title: 12022022_W73102721-V1-2_S175_R1C3_6C_S51


title: 12022022_W73103928-V1-2_S914_R1C3_4M_S274

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
run38_R1BC_count_table.txt
run38_R2BC_count_table.txt
run38_count_table.txt
run38_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: 12022022_W73102387-V1-2_S327_R1C3_6E_S96


title: 12022022_W73102080-V1-2_S403_R1C3_5F_S118


title: 12022022_W73102074-V1-2_S553_R1C3_5H_S163


title: 12022022_W73102079-V1-2_S349_R1C3_12E_S102


title: 12022022_W73102036-V1-2_S797_R1C3_12K_S237


title: 12022022_W73102004-V1-2_S101_R1C3_5B_S28


title: 12022022_W73102001-V1-2_S335_R1C3_8E_S98


title: 12022022_W73101467-V1-2_S286_R1C3_16D_S84


title: 12022022_W73101448-V1-2_S951_R1C3_14M_S284


title: 12022022_W73101432-V1-2_S906_R1C3_2M_S272


title: 12022022_W73101429-V1-2_S198_R1C3_12C_S57


title: 12022022_W73101419-V1-2_S46_R1C3_12A_S12


title: 12022022_W73101264-V1-2_S356_R1C3_14E_S104


title: 12022022_W73101397-V1-2_S499_R1C3_12G_S147


title: 12022022_W73101253-V1-2_S1182_R1C3_16P_S355


title: 12022022_W73101125-V1-2_S804_R1C3_14K_S239


title: 12022022_W73100581-V1-2_S882_R1C3_16L_S264


title: 12022022_W73100578-V1-2_S1158_R1C3_8P_S347


title: 12022022_W73101158-V1-2_S656_R1C3_14I_S194


title: 12022022_W73101226-V1-2_S843_R1C3_3L_S251


title: 12022022_W73101039-V1-2_S506_R1C3_14G_S149


title: 12022022_W73101116-V1-2_S205_R1C3_14C_S59


title: 12022022_W73101236-V1-2_S990_R1C3_3N_S296


title: 12022022_W73100538-V1-2_S436_R1C3_16F_S129


title: 12022022_W73009305-V1-2_S728_R1C3_14J_S217


title: 12022022_W73009243-V1-2_S271_R1C3_11D_S79


title: 12022022_W73009097-V1-2_S937_R1C3_10M_S280


title: 12022022_W73008922-V1-2_S534_R1C3_22G_S157


title: 12022022_W73009280-V1-2_S140_R1C3_18B_S41


title: 12022022_W73009110-V1-2_S592_R1C3_18H_S176


title: 12022022_W73101945-V1-2_S485_R1C3_8G_S143


title: 12022022_W73101814-V1-2_S31_R1C3_8A_S8


title: synthetic control group 6

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.

organism: synthetic construct

source_name: synthetic control

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)

value: synthetic control

tag: sample type


title: 12022022_W73008900-V1-2_S1035_R1C3_18N_S311


title: synthetic control group 2 (part2)

description:
sparseq_control_data_GEOver_part2.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)


title: Myotubes, Ad Flag-Zfp697, mIgG ab, rep1

city: Solna

first: Igor

last: Cervenka

address: Solnavägen 9

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

library_source: genomic

data_processing:
Reads were aligned to the GRCm38.p6 version of the mouse genome using STAR and duplicated reads were removed with MarkDuplicates.
We used MACS3 callpeak for peak calling (q- value < 0.05 and fold change ≥ 1.5).
Bedtools were used to generate coverage tracks.
Assembly: GRCm38.p6
Supplementary files format and content: Excel xlsx files containing peak information
Supplementary files format and content: Bigwig (bw) files containing track coverage information

molecule: genomic DNA

organism: Mus musculus

source_name: mouse primary satellite cells

growth_protocol: Primary mouse myoblasts were seeded on a 6-well plate and differentiated in DMEM supplemented by 5% horse serum

extract_protocol:
Cells were crosslinked by adding 1% formaldehyde directly into the media for 12 minutes at room temperature. Cell pellet was washed and resuspended in 0.5 mL of ChIP Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0) supplemented with protease inhibitor cocktail (Roche, EDTA-free) and homogenized. The chromatin was then submitted to 5 cycles of sonication (Bioruptor Plus, Diagenode; 30 seconds ON, 30 seconds OFF) at low intensity.
The libraries for ChIP-seq were generated using the Takara ThruPLEX DNA-Seq Kit (Takara, R400736)

treatment_protocol: Fully differentiated myotubes were transduced overnight with an adenovirus at an MOI of 100

tag: strain

tag: cell line

value: mouse primary satellite cells

tag: cell type

value: myotubes

tag: genotype

value: wild-type

tag: treatment

value: Adenovirus infection Flag-Zfp697

tag: chip antibody

value: normal rabbit IgG (#2729, Cell Signaling)


title: Myotubes, Ad Flag-Zfp697, mIgG ab, rep2


title: Myotubes, Ad Flag-Zfp697, mIgG ab, rep3


title: 12022022_W73008772-V1-2_S876_R1C3_14L_S262


title: Myotubes, Ad Flag-Zfp697, Flag ab, rep3

value: FLAG (F3165, Sigma)


title: 12022022_W73009448-V1-2_S649_R1C3_12I_S192


title: 12022022_W73008848-V1-2_S119_R1C3_11B_S34


title: 12022022_W73008769-V1-2_S852_R1C3_6L_S254


title: Myotubes, Ad Flag-Zfp697, Input


title: negative supercoils, 36.5C, control, rep2

city: Jinan

first: liangran

last: zhang

state: Shandong

address: Jingshi Street

department: State Key Laboratory of Microbial Technology

country: China

institute: Shandong University

data_processing:
Adaptors and bases with a quality rating of less than 25 were trimmed by Trim-galore.
The filtered reads were aligned to the Saccharomyces cerevisiae reference genome (SacCer2, 2008) using BOWTIE2 (Version 2.4.2; Langmead et al., 2009)
The ChIP and input data were normalized to reads per kilobase per million (RPKM) by using DEEPTOOLS (Version 3.3.2; Zhang et al., 2008)
Peaks were identified using MACS with the following parameters: Nomodel mode, 200 bp extension size, the cutoff of FDR (q-value) at 0.05.
Assembly: SacCer2, 2008
Supplementary files format and content: bedgraph

organism: Saccharomyces cerevisiae

source_name: Budding yeast

growth_protocol: Cultures were either maintained at 30°C or shifted to other temperatures from 2.5h in SPM.

extract_protocol:
Cells were lysed in 1ml of lysis buffer (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate) by Tissue Lyser . Crosslinked chromatin was sheared to 200-500bp by 12 × 10s pulses using a Biorupter sonicator. Genomic DNA was purified after being treated with 100μg/ml RNase A and 100μg/ml proteinase K. 5% purified DNA was treated as input DNA for subsequent experiments. 5μg purified DNA was incubated with 30µl Dynabeads MyOne streptavidin overnight at 4°C. The ChIP–DNA was eluted from the beads with 250µl elution buffer (95% formamide, 10mM EDTA) at 90 °C for 20 min and purified with Qiagen PCR clean up kit.
The library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat# ND607-01) according to the manufacturer’s manual.

treatment_protocol: Cells were treated with 0.1% Sodium azide for 30min at 30°C and permeabilized with 0.1% digitonin for 30min at 30 °C. Collected cells were incubated with bTMP (200µg per 109 cells) in the dark for 30min and cross-linked by 365 nm UV light to form covalent linkage between DNA and bTMP.

value: Budding yeast

tag: antibody

value: bTMP(cat#29986, Thermo Fisher Scientific)

tag: time point

tag: temperature


title: 12022022_W73008722-V1-2_S725_R1C3_13J_S216


title: negative supercoils, 36.5C, IP, rep2


title: Myotubes, Ad Flag-Zfp697, Flag ab, rep2


title: Myotubes, Ad Flag-Zfp697, Flag ab, rep1


title: 12022022_W73008727-V1-2_S873_R1C3_13L_S261


title: 12022022_W73008694-V1-2_S1029_R1C3_16N_S309


title: 12022022_W73008691-V1-2_S740_R1C3_18J_S221


title: 12022022_W73008726-V1-2_S1020_R1C3_13N_S306


title: Zip3, 36.5C, input,rep2

data_processing:
Adaptors and bases with a quality rating of less than 25 were trimmed by Trim-galore.
The filtered reads were aligned to the Saccharomyces cerevisiae reference genome (SacCer2, 2008) using BOWTIE2 (Version 2.4.2; Langmead et al., 2009)
The ChIP and input data were normalized to reads per kilobase per million (RPKM) by using DEEPTOOLS (Version 3.3.2; Zhang et al., 2008)
Fold enrichment for each sample was determined by comparing the signal ratio between normalized ChIP and input for every bin (bin=50bp) across the whole genome using DEEPTOOLS (Version 3.3.2; Ramírez et al., 2016)
Peaks were identified using MACS with the following parameters: Nomodel mode, 200 bp extension size, the cutoff of FDR (q-value) at 0.05.
Assembly: SacCer2, 2008
Supplementary files format and content: bedgraph

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 90 min. The reaction was quenched with glycine. The cells were broken with glass beads in lysis buffer and the chromatin was sheared by sonication.
The library was prepared using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme, Cat# ND607-01) according to the manufacturer’s manual.

