title: coD14_WT_ATAC_rep2

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
The FASTQ data were trimmed by Trim Galore (v0.4.4_dev) and mapped to GRCh37 (hg19) or GCRm38 (mm10) using Bowtie2 (v2.3.4.1). PCR duplicates and mitochondrial DNA were removed, and bam files were generated by samtools (v1.8). Then peaks were called by macs2 (v2.1.2) and differential peaks were identified by R package DiffBind (v 2.10.0) with FDR < 0.05 and |FoldChange| > 2 or 1.5.
bed files were generated using macs2 (v2.1.2)
Assembly: hg19
Supplementary files format and content: narrowPeak

growth_protocol: Human cortical organoid was cultured as followed: H9 cells were dissociated into single cell with accutase, and plated into the ultra-low-attachment 96-well plate (9,000 cells/well) in neural induction media (DMEM-F12 medium, 15% (v/v) KSR, 5% (v/v) FBS, 100 μM β-Mercaptoethanol, 1% (v/v) MEM-NEAA, 1% (v/v) GlutaMax and 1x Penicillin/Streptomycin) supplemented with 100 nM LDN-193189, 10 μM SB-431542, 2 μM XAV-939 and 50 μM Y27632. The media was replenished every other day until day 10 (FBS and Y27632 were omitted on day 2 and 4). On day 10, media were changed to neural differentiation media (1:1 mixture of DMEM-F12 and Neurobasal media, 0.5% (v/v) N2 supplement, 1% (v/v) B27 (minus vitamin A), 0.025% (v/v) Insulin, 50 μM β-Mercaptoethanol, 1% (v/v) MEM-NEAA, 1% (v/v) GlutaMax, and 1% (v/v) Penicillin/Streptomycin).

extract_protocol:
Day 14 cortical organoids (4x for each reaction) were harvested in 1ml DMEM/F12, and digested with Papain (20 units) for 6 minutes at 37°C. Organoids were dissociated into single cells, centrifuged at 300 RCF for 5 minutes, and counted in DPBS.
Day 14 cortical organoids (4x for each reaction) were harvested in 1ml DMEM/F12, and digested with Papain (20 units) for 6 minutes at 37°C. Organoids were dissociated into single cells, centrifuged at 300 RCF for 5 minutes, and counted in DPBS.  ATAC-seq libraries were prepared according to the previously described Omni-ATAC protocol (Corces et al., 2017). In brief, 50,000 viable cells were pellet at 500 RCF at 4°C for 5 min, then resuspended in ATAC-seq resuspension buffer (RSB) (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2) supplemented with 0.1% NP-40,0.1% Tween-20 and 0.01% digitonin. Samples were incubated on ice for 3 min, then washed out with 1 ml RSB supplemented with 0.1% Tween-20. Nuclei were pelleted at 500g for 10 min at 4 °C. The nuclei pellet was resuspended in 50 μl transposition mix (25 μl 2× TD buffer, 5 μl transposase (TTE Mix V50, Vazyme # TD501), 16.5 μl PBS, 0.1 μl 5% digitonin, 0.5 μl 10% Tween-20, 3 μl H2O) and incubated at 37 °C for 30 min in a thermomixer with 1,000 rpm shaking. The reaction was cleaned up using VAHTS DNA Clean Beads (Vazyme # N411-01). Libraries were PCR-amplified using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme # TD501), usually for 10-12 cyles and purified with VAHTS DNA Clean Beads.

value: cortical organoid Day 14


title: coD14_KO_ATAC_rep1

status: Public on Aug 21 2025

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: cell type

value: embryonic stem cells

tag: genotype

tag: treatment


title: coD14_WT_ATAC_rep1


title: coD14_KO_ATAC_rep2


title: coD14_KO_CUTTAG_H3K27me3_rep2

data_processing:
The FASTQ data were trimmed by Trim Galore (v0.4.4_dev) and mapped to GRCh37 (hg19) or GCRm38 (mm10) using Bowtie2 (v2.3.4.1). PCR duplicates and mitochondrial DNA were removed, and bam files were generated by samtools (v1.8). Then peaks were called by macs2 (v2.1.2) (--broad for H3K27me3) and differential peaks were identified by R package DiffBind (v 2.10.0) with FDR < 0.05 and |FoldChange| > 2 or 1.5.
bed files were generated using macs2 (v2.1.2)
Assembly: hg19
Supplementary files format and content: broadPeak, narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Mouse brain tissues and human cortical organoids were digested with Papain to single cell, then about 5 x 104 cells and 0.5-1 μg antibodies or IgG were used for the downstream procedure with 12 cylcles during the final amplification PCR.
Cut&Tag-Seq was performed following manufacturer’s instructions (Vazyme, TD904).

tag: cut&tag antibody


title: coD14_WT_CUTTAG_IgG

value: IgG (CST 2729S)


title: coD14_WT_CUTTAG_H3K27me3_rep2


title: coD14_WT_CUTTAG_H3K27me3_rep1


title: coD14_KO_CUTTAG_H3K27me3_rep1


title: coD14_WT_CUTTAG_H3K4me3_rep2


title: coD14_KO_CUTTAG_H3K4me3_rep2


title: coD14_WT_CUTTAG_H3K4me3_rep1


title: coD14_KO_CUTTAG_H3K4me3_rep1


title: coD14_KO2_RNA_rep2

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 genome assembly using hisat2 and counted by featurecounts, DEGs were analyzed by DESeq2.
Assembly: hg19
Supplementary files format and content: featurecounts and DEGs generated by DESeq2

molecule: polyA RNA

extract_protocol:
Tissues were dissolved in TRI reagent, mixed with chloroform, and centrifuged. The recovered supernatant was applied to RNeasy column to purify the RNA according to the manual.
One microgram total RNA was used for next generation sequencing library preparation according to the manufacturer’s protocol (VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina, Vazyme #NR605-01)


title: coD14_KO2_RNA_rep1


title: coD14_KO1_RNA_rep1


title: coD14_KO1_RNA_rep2


title: dacAybbR-KD_+aTc_#3

city: Omaha

first: Jeonghoon

last: Lee

state: Nebraska

address: 985900 Nebraska Medical Center

department: Pathology, Microbiology, and Immunology

country: USA

institute: University of Nebraska Medical Center

description:
The levels of DacA and YbbR_6xH were decreased.
J10-12_vs_J7-9.xisx

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews S. (2010).
FastQC: a quality control tool for high throughput sequence data; available online at http://www.bioinformatics.babraham.ac.uk/projects/fastqc for quality control.
Assembly: Chlamydia trachomatis 434/Bu bacterial reference genome and annotation files were downloaded from Ensembl (http://bacteria.ensembl.org/Chlamydia_trachomatis_434_bu/Info/Index).
Supplementary files format and content: Excel file showing fold changes and statistical significance between uninduced and induced conditions

molecule: total RNA

source_name: HeLa cell line

growth_protocol: HeLa cells were infected with C. trachomatis L2. Samples were collected at 16 and 24hpi. The infected cells were grown in 1X DMEM containing 10% FBS and 10 ug gentamycin at 37 celcius degree in 5% CO2

extract_protocol:
Total RNA was collected from C. trachomatis infected cell cultures using Trizol. Total RNA was DNased then further purified to remove rRNA using MicrobEnrich, MicrobExpress.
the Illumina Stranded Total RNA Prep protocol

treatment_protocol: 5 nM inducer (Anhydrotetracycline) was treated or not at 10 hpi.

