title: In Vitro SreA GGapt transcript, DMSO, Switch-MaP

city: Ann Arbor

first: Chase

middle: Andrew

last: Weidmann

state: MI

address: 1150 W. Medical Center Drive

department: Biological Chemistry

institute: University of Michigan

description:
RNA was 3' ligated to adapter, cDNA was generated by MaP RT with a template-switching oligo
Lm_SreA_GGapt.fa
Lm_SreA_GGapt_SwitchMaP.shape
Lm_SreA_GGapt_SwitchMaP_structure.ct
Lm_SreA_GGapt_SwitchMaP.pfs
Lm_SreA_GGapt_SwitchMaP_arcplot.pdf
SreA_GGapt_primer_masked_structures.ct

data_processing:
fastqs were processed, aligned, and had mutations counted by shapemapper2 software
SHAPE reactivities were used to inform RNA secondary structure modeling in the RNAStructure software, inclduding Fold, Partition, and ProbabilityPlot
Plots of pairing probability were generated with ArcPlot software (available on GitHub)
Assembly: SreA fasta files used for alignment are included as processed data files. Primer fasta files used for shapemapper2 are also included as processed data files.
Supplementary files format and content: .shape files are tab-separated value normalized SHAPE reactivities for use in RNAStructure software
Supplementary files format and content: .fa files are fasta files containg the SreA and relevant primer sequences used in analysis
Supplementary files format and content: .ct files are RNA structure files used to represent secondary structures (output of RNAStructure)
Supplementary files format and content: .pfs files are the direct output of RNAStructure Partition, while .dp files are text files listing base pairing probabilities for each nucleotide pair (from ProbabilityPlot)
Supplementary files format and content: arcplot.pdf files are the output of arcPlot software, which plots SHAPE reactivity and pairing probabilities onto RNA in a linearized fashion.
Library strategy: Switch-MaP

organism: Listeria monocytogenes

source_name: Listeria monocytogenes

growth_protocol: SreA RNAs were transcribed in solution with T7 RNA polymerase

extract_protocol:
RNAs were buffer exchanged and/or purified by centrifugation filter or column preparation before library preparation
For Switch-MaP, RNAs were ligated to a 3' end adapter including an RT primer binding site and cDNA was generated by MaP RT with Superscript II including a template-switching oligonucleotide. For primer MaP experiments, gene or structure cassette-specific RT primers were used in MaP RT with Superscript II excluding template-switching oligos. Final sequencing libraries were generated by PCR using primers complentary to either  3' adapter and template-switching oligo sequences or gene/cassette-specific sequences, with additional indexing barcodes included in primers.

treatment_protocol: RNAs were folded for 20 minutes at 37C in folding buffer, followed by treatment of 10 mM 1M7 SHAPE reagent or DMSO control for 2 minutes at 37C.

value: 37C folding 20 min, 10% DMSO 37C 2min

value: Listeria monocytogenes


title: In Vitro SreA GG FL transcript, DMSO, Switch-MaP

status: Public on Dec 26 2024

type: SRA

country: USA

description:
RNA was 3' ligated to adapter, cDNA was generated by MaP RT with a template-switching oligo
Lm_SreA_GG_FL.fa
Lm_SreA_GG_FL_SwitchMaP.shape
Lm_SreA_GG_FL_SwitchMaP_structures.ct
Lm_SreA_GG_FL_SwitchMaP.pfs
Lm_SreA_GG_FL_SwitchMaP_arcplot.pdf

library_source: other

molecule: other

tag: treatment

tag: cell type


title: In Vitro SreA FL Cassette transcript, DMSO, primer-MaP, Replicate 2

description:
cDNA was generated by MaP RT
Lm_SreA_cassette.fa
Lm_SreA_cassette_primers.fa
Lm-SreA-FL-cassette-Rep2.shape
Lm-SreA-FL-cassette-NoData_structure_1.ct
Lm-SreA-FL-cassette-NoData_structure_2.ct
Lm-SreA-FL-cassette-Rep2_structure.ct

data_processing:
fastqs were processed, aligned, and had mutations counted by shapemapper2 software
SHAPE reactivities were used to inform RNA secondary structure modeling in the RNAStructure software, inclduding Fold, Partition, and ProbabilityPlot
Plots of pairing probability were generated with ArcPlot software (available on GitHub)
Assembly: SreA fasta files used for alignment are included as processed data files. Primer fasta files used for shapemapper2 are also included as processed data files.
Supplementary files format and content: .shape files are tab-separated value normalized SHAPE reactivities for use in RNAStructure software
Supplementary files format and content: .fa files are fasta files containg the SreA and relevant primer sequences used in analysis
Supplementary files format and content: .ct files are RNA structure files used to represent secondary structures (output of RNAStructure)
Supplementary files format and content: .pfs files are the direct output of RNAStructure Partition, while .dp files are text files listing base pairing probabilities for each nucleotide pair (from ProbabilityPlot)
Supplementary files format and content: arcplot.pdf files are the output of arcPlot software, which plots SHAPE reactivity and pairing probabilities onto RNA in a linearized fashion.
Library strategy: SHAPE-MaP


title: REN174_B1

type: RNA

city: Praha 4

first: Petra

last: Hruba

address: Videnska 1958

department: Transplant Laboratory

country: Czech Republic

institute: Institute for Clinical and Experimental Medicine

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Prime View Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000 7G.

data_processing: The data were analyzed using the “limma”package and R studio version 4.2.2.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: No-rejection, DSA-negative

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA

extract_protocol: Trizol-chloroform extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: kidney biopsy

tag: time from transplantation in days


title: In Vitro SreA GG FL transcript, 1M7, Switch-MaP

value: 37C folding 20 min, 10mM 1M7 37C 2min


title: WT2_15

city: Aachen

first: Matthias

last: Bartneck

address: Pauwelsstraße 30

department: Department of Internal Medicine III

country: Germany

institute: University Hospital RWTH Aachen

library_source: transcriptomic

data_processing:
FASTQ files were generated using bcl2fastq (Illumina). To facilitate reproducible analysis, samples were processed using the publicly available nf-core/RNA-seq pipeline version 3.12 (Ewels et al. 2020) implemented in Nextflow 23.10.0 (Di Tommaso et al. 2017) with the minimal command and deduplication by UMIs. In brief, lane-level reads were trimmed using Trim Galore 0.6.7 (Krueger et al. 2021) and aligned to the mice genome (GRCm39) using STAR 2.7.9a (Dobin et al. 2013). Gene-level and transcript-level quantification was done by Salmon v1.10.1 (Patro et al. 2017). All analysis was performed using custom scripts in R version 4.3.2 using the DESeq2 v.1.32.0 framework (Love, Huber, and Anders 2014).
Assembly: GRCm39
Supplementary files format and content: Excel file contains the normalized reads for all samples.

organism: Mus musculus

source_name: Liver

extract_protocol:
For the isolation of total RNA from cells isolated by fluorescence- activated cell sorting, the RNeasy Plus Micro Kit (Qiagen, 74034), according to manufacturer’s protocol.
3'mRNA sequencing libraries were prepared using Lexogen QuantSeq 3'mRNA-Seq v2 Library Prep Kit FWD with UDIs and the UMI Second Strand Synthesis Module  following the manufacturer's protocol. Prior to library preparation, the concentration of RNA was measured using the Promega Quantus Fluorometer. Additionally, the size distribution of the RNA was assessed using the Agilent TapeStation with an RNA ScreenTape. Quantifiaction and quality assessment were repeated after library preparation, again using the Quantus fluorometer and the Agilent TapeStation with a High Sensitivity D1000 ScreenTape. Libraries were denatured, diluted, and loaded onto a NextSeq High Output v2.5 (75 cycles) flow cell. The 20% PhiX control library was spiked in to improve base calling accuracy. Single-end sequencing was performed with 75 cycles on the Illumina NextSeq platform according to the manufacturer's instructions.