value: Zip3-myc, ndt80D

value: anti-myc


title: 12022022_W73008686-V1-2_S53_R1C3_14A_S14


title: 12022022_W73008695-V1-2_S134_R1C3_16B_S39


title: 12022022_W73009028-V1-2_S421_R1C3_11F_S124


title: negative supercoils, 23C, control, rep2


title: 12022022_W73008683-V1-2_S292_R1C3_18D_S86


title: 12022022_W73008610-V1-2_S541_R1C3_1H_S159


title: Zip3, 23C, IP, rep2


title: 12022022_W73008906-V1-2_S400_R1C3_4F_S117


title: Hop1, 36.5C, input,rep2

value: Hop1-HA, ndt80D

value: anti-HA


title: negative supercoils, 23C, IP, rep2


title: Hop1, 36.5C, IP, rep2


title: 12022022_W73008529-V1-2_S698_R1C3_4J_S207


title: Hop1, 23C, input,rep2


title: Zip3, 36.5C, IP, rep2


title: Hop1, 23C, IP, rep2


title: negative supercoils-36.5C-control-rep1


title: negative supercoils-36.5C-IP-rep1


title: 12022022_W73008527-V1-2_S996_R1C3_5N_S298


title: 12022022_W73008612-V1-2_S415_R1C3_9F_S122


title: 12022022_W73008600-V1-2_S1008_R1C3_9N_S302


title: Zip3, 30C, input, rep2


title: Zip3, 30C, IP, rep2


title: Zip3, 23C, input,rep2


title: 12022022_W73008568-V1-2_S565_R1C3_9H_S167


title: 12022022_W73008372-V1-2_S295_R1C3_19D_S87


title: 12022022_W73008368-V1-2_S1119_R1C3_20O_S335


title: 12022022_W73008604-V1-2_S861_R1C3_9L_S257


title: Zip3-36.5C-IP-rep1


title: 12022022_W73008528-V1-2_S113_R1C3_9B_S32


title: Zip3-30C-input-rep1


title: 12022022_W73008408-V1-2_S707_R1C3_7J_S210


title: 12022022_W73008374-V1-2_S677_R1C3_20I_S200


title: negative supercoils-23C-control-rep1


title: Zip3-23C-input-rep1


title: Zip3-36.5C-input-rep1


title: 12022022_W73008367-V1-2_S527_R1C3_20G_S155


title: 12022022_W73008361-V1-2_S972_R1C3_20M_S290


title: 12022022_W73008370-V1-2_S731_R1C3_15J_S218


title: Zip3-30C-IP-rep1


title: 12022022_W73008364-V1-2_S1098_R1C3_14O_S329


title: 12022022_W73008365-V1-2_S885_R1C3_17L_S265


title: negative supercoils-23C-IP-rep1


title: 12022022_W73008363-V1-2_S442_R1C3_18F_S131


title: 12022022_W73008358-V1-2_S143_R1C3_19B_S42


title: Rec8-36.5C-IP-rep2

value: Rec8-HA, ndt90D


title: 12022022_W73008342-V1-2_S825_R1C3_20K_S245


title: 12022022_W73008338-V1-2_S987_R1C3_2N_S295


title: 12022022_W73008317-V1-2_S1023_R1C3_14N_S307


title: 12022022_W73008315-V1-2_S244_R1C3_2D_S70


title: Rec8-30C-IP-rep2

value: Rec8-HA, ndt86D


title: Rec8-36.5C-IP-rep1

value: Rec8-HA, ndt88D


title: Rec8-36.5C-input-rep2

value: Rec8-HA, ndt91D


title: Zip3-23C-IP-rep1


title: Rec8-30C-input-rep2

value: Rec8-HA, ndt87D


title: 12022022_W73008310-V1-2_S433_R1C3_15F_S128

value: human nasopharyngeal swab

value: BC


title: Rec8-30C-input-rep1

value: Rec8-HA, ndt85D


title: Rec8-36.5C-input-rep1

value: Rec8-HA, ndt89D


title: 12022022_W73008360-V1-2_S1032_R1C3_17N_S310


title: Rec8-30C-IP-rep1

value: Rec8-HA, ndt84D


title: 12022022_W73008195-V1-2_S586_R1C3_16H_S174


title: Rec8-23C-input-rep2

value: Rec8-HA, ndt83D


title: 12022022_W73008193-V1-2_S128_R1C3_14B_S37


title: 12022022_W73008185-V1-2_S1043_R1C3_21N_S314


title: 12022022_W73008181-V1-2_S131_R1C3_15B_S38


title: Rec8-23C-IP-rep1

value: Budding yeast

value: Rec8-HA, ndt80D


title: Hop1-36.5C-input-rep1


title: 12022022_W73008173-V1-2_S601_R1C3_21H_S179


title: Rec8-23C-input-rep1

value: Rec8-HA, ndt81D


title: 12022022_W73008163-V1-2_S149_R1C3_21B_S44


title: Hop1-30C-input-rep2


title: 12022022_W73008170-V1-2_S1196_R1C3_21P_S360


title: Hop1-30C-IP-rep2


title: Hop1-36.5C-IP-rep1


title: Hop1-30C-input-rep1


title: 12022022_W73008152-V1-2_S746_R1C3_20J_S223


title: 12022022_W73008162-V1-2_S298_R1C3_20D_S88


title: Hop1-30C-IP-rep1


title: Hop1-23C-input-rep1


title: 12022022_W73008149-V1-2_S301_R1C3_21D_S89


title: 12022022_W73008159-V1-2_S1193_R1C3_20P_S359


title: Hop1-23C-IP-rep1


title: Red1-36.5C-input-rep2

value: Red1-HA, ndt80D


title: 12022022_W73008148-V1-2_S749_R1C3_21J_S224


title: 12022022_W73008135-V1-2_S283_R1C3_15D_S83


title: Red1-36.5C-IP-rep2


title: Rec8-23C-IP-rep2

value: Rec8-HA, ndt82D


title: Red1-36.5C-input-rep1

value: anti-HA


title: 12022022_W73008127-V1-2_S598_R1C3_20H_S178


title: 12022022_W73008122-V1-2_S888_R1C3_18L_S266


title: 12022022_W73008123-V1-2_S146_R1C3_20B_S43


title: Red1-30C-input-rep2


title: 12022022_W73008103-V1-2_S39_R1C3_10A_S10


title: Red1-30C-IP-rep2


title: 12022022_W73008101-V1-2_S958_R1C3_16M_S286


title: Red1-30C-input-rep1


title: Red1-36.5C-IP-rep1


title: Red1-23C-input-rep2


title: Red1-30C-IP-rep1


title: 12022022_W73008150-V1-2_S896_R1C3_21L_S269


title: 12022022_W73008083-V1-2_S191_R1C3_10C_S55


title: Red1-23C-input-rep1


title: 12022022_W73008060-V1-2_S513_R1C3_16G_S151


title: Red1-23C-IP-rep2


title: 12022022_W73008053-V1-2_S1105_R1C3_16O_S331


title: 12022022_W73008051-V1-2_S212_R1C3_16C_S61


title: NB4_Input

city: Shanghai

first: Peng

last: Jin

address: Ruijin Rd. II

department: Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics

institute: Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing reads were aligned to hg38 by Bowtie2 (version 2.2.9). The uniquely mapped and non-redundant reads were left to conduct peak calling.
ChIP-seq peak regions were called using MACS (version 1.4.2) at a p-value cut off of 10e-10 or 10e-5.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. Peaks.xls files were generated using MACS v1.4.2.
Assembly: hg38
Supplementary files format and content: bigWig or/and peak.txt files (except for input)

organism: Homo sapiens

growth_protocol: NB4 and K562 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, the pellets were then re-suspended in ChIP buffer (Active motif) containing 1 mM PMSF and proteinase inhibitor cocktail (Sigma). Chromatin shearing was performed using a Biorupter Pico ultrasonicator device (Diagenode) with 30s ON then 30s OFF for 30 cycles. Solubilized chromatin was used for immunoprecipitation by incubating overnight at 4 °C with chip antibodies. The immunoprecipitation reaction was transferred to the Protein G agarose Column (53039, Active Motif) and incubated for 2 hours at 4 °C, then each column was washed 4 times with 900 μL Wash Buffer AM1 (Active motif). The ChIPed sample was eluted using 100 μL 37 °C Elution Buffer AM4 (Active Motif). Cross-linking was reversed by adding 5 μL Proteinase K and the sample was incubated overnight at 65 °C. Input and ChIPed DNA were purified using a DNA purification column (Active Motif).
DNA libraries were prepared with the MicroPlex Library Preparation Kit (Diagenode) according to the manufacturer’s instructions. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: NB4 cells were treated with DMSO or ATO or JQ1 for 24 hours, or treated with 4% 1,6-Hexanediol for 30 minutes

value: Acute promyelocytic leukemia (APL) patient-derived cell line


title: 12022022_W73008045-V1-2_S811_R1C3_16K_S241


title: 12022022_W73008041-V1-2_S663_R1C3_16I_S196


title: 12022022_W73008131-V1-2_S451_R1C3_21F_S134


title: NB4_ATO_BRD4_BETHYL

value: ATO

value: BRD4 (Bethyl laboratory, #A301-985)


title: NB4_JQ1_BRD4_BETHYL


title: NB4_DMSO_BRD4_BETHYL

value: DMSO


title: 12022022_W73008026-V1-2_S670_R1C3_18I_S198


title: 12022022_W73008014-V1-2_S818_R1C3_18K_S243


title: 12022022_W73008007-V1-2_S74_R1C3_20A_S20


title: 12022022_W73008098-V1-2_S342_R1C3_10E_S100


title: NB4_1,6-Hex_RNA pol II_BETHYL

value: RNA pol II (Santa Cruz Biotechnology, #sc-17798)


title: 12022022_W73008067-V1-2_S363_R1C3_16E_S106

value: human nasopharyngeal swab


title: Red1-23C-IP-rep1


title: 12022022_W73008004-V1-2_S965_R1C3_18M_S288

value: BC


title: NB4_PBS_RNA pol II_BETHYL

value: PBS


title: 12022022_W73008001-V1-2_S589_R1C3_17H_S175


title: 12022022_W73008006-V1-2_S559_R1C3_7H_S165


title: 12022022_W73008003-V1-2_S1112_R1C3_18O_S333


title: 12022022_W73007992-V1-2_S1191_R1C3_19P_S358


title: NB4_1,6-Hex_BRD4_BETHYL


title: NB4_1,6-Hex_PML_RARα_customized

value: antibody used in PML/RARα ChIP-seq assay was customized by ABclonal Biotechnology


title: 12022022_W73007973-V1-2_S891_R1C3_19L_S267


title: NB4_PBS_PML_RARα_customized


title: NB4_PBS_BRD4_BETHYL


title: 12022022_W73007965-V1-2_S1179_R1C3_15P_S354


title: K562_flag-PML_RARα_FLAG_SIGMA

value: Chronic myeloid leukemia

value: FLAG (Sigma, #F1804)


title: K562_vector_FLAG_SIGMA

value: vector


title: K562_flag-PML_RARα-ΔIDR_FLAG_SIGMA


title: 12022022_W73007956-V1-2_S289_R1C3_17D_S85


title: 12022022_W73007951-V1-2_S571_R1C3_11H_S169


title: NB4_BRD4_BETHYL


title: NB4_JQ1_PML_RARα_customized


title: NB4_ATO_PML_RARα_customized


title: NB4_DMSO_PML_RARα_customized


title: NB4 cells, JQ1, 24h, replicate2

data_processing:
The salmon program was used for quantification of transcript expression.
The reference transcriptome was built with the Ensembl gene annotation file and the hg38 genome (GRCh38.98).
|log2(fold change)| >=0.585 and the FDR < 0.01 were used for determining differentially expressed genes.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing the reads count values and DEseq2 statistics per gene

growth_protocol: NB4 cells were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Valencia, CA). Ribosomal RNAs were depleted according to the manufacturer's protocol (Vazyme, China, N406-01).
RNA-seq libraries were preapared withthe NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, E7530S) according to the manufacturer’s instructions.

treatment_protocol: NB4 cells were treated with DMSO or JQ1 for 24 hours.