value: HeLa cell line

tag: agent

value: Chlamydia trachomatis L2 434/Bu

value: Induced with 5 nM aTc for 14 h (in DMEM)


title: dacAybbR-KD_+aTc_#2


title: coD14_WT_RNA_rep2

description:
coD14_KO1_RNA_DEG.txt.gz
coD14_KO2_RNA_DEG.txt.gz


title: dacAybbR-KD_+aTc_#1


title: dacAybbR-KD_-aTc_#3

description:
Normal Developmental Cycle
J10-12_vs_J7-9.xisx

value: Uninduced condition (in DMEM)


title: dacAybbR6xH_+aTc_#2

description:
DacA and YbbR_6xH are over-expressed.
J4-6_vs_J1-3.xisx

value: Induced with 5 nM aTc for 6 h (in DMEM)


title: dacAybbR-KD_-aTc_#1


title: coD14_KO_CUTTAG_IgG


title: dacAybbR-KD_-aTc_#2


title: dacAybbR6xH_+aTc_#3


title: dacAybbR6xH_+aTc_#1


title: dacAybbR6xH_-aTc_#2

description:
Normal Developmental Cycle
J4-6_vs_J1-3.xisx


title: dacAybbR6xH_-aTc_#3


title: dacAybbR6xH_-aTc_#1


title: LAPC-4, VAN, 5 days, rep1

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
A13-83-8
RTKi_counts.txt
RTKi_tpm.txt

data_processing:
Base calling was performed with RTA v.3.4.4 Illumina run time analysis software.
Demultiplexing was performed using BCL2fatq v.2.20 with the following parameters: --no-lane-splitting -i RunFolder/Data/Intensities/BaseCalls -R RunFolder --barcode-mismatches 1 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --sample-sheet SampleSheet.csv -o Unaligned
Trimming was performed using Trimmomatic v.0.36 with the following parameters: PE -phred33 ILLUMINACLIP:TruSeq_and_nextera_adapters.fa:3:50:10 MINLEN:36
Aligning and mapping was performed using RSEM as a wrapper around STAR v.2.7.0f with the following parameters: rsem-calculate-expression --star --paired-end --star-gzipped-read-file --estimate-rspd -p 30 --output-genome-bam --calc-ci --ci-memory 8192
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene-level TPM values for each sample
Supplementary files format and content: tab-delimited text file includes gene-level count values for each sample

source_name: Prostate

growth_protocol: 22Rv1 and LNCaP cells were maintained in high-glucose RPMI supplemented with 10% serum and 1% L-glutamine. LAPC-4 cells were maintained in IMDM supplemented with 10% serum and 1% L-glutamine. Cells were maintained with antibiotics in a humidified atmosphere with 5% CO2 at 37degC.

extract_protocol:
Total RNA was extracted from cells using the Qiagen RNeasy Plus Mini Kit.
Sequencing libraries were prepared using the TruSeq stranded kit with PolyA capture

treatment_protocol: IC50 values were determined empirically for each drug/cell line combination and dosed at day 0, 1, 3 and 5. Cells treated with 10% CSS (replacing 10% FBS) had media replenished on the same schedule.

tag: tissue

value: Prostate

value: VAN

tag: timepoint

tag: biological replicate


title: LAPC-4, VAN, 1 day, rep1

description:
A13-83-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 3 days, rep1

description:
A13-83-7
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 5 days, rep1

description:
A13-83-4
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 3 days, rep1

description:
A13-83-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 5 days, rep1

description:
A13-80-8
RTKi_counts.txt
RTKi_tpm.txt

value: LNCap

value: GEF


title: 22Rv1, VAN, 0 days, rep1

description:
A13-83-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 1 day, rep1

description:
A13-83-2
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 5 days, rep1

description:
A13-80-4
RTKi_counts.txt
RTKi_tpm.txt

value: ABI


title: LNCap, GEF, 0 days, rep1

description:
A13-80-5
RTKi_counts.txt
RTKi_tpm.txt


title: coD14_WT_RNA_rep1


title: LNCap, ABI, 3 days, rep1

description:
A13-80-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, DAC, 0 days, rep1

description:
A13-57-9
RTKi_counts.txt
RTKi_tpm.txt

value: DAC


title: LNCap, LAP, 3 days, rep1

description:
A13-57-3
RTKi_counts.txt
RTKi_tpm.txt

value: LAP


title: LNCap, DAC, 5 days, rep1

description:
A13-57-12
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, DAC, 3 days, rep1

description:
A13-57-11
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 0 days, rep1

description:
A13-80-1
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 1 day, rep1

description:
A13-80-2
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, LAP, 0 days, rep1

description:
A13-57-1
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, DAC, 1 day, rep1

description:
A13-57-10
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 1 day, rep1

description:
A13-184-1
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 3 days, rep1

description:
A13-184-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 0 days, rep1

description:
A13-183-9
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 5 days, rep2

description:
A13-183-8
RTKi_counts.txt
RTKi_tpm.txt

value: CSS


title: LNCap, LAP, 1 day, rep1

description:
A13-57-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 1 day, rep2

description:
A13-183-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 3 days, rep2

description:
A13-183-7
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 5 days, rep1

description:
A13-184-3
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 0 days, rep1

description:
A13-83-5
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 3 days, rep1

description:
A13-183-3
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 5 days, rep1

description:
A13-183-4
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 0 days, rep2

description:
A13-183-5
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 0 days, rep1

description:
A13-183-13
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 5 days, rep1

description:
A13-183-12
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 1 day, rep1

description:
A13-183-10
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 3 days, rep1

description:
A13-80-7
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 0 days, rep2

description:
A13-161-9
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 5 days, rep2

description:
A13-161-8
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 0 days, rep2

description:
A13-161-5
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 1 day, rep2

description:
A13-161-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 5 days, rep2

description:
A13-161-32
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 3 days, rep2

