title: Day 7 naphthalene Sca1pos 2

extract_protocol:
Lungs were extracted from mice at 2 or 7 days after injection, dissociated into single-cell suspension, and enriched via FACS.
10X Genomics 3' Single Cell RNA Sequencing Protocol Version 3 and 3.1
3' Single Cell RNA Sequencing

value: Epithelial

tag: sorted cell_type

value: Wildtype

value: 200 mg/kg naphthalene

tag: timepoint

value: day 7


title: Control, R23804

status: Public on Apr 08 2026

type: SRA

city: New York City

first: Michael

middle: S

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Library name: R23804

library_source: transcriptomic

data_processing:
Raw sequencing reads were processed using the RAPiD-nf pipeline, with alignment to the GRCh38 reference genome performed using STAR v2.7.3a.
Alignment quality was assessed with RSeQC and Picard. PCR duplicates were marked but not removed prior to quantification.
Gene-level counts were generated using featureCounts (Subread v2.0.1) with GENCODE v32 annotations.
Counts were normalized usingthe VOOM method from the limma package (v3.48.3), and log2-transformed expression matrices were created seperately for DLPFC and hippocampus.
Assembly: GRCh38 (Ensembl release 95)
Supplementary files format and content: tab-delimited text file (T21_raw_counts.txt) includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: DLPFC

extract_protocol:
Total RNA was extracted from frozen dorosolateral prefrontal cortex and hippocampal tissues using the AllPrep DNA/RNA Mini Kit, and only samples with RIN ≥ 9.0 were included.
RNA-seq libraries were generatred from 300 ng of high-quality total RNA using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold.

tag: tissue

value: DLPFC

tag: karyotype

value: Control

tag: rin

tag: gestational age

tag: Sex

value: M

tag: race

value: Caucasian


title: Day 2 corn oil Sca1neg 1

city: Boston

first: margherita

last: paschini

state: MA

address: 1 blackfan circle, Karp Building

department: Hem/Onc

institute: Boston Children's Hospital

library_source: transcriptomic single cell

data_processing:
10X Genomics Cell Ranger 3.1.0 Pipeline was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting.
Assembly: mm10-1.2.0
Supplementary files format and content: h5 files for each library

organism: Mus musculus

source_name: lung

treatment_protocol: Adult mice were given intraperitoneal injections of 200 mg/kg naphthalene in corn oil or corn oil control (of equal volume).

value: lung

tag: cell type

tag: genotype

tag: treatment

value: Corn oil


title: BIS_Discovery_7

type: genomic

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

country: Germany

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

hyb_protocol: The bisulfite treatment and hybridisation was carried out by Life & Brain GmbH

scan_protocol: iscan, carried out by Life & Brain GmbH

data_processing:
ChAMP package in R environment
processed value definition: combat normalised beta methylation values (linked as supplementary file on the Series record)

label: Cy3, Cy5

molecule: genomic DNA

source_name: Blood cells

label_protocol: Labeling was carried out by Life & Brain GmbH

extract_protocol: precipitation with sodium acetate

treatment_protocol: Genomic DNA was extracted from blood cells.

value: BIS

value: Blood cells


title: Control, R18802

description: Library name: R18802


title: BIS_Discovery_8


title: BIS_Discovery_4


title: CLAD lung, CD31 segment, ROI C1E2

city: houston

first: Nirmal

last: Sharma

state: MAtx

address: Baylor college of medicine

institute: Baylor college of medicine

description:
Library name: DSP-1001660018221-A-A03
GeoMx WTA, CLAD, CD31, slide CLAD 1_11.6.24

data_processing:
Raw FASTQ files were processed using the NanoString GeoMx NGS Pipeline (DnD) to generate Digital Count Conversion (DCC) files containing probe-level count data.
DCC files were loaded into NanoString GeoMx DSP software for QC, filtering, and normalization. Third-quartile (Q3) normalization was applied for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: DCC files: NanoString Digital Count Conversion files containing probe-level read counts per area of illumination (AOI).
Supplementary files format and content: geomx_Q3_log2_normalized_matrix.csv: Q3 (upper quartile, 75th percentile) normalized, log2-transformed expression values for all genes across all samples.
Supplementary files format and content: Hs_R_NGS_WTA_v1.0.pkc: NanoString Probe Kit Configuration file mapping probes to target genes for the Human WTA panel.
Library strategy: Spatial Transcriptomics

extract_protocol:
Paraffin-embedded human lung tissue sections (5 um) were placed on GeoMx slides. Tissue was deparaffinized and rehydrated. RNA targets were hybridized with the NanoString GeoMx Human Whole Transcriptome Atlas (WTA) probe panel. Fluorescently labeled antibodies against CD31, PanCK, and CD45 were applied for morphology-guided region of interest (ROI) selection using the GeoMx Digital Spatial Profiler (DSP).
UV-cleaved oligonucleotide tags from selected areas of illumination (AOIs) were collected, indexed, and PCR-amplified to generate sequencing libraries using the NanoString GeoMx NGS Library Prep kit per manufacturer instructions. Panel: (v1.0) Human NGS Whole Transcriptome Atlas RNA.

tag: sample type

value: CLAD

tag: segment

tag: roi

tag: slide

tag: nuclei


title: lung epithelial cells, day 2 corn oil Sca1pos 1

value: day 2


title: BIR_Discovery_6

value: BIR


title: CLAD lung, CD31 segment, ROI C1E1

description:
Library name: DSP-1001660018221-A-A02
GeoMx WTA, CLAD, CD31, slide CLAD 1_11.6.24


title: lung epithelial cells, day 7 corn oil Sca1pos 1


title: Day 7 naphthalene Sca1pos 1


title: Control, R18818

description: Library name: R18818


title: Control, R18801

description: Library name: R18801

value: F


title: NTC, No Template Control, Slide A

description:
Library name: DSP-1001660018221-A-A01
GeoMx WTA, NTC, No Template Control, slide CLAD 1_11.6.24

value: NTC


title: NTC, No Template Control, Slide B

description:
Library name: DSP-1001660018222-B-A01
GeoMx WTA, NTC, No Template Control, slide Normal_11.15.24


title: T21, R13656

description: Library name: R13656


title: Day 2 naphthalene Sca1neg 2

value: Epithelial


title: BIS_Discovery_5


title: RIP-Seq, A549, NAT10 ko

city: Harbin

first: qiong

last: wu

address: No. 92, Xida Street, Nangang District

country: China

institute: Harbin Institute of Technology

description: Library name: Sample 4

data_processing:
STAR v2.7.10a
Assembly: hg38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent.
RNA libraries for RIP-seq were prepared using the SMARTER mRNA-Seq Library Prep Kit following the manufacturer's standard protocols.

tag: cell line

value: human non-small cell lung cancer cells


title: Control, R18815

description: Library name: R18815


title: BIR_Discovery_3


title: Control, R18816

description: Library name: R18816


title: lung epithelial cells, day 7 naphthalene Sca1neg 1

tag: sorted cell_type

value: Wildtype

value: 200 mg/kg naphthalene


title: BIR_Discovery_1


title: Control, R13654

description: Library name: R13654

value: DLPFC


title: A549, NAT10 ko1

description: Library name: Sample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: hg38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

extract_protocol:
Total RNA was extracted using RNAiso Plus reagent.
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seq Library Prep Kitfollowing manufacturer's protocols.


title: BIS_Discovery_2


title: Control, R18811

description: Library name: R18811

value: Control


title: A549,Control

description: Library name: Sample 1


title: lung epithelial cells, day 7 naphthalene Sca1neg 2

tag: timepoint

value: day 7


title: T21, R18800

description: Library name: R18800

tag: tissue

value: Caucasian


title: RIP-Seq, A549,Control

description: Library name: Sample 3


title: lung epithelial cells, day 7 corn oil Sca1neg 1

value: lung


title: Tenderloin, L-type, S0385

status: Public on Apr 07 2026

city: Seoul

first: Suyeon

last: Wy

address: 20, Neungdong-ro, Gwangjin-gu

department: Department of Biomedical Science and Engineering

country: South Korea

institute: Konkuk University

description: Library name: kmp_l_s0385_tenderloin

data_processing:
Raw RNA-seq reads were trimmed using Trimmomatic (v0.36) with the “keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” options. Next, rRNA sequences were filtered employing SortMeRNA (v4.2.0).
The pre-processed RNA-seq reads were assembled using rnaSPAdes (v4.2.0) to build a transcriptome assembly. The transcripts from all samples with TPM values ≥1 were subsequently analyzed. To reduce redundancy, transcripts with ≥98% sequence identity were clustered with CD-HIT (v4.8.1) using the “-c 0.98 -p 1 -d 0 -b 3” options. Lastly, the transcriptome assemblies generated for all tissues were merged with the final de novo assembly using the “tr2aacds.pl” script from EvidentialGene (v23jul15).
Transcript expression profiles for each tissue sample were generated using the Korean minipig transcriptome assembly constructed in this study. Normalized transcript-level expression data (TPM values) were quantified with Salmon (v1.10.0) using RNA-seq reads from all samples .
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes TPM values for each sample
Supplementary files format and content: FASTA file includes transcript sequences for Korean minipig
Supplementary files format and content: tab-delimited text file includes functional annotation of transcripts

organism: Sus scrofa

source_name: Tenderloin

extract_protocol:
Total RNA was extracted using the TRIzol reagent.
Sequencing libraries were prepared with a TruSeq Stranded mRNA LT Sample Prep Kit.

value: Tenderloin


title: Tenderloin, L-type, S0384

description: Library name: kmp_l_s0384_tenderloin


title: Tenderloin, L-type, S0355

description: Library name: kmp_l_s0355_tenderloin


title: Lymph, L-type, S0385

description: Library name: kmp_l_s0385_lymph

source_name: Lymph

value: Lymph


title: Lymph, L-type, S0377

description: Library name: kmp_l_s0377_lymph


title: Tenderloin, L-type, S0349

description: Library name: kmp_l_s0349_tenderloin


title: Loin, L-type, S0385

description: Library name: kmp_l_s0385_loin

source_name: Loin

value: Loin


title: Tenderloin, L-type, S0377

description: Library name: kmp_l_s0377_tenderloin


title: Lymph, L-type, S0349

description: Library name: kmp_l_s0349_lymph


title: Loin, L-type, S0384

description: Library name: kmp_l_s0384_loin


title: Lymph, L-type, S0384

description: Library name: kmp_l_s0384_lymph


title: Brain, L-type, S0385

description: Library name: kmp_l_s0385_brain

source_name: Brain

value: Brain


title: Lymph, L-type, S0355

description: Library name: kmp_l_s0355_lymph


title: Brain, L-type, S0349

description: Library name: kmp_l_s0349_brain


title: Backfat, L-type, S0384

description: Library name: kmp_l_s0384_backfat

source_name: Backfat

value: Backfat


title: Brain, L-type, S0384

description: Library name: kmp_l_s0384_brain


title: Tenderloin, ET-type, S0326

description: Library name: kmp_et_s0326_tenderloin


title: Brain, L-type, S0377

description: Library name: kmp_l_s0377_brain


title: Brain, L-type, S0355

description: Library name: kmp_l_s0355_brain


title: Tenderloin, ET-type, S0309

description: Library name: kmp_et_s0309_tenderloin


title: Backfat, L-type, S0349

description: Library name: kmp_l_s0349_backfat


title: Backfat, L-type, S0355

description: Library name: kmp_l_s0355_backfat


title: Tenderloin, ET-type, S0276

description: Library name: kmp_et_s0276_tenderloin


title: Loin, L-type, S0349

description: Library name: kmp_l_s0349_loin


title: Backfat, L-type, S0377

description: Library name: kmp_l_s0377_backfat


title: Tenderloin, ET-type, S0242

description: Library name: kmp_et_s0242_tenderloin


title: Loin, L-type, S0355

description: Library name: kmp_l_s0355_loin


title: Loin, L-type, S0377

description: Library name: kmp_l_s0377_loin


title: Tenderloin, ET-type, S0235

description: Library name: kmp_et_s0235_tenderloin


title: Backfat, L-type, S0385

description: Library name: kmp_l_s0385_backfat


title: Lymph, ET-type, S0309

description: Library name: kmp_et_s0309_lymph


title: Lymph, ET-type, S0242

description: Library name: kmp_et_s0242_lymph


title: Lymph, ET-type, S0276

description: Library name: kmp_et_s0276_lymph


title: Loin, ET-type, S0326

description: Library name: kmp_et_s0326_loin


title: Lymph, ET-type, S0235

description: Library name: kmp_et_s0235_lymph


title: Loin, ET-type, S0242

description: Library name: kmp_et_s0242_loin


title: Backfat, ET-type, S0242

description: Library name: kmp_et_s0242_backfat


title: Loin, ET-type, S0235

description: Library name: kmp_et_s0235_loin


title: Backfat, ET-type, S0326

description: Library name: kmp_et_s0326_backfat


title: Brain, ET-type, S0235

description: Library name: kmp_et_s0235_brain


title: D425 ATAC-Seq

city: Memphis

first: Pediatric Cancer Dependencies

last: Acclerator

state: TN

address: 262 Danny Thomas Blvd

institute: Pediatric Cancer Dependencies Accelerator

description:
Library name: D425 ATAC-Seq
PDDS_01963

library_source: genomic

data_processing:
ATAC-seq read quality was assessed with FastQC  (v0.11.9). The Illumina adapter (“CTGTCTCTTATACACATCT”) and low-quality bases were trimmed and reads shorter than 60 bp were removed using TrimGalore  (v0.6.10) and Cutadapt  (v3.7). Reads were aligned to the human genome (GRCh38) with Bowtie1  (v1.2.3) using ATAC-seq optimized parameters (--allow-contain --chunkmbs=256 -l=76 -k=2 -m=2 -X=600 --best). Post-alignment filtering removed low-quality, mitochondrial, and duplicate reads, as well as reads overlapping ENCODE blacklist regions, using Samtools  (v1.9) and Bedtools  (v2.30.0). Quality metrics, including transcription start site enrichment, nucleosome profiling, fraction of reads in peaks (FRiP), and library complexity, were calculated using the SEASEQ  (v3.1) QC modules. Within SEQSEQ, genome coverage tracks were generated from paired-end BAM alignments by converting mapped fragments to paired BEDPE format, quantifying fragment coverage in 50 bp bins, and converting the resulting graphs to bigwig format using the UCSC bedGraphToBigWig command-line program.
Assembly: GRCh38
Supplementary files format and content: bigWig tracks with reads-per-million-normalized fragment coverage of 50bp bins