value: Acute promyelocytic leukemia cells


title: 12022022_W73007947-V1-2_S409_R1C3_7F_S120


title: NB4 cells, JQ1, 24h, replicate1


title: 12022022_W73007934-V1-2_S259_R1C3_7D_S75


title: NB4 cells, DMSO, 24h, replicate2


title: 12022022_W73007933-V1-2_S1040_R1C3_20N_S313


title: NB4 cells, DMSO, 24h, replicate1


title: 6122023_H2O-MULTI_S158_F13R39_R3C2_23M_S463_R1_001

description: synthetic control

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_R1BCrpt_count_table.txt; run31_R1BCrpt_count_table.txt; run38_R1BCrpt_count_table.txt; run46_R1BCrpt_count_table.txt; run139_R1BCrpt_count_table.txt; run141p3_R1BCrpt_count_table.txt; run141p6_R1BCrpt_count_table.txt
Supplementary files format and content: run27_R2BCrpt_count_table.txt; run31_R2BCrpt_count_table.txt; run38_R2BCrpt_count_table.txt; run46_R2BCrpt_count_table.txt; run139_R2BCrpt_count_table.txt; run141p3_R2BCrpt_count_table.txt; run141p6_R2BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_count_table.txt; run31_BCrpt_count_table.txt; run38_BCrpt_count_table.txt; run46_BCrpt_count_table.txt; run139_BCrpt_count_table.txt; run141p3_BCrpt_count_table.txt; run141p6_BCrpt_count_table.txt
Supplementary files format and content: run27_BCrpt_pair_analysis_filenames.txt; run31_BCrpt_pair_analysis_filenames.txt; run38_BCrpt_pair_analysis_filenames.txt; run46_BCrpt_pair_analysis_filenames.txt; run139_BCrpt_pair_analysis_filenames.txt; run141p3_BCrpt_pair_analysis_filenames.txt; run141p6_BCrpt_pair_analysis_filenames.txt

value: synthetic control


title: 12022022_W73007904-V1-2_S710_R1C3_8J_S211


title: 6122023_H2O-RT_S23_F1R39_R3C2_23A_S328_R1_001

description: synthetic control


title: 12022022_W73007882-V1-2_S1173_R1C3_13P_S352


title: 12022022_W73007921-V1-2_S104_R1C3_6B_S29


title: 12022022_W73007892-V1-2_S722_R1C3_12J_S215


title: 12022022_W73007958-V1-2_S439_R1C3_17F_S130


title: 6122023_H2O-RT_S46_F3R39_R3C2_23C_S351_R1_001

description: synthetic control


title: 6122023_HEK-200ng-SM1-2p66pg_S114_F9R39_R3C2_23I_S419_R1_001

description: synthetic control


title: 6122023_HEK-200ng-SM1-2p66pg_S158_F7R39_R3C1_23G_S158_R1_001

description: synthetic control


title: 12022022_W73007881-V1-2_S879_R1C3_15L_S263


title: 12022022_W73007917-V1-2_S692_R1C3_2J_S205


title: 6122023_HEK-200ng-SM1-2p66pg_S203_F9R39_R3C1_23I_S203_R1_001

description: synthetic control


title: 6122023_H2O-MULTI_S136_F11R39_R3C2_23K_S441_R1_001

description: synthetic control


title: 12022022_W73007866-V1-2_S719_R1C3_11J_S214


title: 12022022_W73007925-V1-2_S550_R1C3_4H_S162


title: 6122023_NoRT-HEK-200ng-SM1-2p66pg_S69_F5R39_R3C2_23E_S374_R1_001

description: synthetic control


title: 12022022_W73007974-V1-2_S1038_R1C3_19N_S312


title: 6122023_HEK-200ng-SM1-2p66pg_S92_F7R39_R3C2_23G_S397_R1_001

description: synthetic control


title: 12022022_W73007877-V1-2_S737_R1C3_17J_S220


title: 12022022_W73007927-V1-2_S704_R1C3_6J_S209


title: 12022022_W73007868-V1-2_S377_R1C3_20E_S110


title: 6122023_H2O-RT_S68_F3R39_R3C1_23C_S68_R1_001

description: synthetic control


title: 6122023_H2O-MULTI_S293_F13R39_R3C1_23M_S293_R1_001

description: synthetic control


title: 12022022_W73007912-V1-2_S716_R1C3_10J_S213


title: 12022022_W73007864-V1-2_S1026_R1C3_15N_S308


title: 6122023_NoRT-HEK-200ng-SM1-2p66pg_S113_F5R39_R3C1_23E_S113_R1_001

description: synthetic control


title: 12022022_W73007863-V1-2_S116_R1C3_10B_S33


title: 6122023_H2O-MULTI_S248_F11R39_R3C1_23K_S248_R1_001

description: synthetic control


title: 6122023_H2O-RT_S23_F1R39_R3C1_23A_S23_R1_001

description: synthetic control


title: 12022022_W73007858-V1-2_S137_R1C3_17B_S40


title: 6122023_HEK-200ng-SM1-2p66pg_S175_F9R39_R1C3_23I_S175_R1_001

description: synthetic control


title: 12022022_W73007843-V1-2_S122_R1C3_12B_S35


title: 6122023_NoRT-HEK-200ng-SM1-2p66pg_S99_F5R39_R1C3_23E_S99_R1_001

description: synthetic control


title: 12022022_W73007849-V1-2_S226_R1C3_20C_S65


title: 6122023_H2O-RT_S23_F1R39_R1C3_23A_S23_R1_001

description: synthetic control


title: 12022022_W73007787-V1-2_S1185_R1C3_17P_S356


title: 6292023_HEK-200ng-SM1-2p66pg_S160_F7R39_R1C3_23G_S523_R1_001

description: synthetic control


title: 12022022_W73007778-V1-2_S520_R1C3_18G_S153


title: 12022022_W73007745-V1-2_S67_R1C3_18A_S18


title: 6122023_H2O-BC_S251_F13R39_R1C3_23M_S251_R1_001

description: synthetic control


title: 6122023_HEK-200ng-SM1-2p66pg_S137_F7R39_R1C3_23G_S137_R1_001

description: synthetic control


title: 6292023_H2O-RT_S69_F3R39_R1C3_23C_S432_R1_001

description: synthetic control


title: 12022022_W73007739-V1-2_S391_R1C3_1F_S114


title: 6292023_HEK-200ng-SM1-2p66pg_S205_F9R39_R1C3_23I_S568_R1_001

description: synthetic control


title: 6292023_NoRT-HEK-200ng-SM1-2p66pg_S115_F5R39_R1C3_23E_S478_R1_001

description: synthetic control


title: 6122023_H2O-BC_S213_F11R39_R1C3_23K_S213_R1_001

description: synthetic control


title: 12022022_W73007742-V1-2_S370_R1C3_18E_S108


title: 6292023_H2O-RT_S23_F1R39_R1C3_23A_S386_R1_001

description: synthetic control


title: 6292023_H2O-BC_S295_F13R39_R1C3_23M_S658_R1_001

description: synthetic control


title: 6292023_H2O-BC_S250_F11R39_R1C3_23K_S613_R1_001

description: synthetic control


title: 12022022_W73007721-V1-2_S846_R1C3_4L_S252


title: 12022022_W73007730-V1-2_S219_R1C3_18C_S63


title: 12022022_W73007855-V1-2_S107_R1C3_7B_S30


title: 6122023_H2O-RT_S61_F3R39_R1C3_23C_S61_R1_001

description: synthetic control


title: 12022022_W73007718-V1-2_S1170_R1C3_12P_S351


title: 12022022_W73007750-V1-2_S241_R1C3_1D_S69


title: 12022022_W73007743-V1-2_S430_R1C3_14F_S127


title: 6292023_NoRT-HEK-200ng-SM1-2p66pg_S113_F5R39_R3C3_23E_S113_R1_001

description: synthetic control


title: 6292023_HEK-200ng-SM1-2p66pg_S203_F9R39_R3C3_23I_S203_R1_001

description: synthetic control


title: 12022022_W73007711-V1-2_S870_R1C3_12L_S260


title: 12022022_W73007691-V1-2_S556_R1C3_6H_S164


title: 6292023_H2O-RT_S23_F1R39_R3C3_23A_S23_R1_001

description: synthetic control


title: 6292023_H2O-RT_S68_F3R39_R3C3_23C_S68_R1_001

description: synthetic control


title: 6292023_HEK-200ng-SM1-2p66pg_S158_F7R39_R3C3_23G_S158_R1_001

description: synthetic control


title: 6292023_H2O-BC_S248_F11R39_R3C3_23K_S248_R1_001

description: synthetic control


title: 12022022_W73007859-V1-2_S110_R1C3_8B_S31


title: 7042023_HEK-200ng-SM1-2p66pg_S199_F9R39_R3C2_23I_S330_R1_001

description: synthetic control


title: 12022022_W73007705-V1-2_S274_R1C3_12D_S80


title: 7042023_NoRT-HEK-200ng-SM1-2p66pg_S111_F5R39_R3C2_23E_S242_R1_001

description: synthetic control


title: 6292023_H2O-BC_S293_F13R39_R3C3_23M_S293_R1_001

description: synthetic control


title: 12022022_W73007657-V1-2_S448_R1C3_20F_S133


title: 12022022_W73007667-V1-2_S893_R1C3_20L_S268


title: 12022022_W73007672-V1-2_S734_R1C3_16J_S219


title: 12022022_W73007676-V1-2_S544_R1C3_2H_S160


title: 7042023_H2O-RT_S67_F3R39_R3C2_23C_S198_R1_001

description: synthetic control


title: 12022022_W73007637-V1-2_S95_R1C3_3B_S26


title: 7042023_HEK-200ng-SM1-2p66pg_S155_F7R39_R3C2_23G_S286_R1_001

description: synthetic control


title: 12022022_W73007636-V1-2_S695_R1C3_3J_S206


title: 12022022_W73007620-V1-2_S159_R1C3_2C_S47


title: 7042023_H2O-RT_S23_F1R39_R3C2_23A_S154_R1_001

description: synthetic control


title: 7042023_H2O-BC_S243_F11R39_R3C2_23K_S374_R1_001

description: synthetic control


title: 12022022_W73007600-V1-2_S832_R1C3_22K_S247


title: 7042023_H2O-BC_S286_F13R39_R3C2_23M_S417_R1_001

description: synthetic control


title: 7042023_NoRT-HEK-200ng-SM1-2p66pg_S50_F5R39_R3C1_23E_S50_R1_001

description: synthetic control


title: 12022022_W73007684-V1-2_S580_R1C3_14H_S172


title: 12022022_W73007688-V1-2_S1188_R1C3_18P_S357


title: 12022022_W73007677-V1-2_S98_R1C3_4B_S27


title: 12022022_W73007579-V1-2_S684_R1C3_22I_S202


title: 7042023_HEK-200ng-SM1-2p66pg_S66_F7R39_R3C1_23G_S66_R1_001

description: synthetic control


title: 12022022_W73007565-V1-2_S412_R1C3_8F_S121


title: 7042023_H2O-RT_S34_F3R39_R3C1_23C_S34_R1_001

description: synthetic control


title: 12022022_W73007580-V1-2_S1164_R1C3_10P_S349


title: 12022022_W73007560-V1-2_S864_R1C3_10L_S258


title: 7042023_H2O-BC_S114_F13R39_R3C1_23M_S114_R1_001

description: synthetic control


title: 12022022_W73007558-V1-2_S268_R1C3_10D_S78


title: 7042023_H2O-RT_S17_F1R39_R3C1_23A_S17_R1_001

description: synthetic control


title: 7282022_NoRT-HEK-200ng-SM1-2p66pg_S528_F5R39_R3C2_23E_S528

description:
synthetic control
run141p6_R1BC_count_table.txt
run141p6_R2BC_count_table.txt
run141p6_count_table.txt
run141p6_BC_pair_analysis_filenames.txt


title: 12022022_W73007555-V1-2_S577_R1C3_13H_S171


title: 12022022_W73007556-V1-2_S1005_R1C3_8N_S301


title: 12022022_W73007544-V1-2_S7_R1C3_2A_S2


title: 7282022_HEK-200ng-SM1-2p66pg_S573_F9R39_R3C2_23I_S573


title: 12022022_W73007523-V1-2_S424_R1C3_12F_S125


title: 7282022_HEK-200ng-SM1-2p66pg_S551_F7R39_R3C2_23G_S551


title: 12022022_W73007519-V1-2_S1155_R1C3_7P_S346


title: 7042023_H2O-BC_S98_F11R39_R3C1_23K_S98_R1_001

description: synthetic control


title: 7282022_H2O-RT_S505_F3R39_R3C2_23C_S505


title: 7282022_H2O-RT_S482_F1R39_R3C2_23A_S482


title: 7042023_HEK-200ng-SM1-2p66pg_S82_F9R39_R3C1_23I_S82_R1_001

description: synthetic control


title: 7282022_H2O-MULTI_S617_F13R39_R3C2_23M_S617


title: 12022022_W73007508-V1-2_S492_R1C3_10G_S145


title: 12022022_W73007512-V1-2_S701_R1C3_5J_S208


title: 12022022_W73007498-V1-2_S1084_R1C3_10O_S325


title: 7282022_H2O-MULTI_S595_F11R39_R3C2_23K_S595


title: 7282022_NoRT-HEK-200ng-SM1-2p66pg_S209_F5R39_R3C1_23E_S209

description:
synthetic control
run141p3_R1BC_count_table.txt
run141p3_R2BC_count_table.txt
run141p3_count_table.txt
run141p3_BC_pair_analysis_filenames.txt