description:
A13-161-31
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 3 days, rep1

description:
A13-161-3
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 0 days, rep2

description:
A13-161-29
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, VAN, 1 day, rep2

description:
A13-161-30
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 0 days, rep2

description:
A13-161-25
RTKi_counts.txt
RTKi_tpm.txt

value: SUN


title: LAPC-4, SUN, 5 days, rep2

description:
A13-161-28
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 1 day, rep1

description:
A13-183-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 3 days, rep2

description:
A13-161-23
RTKi_counts.txt
RTKi_tpm.txt

value: NER


title: LAPC-4, SUN, 3 days, rep2

description:
A13-161-27
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 5 days, rep2

description:
A13-161-24
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 0 days, rep2

description:
A13-161-21
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 1 day, rep2

description:
A13-161-22
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, CSS, 0 days, rep1

description:
A13-183-1
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 1 day, rep2

description:
A13-161-26
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 3 days, rep1

description:
A13-183-11
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 0 days, rep2

description:
A13-161-17
RTKi_counts.txt
RTKi_tpm.txt

value: ENZ


title: LAPC-4, ENZ, 5 days, rep2

description:
A13-161-20
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 1 day, rep2

description:
A13-161-18
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 3 days, rep1

description:
A13-161-15
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 1 day, rep1

description:
A13-161-14
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 3 days, rep2

description:
A13-161-7
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 0 days, rep1

description:
A13-161-13
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 1 day, rep1

description:
A13-80-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 3 days, rep2

description:
A13-161-11
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 1 day, rep2

description:
A13-161-10
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 5 days, rep1

description:
A13-161-4
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 3 days, rep2

description:
A13-154-3
RTKi_counts.txt
RTKi_tpm.txt

value: AFA


title: LAPC-4, ABI, 0 days, rep1

description:
A13-161-1
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 0 days, rep1

description:
A13-141-9
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 1 day, rep2

description:
A13-154-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ABI, 1 day, rep1

description:
A13-161-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 3 days, rep1

description:
A13-141-7
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 1 day, rep1

description:
A13-141-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 1 day, rep1

description:
A13-141-2
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 3 days, rep2

description:
A13-161-19
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 0 days, rep1

description:
A13-141-13
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 0 days, rep2

description:
A13-154-1
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 3 days, rep1

description:
A13-141-15
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 3 days, rep1

description:
A13-141-11
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 5 days, rep1

description:
A13-141-4
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, ENZ, 5 days, rep1

description:
A13-161-16
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 5 days, rep1

description:
A13-141-8
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, AFA, 0 days, rep1

description:
A13-141-5
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 1 day, rep1

description:
A13-141-14
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, SUN, 5 days, rep1

description:
A13-141-16
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 5 days, rep2

description:
A13-140-8
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 5 days, rep1

description:
A13-141-12
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 0 days, rep2

description:
A13-140-9
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 0 days, rep1

description:
A13-141-1
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, NER, 1 day, rep1

description:
A13-141-10
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 1 day, rep2

description:
A13-140-6
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 3 days, rep2

description:
A13-140-31
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 0 days, rep2

description:
A13-140-5
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 1 day, rep2

description:
A13-140-30
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, DAC, 3 days, rep1

description:
A13-141-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 0 days, rep2

description:
A13-140-29
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 5 days, rep2

description:
A13-140-28
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 1 day, rep2

description:
A13-140-26
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 0 days, rep2

description:
A13-140-25
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 5 days, rep2

description:
A13-140-24
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 3 days, rep2

description:
A13-140-23
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 0 days, rep2

description:
A13-140-21
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 1 day, rep2

description:
A13-140-22
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 5 days, rep2

description:
A13-140-20
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 1 day, rep2

description:
A13-140-18
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 0 days, rep2

description:
A13-140-17
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 5 days, rep2

description:
A13-140-16
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 1 day, rep2

description:
A13-140-14
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 3 days, rep2

description:
A13-140-19
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, GEF, 3 days, rep2

description:
A13-140-7
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 3 days, rep2

description:
A13-140-15
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 0 days, rep2

description:
A13-140-13
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 5 days, rep2

description:
A13-140-12
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ABI, 5 days, rep2

description:
A13-140-32
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 3 days, rep2

description:
A13-140-11
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 5 days, rep2

description:
A13-135-8
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 0 days, rep1

description:
A13-135-9
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 1 day, rep2

description:
A13-135-6
RTKi_counts.txt
RTKi_tpm.txt


title: LAPC-4, LAP, 1 day, rep2

description:
A13-140-10
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 3 days, rep2

description:
A13-135-55
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 3 days, rep2

description:
A13-135-7
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 5 days, rep2

description:
A13-135-56
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 1 day, rep2

description:
A13-135-54
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 0 days, rep2

description:
A13-135-53
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 5 days, rep3

description:
A13-135-52
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 3 days, rep2

description:
A13-140-27
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 3 days, rep3

description:
A13-135-51
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 0 days, rep2

description:
A13-135-5
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 1 day, rep3

description:
A13-135-50
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 3 days, rep2

description:
A13-135-47
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 0 days, rep3

description:
A13-135-49
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 1 day, rep2

description:
A13-135-46
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 3 days, rep1

description:
A13-135-43
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 5 days, rep2

description:
A13-135-48
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, GEF, 0 days, rep2

description:
A13-135-45
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 5 days, rep1

description:
A13-135-4
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 0 days, rep1

description:
A13-135-37
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 5 days, rep1

description:
A13-135-44
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 0 days, rep1

description:
A13-135-41
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 3 days, rep2

description:
A13-135-35
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, ENZ, 1 day, rep1

description:
A13-135-42
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 1 day, rep1

description:
A13-135-38
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 5 days, rep1

description:
A13-135-40
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 0 days, rep2

description:
A13-135-33
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 5 days, rep2

description:
A13-135-32
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 5 days, rep2

description:
A13-135-36
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 3 days, rep2

description:
A13-135-31
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, VAN, 1 day, rep2

description:
A13-135-34
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 1 day, rep2

description:
A13-135-30
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 1day, rep4

description:
A13-135-26
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 0 days, rep4

description:
A13-135-25
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 0 days, rep2

description:
A13-135-29
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 5 days, rep3

description:
A13-135-24
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 3 days, rep4

description:
A13-135-27
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 1day, rep3

description:
A13-135-22
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 0 days, rep3

description:
A13-135-21
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 3 days, rep3

description:
A13-135-23
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, CSS, 3 days, rep1

description:
A13-135-39
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 5 days, rep2

description:
A13-135-20
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 0 days, rep2

description:
A13-135-17
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 1 day, rep2

description:
A13-135-18
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 5 days, rep1