value: Liver

tag: cell line

value: Primary cells

value: Kupffer cell

tag: genotype

value: Control


title: In Vitro SreA FL Cassette transcript, 1M7, primer-MaP, Replicate 2


title: WT2_14


title: primary tumor 3

city: Beijing

first: Xiaohong

last: Chen

address: 1,DongJiaoMinXiang Street, DongCheng District,Beijing, P.R.China.100730

department: Department of Otolaryngology Head and Neck Surgery

country: China

institute: Beijing Tongren Hospital, Capital Medical University

description:
Library name: C11
C11

data_processing:
The sequencing data was filtered with SOAPnuke by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2.
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Expression level of gene was calculated by RSEM (v1.3.1).
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: Ecxel file includes TPM values for each Sample.

source_name: tumor

extract_protocol:
Appropriate tissue samples were collected into corresponding numbered grinding tubes, and 1.5 mL of TRIzol lysis reagent was added. Total RNA was extracted from tissues using TRIzol (Invitrogen, Carlsbad, California, USA) according to manual instruction. The concentration, RNA integrity number, 28S/18S ratio, and fragment size of total RNA were determined using the Agilent 2100 Bioanalyzer.
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). Samples meeting quality standards were used for library construction and sequencing on an MGISEQ-2000RS platform.

value: tumor


title: REN026_B1


title: primary tumor 2

description:
Library name: C10
C10


title: In Vitro SreA GGapt transcript, 1M7, Switch-MaP


title: REN017_B1


title: REN014_B1


title: REN013_B1


title: GFPinactiveTLR4siRNA_11

value: Egfp mRNA + Tlr4 siRNA LNP


title: GFPinactiveTLR4siRNA_10


title: primary normal tissue 11

description:
Library name: AP9
AP9

source_name: normal tissue

value: normal tissue


title: primary normal tissue 10

description:
Library name: AP4
AP4


title: In Vitro SreA GGapt Cassette transcript, DMSO, primer-MaP, Replicate 1

description:
cDNA was generated by MaP RT
Lm_SreA_GGaptamer_cassette.fa
Lm_SreA_GGaptamer_cassette_primers.fa
Lm-SreA-GGapt-cassette-Rep1.shape
Lm-SreA-GGapt-cassette-Rep1_structure.ct


title: primary normal tissue 7

description:
Library name: AP27
AP27


title: GFPinactiveTLR4siRNA_9


title: In Vitro SreA GGapt Cassette transcript, 1M7, primer-MaP, Replicate 2

description:
cDNA was generated by MaP RT
Lm_SreA_GGaptamer_cassette.fa
Lm_SreA_GGaptamer_cassette_primers.fa
Lm-SreA-GGapt-cassette-Rep2.shape
Lm-SreA-GGapt-cassette-Rep2_structure.ct


title: primary tumor 1

description:
Library name: C1
C1


title: In Vitro SreA GGapt Cassette transcript, DMSO, primer-MaP, Replicate 2


title: In Vitro SreA FL Cassette transcript, 1M7, primer-MaP, Replicate 1

description:
cDNA was generated by MaP RT
Lm_SreA_cassette.fa
Lm_SreA_cassette_primers.fa
Lm-SreA-FL-cassette-Rep1.shape
Lm-SreA-FL-cassette-NoData_structure_1.ct
Lm-SreA-FL-cassette-NoData_structure_2.ct
Lm-SreA-FL-cassette-Rep1_structure.ct


title: WT_6


title: REN012_B1


title: primary normal tissue 9

description:
Library name: AP3
AP3


title: In Vitro SreA HH FL transcript, 1M7, primer-MaP

description:
cDNA was generated by MaP RT
Lm_SreA_HH.fa
Lm_SreA_HH_primers.fa
SreA_HH_FL_PrimerMaP.shape
SreA_HH_FL_PrimerMaP_structure.ct
SreA_HH_FL_PrimerMaP.pfs
SreA_HH_FL_PrimerMaP_prob.dp
SreA_HH_FL_PrimerMaP_arcplot.pdf
SreA_HH_FL_PrimerMaP_sim_antiterminator.shape
SreA_HH_FL_PrimerMaP_sim_antiterminator_structure.ct
SreA_HH_FL_PrimerMaP_sim_terminator.shape
SreA_HH_FL_PrimerMaP_sim_terminator_structure.ct


title: GFPinactiveTLR4siRNA_8


title: In Vitro SreA FL Cassette transcript, DMSO, primer-MaP, Replicate 1


title: primary normal tissue 8

description:
Library name: AP28
AP28


title: WT2_13


title: GFPinactiveTLR4siRNA_7


title: In Vitro SreA GGapt Cassette transcript, 1M7, primer-MaP, Replicate 1


title: WT_5


title: primary normal tissue 6

description:
Library name: AP25
AP25


title: In Vitro SreA HH FL transcript, DMSO, primer-MaP


title: WT_4


title: In Vitro SreA GGapt transcript, DMSO, primer-MaP, Replicate 2

description:
cDNA was generated by MaP RT
Lm_SreA_GGaptamer.fa
Lm_SreA_GGaptamer_primers.fa
Lm-SreA-GGapt-primerMaP-Rep2.shape
Lm-SreA-GGapt-primerMaP-Rep2_structures.ct
Lm-SreA-GGapt-primerMaP-Rep2.pfs
Lm-SreA-GGapt-primerMaP-Rep2_prob.dp
Lm-SreA-GGapt-primerMaP-Rep2_arcplot.pdf


title: primary normal tissue 5

description:
Library name: AP24
AP24


title: primary normal tissue 4

description:
Library name: AP19
AP19


title: WT_3


title: In Vitro SreA GGapt transcript, 1M7, primer-MaP, Replicate 2


title: In Vitro SreA GGapt transcript, DMSO, primer-MaP, Replicate 1

description:
cDNA was generated by MaP RT
Lm_SreA_GGaptamer.fa
Lm_SreA_GGaptamer_primers.fa
Lm-SreA-GGapt-primerMaP-Rep1.shape
Lm-SreA-GGapt-primerMaP-Rep1_structures.ct
Lm-SreA-GGapt-primerMaP-Rep1.pfs
Lm-SreA-GGapt-primerMaP-Rep1_prob.dp
Lm-SreA-GGapt-primerMaP-Rep1_arcplot.pdf


title: In Vitro SreA GGapt transcript, 1M7, primer-MaP, Replicate 1


title: primary normal tissue 3

description:
Library name: AP16
AP16


title: WT_1


title: WT_2


title: Pt6_pre

status: Public on Dec 25 2024

city: Trieste

first: Roberto

last: Amadio

address: Padriciano 99

country: Italy

institute: ICGEB Trieste

description: Library name: Sample 11

data_processing:
Library sequencing was performed by Macrogen Europe and raw FTP files containing FastQ were provided.
FastQ files were md5sum checked
FastQC, Trimming by Trimgalore and alignment to GRCh38/hg38 by STAR were performed in R software
Assembly: GRCh38/hg38
Supplementary files format and content: Tab-delimited text file contain normalized reads as count matrix

source_name: PBMCs

growth_protocol: Total PBMCs were collected and shipped in RNA later from San Raffaele Insitute. RNA was extracted by Rneasy micro kit (Qiagen)

extract_protocol:
RNA was harvested using Rneasy micro kit (Qiagen) and 3 ng of total RNA were used for mRNA library preparation
RNA-seq libraries were prepared using mRNA Library Prep Kit (WATCHMAKER) following manufacture instruction.