title: 12022022_W73007497-V1-2_S713_R1C3_9J_S212


title: 7282022_HEK-200ng-SM1-2p66pg_S299_F9R39_R3C1_23I_S299


title: 12022022_W73007490-V1-2_S280_R1C3_14D_S82


title: 12022022_W73007495-V1-2_S311_R1C3_2E_S92


title: 7282022_H2O-RT_S119_F1R39_R3C1_23A_S119


title: 12022022_W73007482-V1-2_S642_R1C3_10I_S190


title: 7282022_H2O-RT_S164_F3R39_R3C1_23C_S164


title: 7282022_HEK-200ng-SM1-2p66pg_S254_F7R39_R3C1_23G_S254


title: 12022022_W73007479-V1-2_S1176_R1C3_14P_S353


title: 7282022_H2O-MULTI_S389_F13R39_R3C1_23M_S389


title: 7132022_NoRT-HEK-200ng-SM1-2p66pg_S469_F5_R39_R2C2_23E_S469

description:
synthetic control
run139_R1BC_count_table.txt
run139_R2BC_count_table.txt
run139_count_table.txt
run139_BC_pair_analysis_filenames.txt


title: 12022022_W73007459-V1-2_S1149_R1C3_5P_S344


title: 7132022_HEK-200ng-SM1-2p66pg_S507_F7_R39_R2C2_23G_S507


title: 12022022_W73007513-V1-2_S1017_R1C3_12N_S305


title: 7132022_H2O-RT_S431_F3_R39_R2C2_23C_S431


title: 12022022_W73007460-V1-2_S790_R1C3_10K_S235


title: 12022022_W73007343-V1-2_S256_R1C3_6D_S74


title: 7132022_HEK-200ng-SM1-2p66pg_S545_F9_R39_R2C2_23I_S545


title: 12022022_W73007457-V1-2_S92_R1C3_2B_S25


title: 7132022_H2O-RT_S393_F1_R39_R2C2_23A_S393


title: 12022022_W73007330-V1-2_S1011_R1C3_10N_S303


title: 7132022_H2O-MULTI_S621_F13_R39_R2C2_23M_S621


title: 12022022_NoRT-HEK-200ng-SM4-2p66pg-V1-2_S238_R2C2_23C_S432

description:
synthetic control
run46_R1BC_count_table.txt
run46_R2BC_count_table.txt
run46_count_table.txt
run46_BC_pair_analysis_filenames.txt


title: 12022022_W73007312-V1-2_S583_R1C3_15H_S173


title: 12022022_W73007321-V1-2_S89_R1C3_1B_S24


title: 7132022_H2O-MULTI_S583_F11_R39_R2C2_23K_S583


title: 12022022_W73007304-V1-2_S1014_R1C3_11N_S304


title: 12022022_W73007194-V1-2_S247_R1C3_3D_S71


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S835_R2C2_23K_S613


title: 12022022_W73007190-V1-2_S547_R1C3_3H_S161


title: 12022022_W73007478-V1-2_S394_R1C3_2F_S115


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S687_R2C2_23I_S568


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S539_R2C2_23G_S523


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S389_R2C2_23E_S478


title: 12022022_W73007126-V1-2_S1126_R1C3_22O_S337


title: 7282022_H2O-MULTI_S344_F11R39_R3C1_23K_S344


title: 12022022_W73007476-V1-2_S849_R1C3_5L_S253


title: 12022022_W73007057-V1-2_S265_R1C3_9D_S77


title: 12022022_W73007140-V1-2_S867_R1C3_11L_S259


title: 12022022_H2O-RT-V1-2_S86_R2C2_23A_S386


title: 12022022_W73006999-V1-2_S397_R1C3_3F_S116


title: 12022022_W73007093-V1-2_S1161_R1C3_9P_S348


title: 12022022_W73006968-V1-2_S1002_R1C3_7N_S300


title: 12022022_NoRT-HEK-200ng-SM4-2p66pg-V1-2_S237_R1C3_23C_S68

description:
synthetic control
run38_R1BC_count_table.txt
run38_R2BC_count_table.txt
run38_count_table.txt
run38_BC_pair_analysis_filenames.txt


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S834_R1C3_23K_S248


title: 12022022_W73006940-V1-2_S855_R1C3_7L_S255


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S686_R1C3_23I_S203


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S538_R1C3_23G_S158


title: 12022022_W73006802-V1-2_S1140_R1C3_2P_S341


title: 12022022_W73006696-V1-2_S1146_R1C3_4P_S343


title: 12022022_H2O-RT-V1-2_S85_R1C3_23A_S23


title: 12022022_HEK-200ng-SM4-2p66pg-V1-2_S388_R1C3_23E_S113


title: 12022022_H2O-multi-V1-2_S981_R1C3_23M_S293


title: 12022022_W73006212-V1-2_S277_R1C3_13D_S81


title: 12022022_W73006208-V1-2_S125_R1C3_13B_S36


title: 12132022_HEK-200ng-SM4-2p66pg-V1-2_S387_R2C2_23E_S239

description:
synthetic control
run31_R1BC_count_table.txt
run31_R2BC_count_table.txt
run31_count_table.txt
run31_BC_pair_analysis_filenames.txt


title: 12132022_NoRT-HEK-200ng-SM4-2p66pg-V1-2_S236_R2C2_23C_S195


title: 12022022_W73006205-V1-2_S427_R1C3_13F_S126


title: 12132022_H2O-multi-V1-2_S537_R2C2_23G_S283


title: 12132022_H2O-RT-V1-2_S84_R2C2_23A_S151


title: 12132022_NoRT-HEK-200ng-SM4-2p66pg-V1-2_S235_R1C3_23C_S34

description:
synthetic control
run27_R1BC_count_table.txt
run27_R2BC_count_table.txt
run27_count_table.txt
run27_BC_pair_analysis_filenames.txt


title: 12022022_H2O-multi-V1-2_S982_R2C2_23M_S658


title: 12022022_W73006122-V1-2_S1137_R1C3_1P_S340


title: 12022022_W73006118-V1-2_S979_R1C3_22M_S292


title: 12132022_HEK-200ng-SM4-2p66pg-V1-2_S386_R1C3_23E_S50


title: 12022022_W73006065-V1-2_S568_R1C3_10H_S168


title: 12132022_H2O-RT-V1-2_S83_R1C3_23A_S17


title: 12022022_W73006101-V1-2_S60_R1C3_16A_S16


title: 12022022_W73006014-V1-2_S384_R1C3_22E_S112


title: 12132022_H2O-multi-V1-2_S536_R1C3_23G_S66


title: 12022022_W73005802-V1-2_S574_R1C3_12H_S170


title: synthetic control group 1 (part2)


title: 12022022_W73005748-V1-2_S81_R1C3_22A_S22


title: synthetic control group 5


title: 12022022_W73005415-V1-2_S418_R1C3_10F_S123


title: 12022022_W73005373-V1-2_S1167_R1C3_11P_S350


title: 12022022_W73005164-V1-2_S233_R1C3_22C_S67


title: 12022022_W73005230-V1-2_S562_R1C3_8H_S166


title: ILC2p_1

city: Cambridge

first: Ana

last: Ferreira

address: Francis Crick Avenue, Cambridge Biomedical Campus

country: United Kingdom

institute: MRC - Laboratory of Molecular Biology

description:
SLX-9191.L2DRBC01.C5KNEANXX.s_4.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx

data_processing:
Samples were sequenced using an Illumina Hiseq4000 running a single-read 50bp protocol
Sequence data were trimmed to remove adaptors and sequences with a quality score below 30 using Trim Galore (v0.50, Babraham Bioinformatics)
sequences were aligned to the mouse genome (GRCm38) using STAR (v2.6.0a, Spliced Transcripts Alignment to a Reference, Alexander Dobin)
differential expression calculated using DEseq2 (v1.18.1)
Supplementary files format and content: GRCm38
Supplementary files format and content: DEseq2 output file

source_name: Bone marrow

extract_protocol: and bar-coded using Ovation Ultralow Library Systems (Nugen)

treatment_protocol: Mice were challenged with IL-33 (Biolegend) (0.25 µg in 40 µl PBS) or PBS (40 µl) intranasally on three consecutive days. Lungs were harvested 24 h after the final dose.ILC2s and pDCs were purified from the lung of IL-33 or PBS intranasally treated mice.

value: Bone marrow

value: WT

value: unchallenged


title: synthetic control group 1

value: preclinical


title: ILC2p_2

description:
SLX-9192.L2DRBC09.C5KNEANXX.s_7.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2 FAT_3

description:
SLX-9195.L2DRBC08.C6DWHANXX.s_3.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx

source_name: Fat

value: Fat


title: 12022022_W73006136-V1-2_S837_R1C3_1L_S249


title: ILC2 FAT_2

description:
SLX-9195.L2DRBC07.C6DWHANXX.s_3.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W73005060-V1-2_S993_R1C3_4N_S297


title: 12022022_W73005205-V1-2_S445_R1C3_19F_S132


title: 12022022_W73005034-V1-2_S250_R1C3_4D_S72


title: 12022022_W73005157-V1-2_S1152_R1C3_6P_S345


title: 12022022_W73005130-V1-2_S595_R1C3_19H_S177


title: ILC2 Lung_3

description:
SLX-9190.L2DRBC01.C5E9JANXX.s_4.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx

source_name: Lung

value: Lung


title: 12022022_W73005033-V1-2_S262_R1C3_8D_S76


title: ILC2 FAT_1

description:
SLX-9194.L2DRBC08.C6DWHANXX.s_2.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W73005015-V1-2_S858_R1C3_8L_S256


title: ILC2 LP_3

description:
SLX-9190.L2DRBC07.C5E9JANXX.s_4.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx

source_name: Lamina propria

value: Lamina propria


title: ILC2 LP_2

description:
SLX-9190.L2DRBC05.C5E9JANXX.s_4.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W73005082-V1-2_S406_R1C3_6F_S119

description:
positive sample
run38_R1BC_count_table.txt
run38_R2BC_count_table.txt
run38_count_table.txt
run38_BC_pair_analysis_filenames.txt


title: ILC2 LP_1

description:
SLX-9190.L2DRBC03.C5E9JANXX.s_4.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2 LN_2

description:
SLX-9189.L2DRBC06.C5E9JANXX.s_1.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx

source_name: Lymph node

value: Lymph node


title: 12022022_W72904754-V1-2_S829_R1C3_21K_S246

value: human nasopharyngeal swab


title: 12022022_W73002972-V1-2_S689_R1C3_1J_S204

value: BC


title: 12022022_W73004299-V1-2_S984_R1C3_1N_S294


title: 12022022_W73004929-V1-2_S743_R1C3_19J_S222


title: 12022022_W73005058-V1-2_S840_R1C3_2L_S250


title: synthetic control group 2


title: 12022022_W72904634-V1-2_S171_R1C3_5C_S50


title: ILC2 Lung_1

description:
SLX-9189.L2DRBC05.C5E9JANXX.s_1.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W73005019-V1-2_S999_R1C3_6N_S299


title: ILC2 LN_3

description:
SLX-9189.L2DRBC08.C5E9JANXX.s_1.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2 LN_1

description:
SLX-9189.L2DRBC04.C5E9JANXX.s_1.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2_PBS_1

description:
SLX-19699.L2V23DRB01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx

value: PBS


title: ILC2_PBS_5

description:
SLX-19699.L2V23DRF01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2_PBS_4

description:
SLX-19699.L2V23DRE01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: pDC_IL33_4

description:
SLX-19699.L2V23DRA01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx

value: pDC


title: ILC2_PBS_3

description:
SLX-19699.L2V23DRD01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: ILC2_PBS_2

description:
SLX-19699.L2V23DRC01.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W72904471-V1-2_S50_R1C3_13A_S13


title: 12022022_W72903930-V1-2_S787_R1C3_9K_S234


title: ILC2 Lung_2

description:
SLX-9189.L2DRBC07.C5E9JANXX.s_1.r
RNAseq2_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W72904418-V1-2_S202_R1C3_13C_S58


title: 12022022_W72904431-V1-2_S1088_R1C3_11O_S326


title: pDC_PBS_3

description:
SLX-19699.L2V23DRB04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W72902341-V1-2_S496_R1C3_11G_S146


title: 12022022_W72904393-V1-2_S976_R1C3_21M_S291


title: pDC_IL33_3

description:
SLX-19699.L2V23DRH04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W72904094-V1-2_S681_R1C3_21I_S201


title: pDC_PBS_4

description:
SLX-19699.L2V23DRC04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: pDC_IL33_1

description:
SLX-19699.L2V23DRE04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: pDC_IL33_2

description:
SLX-19699.L2V23DRF04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: pDC_PBS_1

description:
SLX-19699.L2V23DRH03.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: snRNAseq HEART DMD 12months

city: Creteil

first: Valentina

last: Taglietti

address: 8 rue General Sarrail

country: France

institute: Univ Paris-Est Créteil, INSERM, U955 IMRB

description:
H_DMD_12M
snRNAseq

library_source: transcriptomic single cell

data_processing:
Sequence analysis with Cell Ranger Single Cell Software Suite 3.0.2 by 10X Genomics
Raw base call files were demultiplexed with the cellranger mkfastq pipeline into library specific FASTQ files
The FASTQ files for each library were then processed independently with the cellranger count pipeline.
Assembly: rn6
Supplementary files format and content: For each sample, set of 3 files in format 10X (list of cell barcodes, list of genes and expression matrix (raw counts))

organism: Rattus norvegicus

source_name: Heart, muscle

extract_protocol:
heart nuclei extractionn - 10x Genomics Chromium Next GEM Single Cell 3' V3.1
Chromium Next GEM Single Cell 3' Library kit v3.1

value: DMD

tag: age

value: 12 months

tag: cell types

value: Total nuclei from heart


title: 12022022_W72903927-V1-2_S381_R1C3_21E_S111

description:
positive sample
run38_R1BC_count_table.txt
run38_R2BC_count_table.txt
run38_count_table.txt
run38_BC_pair_analysis_filenames.txt


title: pDC_PBS_2

description:
SLX-19699.L2V23DRA04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: 12022022_W72903776-V1-2_S934_R1C3_9M_S279


title: pDC_PBS_5

description:
SLX-19699.L2V23DRD04.HJ53MBBXY.s_8.r
RNAseq_Mayuri_Gogoi_Normalized_counts.xlsx


title: snRNAseq HEART BMD 12months

description:
H_BMD_12M
snRNAseq

value: BMD


title: 12022022_W72902322-V1-2_S43_R1C3_11A_S11


title: 12022022_W72902160-V1-2_S195_R1C3_11C_S56


title: 12022022_W72902212-V1-2_S1123_R1C3_21O_S336


title: 12022022_W72902306-V1-2_S794_R1C3_11K_S236


title: LOPD_SUNI_PD_14x04xx_X007_S11_L069_B1_T1_P013.pe.q10.sort.rmdup.bam

city: Stanford

first: Eloise

last: Berson

address: 291 Campus Drive

country: USA

institute: Stanford University

description: Bulk ATAC-seq PD Sustantia Nigra

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

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

value: bulk


title: 12022022_W72902161-V1-2_S646_R1C3_11I_S191


title: snRNAseq HEART WT 12months

description:
H_WT_12M
snRNAseq

value: wild-type


title: 12022022_W72901917-V1-2_S1081_R1C3_9O_S324


title: 12022022_W72902029-V1-2_S531_R1C3_21G_S156


title: LOPD_SUNI_PD_13x44xx_X002_S10_L044_B1_T2_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_13x44xx_X002_S10_L043_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72901676-V1-2_S473_R1C3_5G_S140


title: 12022022_W72901644-V1-2_S323_R1C3_5E_S95


title: 12022022_W72902340-V1-2_S941_R1C3_11M_S281


title: LOPD_SUNI_PD_13x17xx_X025_S11_L020_B1_T2_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_13x05xx_X023_S09_L066_B1_T2_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_13x11xx_X024_S10_L092_B1_T2_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72900625-V1-2_S64_R1C3_17A_S17


title: 12022022_W72900631-V1-2_S639_R1C3_9I_S189


title: 12022022_W72900581-V1-2_S187_R1C3_9C_S54


title: LOPD_SUNI_PD_12x42xx_X013_S08_L039_B1_T1_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_12x42xx_X013_S08_L040_B1_T2_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72900572-V1-2_S489_R1C3_9G_S144


title: 12022022_W72900530-V1-2_S216_R1C3_17C_S62


title: LOPD_SUNI_PD_12x22xx_X021_S07_L014_B1_T2_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_12x22xx_X021_S07_L013_B1_T1_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72900517-V1-2_S339_R1C3_9E_S99


title: LOPD_SUNI_PD_12x04xx_X011_S07_L062_B1_T2_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_12x04xx_X011_S07_L061_B1_T1_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72804326-V1-2_S822_R1C3_19K_S244


title: LOPD_SUNI_PD_11x70xx_X020_S02_L051_B1_T1_P037.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72900292-V1-2_S1102_R1C3_15O_S330


title: 12022022_W72803653-V1-2_S457_R1C3_1G_S136


title: 12022022_W72803652-V1-2_S755_R1C3_1K_S226


title: LOPD_SUNI_PD_10x83xx_X009_S01_L002_B1_T2_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_13x17xx_X025_S11_L019_B1_T1_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72900795-V1-2_S771_R1C3_5K_S230


title: 12022022_W72803648-V1-2_S910_R1C3_3M_S273


title: LOPD_SUNI_PD_10x83xx_X009_S01_L001_B1_T1_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_10x76xx_X022_S07_L038_B1_T2_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_SUNI_PD_10x28xx_X012_S04_L008_B1_T2_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72803642-V1-2_S902_R1C3_1M_S271


title: 12022022_W72803650-V1-2_S615_R1C3_3I_S183


title: LOPD_SUNI_PD_13x11xx_X024_S10_L091_B1_T1_P045.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72803636-V1-2_S155_R1C3_1C_S46


title: 12022022_W72900445-V1-2_S955_R1C3_15M_S285


title: 12022022_W72803641-V1-2_S465_R1C3_3G_S138


title: 12022022_W72900617-V1-2_S808_R1C3_15K_S240


title: 12022022_W72803628-V1-2_S35_R1C3_9A_S9


title: LOPD_SUNI_PD_10x28xx_X012_S04_L007_B1_T1_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_MDFG_PD_13x44xx_X018_S02_L004_B1_T2_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_13x44xx_X018_S02_L003_B1_T1_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_14x04xx_X017_S05_L009_B1_T1_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_13x17xx_X013_S11_L046_B1_T2_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_SUNI_PD_11x70xx_X020_S02_L052_B1_T2_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: 12022022_W72803625-V1-2_S763_R1C3_3K_S228


title: LOPD_MDFG_PD_13x17xx_X013_S11_L045_B1_T1_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803619-V1-2_S926_R1C3_7M_S277


title: 12022022_W72803617-V1-2_S1073_R1C3_7O_S322


title: LOPD_MDFG_PD_13x11xx_X006_S06_L036_B1_T2_P013.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803548-V1-2_S19_R1C3_5A_S5


title: 12022022_W72803613-V1-2_S607_R1C3_1I_S181


title: LOPD_MDFG_PD_13x05xx_X020_S08_L064_B1_T2_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803528-V1-2_S623_R1C3_5I_S185


title: LOPD_SUNI_PD_10x76xx_X022_S07_L037_B1_T1_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Sustantia Nigra


title: LOPD_MDFG_PD_13x05xx_X020_S08_L063_B1_T1_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_12x42xx_X028_S02_L004_B1_T2_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803522-V1-2_S1057_R1C3_3O_S318


title: 12022022_W72803632-V1-2_S307_R1C3_1E_S91


title: 12022022_W72803483-V1-2_S163_R1C3_3C_S48


title: LOPD_MDFG_PD_12x42xx_X028_S02_L003_B1_T1_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803463-V1-2_S331_R1C3_7E_S97


title: LOPD_MDFG_PD_12x29xx_X002_S08_L040_B1_T2_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803457-V1-2_S1049_R1C3_1O_S316


title: 12022022_W72803270-V1-2_S11_R1C3_3A_S3


title: LOPD_MDFG_PD_12x22xx_X001_S06_L012_B1_T2_P003.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_12x04xx_X003_S08_L016_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_12x22xx_X001_S06_L011_B1_T1_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_12x29xx_X002_S08_L039_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_13x11xx_X006_S06_L035_B1_T1_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802843-V1-2_S374_R1C3_19E_S109


title: 12022022_W72803101-V1-2_S779_R1C3_7K_S232


title: LOPD_MDFG_PD_12x04xx_X003_S08_L015_B1_T1_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_11x70xx_X022_S04_L032_B1_T2_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_11x70xx_X022_S04_L031_B1_T1_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: LOPD_MDFG_PD_10x83xx_X015_S12_L048_B1_T2_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802840-V1-2_S524_R1C3_19G_S154


title: 12022022_W72802832-V1-2_S969_R1C3_19M_S289


title: LOPD_MDFG_PD_10x83xx_X015_S12_L047_B1_T1_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802811-V1-2_S510_R1C3_15G_S150


title: LOPD_MDFG_PD_10x76xx_X011_S03_L054_B1_T2_P020.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802829-V1-2_S674_R1C3_19I_S199


title: LOPD_MDFG_PD_10x30xx_X030_S12_L072_B1_T2_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802803-V1-2_S517_R1C3_17G_S152


title: LOPD_MDFG_PD_10x76xx_X011_S03_L053_B1_T1_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802804-V1-2_S367_R1C3_17E_S107


title: 12022022_W72802796-V1-2_S346_R1C3_11E_S101


title: LOPD_MDFG_PD_10x28xx_X010_S12_L047_B1_T1_P017.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72803103-V1-2_S481_R1C3_7G_S142


title: 12022022_W72803092-V1-2_S631_R1C3_7I_S187


title: 12022022_W72802790-V1-2_S209_R1C3_15C_S60


title: LOPD_PTMN_PD_14x04xx_X024_S12_L095_B1_T1_P043.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802789-V1-2_S57_R1C3_15A_S15


title: LOPD_PTMN_PD_13x44xx_X004_S04_L031_B1_T1_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_13x44xx_X004_S04_L032_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_13x17xx_X018_S01_L002_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802765-V1-2_S660_R1C3_15I_S195


title: 12022022_W72802755-V1-2_S3_R1C3_1A_S1


title: LOPD_PTMN_PD_13x17xx_X018_S01_L001_B1_T1_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802742-V1-2_S653_R1C3_13I_S193


title: LOPD_PTMN_PD_13x05xx_X008_S10_L092_B1_T2_P011.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_13x05xx_X008_S10_L091_B1_T1_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_12x42xx_X014_S09_L018_B1_T2_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_13x11xx_X021_S05_L010_B1_T2_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802731-V1-2_S1095_R1C3_13O_S328