description:
A13-135-12
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 5 days, rep2

description:
A13-135-16
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 0 days, rep2

description:
A13-135-13
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 1 day, rep1

description:
A13-135-10
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 3 days, rep1

description:
A13-135-3
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 0 days, rep1

description:
A13-135-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 1 day, rep2

description:
A13-135-14
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 3 days, rep1

description:
A13-135-11
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 5 days, rep2

description:
A13-133-8
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ABI, 1 day, rep1

description:
A13-135-2
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 0 days, rep2

description:
A13-133-9
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 0 days, rep2

description:
A13-133-5
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 3 days, rep2

description:
A13-133-7
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 5 days, rep4

description:
A13-135-28
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 1 day, rep2

description:
A13-133-6
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 3 days, rep1

description:
A13-133-31
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 1 day, rep1

description:
A13-133-30
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 0 days, rep1

description:
A13-133-29
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 3 days, rep2

description:
A13-133-3
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 3 days, rep2

description:
A13-135-19
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 1 day, rep1

description:
A13-133-26
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 0 days, rep1

description:
A13-133-25
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 3 days, rep1

description:
A13-133-23
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 5 days, rep1

description:
A13-133-24
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, NER, 3 days, rep1

description:
A13-133-27
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, AFA, 3 days, rep2

description:
A13-135-15
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 1 day, rep2

description:
A13-133-2
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 1 day, rep1

description:
A13-133-22
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 5 days, rep1

description:
A13-133-20
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 1 day, rep1

description:
A13-133-18
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 3 days, rep1

description:
A13-133-19
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 0 days, rep1

description:
A13-133-21
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 3 days, rep2

description:
A13-133-15
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 1 day, rep2

description:
A13-133-14
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 5 days, rep2

description:
A13-133-4
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 0 days, rep1

description:
A13-133-17
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 5 days, rep2

description:
A13-133-16
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 3 days, rep2

description:
A13-133-11
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, SUN, 5 days, rep1

description:
A13-133-32
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 5 days, rep2

description:
A13-133-12
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 1 day, rep2

description:
A13-133-10
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, CSS, 0 days, rep2

description:
A13-133-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 3 days, rep2

description:
A13-132-7
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 0 days, rep2

description:
A13-132-9
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 1 day, rep2

description:
A13-132-6
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 5 days, rep1

description:
A13-132-4
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 0 days, rep2

description:
A13-132-5
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 1 day, rep2

description:
A13-132-10
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 3 days, rep2

description:
A13-132-11
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 1 day, rep1

description:
A13-132-2
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 0 days, rep1

description:
A13-132-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, ENZ, 3 days, rep1

description:
A13-132-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 5 days, rep2

description:
A13-132-12
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 3 days, rep1

description:
A13-130-3
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 1 day, rep1

description:
A13-130-2
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 0 days, rep2

description:
A13-133-13
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 5 days, rep1

description:
A13-130-4
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 5 days, rep1

description:
A13-129-4
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, GEF, 0 days, rep1

description:
A13-130-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 3 days, rep1

description:
A13-112-3
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 1 day, rep1

description:
A13-112-2
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 0 days, rep1

description:
A13-107-9
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 1 day, rep1

description:
A13-129-2
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, LAP, 5 days, rep2

description:
A13-107-8
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, DAC, 0 days, rep1

description:
A13-112-1
RTKi_counts.txt
RTKi_tpm.txt


title: 22Rv1, LAP, 5 days, rep2

description:
A13-132-8
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, LAP, 1 day, rep2

description:
A13-107-6
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, LAP, 0 days, rep2

description:
A13-107-5
RTKi_counts.txt
RTKi_tpm.txt


title: H3K27ac_rep_2

city: New York

first: Bogdan

last: Sieriebriennikov

state: NY

address: 100 Washington Sq E

institute: New York University

description: Library name: H3K27ac_rep_2

data_processing:
FASTQ mapped to the genome using bwa-mem2 mem
output sam sorted and converted to bam using samtools sort
sorted bam converted to BigWig using deeptools bam Coverage
Assembly: v8.6 (GCF_003227715.2)
Supplementary files format and content: coverage tracks in BigWig format
Library strategy: CUT&RUN

organism: Harpegnathos saltator

source_name: antennae

extract_protocol:
Nuclei were isolated from antennae, stained with Hoechst and FACS sorted to separate them from debris. Then, they were processed using the CUT&RUN Assay Kit (Cell Signaling Technology, Cat#86652). Antibodies were purchased from Cell Signaling Technology (Cat#9751, 9733, 8173, 66362).
Libraries were constructed using the manufacturer's protocol for NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs Cat#E7645).

value: antennae


title: LNCap, LAP, 3 days, rep2

description:
A13-107-7
RTKi_counts.txt
RTKi_tpm.txt


title: H3K36me3_rep_1

description: Library name: H3K36me3_rep_1


title: BS_10X_am3, ATAC, sequencing run 1

data_processing:
cellranger-arc mkfastq to generate FASTQ
cellranger-arc count to quantify each sample
cellranger-arc aggr to aggregate the three samples
cellranger aggr to aggregate the RNA-seq portion of the three samples from this experiment with the three wild-type snRNA-seq libraries from GSE235819
Assembly: v8.6 (GCF_003227715.2)
Supplementary files format and content: cellranger-arc count output files for each individual sample; cellranger-arc aggr outputs for the combination of the three multiome samples from this experiment (BS_10X_am1, BS_10X_am2, and BS_10X_am3); cellranger aggr outputs for the combination of the RNA-seq portion of the three multiome samples from this experiment and three wild-type snRNA-seq samples from GSE235819; HSAL70 gene annotations
Library strategy: 10X multiome

extract_protocol:
Nuclei were isolated from dissociated antennae.
Libraries were constructed following the manufacturer's protocol.