source_name: Medulloblastoma

growth_protocol: D425-Cas9 was cultured as a mix of adherent and suspension in DMEM supplemented to a final concentration of 10% FBS, 2mM L-glutamine, and 2mM sodium pyruvate FBS and blasticidin (2μg/ml) at 5% CO2 at 37C.

extract_protocol:
For ATAC sequencing, we follow the protocol established by Buenrostro et al. (Curr. Protoc. Mol. Biol., 2015). Briefly, around 50,000 cells were used for nuclei preparation.
Chromatin tagmentation and library construction were carried out using the Illumina@ Tagment DNA Enzyme and Buffer kit (Illumina). ATACseq DNA libraries were sequenced on the Illumina NextSeq 2000.

value: Medulloblastoma


title: Brain, ET-type, S0242

description: Library name: kmp_et_s0242_brain


title: Loin, ET-type, S0309

description: Library name: kmp_et_s0309_loin


title: Lymph, ET-type, S0326

description: Library name: kmp_et_s0326_lymph


title: Backfat, ET-type, S0309

description: Library name: kmp_et_s0309_backfat


title: Brain, ET-type, S0276

description: Library name: kmp_et_s0276_brain


title: Brain, ET-type, S0326

description: Library name: kmp_et_s0326_brain


title: scCITEseq, metastatic breast cancer organoids, HTO

city: Frankfurt a.M.

first: Francesco

last: Pampaloni

address: Max-von-Laue-Str. 15

institute: Goethe University Frankfurt a.M.

description:
Library name: Rieger_Rhapsody_Run40_BCO_HTO
Hashtag-derived oligonucleotide (HTO), also referred to as sample tag

library_source: other

data_processing:
Following Illumina sequencing, the FASTQ files and reference sequences for mRNAs and ADTs were uploaded to the SevenBridges platform (Seven Bridges Genomics, https://www.sevenbridges.com). The data was processed using the BD Rhapsody analysis pipeline with default settings.
Assembly: References gencodev29-20181205.gtf GRCh38-PhiX-gencodev29.tar.gz
Supplementary files format and content: Comma seperated value files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: Metastatic breast cancer organoids, luminal A and B

growth_protocol: Organoids were grown and treated in the corresponding breast cancer organoid medium (Wächtershäuser et al., 2026).

extract_protocol:
Sorted viable single cells were loaded on the Rhapsody microwell cartridge (BD) to capture 40,000 cells according to manufacturer’s instructions. Oligonucleotide-labeled beads were added, incubated and washed prior to cell lysis by 5 mM DTT. After bead removal, the cDNA was synthesized using the corresponding cDNA kit (BD).
The DNA libraries were produced according to the instructions of the BD Rhapsody whole transcriptome analysis (WTA), ADTs and Sample Tag amplification kit (BD).

treatment_protocol: Treatment was performed for 24 h prior to organoid disruption to single cells. Single cell suspension was labelled with the Invitrogen LIVE/DEAD Fixable Red Dead Cell Stain Kit following manufacturer's instructions. For multiplexing, sample tags were added to the cells in BD Pharmingen™ Stain Buffer (BD) with BSA.

value: Epithelial cells

value: Mixed sample (donor and treatment):non-treated:1.5 % DMSO for 24 h Bi:10 µM Birinapant for 24 h BiE:10 µM Birinapant + 10 µM Emricasan for 24 h H+BiE:pre-treatment:30 µM HOIPIN-8 for 30 min; treatment:10 µM Birinapant + 10 µM Emricasan + 30 µM HOIPIN-8 for 24 h

tag: library type

value: HTO

tag: hto

value: SampleTag01_hs Donor #2 non-treated SampleTag02_hs Donor #2 Bi SampleTag03_hs Donor #2 BiE SampleTag04_hs Donor #2 H+BiE SampleTag05_hs Donor #3 non-treated SampleTag06_hs Donor #3 Bi SampleTag07_hs Donor #3 BiE SampleTag08_hs Donor #3 H+BiE SampleTag09_hs Donor #1 non-treated SampleTag10_hs Donor #1 Bi SampleTag11_hs Donor #1 BiE SampleTag12_hs Donor #1 H+BiE


title: Backfat, ET-type, S0235

description: Library name: kmp_et_s0235_backfat


title: Backfat, ET-type, S0276

description: Library name: kmp_et_s0276_backfat


title: Brain, ET-type, S0309

description: Library name: kmp_et_s0309_brain


title: D458 ATAC-Seq

description:
Library name: D458 ATAC-Seq
PDDS_01964

growth_protocol: D458-Cas9 was cultured as a mix of adherent and suspension in DMEM/F12 supplemented to a final concentration of 15% FBS and blasticidin (4μg/ml) in humidified atmosphere at 5% CO2 at 37C.


title: Loin, ET-type, S0276

description: Library name: kmp_et_s0276_loin


title: scCITEseq, metastatic breast cancer organoids, ADT

description:
Library name: Rieger_Rhapsody_Run40_BCO_ADT
Antibody-derived oligonucleotide (ADT)

value: Metastatic breast cancer organoids, luminal A and B

value: ADT

tag: adt

value: >CD10|MME|AHS0051|pAbO Catalog_940045 CCTGTTTGATGCGTACGGAGATTTAGCGGATTTATG >CD13|ANPEP|AHS0050|pAbO Catalog_940044 ATAATAATAATCGGGTGTTTCGCGGACTGTTGCATG >CD15|FUT4|AHS0196|pAbO Catalog_940274 ATAGGCATGGACGACGTAGATAATAAGTGGCGGGTT >CD18|ITGB2|AHS0091|pAbO Catalog_940086 AGGCGTTCTAAATTGTCGTATGGTGCGGGTATGTCT >CD26|DPP4|AHS0109|pAbO Catalog_940101 TGTAGGTTGCGCGGTTATTAGGGTATTATCGATCTG >CD47|CD47|AHS0087|pAbO Catalog_940082 TGTTAGGTTCGACGTATTATGTGTAGATCCGCAAGG >CD69|CD69|AHS0010|pAbO Catalog_940019 CAATAACGGGTCATAGTAAGTCGCGAGTAAGAGGGC >CD44:L178|CD44|AHS0167|pAbO Catalog_940251 GTGATTGATTAGGACAGTTCGTTGCTTAGTAGTGGG >CD90|THY1|AHS0045|pAbO Catalog_940032 GACTATATGTACGGTGTTAATTCGGGATCCTGCGCT >HLA-A_B_C|HLA-A_B_C|AHS0066|pAbO Catalog_940062 GATATGCATGGCGAGTAGGTAGAACGAAGCTTAGGT >HLA-DR|CD74|AHS0035|pAbO Catalog_940010 TGTTGGTTATTCGTTAGTGCATCCGTTTGGGCGTGG >CD117:YB5.B8|KIT|AHS0064|pAbO Catalog_940051 GGATTAGTTGTCGTTATAGGGAGTGCGTTCTTAGCG >CD9|CD9|AHS0082|pAbO Catalog_940078 GGGTTGTAAGTCGTCGGAAGTGTGAAGCGTATAGTG >CD274|CD274|AHS0004|pAbO Catalog_940035 ATCGTAAGGCTCGTGGTTCGTAAGTAAGTTCGTATC >CD273|PDCD1LG2|AHS0075|pAbO Catalog_940071 TGAGTAACCGTATGTAATCCGTAATCGTAGAAGCGC >CD133:W6B3C1|PROM1|AHS0103|pAbO Catalog_940095 TTTGGTATTGGCACGGTTTGTAGCGAGTTGACGGTC >CD34:581|CD34|AHS0061|pAbO Catalog_940021 TGGGTGTATTACGGTTAGTTTATGCGCGAAGGTGTT >CD25:2A3|IL2RA|AHS0026|pAbO Catalog_940009 AGTTGTATGGGTTAGCCGAGAGTAGTGCGTATGATT >IgG|IGHG1_2_3_4|AHS0059|pAbO Catalog_940027 AGGTAGGTTATCGTAGGGTAGACTTAGCGGGCATTG >CD24|CD24|AHS0042|pAbO Catalog_940028 ACTTTGGGTTGAGCGCATGATTATTCGTGACACTTT


title: scCITEseq, metastatic breast cancer organoids, GEX

description:
Library name: Rieger_Rhapsody_Run40_BCO_GEX
RNA

molecule: polyA RNA

value: RNA


title: SUDIPG24 ATAC-Seq

description:
Library name: SUDIPG24 ATAC-Seq
PDDS_01962

source_name: Diffuse intrinsic pontine glioma (DIPG / diffuse midline glioma)

growth_protocol: SUDIPG24-Cas12 was cultured in the flask coated with 1% Matrigel with medium TSM base media supplemented with growth factors and blasticidin (20μg/ml) at 5% CO2 at 37C.


title: SUDIPG19A ATAC-Seq

description:
Library name: SUDIPG19A ATAC-Seq
PDDS_01960

growth_protocol: SUDIPG19A-Cas12 was cultured in the flask coated with 1% Matrigel  with medium TSM base media supplemented with growth factors and blasticidin (20μg/ml) at 5% CO2 at 37C.

value: Diffuse intrinsic pontine glioma (DIPG / diffuse midline glioma)


title: SUDIPG13 ATAC-Seq

description:
Library name: SUDIPG13 ATAC-Seq
PDDS_01607

growth_protocol: SUDIPG13-Cas12 were cultured in TSM base media supplemented with growth factors and blasticidin (50μg/ml) at 5% CO2 at 37C


title: HSJDDIPG007 ATAC-Seq

description:
Library name: HSJDDIPG007 ATAC-Seq
PDDS_01959

growth_protocol: HSJDDIPG007-Cas12 cultured in TSM base media supplemented with growth factors and blasticidin (30μg/ml) at 5% CO2 at 37C.


title: RD ATAC-Seq

description:
Library name: RD ATAC-Seq
PDDS_01502

source_name: Rhabdomyosarcoma (embryonal)

growth_protocol: RD-Cas9 was cultured as adherent in DMEM/F12 supplemented to a final concentration of 5% FBS, 2mM L-Glutamine, 5ug/mL Insulin, 10mM Selenium, 10mM HEPES, 10nM Hydrocortisone, and 10nM Beta-estradiol.

value: Rhabdomyosarcoma (embryonal)


title: RH30 ATAC-Seq

description:
Library name: RH30 ATAC-Seq
PDDS_01318

source_name: Rhabdomyosarcoma (alveolar)

growth_protocol: RH30-Cas9 was cultured as adherent in RPMI supplemented to a final concentration of 10% FBS and blasticidin (6μg/ml) at 5% CO2 at 37C.

value: Rhabdomyosarcoma (alveolar)


title: SMSCTR ATAC-Seq

description:
Library name: SMSCTR ATAC-Seq
PDDS_01122

growth_protocol: SMSCTR-Cas9 was cultured as adherent in RPMI supplemented to a final concentration of 10% FBS and blasticidin (2μg/ml) at 5% CO2 at 37C.


