4


title: SIG-9188


title: SOD1G93A mouse, Ultrasound treatment3, Day120

city: Shanghai

first: zihao

last: Liu

address: Yishan Road 600

institute: Shanghai jiaotong university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10
Supplementary files format and content: table include RPKM values for each Sample

source_name: motor cortex

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: motor cortex

value: SOD1G93A mouse

value: Ultrasound treatment


title: SOD1G93A mouse, Ultrasound treatment2, Day120


title: SIG-9178

value: blood


title: 12132022_W60603850-V1-2_S757_R1C3_2K_S83

city: Toronto

first: Jeff

last: Wrana

address: 600 University Avenue

institute: Lunenfeld-Tanenbaum Research Institute


title: SIG-9180


title: SOD1G93A mouse, Ultrasound treatment1, Day120


title: SOD1G93A mouse, Control3, Day120

value: Control


title: SIG-9176

value: infected


title: SOD1G93A mouse, Control2, Day120


title: 12132022_W60603844-V1-2_S672_R1C3_19I_S80


title: 12132022_W60603839-V1-2_S813_R1C3_17K_S94


title: SIG-9174

value: f


title: SOD1G93A mouse, Control1, Day120


title: SIG-9171


title: 12132022_W60603834-V1-2_S189_R1C3_10C_S27


title: CE_ingAdipocytes

city: Schwerzenbach

first: Adhideb

last: Ghosh

address: Schorenstrasse 16

department: Health Sciences and Technology

country: Switzerland

institute: ETH Zurich

data_processing:
Mapping was performed by cellranger
Cellbender was used to remove empty droplets and ambient RNA
scDblFinder was used to exclude potential doublets
Downstream analysis was performed by seurat
Assembly: GRCm38.p6
Supplementary files format and content: Raw count matrices from cell ranger

molecule: nuclear RNA

source_name: inguinal adipose tissue

extract_protocol:
mice adipose tissue were miced and homogenized in dounce homogenizer on ice. The homogenized adipose tissue nuclei were washed with 1% BSA in PBS and filtered 35 um straners. Nuclei suspensions were stained with Hoechst 33342 and loaded to FACS sorting and sorted based on RFP fluorecence
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry)
10X snRNAseq

treatment_protocol: gradual cold exposure of UCP1KO mice for 12 days

value: inguinal adipose tissue

value: adipocytes

value: Ucp1KO, AdipoCre, nucRed

value: cold exposure


title: 12132022_W60603829-V1-2_S372_R1C3_19E_S48


title: 995475-1 db/m

city: Indianapolis

first: Neha

last: Mahajan

state: Indiana

address: 1160 W Michigan St

department: Ophthalmology

institute: Indiana University

description: 6 months post-diabetes

data_processing:
The sequencing reads were first quality checked using FastQC (v.0.11.5, Babraham Bioinformatics, Cambridge, UK). The sequence data were then mapped to the mouse reference genome mm10 using the RNA-seq aligner STAR (v.2.7.10a) with the following parameter: “--outSAMmapqUnique 60”.
To evaluate quality of the RNA-seq data, the number of reads that fell into different annotated regions of the reference genome (exonic, intronic, splicing junction, intergenic, UTR, etc.) were assessed using bam-stats (from ngsutilsj v.0.4.17). Uniquely mapped reads were used to quantify gene expression levels employing featureCounts (subread v.2.0.3) with the following parameters: “-s 2 -p –countReadPairs -Q 10”.
The data were normalized using the TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR (v.3.40.2) , and false discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure.
Assembly: mm10
Supplementary files format and content: The excel table including fold change, log2 fold change, p-values, FDR, log2CPM, and raw counts

source_name: LSK Cells

extract_protocol:
The LSK cells were sorted using flow cytometry followed by RNA isolation using Trizol method.
ultralow mRNA