title: BS_10X_am3, GEX, sequencing run 1


title: 22Rv1, DAC, 5 days, rep1

description:
A13-112-4
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 5 days, rep1

description:
A13-107-4
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 3 days, rep1

description:
A13-107-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 1 day, rep1

description:
A13-107-2
RTKi_counts.txt
RTKi_tpm.txt


title: BS_10X_am2, ATAC, sequencing run 1


title: BS_10X_am2, GEX, sequencing run 1


title: LNCap, VAN, 3 days, rep1

description:
A13-129-3
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, SUN, 1 day, rep1

description:
A13-107-10
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, AFA, 0 days, rep1

description:
A13-107-1
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 5 days, rep1

description:
A13-103-8
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, VAN, 0 days, rep1

description:
A13-129-1
RTKi_counts.txt
RTKi_tpm.txt


title: sOrg_8w_rep4

first: Yanjing

last: Zhu

address: No.727 Zhongshan Road

institute: Tongji University

description: Library name: Sample 26

data_processing:
ST-Seq: The FASTQ files were processed using the 10x Genomics Space Ranger pipeline. Reads were aligned to the reference genome. The spaceranger count pipeline was used to perform alignment, tissue detection, fiducial alignment, and spatial barcode/UMI counting. This process generated a feature-spot barcode count matrix and determined the spatial location of each barcode on the tissue image
RNA-Seq: Raw FASTQ reads are checked for quality, adapter content, and other issues using FastQC. Low-quality bases and adapter sequences are removed to improve alignment accuracy. The cleaned reads are mapped to a reference genome using STAR. The number of reads mapping to each gene is counted from the BAM files using Stringtie, producing a the count matrix.
Assembly: mm10, hg38
Supplementary files format and content: Filtered Feature-Barcode Matrix: This contains the gene expression counts for tissue-associated spots.
Supplementary files format and content: Spatial Information Files: These files link the expression matrix to the spatial coordinates on the slide.
Supplementary files format and content: Histology Image: The tissue image used for spatial context.
Supplementary files format and content: Gene count matrix file: a csv-formatted file containing the number of sequencing reads that have been assigned to the human geneset for each of the samples.

source_name: Organoid

extract_protocol:
ST-Seq: spinal cord samples were cryosectioned (10 m) and prepared for spatial transcriptomics using the 10x Genomics Visium platform. Sample quality (morphology & RNA integrity  RIN 7.9-8.8) was confirmed prior to analysis.      RNA-Seq: sOrg and enTsOrg  were sent to BGI for RNA-seq analysis. Total RNA was isolated, mRNA enriched, fragmented, and reverse transcribed into cDNA libraries using standard protocols. Untreated iPSCs served as a control.
ST-Seq: Each slide contained approximately 5,000 spots (55 m diameter, 100 m spacing) for capturing RNA. Permeation times were optimized for each group (6-18 min) using the Visium Tissue Optimization Kit. Libraries were generated with the Visium Spatial Gene Expression Kit and sequenced on an Illumina NextSeq.     RNA-Seq: sequencing was performed on a DNBSEQ system.

value: Organoid


title: LNCap, NER, 0 days, rep1

description:
A13-103-5
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 3 days, rep1

description:
A13-103-7
RTKi_counts.txt
RTKi_tpm.txt


title: sOrg_8w_rep3

description: Library name: Sample 25


title: BS_10X_am1, GEX


title: sOrg_3w_rep3

description: Library name: Sample 22


title: LNCap, DAC, 5 days, rep2

description:
A13-103-4
RTKi_counts.txt
RTKi_tpm.txt


title: LNCap, NER, 1 day, rep1

description:
A13-103-6
RTKi_counts.txt
RTKi_tpm.txt


title: sOrg_8w_rep2

description: Library name: Sample 24


title: sOrg_8w_rep1

description: Library name: Sample 23


title: sOrg_2w_rep1

description: Library name: Sample 17


title: 1039_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-23

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM)

source_name: prostate

extract_protocol:
Total RNA was extracted from cells adhered to caps using the Qiagen RNeasy FFPE kit.
rRNA-depleted RNA was converted into cDNA and assembled into strand-specific libraries using the NEBNext Ultra II Directional RNA-Seq kit.

treatment_protocol: FFPE human prostate tissues were sectioned onto metal frame membrane slides, and regions of interest were excised onto caps using laser capture microdissection.

tag: gender

value: male

tag: case

tag: regionofinterest


title: sOrg_2w_rep3

description: Library name: Sample 19


title: sOrg_3w_rep2

description: Library name: Sample 21


title: 1039_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-25


title: sOrg_3w_rep1

description: Library name: Sample 20


title: 1039_BX5A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-26


title: LNCap, DAC, 3 days, rep2

description:
A13-103-3
RTKi_counts.txt
RTKi_tpm.txt


title: 1039_BX1A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-24


title: 1038_BX13A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-22


title: LNCap, DAC, 0 days, rep2

description:
A13-103-1
RTKi_counts.txt
RTKi_tpm.txt


title: sOrg_2w_rep2

description: Library name: Sample 18


title: 1038_BX11A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-19


title: enTsOrg_3w_rep3

description: Library name: Sample 12


title: enTsOrg_8w_rep2

description: Library name: Sample 14


title: 1038_BX11A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-20


title: 1036_BX15A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-17


title: enTsOrg_8w_rep1

description: Library name: Sample 13


title: 1038_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-21


title: enTsOrg_8w_rep3

description: Library name: Sample 15


title: BS_10X_am1, ATAC


title: enTsOrg_8w_rep4

description: Library name: Sample 16


title: LNCap, DAC, 1 day, rep2

description:
A13-103-2
RTKi_counts.txt
RTKi_tpm.txt


title: enTsOrg_3w_rep1

description: Library name: Sample 10


title: 3KO.7TG late R 2

type: RNA

city: Durham

first: Jean

last: Kwun

state: NC

address: 207 Research Dr, Jones 362

department: Surgery

institute: Duke University

hyb_protocol: 300 ng total RNA was hybridized to gene-specific probes at 65˚C for 18 hours and then purified and deposited onto glass cartridges using the “high sensitivity” setting on the nCounter™ Prep Station (NanoString Technologies, Seattle, WA, USA).

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter™ Digital Analyzer with 555 fields of view setting.

data_processing: Normalization of RNA loading was performed using the geometric mean of 12 internal reference genes (housekeeping genes; ABCF1, G6PD, GUSB, NRDE2, OAZ1, POLR2A, PPIA, SDHA, STK11IP, TBC1D10B, TBP, and UBB).

organism: Macaca mulatta

source_name: Renal, biopsy, FFPE

extract_protocol: Formalin Fixed Paraffin Embedded (FFPE) samples were used for the extraction of total RNA from renal allograft. Samples were included in the final analysis if they passed a priori quality control criteria (260:280 ratio > 1.7).