title: D341 ATAC-Seq

description:
Library name: D341 ATAC-Seq
PDDS_00786

growth_protocol: D341Med-Cas9 was cultured as a mix of adherent and suspension in DMEM/F12 supplemented to a final concentration of 15% FBS and blasticidin (4μg/ml) in humidified atmosphere at 5% CO2 at 37C.


title: HDMB03 ATAC-Seq

description:
Library name: HDMB03 ATAC-Seq
PDDS_01315

growth_protocol: HDMB03-Cas12 was cultured as adherent in RPMI supplemented to a final concentration of 10% FBS and blasticidin (10μg/ml) in humidified atmosphere at 5% CO2 at 37C.


title: D283 ATAC-Seq

description:
Library name: D283 ATAC-Seq
PDDS_00769

growth_protocol: D283MED-Cas9 was cultured as a mix of adherent and suspension in EMEM  supplemented to a final concentration of 10% Fetal Bovine Serum (FBS), 1nM Sodium Pyruvate and blasticidin (4μg/ml) in humidified atmosphere at 5% CO2 at 37C.


city: South San Francisco,

first: Carolina

last: Galan

state: CA

address: 1 DNA Way

institute: Genentech

description: Library name: H358Cas12adTagV148h_EpiGenFactor_CROPseq_FL

data_processing:
scRNA-seq reads were mapped to the reference human genome GRCh38 or a custom reference containing full length pre-crRNA sequences using Cell Ranger v7.1.0
Demultiplexing of pre-crRNA feature barcoding data and assigning pre-crRNA to cells was performed with a custom script as described in Xie et al., 2019 with analysis performed for both full length pre-crRNA sequences or barcodes alone.
Assembly: GRCh38
Supplementary files format and content: CellRanger output files ending in barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz for H358s. Cumulus output files ending in csv.gz for K562s.

growth_protocol: Parental H358 and K562 cell lines were sourced from Genentech cell bank (gCell), where it was maintained under mycoplasma-free conditions. Cell lines were cultured in RPMI-1640 growth medium + 10% heat inactivated FBS (Sigma, F4135) + 2mM L-Glutamine and 100 U/mL Penicillin-streptomycin (Gibco, 15140-122).

extract_protocol:
Cells were resuspended in 1% BSA in 1xPBS to process through the 10x Genomics Chromium Controller according to the manufacturer’s protocol (CG000316 or CG000418) with a recovery aim of 10,000 - 20,000 cells per lane.
Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index) and Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 (Dual Index) (CG000316, CG000418) were used for library construction

treatment_protocol: Cells were cultured in the absence or  presence of 1µM dTAGV-1 (Tocris Bioscience, 6914) for 24h ) dTagV124h) or 48h ( dTagV148h).

value: Human lung


title: SUDIPG25 ATAC-Seq

description:
Library name: SUDIPG25 ATAC-Seq
PDDS_01961

growth_protocol: SUDIPG25-Cas12 was cultured in the flask coated with 1% Matrigel with medium TSM base media supplemented with growth factors and blasticidin (50μg/ml) at 5% CO2 at 37C.


description: Library name: H358Cas12adTagV148h_CellSurfaceReceptors_GEX


title: K562Cas12a_HTO

description:
Library name: K562Cas12a_HTO
Hashtag-derived oligonucleotide (HTO)

value: Human lymphoblast

value: TotalSeq-A0264 anti-human Hashtag 14, TotalSeq-C0278 anti-human Hashtag 18


description: Library name: H358Cas12adTagV124h_EpiGenFactor_CROPseq_FL


description:
Library name: H358Cas12adTagV148h_CellSurfaceReceptors_DCPerturbseq_FL
Hashtag-derived oligonucleotide (HTO)


description: Library name: H358Cas12adTagV148h_EpiGenFactor_CROPseq_BC


title: K562Cas12a_BC

description: Library name: K562Cas12a_BC


description:
Library name: H358Cas12adTagV148h_CellSurfaceReceptors_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-C0251 anti-human Hashtag 1, TotalSeq-A0252 anti-human Hashtag 2


description: Library name: H358Cas12adTagV148h_CellSurfaceReceptors_CROPseq_FL


title: H358Cas12adTagV148h_EpiGenFactor_GEX

description: Library name: H358Cas12adTagV148h_EpiGenFactor_GEX


title: H358Cas12adTagV148h_EpiGenFactor_HTO

description:
Library name: H358Cas12adTagV148h_EpiGenFactor_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-B0256 anti-human Hashtag 6, TotalSeq-C0257 anti-human Hashtag 7, TotalSeq-C0258 anti-human Hashtag 8, TotalSeq-C0259 anti-human Hashtag 9


title: H358Cas12adTagV124h_EpiGenFactor_GEX

description: Library name: H358Cas12adTagV124h_EpiGenFactor_GEX


title: H358Cas12a_EpiGenFactor_GEX

description: Library name: H358Cas12a_EpiGenFactor_GEX


title: H358Cas12a_EpiGenFactor_DCPerturbseq_FL

description: Library name: H358Cas12a_EpiGenFactor_DCPerturbseq_FL


description: Library name: H358Cas12adTagV124h_EpiGenFactor_CROPseq_BC


title: H358Cas12a_EpiGenFactor_DCPerturbseq_BC

description: Library name: H358Cas12a_EpiGenFactor_DCPerturbseq_BC


description: Library name: H358Cas12a_EpiGenFactor_DCPerturbseq_GEX


title: H358Cas12a_EpiGenFactor_CROPseq_BC

description: Library name: H358Cas12a_EpiGenFactor_CROPseq_BC


title: H358Cas12adTagV124h_EpiGenFactor_HTO

description:
Library name: H358Cas12adTagV124h_EpiGenFactor_HTO
Hashtag-derived oligonucleotide (HTO)

value: TotalSeq-A0253 anti-human Hashtag 3, TotalSeq-B0254 anti-human Hashtag 4


title: H358_CellSurfaceReceptors_CROPseq_FL

description: Library name: H358_CellSurfaceReceptors_CROPseq_FL


title: H358_CellSurfaceReceptors_DCCROPseq_FL

description: Library name: H358_CellSurfaceReceptors_DCCROPseq_FL


title: H358Cas12a_EpiGenFactor_CROPseq_FL

description: Library name: H358Cas12a_EpiGenFactor_CROPseq_FL


title: HDMB03 H3K27ac HiChIP

description:
Library name: HDMB03 H3K27ac HiChIP
PDDS_01309

data_processing:
Paired-end HiChIP and HiC sequencing data were processed using HiC-Pro  (v2.11.1). To improve computational efficiency, FASTQ files were split into subsets of 30 million read pairs and processed in parallel. Each read end was independently aligned to the human genome (GRCh38) with Bowtie2  (v2.3.5.1) using sensitive alignment parameters optimized for both global (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder) and local (--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder) mapping. Reads with MAPQ < 10, multi-mapped reads, and PCR duplicates were removed. Valid read pairs generated by HiC-Pro were subsequently converted into .hic format contact maps using the hicpro2juicebox.sh utility.
Assembly: GRCh38
Supplementary files format and content: HiC contact maps in .hic format
Library strategy: HiChIP

extract_protocol:
Chromatin crosslinking was conducted using a final concentration of 2% formaldehyde (Sigma Aldrich, F8775) for 10 minutes and was quenched with Arima Stop Solution 1 at a final concentration of 8.7%. The assay was performed on four million HDMB03-Cas12 or D458-Cas9 cells and on three million D425-Cas9 cells. HiChIP data were generated using the Arima-HiC+ kit (P/N A101020), according to the manufacturer’s protocol. Chromatin was sheared using the Covaris M220 focused ultrasonicator (PIP: 75 W, DF: 10 %, CPB: 200, Treatment time: 240 to 260 seconds, Setpoint Temperature: 7 °C) in 130 μL cold CS Buffer (10 mM Tris-HCl, pH 8.0, 0.1% SDS). Sheared chromatin was precleared at 4 °C for 1 hour on a rotator by adding 880 μL of cold MR1 Buffer (10 mM Tris-HCL, pH 8.0, 159 mM NaCl, 1.14 mM EDTA, 1.14% Triton X-100, 0.1% SDS, 0.114% Sodium Deoxycholate, 1.14% Protease Inhibitor Cocktail) and 30μL of Protein A Beads (Invitrogen, 10002D). Subsequently, each sample was incubated at 4 °C overnight on a rotator with the H3K27ac antibody (Active Motif, #91193) in an antibody:shearing yield ratio of 0.2. The shearing yield concentration was calculated from 10 µL of the sample taken after chromatin shearing. This aliquot worked as an input control in subsequent analysis. Thereafter, each sample was incubated at 4 °C for 4 hours on a rotator with Protein A Beads (Invitrogen, 10002D) previously overnight blocked with R2 Buffer (10 mM Tris-HCL, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate, 1% Protease Inhibitor Cocktail, 5 mg/mL BSA). Bead-bound enriched chromatin underwent several washes with different buffers to remove nonspecific fragments on a thermomixer at 4 °C for 3 minutes with 1000 rpm shaking. Respectively, three R1 Buffer washes (10 mM Tris-HCL, pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate, 1% Protease Inhibitor Cocktail), two R3 Buffer washes (10 mM Tris-HCL, pH 8.0, 300 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), one LC Buffer wash (10 mM Tris-HCL, pH 8.0, 150 mM Lithium Chloride, 1 mM EDTA, 0.5% IGEPAL CO-630, 0.1% Sodium Deoxycholate) and two LTE Buffer washes (10 mM Tris-HCL, pH 8.0, 0.1 mM EDTA). Reverse crosslinking followed the manufacturer’s protocol. Biotin enrichment was carried out using 100μL of Arima Enrichment Beads prior to library construction.
Libraries were prepared as described in the Arima-HiC+ HiChIP Library Preparation protocol, using Swift Accel-NGS® 2S Plus DNA Library Kit (Integrated DNA Technologies, 10009878), KAPA Library Amplification Kit (Roche Sequencing Solutions, 26148) and Swift Single Indexes, with 10 to 13 amplification cycles. Libraries were sequenced as 151 bp paired end reads on the Illumina NovaSeq X Plus system.

value: Medulloblastoma


title: HDMB03 HiC

description:
Library name: HDMB03 HiC
PDDS_01913

data_processing:
Paired-end HiChIP and HiC sequencing data were processed using HiC-Pro  (v2.11.1). To improve computational efficiency, FASTQ files were split into subsets of 30 million read pairs and processed in parallel. Each read end was independently aligned to the human genome (GRCh38) with Bowtie2  (v2.3.5.1) using sensitive alignment parameters optimized for both global (--very-sensitive -L 30 --score-min L,-0.6,-0.2 --end-to-end --reorder) and local (--very-sensitive -L 20 --score-min L,-0.6,-0.2 --end-to-end --reorder) mapping. Reads with MAPQ < 10, multi-mapped reads, and PCR duplicates were removed. Valid read pairs generated by HiC-Pro were subsequently converted into .hic format contact maps using the hicpro2juicebox.sh utility.
Assembly: GRCh38
Supplementary files format and content: HiC contact maps in .hic format

extract_protocol:
Chromatin crosslinking was conducted using a final concentration of 2% formaldehyde (Sigma Aldrich, F8775) for 10 minutes and was quenched with Arima Stop Solution 1 at a final concentration of 8.7%. The assay was performed on one million cells. Hi-C data were generated using the Arima-HiC+ kit (P/N A101020), according to the manufacturer’s protocols. Hi-C DNA was sheared using the Covaris M220 focused ultrasonicator (PIP: 50 W, DF: 25 %, CPB: 200, Treatment time: 65 seconds, Setpoint Temperature: 6 °C) in 100μL cold Elution Buffer. Fragments were size-selected to 200 bp-600 bp prior to biotin enrichment.
Before library construction, size-selected fragments were incubated at room temperature for 15 min with Dynabeads™ MyOne™ Streptavidin T1 beads (Invitrogen, 65601) previously washed three times with 200 µl of Binding Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl). Bead-bound samples were resuspended in 50 µl of Elution Buffer for library preparation using the KAPA HyperPrep Kit (Roche Sequencing Solutions, KK8505) and IDT for Illumina–TruSeq DNA Indexes (Illumina, 20022370), with 6 amplification cycles and DNA cleanup performed using 0.85X AMPure XP Beads (Beckman Coulter, A63881). Libraries were sequenced as 151 bp paired end on the Illumina NovaSeq X Plus system.