value: LSK Cells

value: LSK cells derived from bone marrow

value: homozygous for Leptin receptor


title: SIG-9168


title: 12132022_W60603833-V1-2_S37_R1C3_10A_S10

value: human nasopharyngeal swab


title: SIG-9162

value: m


title: 995475-2 db/m

description: 6 months post-diabetes


title: 995477-2 db/m

description: 6 months post-diabetes


title: 12132022_W60603827-V1-2_S974_R1C3_21M_S111

value: BC


title: 995477-1 db/m

description: 6 months post-diabetes


title: SIG-9159


title: 12132022_W60603827-V1-2_S515_R1C3_17G_S63


title: SIG-9157


title: SIG-9165


title: 995479-1 db/m

description: 6 months post-diabetes

value: B6.BKS(D)-Leprdb/+ db/m

value: heterozygous for Leptin receptor


title: 12132022_W60603827-V1-2_S165_R1C3_4C_S21


title: 12132022_W60603842-V1-2_S333_R1C3_8E_S42


title: 12132022_W60603625-V1-2_S200_R1C3_13C_S29


title: SIG-9154


title: 995478-3 db/m

description: 6 months post-diabetes


title: SIG-9145


title: 995478-2 db/m

description: 6 months post-diabetes


title: SIG-9151


title: 12132022_W60603617-V1-2_S508_R1C3_15G_S62


title: COPTG19859-treated B16F10 tumors D14 rep10 [B71]

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

country: France

institute: Transgene SA

data_processing:
The 3 first bases from read 2 were trimmed using Trimmomatic (3 extra G added by the library preparation protocol)
PCR duplicates were removed using Unique molecular identifiers (UMIs) using the program dedup from the package UMI-tools
Reads were aligned using STAR to an artificial genome containing the whole mouse genome (GRCm39) and mTG6050 viral genome.
Readcount for each murin and viral gene was quantified using HTSeq-count
Assembly: GRCm39
Supplementary files format and content: readcounts in the Htseqcount.txt.gz file

source_name: B16F10-induced tumour

extract_protocol:
Total RNA was extracted from whole tumours using the kit Qiagen kitRNeasy Plus Mini.
Strand specific 3' mRNA sequencing libraries were prepared by Integragen, SA.

value: B16F10-induced tumour


title: 12132022_W60603600-V1-2_S1114_R1C3_19O_S125


title: 12132022_W60603623-V1-2_S48_R1C3_13A_S12


title: SIG-9142

value: blood


title: SIG-9139


title: COPTG19859-treated B16F10 tumors D14 rep9 [B190]


title: 995478-1 db/m

description: 6 months post-diabetes


title: COPTG19859-treated B16F10 tumors D14 rep8 [B981]


title: COPTG19859-treated B16F10 tumors D14 rep7 [B978]


title: SIG-9136


title: SIG-9133


title: 12132022_W60603592-V1-2_S908_R1C3_3M_S99


title: COPTG19859-treated B16F10 tumors D14 rep6 [B214]


title: 12132022_W60603581-V1-2_S1063_R1C3_5O_S116


title: SIG-9130


title: SIG-9127


title: 12132022_W60603575-V1-2_S228_R1C3_21C_S33


title: 12132022_W60603564-V1-2_S820_R1C3_19K_S95


title: SIG-9124


title: 12132022_W60603558-V1-2_S900_R1C3_1M_S97


title: COPTG19859-treated B16F10 tumors D14 rep4 [B800]


title: COPTG19859-treated B16F10 tumors D14 rep3 [B851]


title: 12132022_W60603526-V1-2_S827_R1C3_21K_S96


title: SIG-9120


title: COPTG19859-treated B16F10 tumors D14 rep2 [B557]


title: 12132022_W60603525-V1-2_S479_R1C3_7G_S57


title: SIG-9115


title: 12132022_W60603496-V1-2_S928_R1C3_8M_S104


title: 12132022_W60603599-V1-2_S25_R1C3_7A_S7


title: COPTG19289-treated B16F10 tumors D14 rep10 [B601]


title: 12132022_W60603494-V1-2_S69_R1C3_19A_S15


title: SIG-9113


title: SIG-9111


title: COPTG19859-treated B16F10 tumors D14 rep5 [B799]


title: COPTG19289-treated B16F10 tumors D14 rep8 [B556]


title: SIG-9106


title: SIG-9102


title: 12132022_W60603475-V1-2_S1107_R1C3_17O_S124


title: 12132022_W60603464-V1-2_S1075_R1C3_8O_S119


title: 12132022_W60603435-V1-2_S483_R1C3_8G_S58


title: COPTG19289-treated B16F10 tumors D14 rep5 [B75]