title: 3KO.7TG late R 3


title: 3KO.7TG early bx 3


title: 3KO.7TG late R 1


title: 1037_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-18


title: enTsOrg_3w_rep2

description: Library name: Sample 11


title: 1036_BX13A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-15


title: enTsOrg_2w_rep2

description: Library name: Sample 8


title: 1036_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-14


title: iPSC_rep3

description: Library name: Sample 6

source_name: Cell

value: Cell


title: enTsOrg_2w_rep1

description: Library name: Sample 7


title: H3K4me3_rep_1


title: 1034_BX17A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-9


title: 1KO.1TG early R 1


title: 1KO.1TG early R 2


title: H3K27me3_rep_1


title: 3KO.7TG early bx 2


title: 3KO.7TG early bx 1


title: 1KO.1TG early R 3


title: 1036_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-16


title: iPSC_rep2

description: Library name: Sample 5


title: H3K4me3_rep_3


title: iPSC_rep1

description: Library name: Sample 4


title: 1035_BX12A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-12


title: enTsOrg_2w_rep3

description: Library name: Sample 9


title: Human_HSC_F

city: Shenzhen

first: Haoyue

last: Zhang

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

institute: Shenzhen Bay Lab

data_processing:
The sequencing data was filtered with SOAPnuke(v1.5.6)by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
Bowtie2(2.3.4.3)(parameter: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: tab-delimited text files include FPKM, TPM and read counts of gene expression for each Sample.
Supplementary files format and content: tab-delimited text files include FPKM, TPM and read counts of RNA expression for each Sample.

source_name: tissue derived primary cells

growth_protocol: The hepatic stellate cells were directly isolated from a male patient and a female patient with liver fibrosis. Hepatic stellate cells were sorted through fluorescence activated cell sorting based on Retinoid+/CD45- signals.

extract_protocol:
Total RNAs of hepatic stellate cells were extracted by the RNeasy Mini Kit (Qiagen).
All the RNA samples were then subjected to paired-end RNA-seq by the BGI Genomics.

value: liver

value: hepatic stellate cells

value: F


title: 1035_BX12A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-11


title: IgG_control_rep_1


title: 1034_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-8


title: Human_HSC_M

value: M


title: BS_10X_am3, ATAC, sequencing run 2


title: BS_10X_am2, ATAC, sequencing run 2


title: 1034_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-7


title: 1035_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-13


title: BS_10X_am3, GEX, sequencing run 2


title: BS_10X_am2, GEX, sequencing run 2


title: IgG_control_rep_3


title: 1034_BX20A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-10


title: IgG_control_rep_2


title: skin_C8STINGKO_3

city: Cologne

first: Gianmaria

last: Liccardi

address: Joseph Stelzmann strasse 52, Institute of Biochemistry

country: Germany

institute: Uniklinik, University of Cologne

description:
Library name: sample-28
NA

data_processing:
Sequencing was then carried out on a NovaSeq 6000 platform, employing a single-read (SR) 1x100 bp sequencing strategy.
Assembly: genome mm10
Supplementary files format and content: raw counts after alignement

organism: Mus musculus

source_name: skin

extract_protocol:
RNA was extracted from skin tissue using the RNeasy Plus Mini Kit (74136, Qiagen). Skin was weighted at 30mg, snap frozen in liquid nitrogen and stored at -80°C before lysed. Skin tissues were lysed in lysis buffer (Buffer RLT + 40ul DTT 1M per ml + 0.5% Reagent DX) according to the kit’s manufacturer instructions in TissueLyser II (85300, Qiagen) using 7 mm stainless steel beads (69990, Qiagen). Extracted RNA was stored at -80°C.
Library preparation was performed using the Lexogen QuantSeq 3’ mRNA sequencing protocol.

value: skin

tag: batch


title: skin_C8STINGKO_5

description:
Library name: sample-30
NA


title: skin_C8STINGKO_4

description:
Library name: sample-29
excluded_from_analysis


title: H3K4me3_rep_2


title: SA-TY-021, 1 month, PBMC, perinatal HIV (pHIV), TCR

city: Miami

first: Akshay

last: Iyer

state: FL

institute: University of Miami

description: Library name: SA-TY-021_1m_TCR

data_processing:
Cell Ranger v7 count and aggr funtions to aggregate reads across sequencing lanes. filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+FB/ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv

source_name: Blood

extract_protocol:
10x 5' V2.0 chemistry for cDNA amplification
Library preparation for gene expression profiling and V(D)J sequencing were carried out according to manufacturer’s instructions without modification (10x Genomics PN: 1000263, 1000286, 1000250, 1000215, 1000252,1000253, 1000190, 1000541)

value: Blood

value: PBMC

value: perinatal HIV (pHIV)


title: 1033_BX9A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-6


title: SA-TY-021, 1 month, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: SA-TY-021_1m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)

library_source: other

data_processing:
Cell Ranger v7 count and aggr funtions to aggregate reads across sequencing lanes. filtered_feature_bc_matrix.h5 consists of barcode matrix/counts after read alignment, barcode counting, UMI counting and filtering Downstream processing, integration and analysis was performed in R with packages such as Seurat
Assembly: GRCh38 (hg38)
Supplementary files format and content: CellRanger output files (mRNA+FB/ADT output): raw_feature_bc_matrix.h5, filtered_feature_bc_matrix.h5
Supplementary files format and content: CellRanger output files (VDJ Output): TCR_filtered_contig_annotations.csv, BCR_filtered_contig_annotations.csv
Library strategy: CITE-seq

molecule: protein


title: 1033_BX6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-4


title: H3K27ac_rep_1


title: 1033_BX8A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-5


title: H3K27me3_rep_2


title: skin_C8STINGKO_2

description:
Library name: sample-27
NA


title: skin_CONTROL_4

description:
Library name: sample-24
NA

value: CONTROL


title: SA-AH-029, 1 month, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: SA-AH-029_1m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)


title: SA-TY-021, 1 month, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: SA-TY-021_1m_GEX5


title: SA-AH-029, 1 month, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: SA-AH-029_1m_GEX5


title: skin_CONTROL_5

description:
Library name: sample-25
NA


title: 1033_BX4A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-3


title: SA-TY-021, 1 month, PBMC, perinatal HIV (pHIV), BCR

description: Library name: SA-TY-021_1m_BCR


title: SA-AH-029, 1 month, PBMC, perinatal HIV (pHIV), TCR

description: Library name: SA-AH-029_1m_TCR


title: skin_CONTROL_3

description:
Library name: sample-23
NA


title: 1032_BX21A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-2


title: SA-AH-029, 1 month, PBMC, perinatal HIV (pHIV), BCR

description: Library name: SA-AH-029_1m_BCR


title: skin_CONTROL_2

description:
Library name: sample-22
NA


title: 1032_BX20A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-149-1


title: CP042, 1 month, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP042_1m_GEX5


title: 1032_BX18A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-33


title: CP042, 1 month, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: CP042_1m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)


title: skin_CONTROL_1

description:
Library name: sample-21
excluded_from_analysis


title: 1032_BX18A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-32


title: skin_C8STINGEKO_5

description:
Library name: sample-20
NA


title: CP022, 1 month, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP022_1m_GEX5


title: CP022, 1 month, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: CP022_1m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)


title: CP022, 1 month, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP022_1m_BCR