treatment_protocol: Samples were collected from Wiskott-Aldrich Syndrome patients before and five years after gene therapy.

value: PBMCs

value: WAS


title: primary normal tissue 2

description:
Library name: AP11
AP11


title: primary normal tissue 1

description:
Library name: AP1
AP1


title: Pt6_post

description: Library name: Sample 12

value: WT

value: Gene therapy


title: SK-N-SH_DMSO_control_rep1

type: genomic

city: Kumamoto

first: Kazuya

last: Iwamoto

address: 1-1-1 Honjo, Chuo-ku

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

description: human neuroblastoma cells (SK-N-SH) with 0.06% DMSO

hyb_protocol: Bisulfite converted DNA was amplified, processed and hybridized to Illumina HumanMethylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
Illumina BeadStudio was used, according to the manufacturer's instructions.
Non-normalized data file includes: Unmethylated and methylated signal intensities (same as signalA and signalB on BeadStudio output, respectively).
Normalization: Average Beta values (Beta value was calculated according to the ratio of intensities between methylated and unmethylated alleles, as in the following formula: beta value = methylated intensity/(methylated intensity + unmethylated intensity + 100) ).

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol was used.

growth_protocol: Human neuroblastoma SK-N-SH cells were cultured with Eagle’s minimal essential medium with 10% fetal bovine serum containing antipsychotics for 8 days.

extract_protocol: Genomic DNA was extracted via standard phenol:chloroform methods. The DNA samples were subjected to bisulfite modification by the EZ DNA Methylation Kit D500 (Zymo Research,).

treatment_protocol: We used low and high concentrations of haloperidol (1 uM and 10 uM) and risperidone (3 uM and 30 uM) based on their effective blood concentrations. The antipsychotics were dissolved in dimethyl sulfoxide (DMSO). Final concentrations of DMSO were 0.001% to 0.06%, depending on the dose of antipsychotics. The cells were cultured with or without 0.06% of DMSO as a control.

value: SK-N-SH

value: DMSO


title: SK-N-SH_perospirone_low_rep1

description: human neuroblastoma cells (SK-N-SH) with 10.5 nM perospirone


title: SK-N-SH_DMSO_control_rep3

source_name: human neuroblastoma cells (SK-N-SH) with 0.06% DMSO


title: Pt5_post

description: Library name: Sample 10


title: Pt1_pre

description: Library name: Sample 1


title: Pt3_pre

description: Library name: Sample 5


title: Pt3_post

description: Library name: Sample 6


title: SK-N-SH_perospirone_high_rep1

description: human neuroblastoma cells (SK-N-SH) with 105.5 nM perospirone


title: Pt2_post

description: Library name: Sample 4


title: Pt1_post

description: Library name: Sample 2


title: Pt4_pre

description: Library name: Sample 7


title: Pt2_pre

description: Library name: Sample 3


title: 21335X12_ASPC1_sgDual2_rep2

city: Salt Lake City

first: Eric

middle: L

last: Snyder

state: Utah

address: 2000 Cir of Hope Dr

department: Oncological Sciences

institute: University of Utah

description: Library name: 21335X12_ASPC1_sgDual2_rep2

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 108 (20605R and 20347R) and 110 (21335R) and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCh38
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited matrix

growth_protocol: Cells were grown in RPMI-1640 supplemented with 10% FBS, 1% Glutamax, and 2.5ug/mL of Plasmocin.

extract_protocol:
RNA was isolated via Trizol-chloroform extraction followed by column-based purification. The aqueous phase was brought to a final concentration of 35% ethanol, and RNA was purified using the PureLink RNA Mini kit according to the manufacturer’s instructions (ThermoFisher Scientific).
Library preparation was performed using the NEBNext Ultra II Directional RNA Library Prep with poly(A) mRNA isolation. Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

treatment_protocol: For doxycycline-induced expression of HNF4α P1 and P2 isoforms, BxPC3 cells were treated with 500ng/mL of dox in all conditions, Panc10.05 cells were treated with 25ng/mL of dox for P1-α2 and NC and 12.5ng/mL P2-α8.

value: sgDual


title: 21335X13_ASPC1_sgDual3_rep2

description: Library name: 21335X13_ASPC1_sgDual3_rep2


title: Pt4_post

description: Library name: Sample 8


title: 21335X14_ASPC1_sgNC_rep2

description: Library name: 21335X14_ASPC1_sgNC_rep2

value: sgNC


title: 21335X11_ASPC1_sgP2G_rep2

description: Library name: 21335X11_ASPC1_sgP2G_rep2


title: SK-N-SH_blonanserin_low_rep3

description: human neuroblastoma cells (SK-N-SH) with 1.36 nM blonanserin


title: SK-N-SH_perospirone_high_rep3

source_name: human neuroblastoma cells (SK-N-SH) with 105.5 nM perospirone


title: 21335X9_ASPC1_sgP1J_rep2

description: Library name: 21335X9_ASPC1_sgP1J_rep2


title: 21335X8_ASPC1_sgP1E_rep2

description: Library name: 21335X8_ASPC1_sgP1E_rep2


title: SK-N-SH_perospirone_low_rep2

source_name: human neuroblastoma cells (SK-N-SH) with 10.5 nM perospirone


title: 21335X7_ASPC1_sgNC_rep1

description: Library name: 21335X7_ASPC1_sgNC_rep1


title: Pt5_pre

description: Library name: Sample 9


title: SK-N-SH_DMSO_control_rep2


title: 21335X5_ASPC1_sgDual2_rep1

description: Library name: 21335X5_ASPC1_sgDual2_rep1


title: 21335X6_ASPC1_sgDual3_rep1

description: Library name: 21335X6_ASPC1_sgDual3_rep1


title: 21335X3_ASPC1_sgP2D_rep1

description: Library name: 21335X3_ASPC1_sgP2D_rep1


title: 21335X2_ASPC1_sgP1J_rep1

description: Library name: 21335X2_ASPC1_sgP1J_rep1


title: 20605X5_BxPC3_P2-a8_rep2

description: Library name: 20605X5_BxPC3_P2-a8_rep2

value: 500ng/mL dox


title: 20605X4_BxPC3_P1-a2_rep2

description: Library name: 20605X4_BxPC3_P1-a2_rep2


title: 20605X6_BxPC3_EV-NC_rep2

description: Library name: 20605X6_BxPC3_EV-NC_rep2

value: NC


title: SK-N-SH_perospirone_high_rep2


title: 20347X4_Panc10.05_P1-a2_rep2

description: Library name: 20347X4_Panc10.05_P1-a2_rep2

value: 25ng/mL dox


title: 21335X4_ASPC1_sgP2G_rep1

description: Library name: 21335X4_ASPC1_sgP2G_rep1


title: 20347X6_Panc10.05_GFP-NC_rep2

description: Library name: 20347X6_Panc10.05_GFP-NC_rep2


title: SK-N-SH_blonanserin_low_rep2

source_name: human neuroblastoma cells (SK-N-SH) with 1.36 nM blonanserin


title: 21335X1_ASPC1_sgP1E_rep1

description: Library name: 21335X1_ASPC1_sgP1E_rep1


title: 20605X1_BxPC3_P1-a2_rep1

description: Library name: 20605X1_BxPC3_P1-a2_rep1


title: 20347X3_Panc10.05_GFP-NC_rep1

description: Library name: 20347X3_Panc10.05_GFP-NC_rep1


title: 20347X1_Panc10.05_P1-a2_rep1

description: Library name: 20347X1_Panc10.05_P1-a2_rep1


title: SK-N-SH_blonanserin_low_rep1


title: 23935X16_ASPC1_sgNC_H3K27ac_rep2

description: Library name: 23935X16

library_source: genomic

data_processing:
The paired-end HiChIP sequencing reads were aligned to the human genome hg38 with the HiC-Pro pipeline (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0831-x ).
HiC-DC+ was used to call chromatin loops by binning the genome into 5kb bins (https://www.nature.com/articles/s41467-021-23749-x#citeas).
Chromatin loops were removed if the qvalue < 0.05 or anchors overlapped with ENCODE blacklist regions (https://www.nature.com/articles/s41598-019-45839-z ).
Assembly: hg38
Supplementary files format and content: allValidPairs
Library strategy: HiChIP