title: COPTG19289-treated B16F10 tumors D14 rep6 [B798]


title: COPTG19289-treated B16F10 tumors D14 rep7 [B855]


title: SIG-9117


title: 12132022_W60603430-V1-2_S1055_R1C3_3O_S114


title: SIG-9038


title: SIG-9096


title: COPTG19289-treated B16F10 tumors D14 rep3 [B982]


title: COPTG19289-treated B16F10 tumors D14 rep4 [B187]


title: SIG-9027


title: COPTG19859-treated B16F10 tumors D14 rep1 [B604]


title: 12132022_W60603404-V1-2_S621_R1C3_5I_S71


title: SIG-9040


title: COPTG19289-treated B16F10 tumors D14 rep9 [B605]


title: 12132022_W60603492-V1-2_S939_R1C3_11M_S106


title: COPTG19289-treated B16F10 tumors D14 rep2 [B72]


title: 12132022_W60603399-V1-2_S471_R1C3_5G_S55


title: SIG-9109


title: untreated B16F10 tumors D14 rep9 [B558]

value: untreated


title: 12132022_W60603398-V1-2_S321_R1C3_5E_S39


title: SIG-9026

value: infected


title: untreated B16F10 tumors D14 rep7 [B979]


title: SIG-2134

value: f


title: SIG-8017


title: COPTG19289-treated B16F10 tumors D14 rep1 [B559]


title: untreated B16F10 tumors D14 rep5 [B797]


title: untreated B16F10 tumors D14 rep8 [B980]


title: SIG-2140


title: 12132022_W60603380-V1-2_S916_R1C3_5M_S101


title: 12132022_W60603395-V1-2_S679_R1C3_21I_S81


title: 12132022_W60603391-V1-2_S529_R1C3_21G_S65


title: 12132022_W60603421-V1-2_S9_R1C3_3A_S3


title: 12132022_W60603387-V1-2_S605_R1C3_1I_S67


title: SIG-2137


title: untreated B16F10 tumors D14 rep6 [B189]


title: 12132022_W60603208-V1-2_S806_R1C3_15K_S93


title: untreated B16F10 tumors D14 rep3 [B73]


title: SIG-2125


title: untreated B16F10 tumors D14 rep2 [B560]


title: 12132022_W60603197-V1-2_S1093_R1C3_13O_S122


title: 12132022_W60603384-V1-2_S1051_R1C3_2O_S113


title: SIG-2131


title: SIG-2128


title: SIG-2119


title: untreated B16F10 tumors D14 rep4 [B603]


title: 12132022_W60603205-V1-2_S658_R1C3_15I_S78


title: SIG-2122


title: untreated B16F10 tumors D14 rep1 [B602]


title: SIG-2116


title: 12132022_W60603177-V1-2_S637_R1C3_9I_S75


title: COPTG19859-treated B16F10 tumors D11 rep9 [B209]


title: 12132022_W60603186-V1-2_S953_R1C3_15M_S108


title: SIG-2110


title: 12132022_W60603175-V1-2_S33_R1C3_9A_S9


title: SIG-2113


title: COPTG19859-treated B16F10 tumors D11 rep7 [B206]


title: 12132022_W60602660-V1-2_S41_R1C3_11A_S11


title: COPTG19859-treated B16F10 tumors D11 rep6 [B87]


title: 12132022_W60602553-V1-2_S313_R1C3_3E_S37


title: SIG-2104


title: COPTG19859-treated B16F10 tumors D11 rep5 [B383]


title: SIG-2098


title: 12132022_W60506415-V1-2_S181_R1C3_8C_S25


title: SIG-2077


title: COPTG19859-treated B16F10 tumors D11 rep4 [B382]


title: 12132022_W60506497-V1-2_S609_R1C3_2I_S68


title: COPTG19859-treated B16F10 tumors D11 rep10 [B195]


title: COPTG19859-treated B16F10 tumors D11 rep2 [B419]


title: COPTG19859-treated B16F10 tumors D11 rep3 [B418]


title: 12132022_W60701744-V1-2_S1132_R1C3_24O_S128

description:
negative sample
run27_R1BC_count_table.txt
run27_R2BC_count_table.txt
run27_count_table.txt
run27_BC_pair_analysis_filenames.txt