title: D458 HiC

description:
Library name: D458 HiC
PDDS_01915


title: D458 H3K27ac HiChIP

description:
Library name: D458 H3K27ac HiChIP
PDDS_02013


description: Library name: H358Cas12a_CellSurfaceReceptors_DCCROPseq_FL


title: Patient 11658 Germline PBMC WGS sample

city: Oxford

first: Breeshey

middle: Jane

last: Roskams-Hieter

address: John Radcliffe Hospital/Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description:
Library name: P11658PBMCDNA
PBMC WGS data for patient 11658, used to call somatic mutations and CNVs in the tumour sample

data_processing:
Reads were merged across lanes & then trimmed using TrimGalore! (v0.6.7)
Reads were aligned using bwa-mem2 (v2.2.1)
PCR duplicates were removed using Sambamba (v1.0)
Assembly: hg19
Supplementary files format and content: BAM, aligned sequences to the hg19 reference genome

source_name: Blood

extract_protocol:
WGS: For FT organoids and PBMC samples, the Genomic DNA (gDNA) was extracted with the DNeasy Blood & Tissue Kits (Qiagen), and quantified by Qubit. Tumor bulk RNA seq:Tumor cells around 5,000-20,000 cells were sorted by Epcam+ by FACS. The RNA was extracted by GenElute Single Cell RNA Purification Kit (Sigma-Aldrich) , and quantified by Agilent RNA 6000 Pico Kit.
The WGS libraries were prepared by Novogenes company and sequenced pair-ended on Illumina Novaseq X plus. For the tumor sample, tumor cells were sorted by Epcam+ by FACS, and the DNA was extracted by REPLI-g Advanced DNA Single Cell Kit and quantified by SpectraMax® Quant™ AccuBlue™ Pico dsDNA Assay Kit Cat. We used our in-house method DigiPico to construct the library. Tumor bulk RNA seq:The SMARTer Stranded Total RNA-Seq kit v2 - Pico Input (Takara) was used to prepare sequencing libraries which were indexed, enriched by 15 cycles of amplification, assessed using the Agilent TapeStation, and then quantified by Qubit. Sequenced pair-ended on Illumina Novaseq X plus

value: Blood

value: PBMCs


title: D425 H3K27ac HiChIP

description:
Library name: D425 H3K27ac HiChIP
PDDS_02238


description: Library name: H358Cas12a_CellSurfaceReceptors_DCPerturbseq_FL


description: Library name: H358Cas12a_CellSurfaceReceptors_CROPseq_FL


title: Patient 11658 Fallopian Tube WGS sample

description:
Library name: P11658TumDNA
Tumour WGS data for patient 11658

source_name: Ovary

value: Ovary

value: Epithelial


title: SPG4 cortical organoids

city: Daejeon

first: Youngsun

last: Lee

address: 125, Gwahak-ro, Yuseong-gu

institute: Korea Research Institute of Bioscience and Biotechnology

description: Library name: Sample 2

data_processing:
Sequencing reads were processed with the Cell Ranger version 9.0.0 (10X Genomics, CA) using the Human reference transcriptome GRCh38 that is provided by 10x Genomics. From the gene expression matrix, the downstream analysis was carried out with R version 4.2.2. Quality control, filtering, data clustering and  visualization, and the differential expression analysis was carried out using WinSeurat program (Ebiogen Inc,  Korea) based on Seurat version 4.2.2. R package (Hao et al., Cell) with some custom modifications to the  standard pipeline. For each individual dataset, genes expressed in cells < 500 UMIs and < 300 genes were  removed from the gene expression matrix. In addition, we removed any single cell with > 10% UMIs mapped  to mitochondrial genes and cells with complexity < 0.8. After scTransform-normalizing the data, the expression of each gene was scaled  regressing out the number of UMI in each cell. We performed  PCA on the gene expression matrix and used the first 25 principal components for clustering and visualization. Clustering was performed with a resolution of 0.7 and visualization was done using UMAP (uniform manifold  approximation and projection).
Assembly: Human reference transcriptome GRCh38
Supplementary files format and content: Barcodes (tsv), features (tsv), matrix (mtx)

extract_protocol:
Organoids were dissociated into single-cell suspensions using Accutase
Single-cell suspensions were washed and resuspended in 0.04% BSA in PBS. Cells were counted automatically with Countess III (Thermo Fisher, Waltham, MA) to determine their concentration. Single-cell RNA-sequencing libraries were the prepared using the Chromium GEM-X Single Cell Gene Expression v4 Kit (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. Briefly, the cells were diluted into the Chromium GEM-X Single Cell 3’ Chip as to yield a recovery of ~ 20,000 single-cell. Following the library preparation, the libraries were sequenced in multiplex on the Novaseq X Plus sequencer (Illumina, San Diego, CA) to produce on average a minimum of 50,000 reads per single cell.

value: Cortical organoid


title: Bulk RNA-sequencing of fallopian tube organoid for patient 11658

description:
Library name: P11658FTorgRNA
Bulk RNA-sequencing data for the fallopian tube of patient 11658, used to determine HLA typing during neoantigen prediction. One replicate was generated for this sample.

data_processing:
Reads were trimmed using TrimGalore! (v0.6.7)
Trimmed reads were aligned using STAR (v2.7.8a)
Assembly: hg19
Supplementary files format and content: BAM, RNA-sequencing reads aligned to the hg19 human reference genome

source_name: Fallopian Tube

value: Fallopian Tube


title: Bulk RNA-sequencing of bulk tumour for patient 11658

description:
Library name: P1658TumRNA
Bulk RNA-sequencing data for patient 11658 tumour, used to determine HLA typing for patient 11658. Four technical replicates were generated for this sample.


description: Library name: H358_CellSurfaceReceptors_DCPerturbseq_FL

value: RNA


title: D425 HiC

description:
Library name: D425 HiC
PDDS_01914


title: WT cortical organoids

description: Library name: Sample 1


title: Patient 11658 Tumour DigiPico sample

description:
Library name: P11658FTorgDNA
Fallopian tube WGS data for patient 11658, used to compare mutational profile from PBMCs to tumour

source_name: Fallopian tube

value: Fallopian tube


title: Patient 11642 Fallopian Tube WGS sample

description:
Library name: WGS11642_FT
Fallopian tube WGS data for patient 11642, used to compare mutational profile from PBMCs to tumour


title: Bulk RNA-sequencing of bulk tumour for patient 11642

description:
Library name: P42TRNA
Bulk RNA-sequencing data for patient 11642, used to determine HLA typing for patient 11642. Three technical replicates were generated for this sample.


title: CD8 cells Trilaciclib replicate 2

city: Melbourne

first: Shom

last: Goel

state: Victoria

address: 305 Grattan St

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 11
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_T2_S5

data_processing:
Libraries were sequenced on the Illumina NextSeq 500 platform to obtain 75bp paired-end reads. Sequencing data were demultiplexed using Bcl2fastq (v2.17.1.14) to generate FASTQ files, which were subjected to quality control using FASTQC (v0.11.5).  Sequencing reads were adapter-trimmed and filtered for quality using BBmap (v38.96), using the bbduk.sh script. These reads were aligned to the mouse (mm10) reference genome and tallied using Subread (v2.0.0). Differential gene expression analysis was conducted with DESeq2 (v1.36.0) with comparison of Trilaciclib (n=3) versus Citrate (n=3) buffer groups excluding one replicate from the trilaciclib group due to technical issues resulting in an outlier. The package msigdbr (v7.5.1) was used to load genesets from Hallmarks, Kegg and Immunesig. The fgsea bioconductor package (v1.2.0) was used to conduct Gene set enrichment analysis (GSEA) and generate barcode plots.
Assembly: mm10
Supplementary files format and content: csv file with raw counts for all samples

source_name: CD8 cells

extract_protocol:
Qiagen RNeasy Mini Kit
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

value: CD8 cells

value: immune cells

value: WT

tag: strain

value: Trilaciclib


title: CD8 cells Trilaciclib replicate 3

description:
Library name: Sample 12
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_T3_S6


title: Patient 11642 Germline PBMC WGS sample

description:
Library name: PBMC11642WGS
PBMC WGS data for patient 11642, used to call somatic mutations and CNVs in the tumour sample


title: Patient 11642 Tumour DigiPico sample

description:
Library name: DigiPico_11642
Tumour data for patient 11642, sequenced by DigiPico across 384 wells


title: CD8 cells Citrate Buffer control replicate 1

description:
Library name: Sample 7
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_C1_S1

value: Citrate buffer (control)


title: CD8 cells Trilaciclib replicate 1

description:
Library name: Sample 10
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_T1_S4


title: Bulk RNA-sequencing of fallopian tube organoid for patient 11642

description:
Library name: P11642FTorgRNA
Bulk RNA-sequencing data for the fallopian tube of patient 11642, used to determine HLA typing during neoantigen prediction. One replicate was generated for this sample.


title: CD8 cells Citrate Buffer control replicate 2

description:
Library name: Sample 8
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_C2_S2


title: CD8 cells Citrate Buffer control replicate 3

description:
Library name: Sample 9
column name in fcounts_rawcounts_genesymb_mat.csv: CD8_C3_S3


title: CD4 cells Citrate Buffer control replicate 2

description:
Library name: Sample 2
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_C2_S8

source_name: CD4 cells

value: CD4 cells


title: CD4 cells Citrate Buffer control replicate 3

description:
Library name: Sample 3
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_C3_S9


title: CD4 cells Trilaciclib replicate 1

description:
Library name: Sample 4
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_T1_S10


title: Day3.organoid.Rep3_Cell_765

city: Galveston

first: Marie

last: Kubota

state: TX

address: 301 University Blvd

department: Otolaryngology

institute: University of Texas Medical Branch

description: Library name: Cell_765

data_processing:
Illumina NextGen Sequencing
demultiplexing
STAR alignment v2.5.3a
read quantification: RSEM v1.3.0
Assembly: mm10 (GRCm38)
Supplementary files format and content: text file with raw read counts

source_name: organoid

growth_protocol: Greater epithelial ridge cells, enriched by flow cytometry, were cultured in DMEM/F12-based proliferation medium to induce organoid formation for 1, 3, and 7 days.

extract_protocol:
Harvested organoids were rinsed in PBS and incubated in 0.25% Trypsin-EDTA at 37°C and 5% CO2 for 10-20 min. After the addition of soybean trypsin inhibitor, the samples were mechanically dissociated. Single cells were manually collected using a glass micropipette (50-60µm inner diameter) and transferred into 96-well plates.
SmartSeq2 protocol

treatment_protocol: The growth medium consisted of DMEM/F-12 supplemented with 1x N-2 Supplement, 1x B-27 Supplement, 100 µg/mL ampicillin, growth factors (20 ng/mL EGF, 10 ng/mL FGF2, and 50 ng/mL IGF1), and small molecules (3µM CHIR99021, 500 µM valproic acid, 100 µg/mL 2-phospho-L-ascorbic acid, and 2 µM TGFß receptor inhibitor 616452).

tag: cell source

value: P2 mouse cochlear greater epithelial ridge cells

value: organoid

tag: replicate


title: Day3.organoid.Rep3_Cell_768

description: Library name: Cell_768

tag: cell type


title: Day3.organoid.Rep3_Cell_766

description: Library name: Cell_766


title: CD4 cells Trilaciclib replicate 2

description:
Library name: Sample 5
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_T2_S11

tag: genotype

tag: treatment


title: Day3.organoid.Rep3_Cell_762

description: Library name: Cell_762


title: CD4 cells Trilaciclib replicate 3

description:
Library name: Sample 6
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_T3_S12


title: Day3.organoid.Rep3_Cell_763

description: Library name: Cell_763


title: Day3.organoid.Rep3_Cell_764

description: Library name: Cell_764


title: Day3.organoid.Rep3_Cell_761

description: Library name: Cell_761


title: CD4 cells Citrate Buffer control replicate 1

description:
Library name: Sample 1
column name in fcounts_rawcounts_genesymb_mat.csv: CD4_C1_S7