extract_protocol:
For HiChIP, 6 million cells were collected per replicate. Cells were fixed in 1% formaldehyde for 10min, then quenched with glycine to a final concentration of 125 mM.
HiChIP protocol based on Mumbach et al., 2016, Nature Methods. Cross-linked chromatin was digested with the MboI restriction enzyme followed by end-repair with dNTPs including biotin labeled dATP, ligation using T4 DNA ligase, and sonication to obtain 1kb chromatin fragments using Qsonica (Q800). To enrich for chromatin interactions occurring at active regulatory elements, an anti-H3K27ac antibody (Abcam, ab4729, rabbit polyclonal, 7.5ug/HiChIP) was used for DNA fragment capture. Streptavidin magnetic beads were used to pull down ligated DNA fragments and HiChIP libraries were prepared using Illumina Tagment DNA Enzyme and Buffer Kit. Sequencing was performed with the Illumina Nextera Library preparation.

value: 2D cell line

tag: chip-antibody

value: H3K27ac (abcam, ab4729)


title: 20605X2_BxPC3_P2-a8_rep1

description: Library name: 20605X2_BxPC3_P2-a8_rep1


title: 20605X3_BxPC3_EV-NC_rep1

description: Library name: 20605X3_BxPC3_EV-NC_rep1


title: 20347X5_Panc10.05_P2-a8_rep2

description: Library name: 20347X5_Panc10.05_P2-a8_rep2

value: 12.5ng/mL dox


title: SK-N-SH_blonanserin_high_rep3

description: human neuroblastoma cells (SK-N-SH) with 13.6 nM blonanserin


title: SK-N-SH_blonanserin_high_rep2

source_name: human neuroblastoma cells (SK-N-SH) with 13.6 nM blonanserin


title: 23935X15_ASPC1_sgNC_H3K27ac_rep1

description: Library name: 23935X15


title: 23935X12_ASPC1_sgP2D_H3K27ac_rep1

description: Library name: 23935X12


title: 23935X13_ASPC1_sgDual2_H3K27ac_rep1

description: Library name: 23935X13


title: 23935X14_ASPC1_sgDual2_H3K27ac_rep2

description: Library name: 23935X14


title: 23935X11_ASPC1_sgP1E_H3K27ac_rep2

description: Library name: 23935X11


title: 23935X10_ASPC1_sgP1E_H3K27ac_rep1

description: Library name: 23935X10


title: SK-N-SH_blonanserin_high_rep1


title: 22437X15_ASPC1_sgNC_Input_rep1

description:
Library name: 22437X15
ChIPseq

data_processing:
Fastq alignments were pre-processed with the merge_umi_fastq application from the UMIScripts package (https://github.com/HuntsmanCancerInstitute/UMIScripts) to associate the UMI sequence, provided as the R2 Fastq file, into the read comment.
Reads were aligned using Bowtie2 v2.2.9 to the standard chromosomes of the mouse genome (version mm10) or the human genome (version hg38).
Duplicate alignments based on the UMI code were removed using the bam_umi_dedup application (UMIScripts) allowing for 1 mismatch.
Peaks were called using MACS2 v2.2.7 with a significance of q-value <1e-8 for exogenous experiments and q-value < 0.01 for endogenous experiments.
Coverage tracks were generated with MACS2 as Reads Per Million.
Assembly: hg38
Supplementary files format and content: bigwig, BED files (except for Input samples)

extract_protocol:
For ChIP-seq, 10 million cells were collected per replicate. Cells were washed 3X in cold PBS, then resuspended in 10 ml of 2 mM DSG buffer (1X PBS, 1 mM MgCl2) containing 80μL of 0.25 M disuccinimidyl glutarate (DSG) (Thermo Fisher Scientific) and incubated at room temperature for 35 min. Methanol-free formaldehyde was then added to a final concentration of 1% and cells were crosslinked for 10 min. The cross-linking reaction was quenched with the addition of glycine to a final concentration of 125mM. Cells were washed with cold PBS, then the cell pellet was snap frozen in liquid nitrogen and stored at -80°C. Cell pellets were thawed on ice for 5 minutes then lysed in 1 mL of Farnham lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40) with Pierce Protease Inhibitor (PPI, ThermoFisher Scientific, A32959). Samples were centrifuged at 4°C (1000G) then resuspended in 1mL of RIPA lysis buffer (1X PBS, 1% NP40, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate) with PPI. Chromatin was sonicated with a QSonica Q800R (pulse: 30 s on/30 s off; sonication time: 20 minutes; amplitude: 70%). After sonication, samples were centrifuged at 17,000 x g for 15 minutes and an input was collected from each sample of sheared chromatin. Chromatin from each sample was then immunoprecipitated overnight with 5ug of the following antibodies (per sample) premixed with Protein G Dynabeads (for mouse antibodies; ThermoFisher Scientific, 10004D): HNF4α (Perseus Proteomics PP-H1415) and HNF4α-P1 (Perseus Proteomics PP-K9218) The next day, bound chromatin was washed 5 times with LiCl Wash Buffer (100 mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% sodium deoxycholate). For all samples, crosslinks were reversed by incubating samples in IP Elution Buffer (1% SDS, 0.1% NaHCO3) overnight at 65°C. ChIP DNA was purified using Zymo ChIP DNA Clean and Concentrator Kit (Zymo, D5205).
Library preparation was performed using the ChIP-seq with NEBNext DNA Ultra II library prep kit using Unique Molecular Indexes (UMIs). Sequencing was performed using the Illumina NovaSeq 6000 (150 x 150 bp paired-end sequencing, 25 million reads per sample).

tag: chip antibody

value: No Antibody


title: 22437X13_ASPC1_sgP2D_Input_rep1

description:
Library name: 22437X13
ChIPseq


title: 22437X10_ASPC1_sgNC_HNF4a_rep2

description:
Library name: 22437X10
ChIPseq

value: HNF4α (Perseus Proteomics PP-H1415)


title: 22437X14_ASPC1_sgP2D_Input_rep2

description:
Library name: 22437X14
ChIPseq


title: 22437X11_ASPC1_sgP1E_Input_rep1

description:
Library name: 22437X11
ChIPseq


title: 22437X16_ASPC1_sgNC_Input_rep2

description:
Library name: 22437X16
ChIPseq


title: 22437X12_ASPC1_sgP1E_Input_rep2

description:
Library name: 22437X12
ChIPseq


title: 22437X8_ASPC1_sgP2D_HNF4a_rep2

description:
Library name: 22437X8
ChIPseq


title: 22437X7_ASPC1_sgP2D_HNF4a_rep1

description:
Library name: 22437X7
ChIPseq


title: 22437X6_ASPC1_sgP1E_HNF4a_rep2

description:
Library name: 22437X6
ChIPseq


title: 22437X5_ASPC1_sgP1E_HNF4a_rep1

description:
Library name: 22437X5
ChIPseq


title: SK-N-SH_perospirone_low_rep3


title: 22437X4_ASPC1_sgNC_P1_rep2

description:
Library name: 22437X4
ChIPseq

value: HNF4α-P1 (Perseus Proteomics PP-K9218)