title: SIG-2068


title: 12132022_W60603178-V1-2_S1071_R1C3_7O_S118


title: COPTG19859-treated B16F10 tumors D11 rep1 [B388]


title: COPTG19859-treated B16F10 tumors D11 rep8 [B212]


title: SIG-2059


title: COPTG19289-treated B16F10 tumors D11 rep10 [B194]


title: COPTG19289-treated B16F10 tumors D11 rep9 [B211]


title: SIG-2107


title: SIG-2038


title: SIG-2041


title: SIG-2101


title: Positive human nasopharyngeal swab group 1 (part2)

description:
sparseq_sample_data_GEOver_part2_v3.txt
README_sample_annotations_GEOver_part2.txt
SRR_and_filenames_GEOver_part2_README.txt

data_processing:
Samples sequenced using Illumina NextSeq, MiSeq, and MiniSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were developed to track and quantify key mutations within samples and to aggregate data.
Final anaylsis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1)
Supplementary files format and content: positive sample text file [sparseq_sample_data_GEOver_part2.txt] has 3129 patient samples with bowtie alignment counts and variant analysis pipeline results
Supplementary files format and content: negative control text file [sparseq_negative_data_GEOver_part2.txt] has 283 negative human samples with bowtie alignment counts
Supplementary files format and content: non-patient control text file [sparseq_control_data_GEOver_part2.txt] has 259 total synthetic control samples with bowtie alignment counts
Library strategy: RNAseq with limited amplicons.

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample) and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library) (A66514, Beckman Coulter)

tag: sample type

value: positive sample


title: SIG-2028


title: COPTG19289-treated B16F10 tumors D11 rep8 [B191]


title: Positive human nasopharyngeal swab group 11

data_processing:
Samples sequenced using Illumina NextSeq, MiSeq, and MiniSeq and demultiplexed using bcl2fastq.
Reads were aligned with Bowtie.
Counts were quantified with HTSeq-count (v0.13.5 with settings -f sam -t CDS).
Custom python scripts (python v3.9, available at https://github.com/wrana-lab) were developed to track and quantify key mutations within samples and to aggregate data.
Final anaylsis of data was done in R v4.1.1.
Assembly: Custom genome consists of amplicons targeting GRCh38 and Sars-CoV-2 (Wuhan-Hu-1)
Supplementary files format and content: positive sample text file [sparseq_sample_data_GEOver.txt] has 63036 patient samples with bowtie alignment counts and variant analysis pipeline results
Supplementary files format and content: negative control text file [sparseq_negative_data_GEOver.txt] has 1928 negative human samples with bowtie alignment counts
Supplementary files format and content: non-patient control text file [sparseq_control_data_GEOver.txt] has 2886 total synthetic control samples with bowtie alignment counts
Library strategy: RNAseq with limited amplicons.

extract_protocol:
RNA from positive samples was extracted with MGIEasy Nucleic Acid Extraction Kit.
Libraries were pooled by Biomex Fx. Each sample was pooled (7uL/sample)  and library PCR products were purified twice with SPRIselect beads ratio 1:1 (beads/library)  (A66514, Beckman Coulter)


title: COPTG19289-treated B16F10 tumors D11 rep7 [B90]


title: Positive human nasopharyngeal swab group 10


title: SIG-2025


title: 12132022_W60505956-V1-2_S221_R1C3_19C_S32


title: Positive human nasopharyngeal swab group 8


title: 12132022_W60701738-V1-2_S1128_R1C3_23O_S127


title: SIG-2013


title: SIG-2004


title: Positive human nasopharyngeal swab group 9


title: COPTG19289-treated B16F10 tumors D11 rep6 [B207]


title: COPTG19289-treated B16F10 tumors D11 rep5 [B416]


title: COPTG19289-treated B16F10 tumors D11 rep4 [B86]


title: Negative human nasopharyngeal swab group 1 (part2)

description:
sparseq_negative_data_GEOver_part2.txt
README_sample_annotations_GEOver_part2.txt
SRR_and_filenames_GEOver_part2_README.txt

value: negative sample


title: Positive human nasopharyngeal swab group 2

value: preclinical


title: COPTG19289-treated B16F10 tumors D11 rep3 [B385]