title: LOPD_PTMN_PD_12x42xx_X014_S09_L017_B1_T1_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_MDFG_PD_10x28xx_X010_S12_L048_B1_T2_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle frontal Gyri


title: 12022022_W72802727-V1-2_S948_R1C3_13M_S283


title: 12022022_W72802587-V1-2_S315_R1C3_3E_S93


title: 12022022_W72802795-V1-2_S353_R1C3_13E_S103


title: LOPD_PTMN_PD_12x29xx_X003_S06_L011_B1_T1_P004.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802539-V1-2_S1065_R1C3_5O_S320


title: LOPD_PTMN_PD_12x22xx_X005_S08_L016_B1_T2_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802537-V1-2_S27_R1C3_7A_S7


title: LOPD_PTMN_PD_12x22xx_X005_S08_L015_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802787-V1-2_S360_R1C3_15E_S105


title: 12022022_W72802534-V1-2_S918_R1C3_5M_S275


title: LOPD_PTMN_PD_12x29xx_X003_S06_L012_B1_T2_P008.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_12x04xx_X022_S08_L040_B1_T2_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802532-V1-2_S179_R1C3_7C_S52


title: 12022022_W72802371-V1-2_S78_R1C3_21A_S21


title: 12022022_W72802745-V1-2_S503_R1C3_13G_S148


title: 12022022_W72802372-V1-2_S1116_R1C3_19O_S334


title: LOPD_PTMN_PD_11x70xx_X013_S06_L035_B1_T1_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_12x04xx_X022_S08_L039_B1_T1_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802368-V1-2_S815_R1C3_17K_S242


title: LOPD_PTMN_PD_11x70xx_X013_S06_L036_B1_T2_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802734-V1-2_S801_R1C3_13K_S238


title: 12022022_W72802366-V1-2_S667_R1C3_17I_S197


title: 12022022_W72802352-V1-2_S71_R1C3_19A_S19


title: LOPD_PTMN_PD_10x76xx_X029_S11_L046_B1_T2_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802351-V1-2_S962_R1C3_17M_S287


title: LOPD_PTMN_PD_10x76xx_X029_S11_L045_B1_T1_P057.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_PTMN_PD_10x30xx_X025_S08_L013_B1_T1_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72802347-V1-2_S1109_R1C3_17O_S332


title: LOPD_PTMN_PD_10x30xx_X025_S08_L014_B1_T2_P049.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W72703183-V1-2_S230_R1C3_21C_S66


title: 12022022_W73109769-V1-2_S1134_R1C3_24O_S339

description:
negative sample
run38_R1BC_count_table.txt
run38_R2BC_count_table.txt
run38_count_table.txt
run38_BC_pair_analysis_filenames.txt


title: 12022022_W73109766-V1-2_S1204_R1C3_24P_S363


title: LOPD_PTMN_PD_10x28xx_X028_S05_L009_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: 12022022_W73109757-V1-2_S1201_R1C3_23P_S362


title: LOPD_SMTG_PD_14x04xx_X028_S12_L023_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12022022_W72905871-V1-2_S1130_R1C3_23O_S338


title: LOPD_SMTG_PD_14x04xx_X028_S12_L024_B1_T2_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62204215-V1-2_S100_R2C2_5B_S156

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


title: LOPD_SMTG_PD_13x44xx_X023_S06_L060_B1_T2_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62204092-V1-2_S402_R2C2_5F_S244


title: LOPD_PTMN_PD_10x83xx_X009_S09_L018_B1_T2_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_SMTG_PD_13x11xx_X001_S07_L014_B1_T2_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62204053-V1-2_S694_R2C2_3J_S329


title: LOPD_SMTG_PD_13x11xx_X001_S07_L013_B1_T1_P006.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62204054-V1-2_S989_R2C2_3N_S414


title: LOPD_SMTG_PD_13x05xx_X010_S01_L026_B1_T2_P016.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12022022_W72802355-V1-2_S223_R1C3_19C_S64


title: 12132022_W62204117-V1-2_S842_R2C2_3L_S372


title: 12132022_W62203742-V1-2_S88_R2C2_1B_S152


title: LOPD_SMTG_PD_13x05xx_X010_S01_L025_B1_T1_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_SMTG_PD_13x44xx_X023_S06_L059_B1_T1_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62203755-V1-2_S1136_R2C2_1P_S456


title: LOPD_PTMN_PD_10x83xx_X009_S09_L017_B1_T1_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_SMTG_PD_12x42xx_X013_S10_L044_B1_T2_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62203610-V1-2_S1142_R2C2_3P_S458


title: LOPD_SMTG_PD_12x42xx_X013_S10_L043_B1_T1_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_SMTG_PD_12x22xx_X012_S10_L020_B1_T2_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62203518-V1-2_S246_R2C2_3D_S198


title: 12132022_W62203549-V1-2_S252_R2C2_5D_S200


title: LOPD_PTMN_PD_10x28xx_X028_S05_L010_B1_T2_P056.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Putamen


title: LOPD_SMTG_PD_12x22xx_X012_S10_L019_B1_T1_P022.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_SMTG_PD_11x70xx_X029_S01_L026_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_w62202943-V1-2_S845_R2C2_4L_S373


title: LOPD_SMTG_PD_10x83xx_X025_S07_L012_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62202738-V1-2_S706_R2C2_7J_S333


title: 12132022_W62202315-V1-2_S558_R2C2_7H_S290


title: LOPD_SMTG_PD_11x70xx_X029_S01_L025_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62202113-V1-2_S983_R2C2_1N_S412


title: LOPD_SMTG_PD_10x83xx_X025_S07_L011_B1_T1_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_SMTG_PD_10x76xx_X026_S11_L044_B1_T2_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62202101-V1-2_S836_R2C2_1L_S370


title: 12132022_W62201952-V1-2_S408_R2C2_7F_S246


title: LOPD_SMTG_PD_10x76xx_X026_S11_L043_B1_T1_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62201658-V1-2_S688_R2C2_1J_S327


title: LOPD_SMTG_PD_10x30xx_X014_S06_L011_B1_T1_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_w62201501-V1-2_S992_R2C2_4N_S415


title: LOPD_SMTG_PD_10x28xx_X015_S02_L028_B1_T2_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62201345-V1-2_S94_R2C2_3B_S154


title: LOPD_SMTG_PD_10x28xx_X015_S02_L027_B1_T1_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_SMTG_PD_01x38xx_X009_S12_L024_B1_T2_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: 12132022_W62201339-V1-2_S540_R2C2_1H_S284


title: LOPD_CAUD_PD_14x04xx_X016_S09_L066_B1_T2_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_W62201336-V1-2_S240_R2C2_1D_S196


title: 12132022_W62201299-V1-2_S390_R2C2_1F_S240


title: LOPD_CAUD_PD_14x04xx_X016_S09_L065_B1_T1_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_13x44xx_X019_S04_L032_B1_T2_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_W62201153-V1-2_S258_R2C2_7D_S202


title: 12132022_W62200766-V1-2_S700_R2C2_5J_S331


title: LOPD_CAUD_PD_13x44xx_X019_S04_L031_B1_T1_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62203172-V1-2_S549_R2C2_4H_S287


title: 12132022_W62200764-V1-2_S552_R2C2_5H_S288


title: LOPD_CAUD_PD_13x17xx_X004_S05_L033_B1_T1_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_13x17xx_X004_S05_L034_B1_T2_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200581-V1-2_S543_R2C2_2H_S285


title: LOPD_SMTG_PD_10x30xx_X014_S06_L012_B1_T2_P026.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Middle Temporal Gyri


title: LOPD_CAUD_PD_13x11xx_X002_S07_L038_B1_T2_P007.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_13x11xx_X002_S07_L037_B1_T1_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_13x05xx_X015_S11_L046_B1_T2_P027.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200284-V1-2_S1019_R2C2_13N_S424


title: LOPD_CAUD_PD_13x05xx_X015_S11_L045_B1_T1_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200281-V1-2_S724_R2C2_13J_S339


title: LOPD_CAUD_PD_12x42xx_X012_S07_L014_B1_T2_P023.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200241-V1-2_S273_R2C2_12D_S207


title: 12132022_w62103633-V1-2_S130_R2C2_15B_S166


title: 12132022_w62103630-V1-2_S282_R2C2_15D_S210


title: LOPD_CAUD_PD_12x29xx_X003_S07_L013_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_12x42xx_X012_S07_L013_B1_T1_P021.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200216-V1-2_S115_R2C2_10B_S161


title: LOPD_CAUD_PD_12x22xx_X018_S09_L017_B1_T1_P032.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62103624-V1-2_S300_R2C2_21D_S216


title: 12132022_w62103621-V1-2_S600_R2C2_21H_S304


title: 12132022_w62103619-V1-2_S1163_R2C2_10P_S465


title: LOPD_CAUD_PD_11x70xx_X010_S04_L032_B1_T2_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_11x70xx_X010_S04_L031_B1_T1_P019.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_12x04xx_X023_S11_L069_B1_T1_P042.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62200349-V1-2_S121_R2C2_12B_S163


title: synthetic control group 4

value: synthetic control


title: LOPD_CAUD_PD_10x83xx_X007_S02_L052_B1_T2_P010.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62103605-V1-2_S423_R2C2_12F_S251


title: synthetic control group 3


title: 12132022_w62200335-V1-2_S1010_R2C2_10N_S421


title: 12132022_w62103613-V1-2_S417_R2C2_10F_S249


title: 12132022_w62103594-V1-2_S432_R2C2_15F_S254


title: LOPD_CAUD_PD_10x76xx_X001_S05_L010_B1_T2_P005.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: Rat primary cortical neurons, LV-ICD, Replicate 3

city: Basel

first: Tiago

middle: M

last: Rodrigues

address: Mittlere Strasse 91

country: Switzerland

institute: Institute of Molecular and Clinical Ophthalmology Basel

description: 2 x75 paired-end sequence reads

data_processing:
Read quality was checked for each sample using FastQC (v0.11.9).
Sequenced reads were trimmed for adapter sequences with BBDuk (BBMap, v39.06).
Trimmed reads were mapped with the STAR aligner (v2.7.9) using default settings, against a reference generated from the Rattus norvegicus genome (mRatBN7.2) and annotation (mRatBN7.2.111) and modified to include the transgenes in the lentiviruses used for treatments.
Quantification of aligned reads was done by the STAR aligner, while mapping, using the -quantMode GeneCounts option, to generate gene-level raw counts for each sample.
Assembly: mRatBN7
Supplementary files format and content: For each sample, one tab-delimited text file is provided with raw counts.

source_name: primary cortical neurons

growth_protocol: Primary cortical neurons were isolated from embryos (E17-E18) of pregnant Sprague-Dawley rats (Rattus norvegicus) and cultured in in Neurobasal medium supplemented with 0.5 mM L-glutamine, 25 mM glutamic acid, 2% B-27 supplement and 25 U/mL penicillin/streptomycin.

extract_protocol:
RNA was harvested at DIV10 using the NZY Total RNA Isolation Kit (NYZtech, #MB13402). 1 µg of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina, #RS-122-2001), following the manufacturer's protocols.

treatment_protocol: Cells were transduced at DIV3 with lentiviruses (MOI = 1), either LV-CaMKII-EGFP (LV-GFP) or LV-CaMKII-TrkB-ICD-IRES-ZsGreen1 (LV-ICD), to induce the expression of (1) EGFP or (2) TrkB-ICD and ZsGreen1, respectively. Additionally, we prepared untransduced cells from the same culture batches.