title: 22437X3_ASPC1_sgNC_P1_rep1

description:
Library name: 22437X3
ChIPseq


title: 21025X12_BxPC3_P1-a8_Input_rep2

description:
Library name: 21025X12
ChIPseq


title: 22437X2_ASPC1_sgP2D_P1_rep2

description:
Library name: 22437X2
ChIPseq


title: 22437X9_ASPC1_sgNC_HNF4a_rep1

description:
Library name: 22437X9
ChIPseq


title: 21025X11_BxPC3_P1-a8_Input_rep1

description:
Library name: 21025X11
ChIPseq


title: 21025X9_BxPC3_P1-a2_Input_rep1

description:
Library name: 21025X9
ChIPseq


title: 21025X10_BxPC3_P1-a2_Input_rep2

description:
Library name: 21025X10
ChIPseq


title: 21025X8_BxPC3_P1-a8_HNF4a_rep2

description:
Library name: 21025X8
ChIPseq


title: 21025X5_BxPC3_P1-a2_HNF4a_rep1

description:
Library name: 21025X5
ChIPseq


title: 20904X12_Panc10.05_P2-a8_Input_rep2

description:
Library name: 20904X12
ChIPseq


title: 22437X1_ASPC1_sgP2D_P1_rep1

description:
Library name: 22437X1
ChIPseq


title: 21025X6_BxPC3_P1-a2_HNF4a_rep2

description:
Library name: 21025X6
ChIPseq


title: 20904X7_Panc10.05_P1-a2_HNF4a_rep2

description:
Library name: 20904X7
ChIPseq


title: 20904X8_Panc10.05_P2-a8_HNF4a_rep2

description:
Library name: 20904X8
ChIPseq


title: 20904X10_Panc10.05_P2-a8_Input_rep1

description:
Library name: 20904X10
ChIPseq


title: Non-COVID19-24

city: Jinan

first: Chen

last: Geng

state: State...

address: Shandong Provincial Clinical Medicine Research Center for reproductive health

institute: Shandong University

description:
Library name: Non-24
control group, replicate biosample 17

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, remove the adapter sequence and filter out low quality (low quality, the number of lines with a string quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: granulosa cells

growth_protocol: Granulosa cells were extracted on the day of oocyte retrieval day. Follicular fluid was centrifuged and the precipitates were harvested. The precipitates were then transferred into lymphocyte separation medium. We collected the interlayer phase from lymphocyte separation medium.

extract_protocol:
RNA was harvest using TRIzol® Reagent. Qualification was determined by Nanodrop ND-2000 system and Agilent Bioanalyzer 4150 system.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit following the manufacturer’s instructions.

treatment_protocol: We collected granulosa cells from Non-COVID19 person and COVID19 person.

value: granulosa cells

value: mural granulosa cell

value: Control


title: 20904X6_Panc10.05_P2-a8_HNF4a_rep1

description:
Library name: 20904X6
ChIPseq


title: Non-COVID19-22

description:
Library name: Non-22
control group, replicate biosample 15

value: WT


title: 20904X5_Panc10.05_P1-a2_HNF4a_rep1

description:
Library name: 20904X5
ChIPseq


title: Non-COVID19-23

description:
Library name: Non-23
control group, replicate biosample 16


title: Non-COVID19-19

description:
Library name: Non-19
control group, replicate biosample 14


title: Non-COVID19-11

description:
Library name: Non-11
control group, replicate biosample 9


title: 21025X7_BxPC3_P1-a8_HNF4a_rep1

description:
Library name: 21025X7
ChIPseq


title: Non-COVID19-9

description:
Library name: Non-9
control group, replicate biosample 7


title: Non-COVID19-8

description:
Library name: Non-8
control group, replicate biosample 6


title: Non-COVID19-10

description:
Library name: Non-10
control group, replicate biosample 8


title: Non-COVID19-7

description:
Library name: Non-7
control group, replicate biosample 5


title: 20904X11_Panc10.05_P1-a2_Input_rep2

description:
Library name: 20904X11
ChIPseq


title: Non-COVID19-6

description:
Library name: Non-6
control group, replicate biosample 4


title: COVID19-12

description:
Library name: COV-12
infection group, replicate biosample 9

value: Infection


title: Non-COVID19-1

description:
Library name: Non-1
control group, replicate biosample 1


title: Non-COVID19-3

description:
Library name: Non-3
control group, replicate biosample 2


title: Non-COVID19-5

description:
Library name: Non-5
control group, replicate biosample 3


title: 20904X9_Panc10.05_P1-a2_Input_rep1

description:
Library name: 20904X9
ChIPseq


title: Non-COVID19-17

description:
Library name: Non-17
control group, replicate biosample 13


title: COVID19-8

description:
Library name: COV-8
infection group, replicate biosample 6


title: COVID19-5

description:
Library name: COV-5
infection group, replicate biosample 5


title: Non-COVID19-16

description:
Library name: Non-16
control group, replicate biosample 12


title: COVID19-2

description:
Library name: COV-2
infection group, replicate biosample 2


title: COVID19-1

description:
Library name: COV-1
infection group, replicate biosample 1


title: COVID19-11

description:
Library name: COV-11
infection group, replicate biosample 8


title: COVID19-4

description:
Library name: COV-4
infection group, replicate biosample 4


title: COVID19-10

description:
Library name: COV-10
infection group, replicate biosample 7


title: COVID19-3

description:
Library name: COV-3
infection group, replicate biosample 3


title: K31_OE

city: Kashiwa

first: Kenji

last: Harada

state: Chiba

address: 6-5-1 Kashiwanoha

department: Exploratory Oncology Research & Clinical Trial Center

institute: National Cancer Center

data_processing:
The quality of the raw paired-end sequence reads was assessed using FastQC (Version 0.11.7).
Low quality (< 20) bases and adapter sequences were removed using Trimmomatic software (Version 0.38).
The trimmed reads were aligned to the reference genome using HISAT2 (Version 2.1.0).
The HISAT2-resultant .sam files were converted into .bam files using Samtools (Version 1.9).
The .bam files were used to estimate the abundance of uniquely mapped reads using featureCounts (Version 1.6.3).
The raw read counts were normalized with transcripts per million (TPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: gastric cancer organoid

growth_protocol: All cell lines were maintained as described previously in a humidified atmosphere of 5% CO2 and 95% air at 37 °C. Human gastric cancer organoids were established and cultured in organoid media containing the niche factors.

extract_protocol:
Total RNA was extracted from cell lines and GCOs using the Nucleo Spin RNA Plus Kit (TaKaRa Bio) according to the manufacturer's instructions.
The RNA-seq library was prepared using Non-stranded library preparation method.