title: skin_C8STINGKO_1

description:
Library name: sample-26
NA


title: 1032_BX16A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-31


title: CP017, 2 months, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP017_2m_TCR


title: CP042, 1 month, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP042_1m_BCR


title: 1032_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-29


title: 1032_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-30


title: CP042, 1 month, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP042_1m_TCR


title: CP017, 2 months, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP017_2m_BCR


title: skin_C8STINGEKO_3

description:
Library name: sample-18
excluded_from_analysis


title: skin_C8STINGEKO_1

description:
Library name: sample-16
NA


title: skin_C8STINGEKO_2

description:
Library name: sample-17
NA


title: CP016, 2 months, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP016_2m_TCR


title: CP016, 2 months, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP016_2m_GEX5


title: 1030_BX18A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-27


title: skin_not_discosed_5

description:
Library name: sample-15
normalization_only


title: CP022, 1 month, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP022_1m_TCR


title: 1030_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-26


title: 1031_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-28


title: skin_C8STINGEKO_4

description:
Library name: sample-19
NA


title: skin_not_discosed_4

description:
Library name: sample-14
normalization_only


title: 1030_BX13A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-25


title: CP011, 2 months, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP011_2m_TCR


title: skin_C8_5

description:
Library name: sample-10
NA


title: CP016, 2 months, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP016_2m_BCR


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 4 hours, batch 2, replicate 2

description: Library name: A17-H-3-32

data_processing:
Base calling was performed with RTA v.4 Illumina run time analysis software.
Demultiplexing was performed using BCL2fatq v.2.20 with the following parameters: --no-lane-splitting -i RunFolder/Data/Intensities/BaseCalls -R RunFolder --barcode-mismatches 1 --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --sample-sheet SampleSheet.csv -o Unaligned
Trimming was performed using Trimmomatic v.0.36 with the following parameters: PE -phred33 ILLUMINACLIP:TruSeq_and_nextera_adapters.fa:3:50:10 MINLEN:36
Aligning and mapping was performed using RSEM as a wrapper around STAR v.2.7.0f with the following parameters: rsem-calculate-expression --star --paired-end --star-gzipped-read-file --estimate-rspd -p 30 --output-genome-bam --calc-ci --ci-memory 8192
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene-level TPM values for each sample
Supplementary files format and content: tab-delimited text file includes gene-level count values for each sample

source_name: LNCaP

growth_protocol: LNCap cells were propagated in RPMI-1640 Medium (ATCC, #30-2001) supplemented with 10% FBS (HyClone, #SH30071.03), 1% L-Glutamine (Corning, #25-005-CI) and 1% Penicillin Streptomycin (Corning, #30-002-CI).  LNCaP cells were plated day 1.

extract_protocol:
After treatment cells were washed with PBS and either lysed RNA using the RNeasy Plus Mini protocol.
Illumina mRNA Ligation Kit for polyA capture and strans-specific sequencing.

treatment_protocol: Day 2, the cells were washed two times with PBS and media was replaced with media supplemented with 10% Charcoal/Dextran Treated FBS (HyClone, #SH30063.03). Day 3, cells were treated with 100ng/ml EGF (R&D, #236-EG) or 100ng/ml NRG-1 (R&D, #396-HB) for 5’, 1hr, or 4 hr.

value: LNCaP

tag: serum

value: CSS

tag: growth factor

value: NRG-1 100ng/ml

tag: treatment time

value: 4 hours


title: 1029_BX23A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-22


title: CP013, 1 month, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP013_1m_GEX5


title: 1029_BX17A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-21


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 1 hour, batch 2, replicate 2

description: Library name: A17-H-3-31

value: 1 hour


title: CP011, 2 months, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP011_2m_BCR


title: skin_C8_4

description:
Library name: sample-9
excluded_from_analysis


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 4 hours, batch 2, replicate 2

description: Library name: A17-H-3-29

value: EGF 100ng/ml


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 5 minutes, batch 2, replicate 2

description: Library name: A17-H-3-30

value: 5 minutes


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 1 hour, batch 2, replicate 2

description: Library name: A17-H-3-28


title: 1029_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-19

value: male


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 5 minutes, batch 2, replicate 2

description: Library name: A17-H-3-27


title: skin_C8_3

description:
Library name: sample-8
NA


title: RNA-Seq of LNCaP cells grown in CSS, batch 2, replicate 2

description: Library name: A17-H-3-26


title: skin_C8_2

description:
Library name: sample-7
NA


title: 1028_BX21A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-18


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 4 hours, batch 2, replicate 1

description: Library name: A17-H-3-24


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 1 hour, batch 2, replicate 1

description: Library name: A17-H-3-23


title: skin_C8TNFR1_5

description:
Library name: sample-5
NA


title: 1028_BX18A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-17


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 5 minutes, batch 2, replicate 1

description: Library name: A17-H-3-22


title: 1029_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-20


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 4 hours, batch 2, replicate 1

description: Library name: A17-H-3-21


title: 1028_BX18A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-16


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 1 hour, batch 2, replicate 1

description: Library name: A17-H-3-20


title: RNA-Seq of LNCaP cells grown in FBS, batch 2, replicate 2

description: Library name: A17-H-3-25

value: FBS


title: 1028_BX15A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-15


title: RNA-Seq of LNCaP cells grown in CSS, batch 2, replicate 1

description: Library name: A17-H-3-18


title: skin_C8TNFR1_3

description:
Library name: sample-3
NA


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 5 minutes, batch 2, replicate 1

description: Library name: A17-H-3-19


title: RNA-Seq of LNCaP cells grown in FBS, batch 2, replicate 1

description: Library name: A17-H-3-17


title: CP017, 2 months, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP017_2m_GEX5


title: 1028_BX13A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-14


title: skin_C8_1

description:
Library name: sample-6
NA


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 4 hours, batch 1, replicate 2

description: Library name: A17-H-3-16


title: 1028_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-13


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 1 hour, batch 1, replicate 2

description: Library name: A17-H-3-15


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 5 minutes, batch 1, replicate 2

description: Library name: A17-H-3-14


title: CP013, 1 month, PBMC, perinatal HIV (pHIV), TCR

description: Library name: CP013_1m_TCR


title: skin_C8TNFR1_1

description:
Library name: sample-1
excluded_from_analysis


title: skin_C8TNFR1_4

description:
Library name: sample-4
NA


title: skin_C8TNFR1_2

description:
Library name: sample-2
NA


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 4 hours, batch 1, replicate 2

description: Library name: A17-H-3-13


title: 1027_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-12


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 1 hour, batch 1, replicate 2

description: Library name: A17-H-3-12


title: 1027_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-11


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 5 minutes, batch 1, replicate 2