title: Day3.organoid.Rep3_Cell_760

description: Library name: Cell_760


title: Day3.organoid.Rep3_Cell_767

description: Library name: Cell_767


title: Day3.organoid.Rep3_Cell_758

description: Library name: Cell_758


title: Day3.organoid.Rep3_Cell_757

description: Library name: Cell_757


title: Day3.organoid.Rep3_Cell_756

description: Library name: Cell_756


title: Day3.organoid.Rep3_Cell_759

description: Library name: Cell_759


title: Day3.organoid.Rep3_Cell_750

description: Library name: Cell_750


title: Day3.organoid.Rep3_Cell_747

description: Library name: Cell_747


title: Day3.organoid.Rep3_Cell_748

description: Library name: Cell_748


title: Day3.organoid.Rep3_Cell_740

description: Library name: Cell_740


title: Day3.organoid.Rep3_Cell_752

description: Library name: Cell_752


title: Day3.organoid.Rep3_Cell_751

description: Library name: Cell_751


title: Day3.organoid.Rep3_Cell_739

description: Library name: Cell_739


title: Day3.organoid.Rep3_Cell_738

description: Library name: Cell_738


title: Day3.organoid.Rep3_Cell_745

description: Library name: Cell_745


title: Day3.organoid.Rep3_Cell_737

description: Library name: Cell_737


title: Day3.organoid.Rep3_Cell_749

description: Library name: Cell_749


title: Day3.organoid.Rep3_Cell_743

description: Library name: Cell_743


title: Day3.organoid.Rep3_Cell_742

description: Library name: Cell_742


title: Day3.organoid.Rep3_Cell_741

description: Library name: Cell_741


title: Day3.organoid.Rep3_Cell_735

description: Library name: Cell_735


title: Day3.organoid.Rep3_Cell_734

description: Library name: Cell_734


title: Day3.organoid.Rep3_Cell_754

description: Library name: Cell_754


title: Day3.organoid.Rep3_Cell_733

description: Library name: Cell_733


title: Day3.organoid.Rep3_Cell_736

description: Library name: Cell_736


title: Day3.organoid.Rep3_Cell_744

description: Library name: Cell_744


title: Day3.organoid.Rep3_Cell_746

description: Library name: Cell_746


title: Day3.organoid.Rep3_Cell_753

description: Library name: Cell_753


title: Day3.organoid.Rep3_Cell_731

description: Library name: Cell_731


title: Day3.organoid.Rep3_Cell_729

description: Library name: Cell_729


title: Day3.organoid.Rep3_Cell_730

description: Library name: Cell_730


title: Day3.organoid.Rep3_Cell_727

description: Library name: Cell_727


title: Day3.organoid.Rep3_Cell_726

description: Library name: Cell_726


title: Day3.organoid.Rep3_Cell_728

description: Library name: Cell_728


title: Day3.organoid.Rep3_Cell_732

description: Library name: Cell_732


title: Day3.organoid.Rep3_Cell_725

description: Library name: Cell_725


title: Day3.organoid.Rep3_Cell_723

description: Library name: Cell_723


title: Day3.organoid.Rep3_Cell_719

description: Library name: Cell_719


title: Day3.organoid.Rep3_Cell_755

description: Library name: Cell_755


title: Day3.organoid.Rep3_Cell_717

description: Library name: Cell_717


title: Day3.organoid.Rep3_Cell_722

description: Library name: Cell_722


title: Day3.organoid.Rep3_Cell_721

description: Library name: Cell_721


title: Day3.organoid.Rep3_Cell_720

description: Library name: Cell_720


title: Day3.organoid.Rep3_Cell_715

description: Library name: Cell_715


title: Day3.organoid.Rep3_Cell_716

description: Library name: Cell_716


title: Day3.organoid.Rep3_Cell_713

description: Library name: Cell_713


title: Day3.organoid.Rep3_Cell_718

description: Library name: Cell_718


title: Day3.organoid.Rep3_Cell_711

description: Library name: Cell_711


title: Day3.organoid.Rep3_Cell_712

description: Library name: Cell_712


title: Day3.organoid.Rep3_Cell_724

description: Library name: Cell_724


title: Day3.organoid.Rep3_Cell_709

description: Library name: Cell_709


title: Day3.organoid.Rep3_Cell_714

description: Library name: Cell_714


title: Day3.organoid.Rep3_Cell_710

description: Library name: Cell_710


title: Day3.organoid.Rep3_Cell_705

description: Library name: Cell_705


title: Day3.organoid.Rep3_Cell_707

description: Library name: Cell_707


title: Day3.organoid.Rep3_Cell_708

description: Library name: Cell_708


title: Day3.organoid.Rep3_Cell_706

description: Library name: Cell_706


title: Day3.organoid.Rep3_Cell_703

description: Library name: Cell_703


title: Day3.organoid.Rep3_Cell_704

description: Library name: Cell_704


title: Day3.organoid.Rep3_Cell_699

description: Library name: Cell_699


title: Day3.organoid.Rep3_Cell_701

description: Library name: Cell_701


title: Day3.organoid.Rep3_Cell_700

description: Library name: Cell_700


title: Day3.organoid.Rep3_Cell_702

description: Library name: Cell_702


title: Day3.organoid.Rep3_Cell_698

description: Library name: Cell_698


title: Day3.organoid.Rep3_Cell_697

description: Library name: Cell_697


title: Day3.organoid.Rep3_Cell_695

description: Library name: Cell_695


title: Day3.organoid.Rep3_Cell_696

description: Library name: Cell_696


title: Day3.organoid.Rep3_Cell_693

description: Library name: Cell_693


title: Day3.organoid.Rep3_Cell_694

description: Library name: Cell_694


title: Day3.organoid.Rep3_Cell_691

description: Library name: Cell_691


title: Day3.organoid.Rep3_Cell_688

description: Library name: Cell_688


title: Day3.organoid.Rep3_Cell_692

description: Library name: Cell_692


title: Day3.organoid.Rep3_Cell_689

description: Library name: Cell_689


title: Day3.organoid.Rep3_Cell_686

description: Library name: Cell_686


title: Day3.organoid.Rep3_Cell_684

description: Library name: Cell_684


title: Day1.organoid.Rep3_Cell_683

description: Library name: Cell_683


title: Day3.organoid.Rep3_Cell_687

description: Library name: Cell_687


title: Day1.organoid.Rep3_Cell_682

description: Library name: Cell_682


title: Day3.organoid.Rep3_Cell_685

description: Library name: Cell_685


title: Day3.organoid.Rep3_Cell_690

description: Library name: Cell_690


title: Day1.organoid.Rep3_Cell_680

description: Library name: Cell_680


title: Day1.organoid.Rep3_Cell_676

description: Library name: Cell_676


title: Day1.organoid.Rep3_Cell_672

description: Library name: Cell_672


title: Day1.organoid.Rep3_Cell_674

description: Library name: Cell_674


title: Day1.organoid.Rep3_Cell_677

description: Library name: Cell_677


title: Day1.organoid.Rep3_Cell_673

description: Library name: Cell_673


title: Day1.organoid.Rep3_Cell_675

description: Library name: Cell_675


title: Day1.organoid.Rep3_Cell_678

description: Library name: Cell_678


title: Day1.organoid.Rep3_Cell_670

description: Library name: Cell_670


title: Day1.organoid.Rep3_Cell_679

description: Library name: Cell_679


title: Day1.organoid.Rep3_Cell_669

description: Library name: Cell_669


title: Day1.organoid.Rep3_Cell_671

description: Library name: Cell_671


title: Day1.organoid.Rep3_Cell_666

description: Library name: Cell_666


title: Day1.organoid.Rep3_Cell_668

description: Library name: Cell_668


title: Day1.organoid.Rep3_Cell_663

description: Library name: Cell_663


title: Day1.organoid.Rep3_Cell_664

description: Library name: Cell_664


title: Day1.organoid.Rep3_Cell_665

description: Library name: Cell_665


title: Day1.organoid.Rep3_Cell_667

description: Library name: Cell_667


title: Day1.organoid.Rep3_Cell_662

description: Library name: Cell_662


title: Day1.organoid.Rep3_Cell_681

description: Library name: Cell_681


title: Day1.organoid.Rep3_Cell_659

description: Library name: Cell_659


title: Day1.organoid.Rep3_Cell_658

description: Library name: Cell_658


title: Day1.organoid.Rep3_Cell_657

description: Library name: Cell_657


title: Day1.organoid.Rep3_Cell_661

description: Library name: Cell_661


title: Day1.organoid.Rep3_Cell_660

description: Library name: Cell_660


title: Day1.organoid.Rep3_Cell_653

description: Library name: Cell_653


title: Day1.organoid.Rep3_Cell_651

description: Library name: Cell_651


title: Day1.organoid.Rep3_Cell_644

description: Library name: Cell_644


title: Day1.organoid.Rep3_Cell_649

description: Library name: Cell_649


title: Day1.organoid.Rep3_Cell_655

description: Library name: Cell_655


title: Day1.organoid.Rep3_Cell_645

description: Library name: Cell_645


title: Day1.organoid.Rep3_Cell_652

description: Library name: Cell_652


title: Day1.organoid.Rep3_Cell_648

description: Library name: Cell_648


title: Day1.organoid.Rep3_Cell_642

description: Library name: Cell_642


title: Day1.organoid.Rep3_Cell_650

description: Library name: Cell_650


title: Day1.organoid.Rep3_Cell_641

description: Library name: Cell_641


title: Day1.organoid.Rep3_Cell_646

description: Library name: Cell_646


title: Day1.organoid.Rep3_Cell_643

description: Library name: Cell_643


title: Day1.organoid.Rep3_Cell_647

description: Library name: Cell_647


title: Day1.organoid.Rep3_Cell_654

description: Library name: Cell_654


title: Day1.organoid.Rep3_Cell_639

description: Library name: Cell_639


title: Day1.organoid.Rep3_Cell_640

description: Library name: Cell_640


title: Day3.organoid.Rep2_Cell_636

description: Library name: Cell_636


title: Day1.organoid.Rep3_Cell_637

description: Library name: Cell_637


title: Day3.organoid.Rep2_Cell_635

description: Library name: Cell_635


title: Day1.organoid.Rep3_Cell_638

description: Library name: Cell_638


title: Day3.organoid.Rep2_Cell_633

description: Library name: Cell_633


title: Day3.organoid.Rep2_Cell_634

description: Library name: Cell_634


title: Day3.organoid.Rep2_Cell_632

description: Library name: Cell_632


title: Day3.organoid.Rep2_Cell_630

description: Library name: Cell_630


title: Day1.organoid.Rep3_Cell_656

description: Library name: Cell_656


title: Day3.organoid.Rep2_Cell_629

description: Library name: Cell_629


title: Day3.organoid.Rep2_Cell_631

description: Library name: Cell_631


title: Day3.organoid.Rep2_Cell_628

description: Library name: Cell_628


title: Day3.organoid.Rep2_Cell_627

description: Library name: Cell_627


title: Day3.organoid.Rep2_Cell_621

description: Library name: Cell_621


title: Day3.organoid.Rep2_Cell_624

description: Library name: Cell_624


title: Day3.organoid.Rep2_Cell_625

description: Library name: Cell_625


title: Day3.organoid.Rep2_Cell_626

description: Library name: Cell_626


title: Day3.organoid.Rep2_Cell_619

description: Library name: Cell_619


title: Day3.organoid.Rep2_Cell_616

description: Library name: Cell_616


title: Day3.organoid.Rep2_Cell_612

description: Library name: Cell_612


title: Day3.organoid.Rep2_Cell_623

description: Library name: Cell_623


title: Day3.organoid.Rep2_Cell_622

description: Library name: Cell_622


title: Day3.organoid.Rep2_Cell_617

description: Library name: Cell_617


title: Day3.organoid.Rep2_Cell_615

description: Library name: Cell_615


title: Day3.organoid.Rep2_Cell_610

description: Library name: Cell_610


title: Day3.organoid.Rep2_Cell_614

description: Library name: Cell_614


title: Day3.organoid.Rep2_Cell_620

description: Library name: Cell_620


title: Day3.organoid.Rep2_Cell_618

description: Library name: Cell_618


title: Day3.organoid.Rep2_Cell_613

description: Library name: Cell_613


title: Day3.organoid.Rep2_Cell_611

description: Library name: Cell_611


title: Day3.organoid.Rep2_Cell_609

description: Library name: Cell_609


title: Day3.organoid.Rep2_Cell_608

description: Library name: Cell_608


title: Day3.organoid.Rep2_Cell_606

description: Library name: Cell_606


title: Day3.organoid.Rep2_Cell_605

description: Library name: Cell_605


title: Day3.organoid.Rep2_Cell_607

description: Library name: Cell_607


title: Day3.organoid.Rep2_Cell_604

description: Library name: Cell_604


title: Day3.organoid.Rep2_Cell_601

description: Library name: Cell_601


title: Day3.organoid.Rep2_Cell_591

description: Library name: Cell_591


title: Day3.organoid.Rep2_Cell_602

description: Library name: Cell_602


title: Day3.organoid.Rep2_Cell_596

description: Library name: Cell_596


title: Day3.organoid.Rep2_Cell_597

description: Library name: Cell_597


title: Day3.organoid.Rep2_Cell_599