value: gastric cancer organoid

value: gastric cancer

value: PI3 overexpression


title: Non-COVID19-15

description:
Library name: Non-15
control group, replicate biosample 11


title: K24_OE


title: K31_Ctrl


title: Non-COVID19-12

description:
Library name: Non-12
control group, replicate biosample 10


title: K24_Ctrl


title: HSC44PE_Ctrl

source_name: gastric cancer cell line

value: gastric cancer cell line


title: MKN45_OE


title: HSC44PE_OE


title: K1_OE


title: MKN45_Ctrl


title: MKN1_OE


title: MKN1_Ctrl


title: U937_NTc_S3_L001

city: San Diego

first: Maria

middle: Cecilia

last: Marcondes

state: CA

address: 3525 John Hopkins Ct. #200

institute: San Diego Biomedical Research Institute

description:
U937 parent
U937_NT_filtered_feature_bc_matrix.h5

library_source: transcriptomic single cell

data_processing:
Cell Ranger
Assembly: GRChg38 GCA_000001405.15 GCF_000001405.26
Supplementary files format and content: h5

growth_protocol: Complete RPMI

extract_protocol:
Following stimulation, the cells were collected by centrifugation, and washed with PBS containing 2% of BSA. 10000 cells were processed freshly on Chromium controller (www.10x genomics.com) by using Chromium single cell 3’ Reagent kits with v3.1 Chemistry Dual Index, followed by library preparation.
10X Gene Expression library contruction protocol

treatment_protocol: Dopamine (Sigma Aldrich,  was provided at 1 uM or 10uM. MRP8/14 was provided at 1 uM or 10 uM.

value: Promonocytes

value: Caucasian

value: No treatment


title: U937_NTp_S1_L001


title: U937_DAp_S2_L002

description:
U937 parent
U937_DA_filtered_feature_bc_matrix.h5

value: DA 10uM


title: U937_DAp_S2_L001


title: U937_DAc_S4_L002


title: U937_DAc_S4_L001


title: U1_NTc_S3_L002

description:
U937 cells that is latently infected with HIV-1 isolate NY-5.
U1_NT_filtered_feature_bc_matrix.h5


title: U1-MRPc_S8_L002

description:
U937 cells that is latently infected with HIV-1 isolate NY-5.
U1_MRP8_14_filtered_feature_bc_matrix.h5


title: U1-MRPp_S6_L002


title: U1-DAp_S5_L001

description:
U937 cells that is latently infected with HIV-1 isolate NY-5.
U1_DA_filtered_feature_bc_matrix.h5


title: U1-DAp_S5_L002


title: U1_NTp_S1_L002


title: U1-DAc_S7_L002


title: U251MG cells, Radioresistant, replicate 3

city: Shanghai

first: Zhou

last: Yuchuan

address: No.2094 Xie-Tu Road

department: Institute of Radiation Medicine

institute: Fudan University

data_processing:
The library was sequenced using NovaSeq 6000 (Illumina, San Diego, CA, USA)
Reads containing adapters, poly-N, and low-quality reads were removed with Trim Galore software (v0.6.6)
Clean reads were mapped to the human reference genome (hg38) using TopHat soft-ware and Cufflinks software (v2.2.1)
featureCount software was used to obtain read counts/fragments per kilobase of transcript per million fragments mapped (FPKM)/transcripts per million (TPM) for each noticed gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes TPM values for each Sample

growth_protocol: U251MG cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
Total cellular RNA was extracted using Trizol reagent (Invitrogen, San Diego, CA, USA)
The NEBNext Ultra mRNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was used for RNA library construction.

treatment_protocol: U251MG cells were developed into radioresistant GBM cells by exposure to 2 Gy of X-rays per day for 30 fractions, for a total dose of 60 Gy.

value: Glioblastoma cells

value: Radioresistance


title: U1-DAc_S7_L001


title: U251MG cells, Control, replicate 3


title: K1_Ctrl


title: U251MG cells, Radioresistant, replicate 1


title: Input3

city: Pokfulam

first: Lydia

last: Cheung

address: 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: University of Hong Kong

data_processing:
Original raw data from Illumina platform were transformed to Raw Reads by base calling of CASAVA and are recorded in FASTQ file.
Basic quality of the raw reads was checked by FastQC and then skewer 0.1.126 was used for raw data trimming. Adapter sequence at the 3’-end was trimmed. Reads with length less than 18nt after trimming were discarded. Reads with proportion of low quality bases larger than 50% and N ratio (unsure base) larger than 15% were discarded.
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA 0.7.12.
bigWig files were generated by deeptool (1.5.11) bamcoverage for bam-to-bigWig conversion
Assembly: hg38
Supplementary files format and content: bigWig(.bw)

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Chromatin was sonicated using Diagnode bioruptor pico sonicator after quenching and cell lysis. The purified DNA was used for ChIP-seq library preparation.
ChIP-Seq library preparation was performed by Novogene Corporation Inc (China). After the construction of the library, initial quantification was done with Qubit 2.0 and the library was diluted to 1ng/l. The insertion size of the library was detected with NGS3K.

tag: disease

value: Human ovarian carcinoma

value: Ovarian cancer cells

value: p85beta stable expression


title: Input1


title: HA3

value: Abcam, Ab9110


title: 20347X2_Panc10.05_P2-a8_rep1

description: Library name: 20347X2_Panc10.05_P2-a8_rep1

value: 12.5ng/mL dox


title: Input2


title: U251MG cells, Control, replicate 1

value: WT

value: Control


title: BCLAF1_3

value: Bethyl, A300-608A


title: U251MG cells, Control, replicate 2


title: BCLAF1_2


title: U1-MRPp_S6_L001


title: U1-MRPc_S8_L001


title: HA1


title: BCLAF1_1


title: Sample 11_R2OX, siBCLAF1 2

data_processing:
Sequencing reads were first filtered for adapter sequence, low quality sequence and rRNA sequence. Reads with read length ≥40 bp retained were aligned to the human genome GRCh38 using STAR version 2.5.2. Differentially expressed genes were identified using DESeq2 version 1.26.0.
Assembly: hg38
Supplementary files format and content: FPKM values and gene ID

source_name: Ovarian cancer

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen).
2ug RNA was used for library preparation using KAPA Stranded mRNA-Seq Kit (Roche).
RNA sequencing was performed on the Illumina NovaSeq 6000 system.

value: Ovarian cancer

value: p85beta stable expression + BCLAF1 knockdown


title: HA2


title: Sample 12_R2OX, siBCLAF1 3


title: U251MG cells, Radioresistant, replicate 2


title: Sample 10_R2OX, siBCLAF1 1


title: Sample 9_R2OX, mock 3


title: Sample 7_R2OX, mock 1


title: Sample 8_R2OX, mock 2


title: R513H/WT forebrain organoids, CUTTag IgG negative control, library 2

city: San Francisco

first: Kelsey

last: Hennick

address: 1651 4th St room 521A

institute: UCSF

description:
Library name: R513H-CUTTag-IgG-rep2
One pool of cells split into two technical replicates for library prep

data_processing:
CUT&Tag data was processed by trimming adaptors with trimGalore, aligning to hg38 with bowtie2, marking and removing duplicates with picard, and calling peaks with MACS2
Assembly: hg38
Supplementary files format and content: narrowPeak output from MACS2 peak calling
Library strategy: CUT&Tag

source_name: hiPSC-derived forebrain organoid

extract_protocol:
Fragmented DNA was purified using phenol chloroform
Libraries were constructed using the Nextera XT Index Kit v2 Set A

value: hiPSC-derived forebrain organoid

value: CRISPR isogenic 13234 clone

value: hiPSC

value: forebrain organoid differentiation


title: R513H/WT forebrain organoids, CUTTag for H3K27me3, library 2

description:
Library name: R513H-CUTTag-H3K27me3-rep2
One pool of cells split into two technical replicates for library prep


title: Sample 6_Vector, siBCLAF1 3

value: BCLAF1 knockdown


title: R513H/WT forebrain organoids, CUTTag IgG negative control, library 1

description:
Library name: R513H-CUTTag-IgG-rep1
One pool of cells split into two technical replicates for library prep