description: Library name: A17-H-3-11


title: skin_TPC8STING_5

description:
Library name: sample_23
yes


title: RNA-Seq of LNCaP cells grown in CSS, batch 1, replicate 2

description: Library name: A17-H-3-10


title: skin_TPC8STING_4

description:
Library name: sample_22
yes


title: RNA-Seq of LNCaP cells grown in FBS, batch 1, replicate 2

description: Library name: A17-H-3-9


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 4 hours, batch 1, replicate 1

description: Library name: A17-H-3-8


title: skin_TPC8TNFR1_5

description:
Library name: sample_21
yes


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 1 hour, batch 1, replicate 1

description: Library name: A17-H-3-7


title: 1026_BX16A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-10


title: RNA-Seq of LNCaP cells grown in CSS, treated with NRG-1 100ng/ml for 5 minutes, batch 1, replicate 1

description: Library name: A17-H-3-6


title: skin_TPC8TNFR1_4

description:
Library name: sample_20
yes


title: 1025_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-8


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 4 hours, batch 1, replicate 1

description: Library name: A17-H-3-5


title: skin_TPC8_5

description:
Library name: sample_19
yes


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 1 hour, batch 1, replicate 1

description: Library name: A17-H-3-4


title: RNA-Seq of LNCaP cells grown in CSS, treated with EGF 100ng/ml for 5 minutes, batch 1, replicate 1

description: Library name: A17-H-3-3


title: 1025_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-7


title: 1024_BX6A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-6


title: skin_TPC8_4

description:
Library name: sample_18
yes


title: NSC,ASXL3

city: Cincinnati

first: Jason

last: Tchieu

address: 240 Albert Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Raw FASTQ files were quality checked using FastQC. Adapter sequences were trimmed using fastp with parameters "-q 20 -n7". Trimmed reads were then aligned to hg38 using HISAT2 with default parameters. The raw count files was generated using featureCounts in Subread with default parameters.
Genes with no raw counts in >= 75% samples were filtered out. Differential gene expression analysis was performed using "DESeq2" with p.adjust < 0.05 and fold change > 1.5.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

growth_protocol: Human embryonic stem cells (hESCs) were maintained in Essential 8 medium in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA-Seq libraries (poly A enrichment) for hESCs were prepared using TruSeq Stranded mRNA library kit and sequenced at Roy J. Carver Biotechnology Center (CBC) at the University of Illinois at Urbana-Champaign (UIUC) for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform. mRNA-Seq libraries (poly A enrichment) for NSCs were prepared by Novogene for 150bp paired-end (PE) sequencing on an Illumina NovaSeq platform.

treatment_protocol: Cortical neural stem cells (NSCs) were directly differentiated from hESCs using dual-SMAD strategies for the first 8 days, and subsequently treated with FGF8 to pattern prefrontal cortical lineage until day 18. For overexpression studies, doxycycline treatment starts at d15 till d18.

value: cortical neural stem cells

value: ASXL3 -/-

value: cortical differentiation


title: RNA-Seq of LNCaP cells grown in FBS, batch 1, replicate 1

description: Library name: A17-H-3-1


title: 1026_BX14A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-9


title: skin_TPCONTROL_5

description:
Library name: sample_17
yes

value: skin

value: TPCONTROL


title: NSC,KDM5B,clone2

value: KDM5B -/-


title: skin_TPCONTROL_4

description:
Library name: sample_16
yes


title: NSC,KDM5B,clone1


title: NSC,CUL3,2


title: CP013, 1 month, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: CP013_1m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)

value: Blood

value: PBMC

value: perinatal HIV (pHIV)


title: 1024_BX3A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-4


title: NSC,CUL3,1


title: skin_TPCONTROL_3

description:
Library name: sample_15
yes


title: RNA-Seq of LNCaP cells grown in CSS, batch 1, replicate 1

description: Library name: A17-H-3-2

value: LNCaP

value: CSS


title: 1024_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-3


title: CP017, 2 months, PBMC, perinatal HIV (pHIV), Feature Barcode/Antibody Derived Tag (FB/ADT)

description:
Library name: CP017_2m_FB5
see GEX sample for processed data; ADT antibodies - TotalSeq-C Human Universal Cocktail (Biolegend, Cat# 399905)


title: NSC,RELN,clone1

value: RELN -/-


title: NSC,RELN,clone2


title: skin_not_discosed_3

description:
Library name: sample-13
normalization_only


title: CP013, 1 month, PBMC, perinatal HIV (pHIV), BCR

description: Library name: CP013_1m_BCR


title: 1023_BX1A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-2


title: skin_TPCONTROL_2

description:
Library name: sample_14
excluded_from_analysis


title: NSC,DEAF1,1

value: DEAF1 -/-


title: NSC,DEAF1,2


title: NSC,ASH1L,2

value: ASH1L -/-


title: skin_TPCONTROL_1

description:
Library name: sample_13
yes


title: 1022_BX23A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-1


title: NSC,ASH1L,1


title: 1024_BX3A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-5


title: NSC,UMOD,clone1,2

value: WT


title: skin_not_discosed_2

description:
Library name: sample-12
normalization_only


title: NSC,UMOD,clone3


title: skin_non_disclosed_1

description:
Library name: sample_10
normalization_only


title: NSC,FLAG,dox,2

value: cortical differentiation, dox (200ng/ml) for 3 days


title: 1022_BX19A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-32

value: male


title: NSC,UMOD,clone1,1

value: cortical neural stem cells


title: NSC,UMOD,clone2


title: 1022_BX18A-2

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-147-31


title: NSC,FLAG,no,dox,1

value: cortical differentiation, with no dox


title: skin_TPC8TNFR1_2

description:
Library name: sample_8
yes


title: CP011, 2 months, PBMC, perinatal HIV (pHIV), Gene Expression (GEX)

description: Library name: CP011_2m_GEX5


title: NSC,FLAG,dox,1


title: NSC,FLAG,no,dox,2


title: NSC,Homo,4

value: ZMYND11 -/-

value: cortical differentiation


title: 1029_BX24A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-23


title: NSC,Homo,3


title: 1030_BX13A-1

description:
Total RNA was extracted from laser capture microdissected tisuse, using the Qiagen RNeasy FFPE kit. Up to 100ng of RNA was prepared into libraries at NCI CCR Illumina Sequencing Core Facility uisng the NEBNext Ultra II Directional RNA-Seq kit. Sequence reads were then filtered to remove low quality reads, followed by the trimming of low quality bases and bases corresponding to sequencing adaptors. RNA Sequence reads were aligned with STAR to the human genome, hg19. The RSEM algorithm was applied to compute the raw reads count and transcripts per million (TPM) value.
processed_TPM.txt
A9-148-24