description: Library name: Cell_599


title: Day3.organoid.Rep2_Cell_594

description: Library name: Cell_594


title: Day3.organoid.Rep2_Cell_595

description: Library name: Cell_595


title: Day3.organoid.Rep2_Cell_600

description: Library name: Cell_600


title: Day3.organoid.Rep2_Cell_592

description: Library name: Cell_592


title: Day3.organoid.Rep2_Cell_603

description: Library name: Cell_603


title: Day3.organoid.Rep2_Cell_589

description: Library name: Cell_589


title: Day3.organoid.Rep2_Cell_586

description: Library name: Cell_586


title: Day3.organoid.Rep2_Cell_587

description: Library name: Cell_587


title: Day3.organoid.Rep2_Cell_588

description: Library name: Cell_588


title: Day3.organoid.Rep2_Cell_593

description: Library name: Cell_593


title: Day3.organoid.Rep2_Cell_590

description: Library name: Cell_590


title: Day3.organoid.Rep2_Cell_585

description: Library name: Cell_585


title: Day3.organoid.Rep2_Cell_584

description: Library name: Cell_584


title: Day3.organoid.Rep2_Cell_598

description: Library name: Cell_598


title: Day3.organoid.Rep2_Cell_578

description: Library name: Cell_578


title: Day3.organoid.Rep2_Cell_582

description: Library name: Cell_582


title: Day3.organoid.Rep2_Cell_583

description: Library name: Cell_583


title: Day3.organoid.Rep2_Cell_581

description: Library name: Cell_581


title: Day3.organoid.Rep2_Cell_576

description: Library name: Cell_576


title: Day3.organoid.Rep2_Cell_574

description: Library name: Cell_574


title: Day3.organoid.Rep2_Cell_575

description: Library name: Cell_575


title: Day3.organoid.Rep2_Cell_571

description: Library name: Cell_571


title: Day3.organoid.Rep2_Cell_579

description: Library name: Cell_579


title: Day3.organoid.Rep2_Cell_566

description: Library name: Cell_566


title: Day3.organoid.Rep2_Cell_561

description: Library name: Cell_561


title: Day3.organoid.Rep2_Cell_572

description: Library name: Cell_572


title: Day3.organoid.Rep2_Cell_568

description: Library name: Cell_568


title: Day3.organoid.Rep2_Cell_562

description: Library name: Cell_562


title: Day3.organoid.Rep2_Cell_580

description: Library name: Cell_580


title: Day3.organoid.Rep2_Cell_570

description: Library name: Cell_570


title: Day3.organoid.Rep2_Cell_567

description: Library name: Cell_567


title: Day3.organoid.Rep2_Cell_573

description: Library name: Cell_573


title: Day3.organoid.Rep2_Cell_577

description: Library name: Cell_577


title: Day3.organoid.Rep2_Cell_560

description: Library name: Cell_560


title: Day3.organoid.Rep2_Cell_564

description: Library name: Cell_564


title: Day3.organoid.Rep2_Cell_569

description: Library name: Cell_569


title: Day3.organoid.Rep2_Cell_565

description: Library name: Cell_565


title: Day3.organoid.Rep2_Cell_559

description: Library name: Cell_559


title: Day3.organoid.Rep2_Cell_563

description: Library name: Cell_563


title: Day3.organoid.Rep2_Cell_557

description: Library name: Cell_557


title: Day3.organoid.Rep2_Cell_556

description: Library name: Cell_556


title: Day3.organoid.Rep2_Cell_558

description: Library name: Cell_558


title: Day3.organoid.Rep2_Cell_555

description: Library name: Cell_555


title: Day1.organoid.Rep2_Cell_553

description: Library name: Cell_553


title: Day1.organoid.Rep2_Cell_551

description: Library name: Cell_551


title: Day1.organoid.Rep2_Cell_549

description: Library name: Cell_549


title: Day1.organoid.Rep2_Cell_554

description: Library name: Cell_554


title: Day1.organoid.Rep2_Cell_552

description: Library name: Cell_552


title: Day1.organoid.Rep2_Cell_550

description: Library name: Cell_550


title: Day1.organoid.Rep2_Cell_547

description: Library name: Cell_547


title: Day1.organoid.Rep2_Cell_544

description: Library name: Cell_544


title: Day1.organoid.Rep2_Cell_545

description: Library name: Cell_545


title: Day1.organoid.Rep2_Cell_540

description: Library name: Cell_540


title: Day1.organoid.Rep2_Cell_542

description: Library name: Cell_542


title: Day1.organoid.Rep2_Cell_548

description: Library name: Cell_548


title: Day1.organoid.Rep2_Cell_543

description: Library name: Cell_543


title: Day1.organoid.Rep2_Cell_541

description: Library name: Cell_541


title: Day1.organoid.Rep2_Cell_537

description: Library name: Cell_537


title: Day1.organoid.Rep2_Cell_536

description: Library name: Cell_536


title: Day1.organoid.Rep2_Cell_535

description: Library name: Cell_535


title: Day1.organoid.Rep2_Cell_538

description: Library name: Cell_538


title: Day1.organoid.Rep2_Cell_539

description: Library name: Cell_539


title: Day1.organoid.Rep2_Cell_534

description: Library name: Cell_534


title: Day1.organoid.Rep2_Cell_531

description: Library name: Cell_531


title: Day1.organoid.Rep2_Cell_546

description: Library name: Cell_546


title: Day1.organoid.Rep2_Cell_529

description: Library name: Cell_529


title: Day1.organoid.Rep2_Cell_533

description: Library name: Cell_533


title: Day1.organoid.Rep2_Cell_530

description: Library name: Cell_530


title: Day1.organoid.Rep2_Cell_532

description: Library name: Cell_532


title: Day1.organoid.Rep2_Cell_527

description: Library name: Cell_527


title: Day1.organoid.Rep2_Cell_523

description: Library name: Cell_523


title: Day1.organoid.Rep2_Cell_528

description: Library name: Cell_528


title: Day1.organoid.Rep2_Cell_521

description: Library name: Cell_521


title: Day1.organoid.Rep2_Cell_524

description: Library name: Cell_524


title: Day1.organoid.Rep2_Cell_525

description: Library name: Cell_525


title: Day1.organoid.Rep2_Cell_519

description: Library name: Cell_519


title: Day1.organoid.Rep2_Cell_518

description: Library name: Cell_518


title: Day1.organoid.Rep2_Cell_526

description: Library name: Cell_526


title: Day1.organoid.Rep2_Cell_522

description: Library name: Cell_522


title: Day1.organoid.Rep2_Cell_520

description: Library name: Cell_520


title: Day1.organoid.Rep2_Cell_517

description: Library name: Cell_517


title: Day1.organoid.Rep2_Cell_514

description: Library name: Cell_514


title: Day1.organoid.Rep2_Cell_513

description: Library name: Cell_513


title: Day1.organoid.Rep2_Cell_515

description: Library name: Cell_515


title: Day1.organoid.Rep2_Cell_516

description: Library name: Cell_516


title: Day1.organoid.Rep2_Cell_512

description: Library name: Cell_512


title: Day1.organoid.Rep2_Cell_511

description: Library name: Cell_511


title: Day1.organoid.Rep2_Cell_510

description: Library name: Cell_510


title: Day1.organoid.Rep2_Cell_509

description: Library name: Cell_509


title: Day1.organoid.Rep2_Cell_501

description: Library name: Cell_501


title: Day1.organoid.Rep2_Cell_503

description: Library name: Cell_503


title: Day1.organoid.Rep2_Cell_508

description: Library name: Cell_508


title: Day1.organoid.Rep2_Cell_498

description: Library name: Cell_498


title: Day1.organoid.Rep2_Cell_504

description: Library name: Cell_504


title: Day1.organoid.Rep2_Cell_506

description: Library name: Cell_506


title: Day1.organoid.Rep2_Cell_505

description: Library name: Cell_505


title: Day1.organoid.Rep2_Cell_507

description: Library name: Cell_507


title: Day1.organoid.Rep2_Cell_499

description: Library name: Cell_499


title: Day1.organoid.Rep2_Cell_497

description: Library name: Cell_497


title: Day1.organoid.Rep2_Cell_502

description: Library name: Cell_502


title: Day1.organoid.Rep2_Cell_495

description: Library name: Cell_495


title: Day1.organoid.Rep2_Cell_491

description: Library name: Cell_491


title: Day1.organoid.Rep2_Cell_492

description: Library name: Cell_492


title: Day1.organoid.Rep2_Cell_493

description: Library name: Cell_493


title: Day1.organoid.Rep2_Cell_500

description: Library name: Cell_500


title: Day1.organoid.Rep2_Cell_494

description: Library name: Cell_494


title: Day1.organoid.Rep2_Cell_496

description: Library name: Cell_496


title: Day1.organoid.Rep2_Cell_489

description: Library name: Cell_489


title: Day1.organoid.Rep2_Cell_486

description: Library name: Cell_486


title: Day1.organoid.Rep2_Cell_490

description: Library name: Cell_490


title: Day1.organoid.Rep2_Cell_485

description: Library name: Cell_485


title: Day1.organoid.Rep2_Cell_488

description: Library name: Cell_488


title: Day1.organoid.Rep2_Cell_484

description: Library name: Cell_484


title: Day1.organoid.Rep2_Cell_475

description: Library name: Cell_475


title: Day1.organoid.Rep2_Cell_476

description: Library name: Cell_476


title: Day1.organoid.Rep2_Cell_483

description: Library name: Cell_483


title: Day1.organoid.Rep2_Cell_480

description: Library name: Cell_480


title: Day1.organoid.Rep2_Cell_479

description: Library name: Cell_479


title: Day1.organoid.Rep2_Cell_487

description: Library name: Cell_487


title: Day1.organoid.Rep2_Cell_482

description: Library name: Cell_482


title: Day1.organoid.Rep2_Cell_478

description: Library name: Cell_478


title: Day1.organoid.Rep2_Cell_473

description: Library name: Cell_473


title: Day1.organoid.Rep2_Cell_472

description: Library name: Cell_472


title: Day1.organoid.Rep2_Cell_474

description: Library name: Cell_474


title: Day1.organoid.Rep2_Cell_471

description: Library name: Cell_471


title: Day1.organoid.Rep2_Cell_470

description: Library name: Cell_470


title: Day1.organoid.Rep2_Cell_477

description: Library name: Cell_477


title: Day1.organoid.Rep2_Cell_481

description: Library name: Cell_481


title: Day1.organoid.Rep2_Cell_465

description: Library name: Cell_465


title: Day7.organoid.Rep5_Cell_464

description: Library name: Cell_464


title: Day1.organoid.Rep2_Cell_468

description: Library name: Cell_468


title: Day1.organoid.Rep2_Cell_469

description: Library name: Cell_469


title: Day7.organoid.Rep5_Cell_463

description: Library name: Cell_463


title: Day7.organoid.Rep5_Cell_462

description: Library name: Cell_462


title: Day7.organoid.Rep5_Cell_460

description: Library name: Cell_460


title: Day1.organoid.Rep2_Cell_466

description: Library name: Cell_466


title: Day1.organoid.Rep2_Cell_467

description: Library name: Cell_467


title: Day7.organoid.Rep5_Cell_458

description: Library name: Cell_458


title: ChIP_22_Pol2_TIMM13_KO1_Hypoxia

status: Public on Apr 10 2026

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Library name: ChIP_22_Pol2_TIMM13_KO1_Hypoxia

data_processing:
Basecalls were performed using Illumina bcl2fastq v.2.19 for NextSeq2000 output
For samples with a spike-in normalization, reads were trimmed using Cutadapt v.4.1  with parameters --nextseq-trim=30 --minimum-length=20. Spike-in containing samples were aligned using Bowtie2 v.2.2.6 with parameters --sensitive --no-unal,  Non-spiked-in samples were aligned using Bowtie v.1.1.2 with parameters -m 1 -v 2.
bigWig files were generated using package deepTools v.3.5.1 and function bamCoverage, with a parameter to extend reads length -extLen=150. Normalization applied using parameter --scaleFactor, which was calculated from D.melanogaster spike-in reads (bigWig files tagged with "Rx)"
Assembly: hg38, dm6 spike-in
Supplementary files format and content: bigWig

source_name: Large intestine; Colon

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) (Millipore Sigma, cat# D6429) supplemented with 10% fetal bovine serum (FBS) (Millipore Sigma, cat# F2442). DLD-1 cells were grown at 37°C in a humidified incubator with 5% CO₂ to maintain normoxic conditions.

extract_protocol:
Immunoprecipitated DNA was extracted using ChIP-DNA purification kit (Zymo Research, cat# D5205) following manufacturer’s instructions. DNA was eluted using in 10mM Tris-HCL pH 8 and quantified using qubit.
ChIP-seq libraries were made using the KAPA HTP Biosystems Library Prep kit (Roche, KK8234) using Perkin Elmer Unique Dual Index Barcodes compatible with Illumina systems. DNA libraries were sequenced on Illumina NextSeq 2000 instruments as paired end 50b reads.

treatment_protocol: For hypoxic culture, cells were incubated at 37°C in a controlled atmosphere with 1% O₂.