title: Sample 5_Vector, siBCLAF1 2


title: R513H/WT forebrain organoids, CUTTag for FOXP4, library 2

description:
Library name: R513H-CUTTag-FOXP4-rep2
One pool of cells split into two technical replicates for library prep


title: R513H/WT forebrain organoids, CUTTag for H3K27me3, library 1

description:
Library name: R513H-CUTTag-H3K27me3-rep1
One pool of cells split into two technical replicates for library prep


title: Sample 4_Vector, siBCLAF1 1


title: R513H/WT forebrain organoids, CUTTag for FOXP4, library 1

description:
Library name: R513H-CUTTag-FOXP4-rep1
One pool of cells split into two technical replicates for library prep


title: R513H/WT forebrain organoids, CUTTag for FOXP1, library 2

description:
Library name: R513H-CUTTag-FOXP1-rep2
One pool of cells split into two technical replicates for library prep


title: R513H/WT forebrain organoids, CUTTag for FOXP1, library 1

description:
Library name: R513H-CUTTag-FOXP1-rep1
One pool of cells split into two technical replicates for library prep


title: Sample 3_Vector, mock 3


title: Sample 1_Vector, mock 1


title: WT forebrain organoids, CUTTag IgG negative control, library 1

description:
Library name: WT-CUTTag-IgG-rep1
One pool of cells split into two technical replicates for library prep

value: WT/WT


title: A549 cancer cell, sgCtrl, rep3

first: Zexian (Davis)

last: Zeng

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
RNA-Seq immune analysis pipeline (RIMA)
sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d
Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized abundance measurements generated by DESeq2

molecule: polyA RNA

extract_protocol:
RNA was harvested using the Rneasy mini plus kit by Qiagen. A total of 1.3 micrograms (μg) of RNA was utilized for the construction of sequencing libraries, which is a process for preparing RNA samples for next-generation sequencing.
The libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit, adhering strictly to the protocols provided by the manufacturer. This step involves converting RNA into a library of cDNA fragments with adaptors attached to each end, a prerequisite for sequencing.

value: lung cancer cell

value: control knockout


title: WT forebrain organoids, CUTTag for H3K27me3, library 1

description:
Library name: WT-CUTTag-H3K27me3-rep1
One pool of cells split into two technical replicates for library prep


title: WT forebrain organoids, CUTTag for H3K27me3, library 2

description:
Library name: WT-CUTTag-H3K27me3-rep2
One pool of cells split into two technical replicates for library prep


title: A549 cancer cell, sgCtrl, rep1


title: A549 cancer cell, sgCtrl, rep2


title: WT forebrain organoids, CUTTag for FOXP4, library 2

description:
Library name: WT-CUTTag-FOXP4-rep2
One pool of cells split into two technical replicates for library prep


title: A549 cancer cell, sgTNFAIP3-2, rep2

value: TNFAIP3 knockout


title: A549 cancer cell, sgTNFAIP3-2, rep1


title: WT forebrain organoids, CUTTag for FOXP1, library 2

description:
Library name: WT-CUTTag-FOXP1-rep2
One pool of cells split into two technical replicates for library prep


title: A549 cancer cell, sgTNFAIP3-1, rep3


title: A549 cancer cell, sgTNFAIP3-2, rep3


title: WT forebrain organoids, CUTTag for FOXP1, library 1

description:
Library name: WT-CUTTag-FOXP1-rep1
One pool of cells split into two technical replicates for library prep


title: WT forebrain organoids, CUTTag for FOXP4, library 1

description:
Library name: WT-CUTTag-FOXP4-rep1
One pool of cells split into two technical replicates for library prep


title: A549 cancer cell, sgTNFAIP3-1, rep2


title: WT forebrain organoids, scRNA-seq, library 2

description:
Library name: WT-scRNAseq-rep2
wt7 in metadata, one pool of cells split into two technical replicates for library prep

data_processing:
scRNA-seq data was first processed using PIPseeker for quality control, and then following the Seurat pipeline.
Assembly: hg38
Supplementary files format and content: scRNA-seq: csv file with cell metadata

extract_protocol:
RNA was extracted following the Fluent PIP-seq protocol (PMID: 36879006)
Libraries were constructed using the Fluent PIP-seq reagents (PMID: 36879006)


title: A549 cancer cell, sgTNFAIP3-1, rep1


title: R513H/WT forebrain organoids, scRNA-seq, library 2

description:
Library name: R513H-scRNAseq-rep2
het3 in metadata, labeled R514H (same residue, different isoform), one pool of cells split into two technical replicates for library prep


title: AML20, scRNAseq

city: Taipei

first: Chung-Hsing

address: No.1 Ai-Guo West Road

department: Department of Mathematics

country: Taiwan

institute: University of Taipei

data_processing:
The scRNA-seq data were processed and integrated using Cell Ranger Suite 6.0.1 along with the GRCh38 reference genome, resulting in the generation of unique molecular identifier (UMI) count matrices. Following barcode demultiplexing, the UMI matrices were imported into the R package Seurat (version 4.0.1), which is an R toolkit utilized for quality control, analysis, and exploration of scRNA-seq data. Cells expressing fewer than 500 genes, with total UMI counts below 1000, or with over 10% of total UMI counts in the mitochondrial genome were considered low-quality or indicative of dead or dying cells. Doublets within each sample were identified using DoubletFinder. These identified cells were subsequently excluded from further analyses.
Assembly: GRCh38
Supplementary files format and content: cell barcodes (barcodes.tsv.gz), genes (genes.tsv.gz), and count matrix (matrix.mtx.gz)

source_name: Bone marrow mononuclear cells

extract_protocol:
AML cells were collected using a BD Vacutainer CPT mononuclear cell preparation tube (Franklin Lakes, NJ, USA) to enrich the concentration of myeloblast cells from the bone marrow sample. After performing density gradient centrifugation, the mononuclear cells were isolated and suspended in CELLBANKER (Zenogen Pharma, Fukushima, Japan).
Each bone marrow specimen's cell suspension was labeled with Cell Multiplex oligos (10x Genomics CG000391, Rev B), and 4-7 samples were multiplexed onto a 10x Genomics Chromium Single Cell Instrument (10x Genomics, Pleasanton, CA, USA).

value: Bone marrow mononuclear cells

tag: age

tag: gender

value: Female

tag: wbc

tag: bm

tag: pb

tag: fab

tag: cytogenetics risk

value: Intermediate


title: AML19, scRNAseq

description: cell barcodes (barcodes.tsv.gz), genes (genes.tsv.gz), and count matrix (matrix.mtx.gz)

value: Male

value: Adverse


title: Sample 2_Vector, mock 2

value: Ovarian cancer cells

value: WT


title: WT forebrain organoids, scRNA-seq, library 1

description:
Library name: WT-scRNAseq-rep1
wt7 in metadata, one pool of cells split into two technical replicates for library prep


title: R513H/WT forebrain organoids, scRNA-seq, library 1

description:
Library name: R513H-scRNAseq-rep1
het3 in metadata, labeled R514H (same residue, different isoform), one pool of cells split into two technical replicates for library prep


title: WT forebrain organoids, CUTTag IgG negative control, library 2

description:
Library name: WT-CUTTag-IgG-rep2
One pool of cells split into two technical replicates for library prep


title: AML17, scRNAseq


title: AML18, scRNAseq

value: Favorable


title: S2_5_mouse5

city: Osaka

first: Yu-Tung

last: Li

address: 2-2 Yamada-oka, Suita

institute: Osaka University

data_processing:
Sequencing outputs were demultiplexed using bcl2fastq2 (https://jp.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html)
reads were aligned on the mouse reference genome using STAR and the mapped reads were quantified using RSEM.
Assembly: GRCm38
Supplementary files format and content: Processed data files are RSEM output (.genes.results)

source_name: Mouse 5

growth_protocol: (cells were isolated directly from tissues without culture)

extract_protocol:
RNA was harvested using RNeasy Plus Micro Kit (Cat#74034).
Libraries were constructed following the Smart-seq2 protocol (Picelli S, et al. Nature. 2014) with minor modifications. First-strand cDNA were synthesized adding oligo dT primer and template switching oligo. Then, full-length ds cDNA were amplified by IS-PCR. Amplified cDNA were purified using magnetic beads. cDNA libraries were constructed using Nextera XT DNA Library Prep Kit (illumina, Cat#.FC-131-1096), and finally purified and size selected using magnetic beads. Libraries were sequenced on the Illumina NextSeq2000 following the manufacturer's protocols.