title: SIG_8 SIG-2018

data_processing:
Reads were quality checked with package FastQC (version 0.11.4), then trimmed using Trimgalore (version 0.4.4) with default settings.
Trimmed reads were mapped to human genome annotation hg38 (ENSMBL hg38 release 91) using STAR (version 2.5.2b, (Dobin and Gingeras, 2015)) with default settings.
Mapped reads were counted using RsubRead (version 1.32.4, (Liao et al., 2019)). Reads for beta-globin were set to 1000. Raw counts were then normalized using DESeq2 (version 1.16.1, (Love et al., 2014)).
Sex was validated by gene expression for Y-specific genes and corrected if different from recorded sex.
Genome_build: ENSMBL hg38 release 91
Supplementary_files_format_and_content: txt matrix with log2 normalized values per sample

treatment_protocol: Blood samples from patients and controls were collected and stored in PAX tubes. Project SIG-2018

tag: status


title: SIG-1565


title: Positive human nasopharyngeal swab group 3


title: SIG_9 SIG-2018


title: SIG_7 SIG-2018


title: COPTG19289-treated B16F10 tumors D11 rep2 [B387]


title: untreated B16F10 tumors D11 rep10 [B210]


title: SIG_80 SIG-2018


title: Negative human nasopharyngeal swab group 2


title: untreated B16F10 tumors D11 rep9 [B215]


title: COPTG19289-treated B16F10 tumors D11 rep1 [B390]


title: Negative human nasopharyngeal swab group 4


title: untreated B16F10 tumors D11 rep7 [B88]


title: SIG-2001


title: untreated B16F10 tumors D11 rep8 [B208]


title: SIG_6 SIG-2018


title: Positive human nasopharyngeal swab group 7


title: Negative human nasopharyngeal swab group 1


title: Positive human nasopharyngeal swab group 2 (part2)


title: SIG_5 SIG-2018


title: untreated B16F10 tumors D11 rep6 [B192]


title: SIG_41 SIG-2018


title: SIG_42 SIG-2018


title: untreated B16F10 tumors D11 rep5 [B417]


title: Positive human nasopharyngeal swab group 6


title: Negative human nasopharyngeal swab group 2 (part2)


title: SIG_40 SIG-2018


title: Positive human nasopharyngeal swab group 1


title: untreated B16F10 tumors D11 rep4 [B386]


title: Negative human nasopharyngeal swab group 6


title: untreated B16F10 tumors D11 rep3 [B384]


title: SIG_4 SIG-2018


title: Hh_4

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from MajorBio company. 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 of MajorBio.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: breast

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. Illumina NovaSeq X Plus was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: breast

tag: cell line

value: overexpression of TFCP2L1 in Hs578T breast cancer cells


title: untreated B16F10 tumors D11 rep2 [B420]

tag: timepoint


title: Hh_3


title: SIG_39 SIG-2018


title: untreated B16F10 tumors D11 rep1 [B381]


title: SIG_38 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep10 [630]

source_name: CT26-induced tumour

value: CT26-induced tumour

value: BALB/c


title: HPB_1

value: Empty group Hs578T breast cancer cells


title: HPB_2


title: SIG_35 SIG-2018

value: m


title: SIG_36 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep9 [106]


title: SIG_34 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep7 [743]


title: SIG_31 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep6 [103]


title: COPTG19859-treated CT26 tumors D17 rep8 [969]


title: COPTG19859-treated CT26 tumors D17 rep5 [559]


title: SIG_33 SIG-2018


title: SIG_28 SIG-2018


title: SIG_30 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep3 [971]


title: SIG_22 SIG-2018


title: COPTG19859-treated CT26 tumors D17 rep4 [633]


title: COPTG19859-treated CT26 tumors D17 rep2 [741]


title: TA4357_2|020|PanCK+

type: RNA

city: brisbane

first: Arutha

last: Kulasinghe

address: 37 kent st

institute: University of Queensland

data_processing:
Adapter trimming with trim galore,  trimGaloreOpts =  --hardtrim5 26 --dont_gzip
If paired-end, merge overlapping R1 and R2 with flash2, flash2Opts =  -m 26 -e 26 -f 26 -s 1 -r 27”
Extract UMIs in bowtie2, umiExtractOpts =  --bc-pattern=NNNNNNNNNNNNNN
Align RTS_IDs (probe barcodes) using bowtie2, bowtie2Opts =  --end-to-end -L 4 --trim5 0 --trim3 0 --norc
Deduplication using UMI-tools, umiDedupOpts =  --edit-distance-threshold=1“
sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached NanoString GeoMx Hs_R_NGS_WTA_v1.0 file
4357_WTA_QC.csv: raw count data, normalised_4357_WTA_QC.csv: normalised count data