value: Large intestine; Colon

value: epithelial

value: hypoxia

tag: antibody

value: RPB1_NTD (CST, cat# D8L4Y)


title: Day7.organoid.Rep5_Cell_453

description: Library name: Cell_453


title: Day7.organoid.Rep5_Cell_455

description: Library name: Cell_455


title: Day7.organoid.Rep5_Cell_456

description: Library name: Cell_456


title: Day7.organoid.Rep5_Cell_461

description: Library name: Cell_461


title: Day7.organoid.Rep5_Cell_459

description: Library name: Cell_459


title: Day7.organoid.Rep5_Cell_457

description: Library name: Cell_457


title: Day7.organoid.Rep5_Cell_448

description: Library name: Cell_448


title: Day7.organoid.Rep5_Cell_452

description: Library name: Cell_452


title: Day7.organoid.Rep5_Cell_451

description: Library name: Cell_451


title: Day7.organoid.Rep5_Cell_454

description: Library name: Cell_454


title: Day7.organoid.Rep5_Cell_450

description: Library name: Cell_450


title: Day7.organoid.Rep5_Cell_444

description: Library name: Cell_444


title: Day7.organoid.Rep5_Cell_449

description: Library name: Cell_449


title: Day7.organoid.Rep5_Cell_440

description: Library name: Cell_440


title: Day7.organoid.Rep5_Cell_447

description: Library name: Cell_447


title: Day7.organoid.Rep5_Cell_436

description: Library name: Cell_436


title: Day7.organoid.Rep5_Cell_445

description: Library name: Cell_445


title: Day7.organoid.Rep5_Cell_435

description: Library name: Cell_435


title: Day7.organoid.Rep5_Cell_442

description: Library name: Cell_442


title: Day7.organoid.Rep5_Cell_443

description: Library name: Cell_443


title: Day7.organoid.Rep5_Cell_446

description: Library name: Cell_446


title: Day7.organoid.Rep5_Cell_434

description: Library name: Cell_434


title: Day7.organoid.Rep5_Cell_437

description: Library name: Cell_437


title: Day7.organoid.Rep5_Cell_438

description: Library name: Cell_438


title: Day7.organoid.Rep5_Cell_441

description: Library name: Cell_441


title: Day7.organoid.Rep5_Cell_431

description: Library name: Cell_431


title: Day7.organoid.Rep5_Cell_439

description: Library name: Cell_439


title: Day7.organoid.Rep5_Cell_432

description: Library name: Cell_432


title: Day7.organoid.Rep5_Cell_433

description: Library name: Cell_433


title: Day7.organoid.Rep5_Cell_425

description: Library name: Cell_425


title: Day7.organoid.Rep5_Cell_427

description: Library name: Cell_427


title: Day7.organoid.Rep5_Cell_420

description: Library name: Cell_420


title: Day7.organoid.Rep5_Cell_421

description: Library name: Cell_421


title: Day7.organoid.Rep5_Cell_413

description: Library name: Cell_413


title: Day7.organoid.Rep5_Cell_426

description: Library name: Cell_426


title: Day7.organoid.Rep5_Cell_418

description: Library name: Cell_418


title: Day7.organoid.Rep5_Cell_429

description: Library name: Cell_429


title: Day7.organoid.Rep5_Cell_419

description: Library name: Cell_419


title: Day7.organoid.Rep5_Cell_416

description: Library name: Cell_416


title: Day7.organoid.Rep5_Cell_424

description: Library name: Cell_424


title: Day7.organoid.Rep5_Cell_405

description: Library name: Cell_405


title: Day7.organoid.Rep5_Cell_410

description: Library name: Cell_410


title: Day7.organoid.Rep5_Cell_430

description: Library name: Cell_430


title: Day7.organoid.Rep5_Cell_428

description: Library name: Cell_428


title: Day7.organoid.Rep5_Cell_415

description: Library name: Cell_415


title: Day7.organoid.Rep5_Cell_412

description: Library name: Cell_412


title: Day7.organoid.Rep5_Cell_406

description: Library name: Cell_406


title: Day7.organoid.Rep5_Cell_411

description: Library name: Cell_411


title: Day7.organoid.Rep5_Cell_407

description: Library name: Cell_407


title: Day7.organoid.Rep5_Cell_414

description: Library name: Cell_414


title: Day7.organoid.Rep5_Cell_423

description: Library name: Cell_423


title: Day7.organoid.Rep5_Cell_409

description: Library name: Cell_409


title: Day7.organoid.Rep5_Cell_408

description: Library name: Cell_408


title: Day7.organoid.Rep5_Cell_403

description: Library name: Cell_403


title: Day7.organoid.Rep5_Cell_422

description: Library name: Cell_422


title: Day7.organoid.Rep5_Cell_398

description: Library name: Cell_398


title: Day7.organoid.Rep5_Cell_400

description: Library name: Cell_400


title: Day7.organoid.Rep5_Cell_393

description: Library name: Cell_393


title: Day7.organoid.Rep5_Cell_401

description: Library name: Cell_401


title: Day7.organoid.Rep5_Cell_397

description: Library name: Cell_397


title: Day7.organoid.Rep5_Cell_417

description: Library name: Cell_417


title: Day7.organoid.Rep5_Cell_394

description: Library name: Cell_394


title: Day7.organoid.Rep5_Cell_390

description: Library name: Cell_390


title: Day7.organoid.Rep5_Cell_404

description: Library name: Cell_404


title: Day7.organoid.Rep5_Cell_389

description: Library name: Cell_389


title: Day7.organoid.Rep5_Cell_385

description: Library name: Cell_385


title: Day7.organoid.Rep5_Cell_399

description: Library name: Cell_399


title: Day7.organoid.Rep5_Cell_391

description: Library name: Cell_391


title: Day3.organoid.Rep1_Cell_384

description: Library name: Cell_384


title: Day7.organoid.Rep5_Cell_402

description: Library name: Cell_402


title: Day7.organoid.Rep5_Cell_386

description: Library name: Cell_386


title: Day7.organoid.Rep5_Cell_392

description: Library name: Cell_392


title: Day3.organoid.Rep1_Cell_383

description: Library name: Cell_383


title: Day7.organoid.Rep5_Cell_395

description: Library name: Cell_395


title: Day3.organoid.Rep1_Cell_381

description: Library name: Cell_381


title: Day7.organoid.Rep5_Cell_396

description: Library name: Cell_396


title: Day7.organoid.Rep5_Cell_388

description: Library name: Cell_388


title: Day3.organoid.Rep1_Cell_382

description: Library name: Cell_382


title: Day3.organoid.Rep1_Cell_380

description: Library name: Cell_380


title: Day7.organoid.Rep5_Cell_387

description: Library name: Cell_387


title: Day3.organoid.Rep1_Cell_378

description: Library name: Cell_378


title: Day3.organoid.Rep1_Cell_379

description: Library name: Cell_379


title: Day3.organoid.Rep1_Cell_377

description: Library name: Cell_377


title: Day3.organoid.Rep1_Cell_373

description: Library name: Cell_373


title: Day3.organoid.Rep1_Cell_376

description: Library name: Cell_376


title: Day3.organoid.Rep1_Cell_375

description: Library name: Cell_375


title: Day3.organoid.Rep1_Cell_374

description: Library name: Cell_374


title: Day3.organoid.Rep1_Cell_370

description: Library name: Cell_370


title: Day3.organoid.Rep1_Cell_368

description: Library name: Cell_368


title: Day3.organoid.Rep1_Cell_371

description: Library name: Cell_371


title: Day3.organoid.Rep1_Cell_372

description: Library name: Cell_372


title: Day3.organoid.Rep1_Cell_362

description: Library name: Cell_362


title: Day3.organoid.Rep1_Cell_369

description: Library name: Cell_369


title: Day3.organoid.Rep1_Cell_363

description: Library name: Cell_363


title: Day3.organoid.Rep1_Cell_360

description: Library name: Cell_360


title: Day3.organoid.Rep1_Cell_358

description: Library name: Cell_358


title: Day3.organoid.Rep1_Cell_361

description: Library name: Cell_361


title: Day3.organoid.Rep1_Cell_367

description: Library name: Cell_367


title: Day3.organoid.Rep1_Cell_364

description: Library name: Cell_364


title: Day3.organoid.Rep1_Cell_357

description: Library name: Cell_357


title: Day3.organoid.Rep1_Cell_366

description: Library name: Cell_366


title: Day3.organoid.Rep1_Cell_356

description: Library name: Cell_356


title: Day3.organoid.Rep1_Cell_355

description: Library name: Cell_355


title: Day3.organoid.Rep1_Cell_365

description: Library name: Cell_365


title: Day3.organoid.Rep1_Cell_359

description: Library name: Cell_359


title: Day3.organoid.Rep1_Cell_354

description: Library name: Cell_354


title: Day3.organoid.Rep1_Cell_353

description: Library name: Cell_353


title: Day3.organoid.Rep1_Cell_352

description: Library name: Cell_352


title: Day3.organoid.Rep1_Cell_351

description: Library name: Cell_351


title: Day3.organoid.Rep1_Cell_350

description: Library name: Cell_350


title: Day3.organoid.Rep1_Cell_344

description: Library name: Cell_344


title: Day3.organoid.Rep1_Cell_341

description: Library name: Cell_341


title: Day3.organoid.Rep1_Cell_349

description: Library name: Cell_349


title: Day3.organoid.Rep1_Cell_348

description: Library name: Cell_348


title: Day3.organoid.Rep1_Cell_337

description: Library name: Cell_337


title: Day3.organoid.Rep1_Cell_339

description: Library name: Cell_339


title: Day3.organoid.Rep1_Cell_335

description: Library name: Cell_335


title: Day3.organoid.Rep1_Cell_347

description: Library name: Cell_347


title: Day3.organoid.Rep1_Cell_340

description: Library name: Cell_340


title: Day3.organoid.Rep1_Cell_342

description: Library name: Cell_342


title: Day3.organoid.Rep1_Cell_343

description: Library name: Cell_343


title: Day3.organoid.Rep1_Cell_346

description: Library name: Cell_346


title: Day3.organoid.Rep1_Cell_334

description: Library name: Cell_334


title: Day3.organoid.Rep1_Cell_338

description: Library name: Cell_338


title: Day3.organoid.Rep1_Cell_336

description: Library name: Cell_336


title: Day3.organoid.Rep1_Cell_332

description: Library name: Cell_332


title: Day3.organoid.Rep1_Cell_345

description: Library name: Cell_345


title: Day3.organoid.Rep1_Cell_333

description: Library name: Cell_333


title: Day3.organoid.Rep1_Cell_331

description: Library name: Cell_331


title: Day3.organoid.Rep1_Cell_329

description: Library name: Cell_329


title: Day3.organoid.Rep1_Cell_330

description: Library name: Cell_330


title: Day3.organoid.Rep1_Cell_325

description: Library name: Cell_325


title: Day3.organoid.Rep1_Cell_328

description: Library name: Cell_328


title: Day3.organoid.Rep1_Cell_327

description: Library name: Cell_327


title: Day3.organoid.Rep1_Cell_322

description: Library name: Cell_322


title: Day3.organoid.Rep1_Cell_319

description: Library name: Cell_319


title: Day3.organoid.Rep1_Cell_321

description: Library name: Cell_321


title: Day3.organoid.Rep1_Cell_324

description: Library name: Cell_324


title: Day3.organoid.Rep1_Cell_326

description: Library name: Cell_326


title: Day3.organoid.Rep1_Cell_323

description: Library name: Cell_323


title: Day3.organoid.Rep1_Cell_320

description: Library name: Cell_320


title: Day3.organoid.Rep1_Cell_317

description: Library name: Cell_317


title: Day3.organoid.Rep1_Cell_315

description: Library name: Cell_315


title: Day3.organoid.Rep1_Cell_318

description: Library name: Cell_318


title: Day3.organoid.Rep1_Cell_316

description: Library name: Cell_316


title: Day3.organoid.Rep1_Cell_312

description: Library name: Cell_312


title: Day3.organoid.Rep1_Cell_311

description: Library name: Cell_311


title: Day3.organoid.Rep1_Cell_310

description: Library name: Cell_310


title: Day3.organoid.Rep1_Cell_308

description: Library name: Cell_308


title: Day3.organoid.Rep1_Cell_309

description: Library name: Cell_309


title: Day3.organoid.Rep1_Cell_307

description: Library name: Cell_307


title: Day3.organoid.Rep1_Cell_314

description: Library name: Cell_314


title: Day3.organoid.Rep1_Cell_306

description: Library name: Cell_306


title: Day3.organoid.Rep1_Cell_305

description: Library name: Cell_305


title: Day3.organoid.Rep1_Cell_304

description: Library name: Cell_304


title: Day3.organoid.Rep1_Cell_302

description: Library name: Cell_302


title: Day3.organoid.Rep1_Cell_313

description: Library name: Cell_313


title: Day7.organoid.Rep4_Cell_296

description: Library name: Cell_296


title: hepg2_pr_wt_lig_1

city: Rehovot

first: Naama

last: Barkai

state: HaMerkaz

address: Herzl 234

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

description:
Library name: hepg2_pr_wt_lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