value: primary cortical neurons

tag: cell source

value: WT

value: Transduction with LV-ICD


title: Rat primary cortical neurons, LV-GFP, Replicate 2

description: 2 x75 paired-end sequence reads

value: Transduction with LV-GFP


title: Rat primary cortical neurons, LV-ICD, Replicate 1

description: 2 x75 paired-end sequence reads


title: 12132022_W62103560-V1-2_S396_R2C2_3F_S242


title: 12132022_w62103628-V1-2_S267_R2C2_10D_S205


title: Rat primary cortical neurons, LV-ICD, Replicate 2

description: 2 x75 paired-end sequence reads


title: Rat primary cortical neurons, LV-GFP, Replicate 3

description: 2 x75 paired-end sequence reads


title: LOPD_CAUD_PD_10x76xx_X001_S05_L009_B1_T1_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_10x83xx_X007_S02_L051_B1_T1_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_12x22xx_X018_S09_L018_B1_T2_P033.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: LOPD_CAUD_PD_10x30xx_X028_S07_L014_B1_T2_P053.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: Rat primary cortical neurons, Untransduced, Replicate 3

description: 2 x75 paired-end sequence reads


title: Rat primary cortical neurons, LV-GFP, Replicate 1

description: 2 x75 paired-end sequence reads


title: LOPD_CAUD_PD_10x30xx_X028_S07_L013_B1_T1_P052.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62103554-V1-2_S426_R2C2_13F_S252


title: 12132022_w62103551-V1-2_S582_R2C2_15H_S298


title: 12132022_w62103542-V1-2_S1172_R2C2_13P_S468


title: WT-biol rep3

city: Iowa city

first: Craig

middle: D

last: Ellermeier

state: Iowa

address: 431 Newton Road, Room 200 E

department: Department of Microbiology and Immunology

institute: University of Iowa

data_processing:
Demultiplexing and adapter trimming was performed with bcl-convert
fastp was then used to further trim and filter the files
Read alignments were performed using Bowtie2
All subsequent analysis was performed in Excel.
Assembly: FN545816
Supplementary files format and content: .xlsx file contains Base mean reads, log2 fold change, and adjusted P-value

organism: Clostridioides difficile

source_name: Bacterial

growth_protocol: All cultures were grown in tryptone-yeast extract broth at 37C under anaerobic conditions.

extract_protocol:
Cultures were fixed by mixing with an equal volume of cells with ice-cold 1:1 ethanol:acetone. RNA was extracted with the Qiagen RNeasy kit. All samples had a RIN of 8.0 or higher (Agilent Bioanalyzer).
Illumina Stranded RNA library preparation paired with RiboZero Plus  was prepared per manufacturer's specifications.

treatment_protocol: Strains were subcultured 1:50 and grwon to an OD600=0.6 when they were then harvested.

value: Bacterial

value: Wildtype


title: Ldt1-3 mutant-biol repl3


title: Rat primary cortical neurons, Untransduced, Replicate 1

description: 2 x75 paired-end sequence reads


title: Ldt1-3 mutant-biol repl2


title: LOPD_CAUD_PD_10x28xx_X024_S11_L094_B1_T2_P044.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: WT-biol rep2


title: 12132022_w62103523-V1-2_S576_R2C2_13H_S296

value: human nasopharyngeal swab

value: BC


title: Ldt1-3 mutant-biol repl1


title: LOPD_CAUD_PD_10x28xx_X024_S11_L093_B1_T1_P045.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Caudate


title: 12132022_w62103491-V1-2_S697_R2C2_4J_S330


title: WT-biol rep1


title: LOPD_HIPP_PD_14x04xx_X022_S03_L030_B1_T2_P041.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: 12132022_w62103302-V1-2_S986_R2C2_2N_S413


title: 12132022_w62103293-V1-2_S748_R2C2_21J_S347


title: Rat primary cortical neurons, Untransduced, Replicate 2

description: 2 x75 paired-end sequence reads


title: LOPD_HIPP_PD_14x04xx_X022_S03_L029_B1_T1_P045.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: Ac, N , RNA-seq-N1

city: Shenzhen

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

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

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: Ac, m1A-seq-TGIRT-input-2

data_processing:
The raw sequencing reads obtained from m1A-seq-TGIRT experiments were first processed for quality control using Trim Galore with the parameters ‘-q 25 -e 0.1 --stringency 3’ to remove adapter sequences and low-quality reads.
The trimmed reads were then aligned to the reference genome of A. carterae (Ac.genome.v1.fa) using STAR with the parameters ‘--outFilterMismatchNmax 3 --outSAMmultNmax 1’, allowing a maximum of three mismatches per read and ensuring that only the best alignment per read was retained.
Following alignment, ‘samtools mpileup’ was used with the parameters ‘-d 100000 -a’ to generate a pileup file that provided detailed information about the coverage and mismatch count for each base in the reference genome. From this file, the coverage and mismatch data for each base located within exon regions were extracted.
For each adenosine (A) site within annotated transcripts, the data were filtered to retain only those sites where the coverage exceeded 10 reads per sample, and there were at least 2 mismatches with a mismatch rate greater than 10%. These criteria identified potential m1A modification sites, which were pooled together as candidates for further analysis.
Assembly: Acart.genome.v1.fa.gz
Supplementary files format and content: TGIRT-Seq_defined_m1A_sites.bed
Library strategy: MeRIP-seq

molecule: polyA RNA

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. Poly(A)+ RNA of A. carterae was isolated using VAHTS mRNA Capture Beads (Vazyme Biotech, Nanjing, China), fragmented at 70 °C for 10 minutes using RNA fragmentation reagent (Invitrogen) in a 10 µL reaction mixture and purified with the RNA Clean & Concentrator-5 kit (Zymo Research).
For m1A-seq-TGIRT, 25 µL of prewashed Protein A/G Dynabeads were incubated with 3 µL of anti-m1A antibody (MBL #D345-3) at 4 °C for two hours. Subsequently, 500 ng of fragmented mRNA was used for immunoprecipitation, with 50 ng of purified mRNA taken as input. After digestion with Proteinase K, the RNA was purified using RNA Extraction Reagent (Shanghai Acmec Biochemical Co., Ltd, China) and then subjected to library construction. Briefly, the purified mRNA was treated with Antarctic Phosphatase (NEB) and T4 PNK (NEB) at 37 °C for 30 minutes, followed by purification using the Oligo Clean & Concentrator kit (Zymo Research). The dephosphorylated RNA was then ligated to the 3'-RNA adaptor (/5'Phosphate/AGAUCGGAAGAGCGUCGUG/ddC) using T4 RNA Ligase I (NEB) at 23°C for two hours, purified by Oligo Clean & Concentrator again, and reverse transcribed using TGIRT-III (Haigne, China) with the RT primer (5'-ACACGACGCTCTTCCGA-3') in RT reaction buffer (50 mM Tris–HCl pH 8.3, 75 mM KCl, and 3 mM MgCl2) at 57 °C for two hours. The reaction was terminated with 25 mM EDTA and RNA was degraded with 150 mM NaOH, heated to 70 °C for 12 minutes, and purified with Oligo Clean & Concentrator kit. The 5'-DNA adaptor (/5'Phosphate/AGATCGGAAGAGCACACGTCTG/ddC) was ligated using T4 RNA ligase I (NEB) at 23 °C overnight. The single-stranded cDNA was then amplified by PCR using specific primers (5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3' and 5'-CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3', NNNNNN denotes the 6-bp barcode sequence), and the product was purified with AMPure XP beads (0.9×). Both input and IP samples were sequenced by GenePlus (Shenzhen, China) on DNBSEQ-T7 platform with paired-end 150 bp mode.

tag: rip antibody

value: none (input)

value: normal


title: Ac, m1A-seq-TGIRT-IP-2

tag: tissue

value: anti-m1A antibody (MBL #D345-3)


title: Ac, m1A-seq-TGIRT-input-1


title: LOPD_HIPP_PD_13x11xx_X017_S10_L019_B1_T1_P029.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus

value: brain


title: Ac, m1A-seq-TGIRT-IP-1


title: 12132022_W62103288-V1-2_S1154_R2C2_7P_S462

tag: bc run_id


title: 12132022_w62103291-V1-2_S1157_R2C2_8P_S463

tag: pipeline version


title: Ac, F2 , RNA-seq-F3


title: Ac, N , RNA-seq-N2


title: LOPD_HIPP_PD_12x42xx_X023_S03_L054_B1_T2_P040.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus

value: bulk


title: 12132022_w62103286-V1-2_S109_R2C2_8B_S159


title: LOPD_HIPP_PD_12x42xx_X023_S03_L053_B1_T1_P039.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: Ac, F2 , RNA-seq-F2


title: 12132022_W62103281-V1-2_S585_R2C2_16H_S299


title: LOPD_HIPP_PD_11x70xx_X012_S11_L021_B1_T1_P025.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: 12132022_w62103278-V1-2_S91_R2C2_2B_S153


title: LOPD_HIPP_PD_10x83xx_X003_S11_L022_B1_T2_P009.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: RNA-seq human CD8+ T  donor2-4-4-20-4h

city: Bethesda

first: Jyothi

last: Padiadpu

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
Sequenced reads were  mapped to the human genome hg38 (GRCh38, Dec. 2013) using Bowtie2 and Tophat2.
Only uniquely mapped reads were retained.
Assembly: hg38
Supplementary files format and content: tab limited file contains read counts in .txt file

source_name: PBMC

extract_protocol:
For RNA-Seq experiments, 5´105 purified human CD8+ T cells were cultured in complete RPMI 1640 medium and stimulated for 4 or 24 hr with 1 µM IL-2 or 0.5 µM (equivalent stoichiometric quantity) Control IC or F10 IC. Total RNA was isolated using Direct-zol RNA Microprep Kit (R2061, ZYMO Research), and RNA-Seq libraries were prepared using 120 ng of total RNA and Kapa mRNA HyperPrep Kit (Kapa Biosystems). Each library was indexed using NEXTflex DNA Barcodes-24 (BIOO Scientific) and amplified by PCR. Amplified libraries between 250-400 bp were recovered using 2% E-Gel pre-cast gels (ThermoFisher), purified with Zymoclean Gel DNA Recovery Kit (Zymo Research), and quantified by Qubit 3 Fluorometer (ThermoFisher).
After quantification by Qubit (Invitrogen), barcoded samples were mixed and sequenced on an Illumina NovaSeq system.

treatment_protocol: Purified human CD8+ T cells were cultured in complete RPMI 1640 medium and stimulated for 4 or 24 hr with 1 µM IL-2 or 0.5 µM (equivalent stoichiometric quantity) Control IC or F10 IC.

value: PBMC

value: CD8 + T cells

value: Healthy donors


title: RNA-seq human CD8+ T  donor2-IL2 -24h


title: RNA-seq human CD8+ T  donor2-F10-24h


title: RNA-seq human CD8+ T  donor2-F10-4h


title: RNA-seq human CD8+ T  donor2-4-4-20-24h


title: Ac, N , RNA-seq-N3


title: LOPD_HIPP_PD_13x05xx_X008_S08_L087_B1_T1_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: RNA-seq human CD8+ T  donor2-IL2 -4h


title: 12132022_w62103277-V1-2_S103_R2C2_6B_S157

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: RNA-seq human CD8+ T  donor2 -Control

value: Control


title: LOPD_HIPP_PD_10x28xx_X025_S05_L010_B1_T2_P046.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: 12132022_W62103274-V1-2_S435_R2C2_16F_S255


title: RNA-seq human CD8+ T  donor1-IL2 -24h


title: RNA-seq human CD8+ T  donor1-4-4-20-24h


title: RNA-seq human CD8+ T  donor1-F10-24h


title: Ac, F2 , RNA-seq-F1


title: RNA-seq human CD8+ T  donor1-4-4-20-4h


title: 12132022_W62103220-V1-2_S1181_R2C2_16P_S471


title: RNA-seq human CD8+ T  donor1 -Control


title: CTRL_SUNI_PD_16x32xx_X007_S12_L071_B1_T1_P014.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: RNA-seq human CD8+ T  donor1-IL2 -4h


title: CTRL_SUNI_PD_16x32xx_X007_S12_L072_B1_T2_P012.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: LOPD_HIPP_PD_10x28xx_X025_S05_L009_B1_T1_P048.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq PD Hippocampus


title: 12132022_W62103271-V1-2_S285_R2C2_16D_S211


title: WaGa-RB1kd dox-induced TA k.d.