source_name: HNSCC

label_protocol: Each collection of oligo tags from one well (representing an AOI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

extract_protocol: Samples were incubated with DNA-oligo barcoded RNA-ISH probes which were conjugated with a UV-photocleavable linker following standard ISH protocols, along with fluorescently labeled antibodies for visualization of morphological structures. Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)

value: head and neck cancer tumour samples from patients who received immunotherapy

tag: aoisurfacearea

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

tag: scanoffsety

value: SCC

value: pos

value: PR


title: SIG_21 SIG-2018

tag: Sex

tag: status


title: SIG_23 SIG-2018


title: TA4357_2|017|PanCK-

tag: tissue

value: SD


title: TA4357_2|017|PanCK+

tag: aoisurfacearea


title: SIG_20 SIG-2018


title: SIG_2 SIG-2018


title: COPTG19289-treated CT26 tumors D17 rep10 [420]

tag: strain

tag: treatment

tag: timepoint


title: TA4357_2|020|PanCK-

tag: aoinucleicount

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads


title: TA4357_2|019|PanCK-

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads


title: COPTG19289-treated CT26 tumors D17 rep9 [897]


title: COPTG19859-treated CT26 tumors D17 rep1 [973bis]


title: SIG_17 SIG-2018


title: SIG_169 SIG-2018


title: COPTG19289-treated CT26 tumors D17 rep6 [296]


title: SIG_168 SIG-2018


title: COPTG19289-treated CT26 tumors D17 rep7 [581]


title: TA4357_2|016|PanCK+

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

tag: scanoffsetx

value: Recurrent SCC


title: TA4357_2|016|PanCK-

tag: tissue

tag: scanoffsety


title: TA4357_2|015|PanCK+

tag: aoisurfacearea

value: Metastatic SCC

value: PD


title: TA4357_2|015|PanCK-


title: TA4357_2|018|PanCK-


title: TA4357_2|014|PanCK-


title: TA4357_2|014|PanCK+


title: COPTG19289-treated CT26 tumors D17 rep5 [733]

tag: strain

tag: treatment


title: COPTG19289-treated CT26 tumors D17 rep4 [687]

tag: timepoint


title: TA4357_2|013|PanCK+

tag: aoinucleicount

tag: roicoordinatex

value: neg


title: SIG_165 SIG-2018

tag: Sex

tag: status


title: SIG_164 SIG-2018


title: COPTG19289-treated CT26 tumors D17 rep1 [686]


title: COPTG19289-treated CT26 tumors D17 rep3 [736]


title: SIG_163 SIG-2018

value: f


title: TA4357_2|013|PanCK-

tag: roicoordinatey

tag: rawreads

tag: alignedreads

tag: deduplicatedreads


title: TA4357_2|012|PanCK-

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth


title: COPTG19289-treated CT26 tumors D17 rep8 [424]

tag: tissue


title: untreated CT26 tumors D17 rep10 [293]

value: untreated


title: SIG_162 SIG-2018


title: TA4357_2|012|PanCK+

tag: aoisurfacearea

tag: scanheight

tag: scanoffsetx

tag: scanoffsety


title: TA4357_2|010|PanCK-

tag: aoinucleicount


title: untreated CT26 tumors D17 rep9 [414]

tag: strain

tag: treatment

tag: timepoint


title: SIG_161 SIG-2018

tag: Sex

tag: status


title: SIG_160 SIG-2018


title: TA4357_2|011|PanCK+

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads

value: Metastatic/recurrent SCC with basaloid features


title: untreated CT26 tumors D17 rep8 [684]


title: SIG_167 SIG-2018


title: TA4357_2|011|PanCK-

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: TA4357_2|010|PanCK+

tag: tissue

tag: aoisurfacearea

tag: scanwidth

tag: scanheight


title: untreated CT26 tumors D17 rep7 [412]