data_processing:
demultiplexing with bcl2fastq
filtering of adapter dimers using cutadapt
ChEC-seq: genome coverage with bedtools (-5 -fs 1 -d) for yeast and deeptools bamtoBigWig for mammalian samples
Assembly: Yeast-GCA_000146045.2 (R64), Mouse-mm10, Human-hg38
Supplementary files format and content: Yeast - .out file contains  genome coverage for all 12,157,105 bases in the S. cerevisiae genome (Chr 1-16+mitochondria), the vector is ordered by the order of chromosomes from 1 to the length of the genome
Supplementary files format and content: Mammalian- bw files contain averaged between repeats BigWIg files using CPM and bin size of 1 bp

growth_protocol: Yeast - Overnight cultures from fresh colonies were diluted (>1:10000) and grown to OD 0.4 in SC medium with glucose; Mammalian- cells were deluted and grown until ~1.4 M cells

extract_protocol:
ChEC-seq: phenol chloroform
One tube library construction based on Skeene et al. 2017 as described in Gera 2021

treatment_protocol: ChEC-Seq protocol as described in Zentner et al. MNase-seq modified from Yaakov et al. 2021

value: incubation in 100nM of Progesterone for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day3.organoid.Rep1_Cell_301

description: Library name: Cell_301


title: hepg2_pr_dlbd_2

description:
Library name: hepg2_pr_dlbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: permeabilization followed by 2min Ca2+ Mnase incubation


title: hepg2_pr_dlbd_3

description:
Library name: hepg2_pr_dlbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_pr_dlbd_1

description:
Library name: hepg2_pr_dlbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day3.organoid.Rep1_Cell_300

description: Library name: Cell_300


title: Day3.organoid.Rep1_Cell_297

description: Library name: Cell_297


title: Day3.organoid.Rep1_Cell_298

description: Library name: Cell_298


title: hepg2_pr_wt_lig_3

description:
Library name: hepg2_pr_wt_lig_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_pr_wt_lig_2

description:
Library name: hepg2_pr_wt_lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day3.organoid.Rep1_Cell_303

description: Library name: Cell_303


title: hepg2_pr_wt_3

description:
Library name: hepg2_pr_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day3.organoid.Rep1_Cell_299

description: Library name: Cell_299


title: Day7.organoid.Rep4_Cell_294

description: Library name: Cell_294


title: Day7.organoid.Rep4_Cell_295

description: Library name: Cell_295


title: Day7.organoid.Rep4_Cell_293

description: Library name: Cell_293


title: hepg2_pr_wt_1

description:
Library name: hepg2_pr_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_291

description: Library name: Cell_291


title: hepg2_pr_dbd_2

description:
Library name: hepg2_pr_dbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_292

description: Library name: Cell_292


title: hepg2_gr_dlbd_3

description:
Library name: hepg2_gr_dlbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_290

description: Library name: Cell_290


title: Day7.organoid.Rep4_Cell_287

description: Library name: Cell_287


title: Day7.organoid.Rep4_Cell_285

description: Library name: Cell_285


title: hepg2_gr_dlbd_2

description:
Library name: hepg2_gr_dlbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_pr_dbd_1

description:
Library name: hepg2_pr_dbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_pr_wt_2

description:
Library name: hepg2_pr_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_gr_wt_2

description:
Library name: hepg2_gr_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_283

description: Library name: Cell_283


title: hepg2_gr_wt__lig_2

description:
Library name: hepg2_gr_wt__lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: incubation in 100nM of Dex (dexamethasone ) for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep4_Cell_286

description: Library name: Cell_286


title: hepg2_gr_wt__lig_1

description:
Library name: hepg2_gr_wt__lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_288

description: Library name: Cell_288


title: hepg2_gr_wt_3

description:
Library name: hepg2_gr_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_289

description: Library name: Cell_289


title: Day7.organoid.Rep4_Cell_284

description: Library name: Cell_284


title: hepg2_gr_dlbd_1

description:
Library name: hepg2_gr_dlbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_gr_dbd_2

description:
Library name: hepg2_gr_dbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_gr_wt_1

description:
Library name: hepg2_gr_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_282

description: Library name: Cell_282


title: hepg2_gr_dbd_3

description:
Library name: hepg2_gr_dbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_280

description: Library name: Cell_280


title: Day7.organoid.Rep4_Cell_281

description: Library name: Cell_281


title: Day7.organoid.Rep4_Cell_277

description: Library name: Cell_277


title: hepg2_ar_dlbd_3

description:
Library name: hepg2_ar_dlbd_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_274

description: Library name: Cell_274


title: hepg2_gr_dbd_1

description:
Library name: hepg2_gr_dbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_271

description: Library name: Cell_271


title: hepg2_ar_wt_lig_3

description:
Library name: hepg2_ar_wt_lig_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system

value: incubation in 100nM of DHT (Dihydrotestosterone) for 1h followed by permeabilization followed by 2min Ca2+ Mnase incubation


title: Day7.organoid.Rep4_Cell_279

description: Library name: Cell_279


title: Day7.organoid.Rep4_Cell_273

description: Library name: Cell_273


title: hepg2_ar_dlbd_2

description:
Library name: hepg2_ar_dlbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_278

description: Library name: Cell_278


title: hepg2_ar_wt_lig_1

description:
Library name: hepg2_ar_wt_lig_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_ar_wt_1

description:
Library name: hepg2_ar_wt_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: hepg2_ar_dbd_2

description:
Library name: hepg2_ar_dbd_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_270

description: Library name: Cell_270


title: hepg2_ar_wt_lig_2

description:
Library name: hepg2_ar_wt_lig_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_276

description: Library name: Cell_276


title: hepg2_ar_wt_3

description:
Library name: hepg2_ar_wt_3
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_275

description: Library name: Cell_275


title: Day7.organoid.Rep4_Cell_269

description: Library name: Cell_269


title: Day7.organoid.Rep4_Cell_272

description: Library name: Cell_272


title: hepg2_ar_wt_2

description:
Library name: hepg2_ar_wt_2
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: Day7.organoid.Rep4_Cell_268

description: Library name: Cell_268


title: hepg2_ar_dbd_1

description:
Library name: hepg2_ar_dbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: 1955_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_312h-pae_set3_flask3_1955

city: Aurora

first: Jo

last: Hendrix

state: CO

department: Pulmonology

institute: University of Colorado

description: Library name: NW_862

data_processing:
After sequencing, bacterial reads were trimmed by Skewer v0.2.2 using an adapter sequence of 5’- CTGTCTCTTATACACATCT-3’, a length of 50-175 bases, and an end quality of 20.
Individual reads were reunited with their mate pair using PairFQ lite v0.17.0.
Paired-end reads were then aligned to the 2016 Mtb Erdman reference assembly using Bowtie2 v2.5.0 with default parameters.
Mapped sequences were counted using HtSeq v1.0 with the default parameters.
The SEARCH-TB panel amplifies Mtb 3,568 genes. In this experiment, 12 genes had high incidences of 0 expression values, so our analysis included 3,552 genes.
Assembly: 2016 Mtb Erdman reference assembly
Supplementary files format and content: Read counts per Mtb Erdman gene are providedin .txt format

organism: Mycobacterium tuberculosis str. Erdman = ATCC 35801

source_name: Erdman

growth_protocol: Mtb Erdman cells were inoculated into 7H9 media and grown to mid-log. At mid-log, starter cultures were split into separate sterile 125 ml Erlenmeyer flasks, one each for no drug control, 6-hour and 48-hour drug exposure arms each adjusted to an OD600 of 0.05 in 50 ml fresh 7H9. Cultures were then outgrown for 18 h at 37C prior to drug addition. Following drug wash out, cultures were returned to the incubator and grown at 37C until cultures reached an OD600 of 2.0 or exceeded 15 days.

extract_protocol:
RNA was isolated with Precellys Evolution in RLT-TCEP buffer followed by RNA purification with the Maxwell Simply RNA cell kit from Promega.
Extracted RNA was reverse transcribed and prepared for sequencing with Illumina AmpliSeq custom panel library preparation protocol.

treatment_protocol: For drug exposed cultures, a 50 µl drug suspension was added from a 1000X sterile stock solution containing the following: 0.05 mg/ml isoniazid (Sigma-Aldrich), 0.05 mg/ml rifampicin (Chem-Impex-Int’l), 1.6 mg/ml pyrazinamide (MP Biomedicals), 2.0 mg/ml ethambutol (MP Biomedicals). Drugs were suspended in DMSO at the indicated concentrations, sterilized using a 0.22 µm nylon syringe filter, and stored at -80C prior to use. Control non-drug exposed cultures were collected by centrifugation for 5 min at 3220 x g, washed 2 times with 50 ml 7H9 and then resuspended in 50 ml fresh 7H9 to an OD600 of 0.05. Cultures were returned to the incubator and grown at 37C for the pre-defined drug exposure period. At the end of the defined drug exposure period, cultures were collected by centrifugation, washed 2 times with 50 ml 7H9 to remove residual drug and then resuspended in 50 ml fresh 7H9 to an OD600 of 0.05.

value: Erdman

value: HRZE

tag: batch


title: 1953_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_312h-pae_set1_flask3_1953

description: Library name: NW_860


title: Day7.organoid.Rep4_Cell_266

description: Library name: Cell_266


title: 1956_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_312h-pae_set4_flask3_1956

description: Library name: NW_863


title: Day7.organoid.Rep4_Cell_261

description: Library name: Cell_261


title: 1954_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_312h-pae_set2_flask3_1954

description: Library name: NW_861


title: 1952_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_192h-pae_set4_flask3_1952

description: Library name: NW_859


title: 1158_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_96h-pae_set4_flask3_1158

description: Library name: NW_855


title: Day7.organoid.Rep4_Cell_263

description: Library name: Cell_263


title: Day7.organoid.Rep4_Cell_262

description: Library name: Cell_262


title: Day7.organoid.Rep4_Cell_259

description: Library name: Cell_259


title: Day7.organoid.Rep4_Cell_265

description: Library name: Cell_265


title: 1157_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_96h-pae_set3_flask3_1157

description: Library name: NW_854


title: 1951_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_192h-pae_set3_flask3_1951

description: Library name: NW_858


title: 1949_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_192h-pae_set1_flask3_1949

description: Library name: NW_856


title: Day7.organoid.Rep4_Cell_257

description: Library name: Cell_257


title: 1149_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_48h-pae_set3_flask3_1149

description: Library name: NW_852


title: Day7.organoid.Rep4_Cell_258

description: Library name: Cell_258


title: Day7.organoid.Rep4_Cell_260

description: Library name: Cell_260


title: Day7.organoid.Rep4_Cell_255

description: Library name: Cell_255


title: Day7.organoid.Rep4_Cell_256

description: Library name: Cell_256


title: 1150_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_48h-pae_set4_flask3_1150

description: Library name: NW_853


title: 1950_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_192h-pae_set2_flask3_1950

description: Library name: NW_857


title: 1145_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_24h-pae_set3_flask3_1145

description: Library name: NW_850


title: hepg2_ar_dlbd_1

description:
Library name: hepg2_ar_dlbd_1
ChEC-seq in cell culture proteins were inserted using PiggyBack super transposon system


title: 1137_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_0h-pae-PreWash_set3_flask3_1137

description: Library name: NW_848


title: 1138_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_0h-pae-PreWash_set4_flask3_1138

description: Library name: NW_849


title: Day7.organoid.Rep4_Cell_253

description: Library name: Cell_253


title: 1146_In vitro PAE_48hrWash_in-vitro-PAE_erdman_7H9Tw_48h-hrze-1x-mic_24h-pae_set4_flask3_1146

description: Library name: NW_851


title: Day7.organoid.Rep4_Cell_254

description: Library name: Cell_254


title: Day7.organoid.Rep4_Cell_251

description: Library name: Cell_251


title: 959_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_138h-pae_set4_flask2_959

description: Library name: NW_847


title: Day7.organoid.Rep4_Cell_250

description: Library name: Cell_250


title: 943_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_90h-pae_set4_flask2_943

description: Library name: NW_845


title: Day7.organoid.Rep4_Cell_267

description: Library name: Cell_267


title: Day7.organoid.Rep4_Cell_252

description: Library name: Cell_252


title: 927_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_42h-pae_set4_flask2_927

description: Library name: NW_843


title: Day7.organoid.Rep4_Cell_249

description: Library name: Cell_249


title: 942_In vitro PAE_6hrWash_in-vitro-PAE_erdman_7H9Tw_6h-hrze-1x-mic_90h-pae_set3_flask2_942

description: Library name: NW_844


title: Day7.organoid.Rep4_Cell_248

description: Library name: Cell_248


title: Day7.organoid.Rep4_Cell_247

description: Library name: Cell_247