city: Heidelberg

first: Jürgen

last: Becker

address: Im Neuenheimer Feld 280

country: Germany

institute: Deutsches Krebsforschungszentrum

data_processing:
Sequenced reads were analyzed using CellRanger 7.1.0.
Assembly: hs1
Supplementary files format and content: tab-delimited text files include gene count matrix and cell meta data.

extract_protocol:
Following infection of LoKe cells a pure transduced population was selected by fluorescence activated cell sorting of GFP-positive cells. Single nuclei were stained using trypan blue for visualization, counting and viability assessment using the Countess II Automated Cell Counter and diluted as needed to a final concentration of 700-1200 nuclei/μL in 1x PBS + 0.04% BSA. A minimum of two reproducible counts (defined as standard deviation <25%) were required before droplet preparation, and <5% of input should be viable cells.
RNA library was prepared using 10X Chromium library preparation kit following the manufacturer's protocols.

value: Dox-induced at 24, 48 and 72 h


title: CTRL_SUNI_PD_15x78xx_X026_S01_L024_B1_T2_P051.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: RNA-seq human CD8+ T  donor1-F10-4h


title: 12132022_w62103178-V1-2_S1190_R2C2_19P_S474

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: CTRL_SUNI_PD_15x78xx_X026_S01_L023_B1_T1_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62103258-V1-2_S249_R2C2_4D_S199


title: CTRL_SUNI_PD_09x50xx_X020_S06_L060_B1_T2_P034.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_W62103162-V1-2_S564_R2C2_9H_S292


title: WaGa-RB1kd uninduced control

value: Without dox treatment


title: MDA-MB-468 inerferrred with control siRNA oligo replica 2

city: Milano

first: Stefano

last: Confalonieri

address: Via Adamello 16

department: Department of Experimental Oncology

country: Italy

institute: IEO, European Institute of Oncology IRCCS, Via Ripamonti 435, 20141, Milan, Italy.

data_processing:
Assembly: GCF_000001405.39_GRCh38.p13
The estimation of gene expression abundance was carried out using RSEM (version 1.3.3) with default parameters
Supplementary files format and content: gene_id, expected_count, TPM, FPKM

extract_protocol:
RNA was extracted from MDA-MB-468  cells using the Maxwell RSC miRNA Tissue kit (Promega, AS1460) with the Maxwell RSC Instrument (Promega, AS4500)
RNAseq libraries were prepared with the TruSeq Stranded Total RNA kit from Illumina (San Diego, CA, USA)

value: control siRNA oligo


title: MDA-MB-468 inerferrred with control siRNA oligo replica 3


title: MDA-MB-468 inerferrred with control siRNA oligo replica 1


title: 12132022_w62103126-V1-2_S279_R2C2_14D_S209


title: MDA-MB-468 inerferrred with specific siRNA oligo against TBC1D7 replica 2

value: siRNA oligo against TBC1D7


title: MDA-MB-468 inerferrred with specific siRNA oligo against TBC1D7 replica 3


title: 12132022_w62103108-V1-2_S127_R2C2_14B_S165

value: human nasopharyngeal swab


title: CTRL_SUNI_PD_09x50xx_X020_S06_L059_B1_T1_P037.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CTRL_SUNI_PD_09x35xx_X021_S02_L004_B1_T2_PMRG.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 786O_KO_3

city: Gainesville

first: Ryan

last: Kolb

state: FL

address: 1275 Center Drive, M656

department: Pathology, Immunology and Laboratory Medicine

institute: University of Florida

data_processing:
Raw FastQ sequencing data was aligned to the hg38 genome using Kallisto pseudoalignment
Differential gene expression analysis was conducted using limma package
Assembly: hg38
Supplementary files format and content: Tab-delimited text files indluce TPM values for each sample

growth_protocol: CAKi-1 and 786O cells were grown in RPMI media supplemented with 10% fetal bovine sereum plus antibitotics in a humidified incubator at 5%  CO2 and 37 ºC.

extract_protocol:
RNA was isolated from cells using the NucleoSpin RNA mini kit (Macherey-Nagel, Duren Germany).
RNA concentration was determined by Qubit and quality was determined using a Bioanalyzer RNA assay. Samples with a RIN score ≥ 8 were used for library preparation. Library preparation was done using the NEBNext Poly(A) mRNA isolation module (New England Biolabs, Ipswich MA) and NEBNext Ultra II Library prep Kit (New England Biolabs).
Libraries were sequenced at 150 paired end reads at 3 million reads/sample using an Illumina Novaseq 6000 (Illumina, San Diego CA).

treatment_protocol: Cells were grown to log phase and harvested when reaching approximnately 70% confluency.

value: ccRCC cell line

value: ANGPTL4 KO


title: 12132022_w62103106-V1-2_S1016_R2C2_12N_S423

value: BC


title: 786O_KO_2


title: MDA-MB-468 inerferrred with specific siRNA oligo against TBC1D7 replica 1


title: CTRL_SUNI_PD_09x35xx_X021_S02_L003_B1_T1_P038.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 786O_WT_3

value: WT


title: 12132022_w62103095-V1-2_S1169_R2C2_12P_S467


title: 786O_KO_1


title: 786O_WT_2


title: 12132022_w62102971-V1-2_S579_R2C2_14H_S297


title: CAKI_1_KO_5


title: 12132022_w62102937-V1-2_S429_R2C2_14F_S253


title: CTRL_SUNI_PD_07x28xx_X030_S09_L065_B1_T1_P055.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CAKI_1_KO_4


title: CAKI_1_KO_3


title: CTRL_SUNI_PD_06x57xx_X026_S05_L032_B1_T2_P050.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62102929-V1-2_S869_R2C2_12L_S381


title: CAKI_1_KO_2


title: CTRL_SUNI_PD_05x16xx_X003_S10_L020_B1_T2_P002.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CAKI_1_KO_1


title: 12132022_W62102900-V1-2_S1148_R2C2_5P_S460


title: CAKI_1_WT_3


title: CTRL_SUNI_PD_05x16xx_X003_S10_L019_B1_T1_P001.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CAKI_1_WT_2


title: CAKI_1_WT_1


title: 786O_WT_1


title: 12132022_W62102787-V1-2_S995_R2C2_5N_S416


title: 12132022_w62102785-V1-2_S1037_R2C2_19N_S430


title: CTRL_SUNI_PD_03x66xx_X018_S06_L011_B1_T1_P035.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CTRL_SUNI_PD_07x28xx_X030_S09_L066_B1_T2_P054.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CTRL_SUNI_PD_04x38xx_X016_S10_L067_B1_T1_P028.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CTRL_SUNI_PD_03x41xx_X017_S11_L022_B1_T2_P036.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62102782-V1-2_S142_R2C2_19B_S170


title: 12132022_w62102714-V1-2_S736_R2C2_17J_S343


title: CTRL_SUNI_PD_03x39xx_X019_S11_L046_B1_T2_P031.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CTRL_SUNI_PD_06x57xx_X026_S05_L031_B1_T1_P047.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: 12132022_w62102750-V1-2_S555_R2C2_6H_S289


title: 12132022_w62102772-V1-2_S1195_R2C2_21P_S475


title: CTRL_SUNI_PD_03x66xx_X018_S06_L012_B1_T2_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: CAKI_1_WT_4


title: 12132022_w62102894-V1-2_S839_R2C2_2L_S371


title: CTRL_SUNI_PD_03x39xx_X019_S11_L045_B1_T1_P030.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra


title: healthy donor CD8+ CD4- CD56- T cells transduced with a3a TCR; antigen-exposed

city: Vancouver

first: Govinda

last: Sharma

address: 7th floor, 675 W 10th Ave

department: Michael Smith Genome Sciences Centre

institute: British Columbia Cancer Research Institute

data_processing:
Trimmomatic v0.36 run in paired end mode. Seed mismatches set to 2. Palindrome clipping threshold set to 30 matches. Simple clip threshold to 10 matches. Minimum adapter length to 1bp with the “keepBothPairs” option enabled. Leading and Trailing qualities set to 3. Sliding window size set to 4bp (required quality of 15). Minimum read length was thresholded at 30bp.
Trimmed reads mapped to reference genome using STAR aligner v2.5.2b run with default parameters
Alignment output sorted and indexed with Samtools. Unique gene hit counts calculated with featureCounts from Subread package v1.5.2. Largest overlap option turned on.
Differential analysis was performed using DESeq2 v1.30.0 with default parameters
Assembly: GRCh38
Supplementary files format and content: Pairwise DESeq2 normalized read counts for samples to be compared, in csv format

source_name: Peripheral blood

growth_protocol:
All cells maintained in RPMI-1640 supplemented with 2 mM GlutaMAX, 1 mM sodium pyruvate, 50 μM β-mercaptoethanol, 10 mM HEPES, 100 U/mL penicillin, 100 U/mL streptomycin, 1X MycoZap™ Prophylactic (Lonza) and 10% heat-inactivated fetal bovine serum
Primary T cells were directly isolated from healthy donor PBMC samples by FACS, stimulated on anti-CD3/28 mAb coated plates for 24h, and allowed to expand for 12 days prior to analysis

extract_protocol:
Flash-frozen pellets were shipped on dry-ice to Azenta/Genewiz. RNA extraction and QC was conducted according to supplier SOPs (July 2022)
polyA selection and RNA-seq library construction were conducted according to supplier SOPs (Azenta/Genewiz, August 2022)

treatment_protocol: Cells were either co-cultured with K562-based APC expressing HLA-A*01:01 transgene and MAGEA3 antigen for 12h or left non-co-cultured. All conditions were FACS re-purified and immediately flash frozen

value: Peripheral blood

value: anti-CD3/28 expansion, 12 days + 12 hour co-culture with target APC expressing known cognate epitope from MAGEA3


title: CTRL_SUNI_PD_04x38xx_X016_S10_L068_B1_T2_P024.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra

value: brain


title: YT-Indy cell line, unmodified, untreated

description: YT-Indy

source_name: YT-Indy

value: YT-Indy


title: 12132022_w62102687-V1-2_S742_R2C2_19J_S345

source_name: human nasopharyngeal swab


title: CTRL_SUNI_PD_03x15xx_X009_S03_L006_B1_T2_P015.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra

value: bulk


title: healthy donor CD8+ CD4- CD56- T cells transduced with a3a TCR

value: anti-CD3/28 expansion, 12 days


title: YT-Indy transduced with CD3, CD8, a3a TCR


title: 12132022_w62102686-V1-2_S444_R2C2_19F_S258


title: 12132022_w62102780-V1-2_S890_R2C2_19L_S388


title: CTRL_SUNI_PD_03x15xx_X009_S03_L005_B1_T1_P018.pe.q10.sort.rmdup.bam

description: Bulk ATAC-seq CTRL Sustantia Nigra