tag: strain


title: SIG_166 SIG-2018


title: SIG_159 SIG-2018


title: SIG_158 SIG-2018


title: COPTG19289-treated CT26 tumors D17 rep2 [416]

tag: treatment


title: TA4357_2|009|PanCK-

tag: aoinucleicount

tag: scanoffsetx

tag: scanoffsety


title: SIG_1573 SIG-2018

tag: Sex

tag: status

value: infected


title: untreated CT26 tumors D17 rep4 [197]

value: CT26-induced tumour

tag: timepoint


title: SIG_1572 SIG-2018


title: SIG_1571 SIG-2018


title: TA4357_2|009|PanCK+

tag: roicoordinatex

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: TA4357_2|008|PanCK-

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: untreated CT26 tumors D17 rep3 [415]

tag: tissue

value: BALB/c


title: SIG_1570 SIG-2018


title: untreated CT26 tumors D17 rep2 [447]

tag: strain


title: untreated CT26 tumors D17 rep1 [341]

tag: treatment


title: TA4357_2|007|PanCK-

tag: aoisurfacearea

tag: aoinucleicount

tag: scanwidth

tag: scanheight


title: SIG_157 SIG-2018

tag: Sex

tag: status


title: TA4357_2|007|PanCK+

tag: roicoordinatex

tag: scanoffsetx

tag: scanoffsety


title: TA4357_2|006|PanCK-

tag: roicoordinatey

tag: rawreads

tag: alignedreads


title: SIG_1568 SIG-2018


title: untreated CT26 tumors D17 rep6 [294]

tag: timepoint


title: COPTG19859-treated CT26 tumors D15 rep8 [515]


title: SIG_1567 SIG-2018


title: TA4357_2|006|PanCK+

tag: deduplicatedreads

tag: trimmedreads

tag: stitchedreads

tag: sequencingsaturation


title: COPTG19859-treated CT26 tumors D15 rep10 [744]

tag: tissue

tag: strain

tag: treatment


title: SIG_1569 SIG-2018


title: SIG_1566 SIG-2018


title: TA4357_2|005|PanCK-

tag: aoisurfacearea

tag: aoinucleicount

tag: scanwidth

tag: scanheight


title: COPTG19859-treated CT26 tumors D15 rep9 [557]


title: untreated CT26 tumors D17 rep5 [161]


title: TA4357_2|005|PanCK+

tag: roicoordinatex

tag: scanoffsetx


title: TA4357_2|004|PanCK-

tag: roicoordinatey

tag: scanoffsety

value: Residual SCC


title: SIG_1565 SIG-2018

tag: Sex

value: m

tag: status


title: COPTG19859-treated CT26 tumors D15 rep7 [745]

tag: timepoint


title: TA4357_2|008|PanCK+

value: head and neck cancer tumour samples from patients who received immunotherapy

tag: rawreads

tag: alignedreads

tag: deduplicatedreads

tag: trimmedreads


title: SIG_156 SIG-2018


title: GB1_4

description:
AD_vs_CTL.CG.DMR.bed
AD_vs_CTL.CHG.DMR.bed
AD_vs_CTL.CHH.DMR.bed

data_processing:
The original images obtained from high-throught sequencing platform are transformed into sequenced reads by CASAVA base calling. Bismark software (Krueger, 2011) is used to perform alignments of bisulfite-treated reads to a reference genome.
Assembly: HG38
Supplementary files format and content: bed files containing the DMR between AD and CTL

source_name: iPSC

growth_protocol: iPSC cells

extract_protocol:
the DNA was extracted using Quiagen DNA kits according to the manufacturer instructions.
cDNA was prepared according to the manufacturer’s instructions (NEB library).

tag: cell type

value: iPSC

tag: genotype

value: CTL


title: COPTG19859-treated CT26 tumors D15 rep4 [366]

tag: tissue

tag: strain

tag: treatment


title: COPTG19859-treated CT26 tumors D15 rep6 [364]


title: GB2_1


title: TA4357_2|003|PanCK-

tag: aoisurfacearea

tag: aoinucleicount

tag: stitchedreads

tag: sequencingsaturation

tag: scanwidth

tag: scanheight

value: SCC

value: pos