treatment_protocol: Samples are from healthy skin digested in 0.3% collagenase-A, 0.25mg/ml Dispase-II, 10U/ml DNaseI and 2%FBS in RPMI for one hour to obtain single cell suspension. FcR was blocked with 2.4G2 before antibody staining.

value: Skin

tag: strain

value: dermal macrophage


title: AML16, scRNAseq


title: AML15, scRNAseq


title: S1_mouse5


title: S3_mouse5


title: AML13, scRNAseq


title: AML14, scRNAseq


title: S2_5_mouse4

source_name: Mouse 4


title: S3_mouse4


title: S2_5_mouse3

source_name: Mouse 3


title: AML10, scRNAseq


title: S2_5_mouse2

source_name: Mouse 2


title: S1_mouse2


title: S3_mouse1

source_name: Mouse 1


title: AML11, scRNAseq


title: AML9, scRNAseq


title: S1_mouse1


title: AML6, scRNAseq


title: S2_5_mouse1


title: GFRa1+/Kit-, cryptorchid RNA, rep05

city: Yokohama

first: Shin-ichi

last: Tomizawa

state: Kanagawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

data_processing:
RNA-seq reads were quality-checked with FastQC (version 0.11.8, Babraham Bioinformatics), trimmed using Trim Galore! (version 0.6.6, Babraham Bioinformatics) and mapped with Hisat2 (version 2.1.0) on the mm10 mouse genome using default parameters. Read count (log2 RPM) was performed by using SeqMonk (version 1.48.1, Babraham Bioinformatics) for protein coding genes.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes log2-transformed rpm values for each sample.

source_name: Testis

growth_protocol: GFRa1+/Kit- spermatogonia were sorted from control testes and surgically-induced cryptorchid testes (day 10 after surgery).

extract_protocol:
RNA-seq
Nextera XT DNA Library Prep Kit

treatment_protocol: Total RNA from ~200 cells was used for RNA-seq library preparation using the Smart-seq2 protocol.

value: Testis

value: Spermatogonia

value: Cryptorchid


title: GFRa1+/Kit-, cryptorchid RNA, rep06


title: GFRa1+/Kit-, cryptorchid RNA, rep07


title: S3_mouse2


title: 21335X10_ASPC1_sgP2D_rep2

description: Library name: 21335X10_ASPC1_sgP2D_rep2


title: S1_mouse4


title: S3_mouse3


title: GFRa1+/Kit-, cryptorchid RNA, rep04


title: AML5, scRNAseq


title: AML12, scRNAseq


title: L_mouse4

treatment_protocol: Samples are from healthy, vehicle/treated AD skin regions or femur/tibia bone marrow. Skin samples were digested in 0.3% collagenase-A, 0.25mg/ml Dispase-II, 10U/ml DNaseI and 2%FBS in RPMI for one hour to obtain single cell suspension. FcR was blocked with 2.4G2 before antibody staining.

value: AD skin, LN

value: eosinophil


title: L_mouse3


title: C_mouse4

value: AD skin, ctrl


title: GFRa1+/Kit-, control RNA, rep05


title: H_mouse4

value: healthy skin


title: AML7, scRNAseq

value: Bone marrow mononuclear cells


title: GFRa1+/Kit-, control RNA, rep04


title: BM_mouse4

value: bone marrow


title: AML4, scRNAseq


title: S1_mouse3


title: AML8, scRNAseq

value: Female


title: AML3, scRNAseq

value: Male


title: C_mouse3


title: BM_mouse3


title: H_mouse3


title: AML2, scRNAseq

value: Intermediate


title: GFRa1+/Kit-, input, rep01

data_processing:
ChIP-seq reads were quality-checked (FastQC; Babraham Bioinformatics), adapter- and quality-trimmed (Trim Galore! version 0.6.6; Babraham Bioinformatics), and mapped onto the mouse genome (mm10) using Bowtie 2 version 2.5.1 with the parameter -N 1. After quality filtering, duplicates were removed with Picard. ChIP-seq peak identification and read count were performed using SeqMonk/MACS2 (version 1.48.1, Babraham Bioinformatics) with the default parameter.
Assembly: mm10
Supplementary files format and content: Bigwig

extract_protocol:
ChIP-seq
ChIP-seq libraries were constructed with the CATCH-seq method (Nat Cell Biol, doi: 10.1038/s41556-024-01553-1).

treatment_protocol: About 1,000 to 2,000 cells were used for H3K27me3 and H3K9me3 ChIP-seq experiments.

tag: treatment

value: Input


title: H_mouse2

tag: cell type


title: AML1, scRNAseq

tag: tissue

value: Adverse


title: GFRa1+/Kit-, cryptorchid H3K9me3, rep02


title: GFRa1+/Kit-, control H3K9me3, rep02

value: WT


title: L_mouse2


title: EM, 5

city: Guangzhou

first: Jiayi

last: Guo

state: Guangdong

address: 员村二横路26号中山大学附属第六医院No.26, Erheng Road, Yuancun

department: Reproductive Medicine Research Center

institute: the Sixth Affiliated Hospital of Sun Yat-sen University

data_processing:
FastQC (v0.11.7, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was employed to process raw sequencing data.
Trimmed data were mapped onto Homo sapiens (assembly GRCh37) using Hisat2 (v2.1.0)
Read counts and transcripts with fragments per kilobase of exon per million read mapped were generated for further analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: granulosa cells isolated from follicular fluid

extract_protocol:
Total RNA from each sample was extracted by TRIzol reagent (Invitrogen). Ribosomal RNA was removed by RiboZero Magnetic Gold Kit (Epidemiology). Subsequently, 1 μg RNA from each sample was extracted and enriched using NEB Next Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
The sequencing libraries were generated by KAPA Stranded RNA-Seq Library Prep Kit (Illumina) according to the manufacturer's recommendations.

tag: disease state

value: endometriosis

value: granulosa cells


title: C_mouse1


title: EM, 3


title: Macrophages, OI_VSV_2

first: Shulei

last: Yin

state: Shanghai

address: No.800 Xiangyin Road, Yangpu District

department: Department of Immunology

institute: Naval Medical University

description: OI_VSV_2 FPKM

data_processing:
High-quality reads were aligned to the mouse reference genome (GRCm38.p6) using Bowtie2
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM) using RNA-Seq by Expectation Maximization (RSEM).
Assembly: mm10
Supplementary files format and content: FPKM values for each sample

source_name: macrophages

growth_protocol: macrophages were maintatined in DMEM supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (QIAGEN)
cDNA library construction and sequencing were performed by Beijing Genomics Institute using MGISEQ-2000RS platform.

treatment_protocol: macrophages were treated with DMSO or OI for 12 hours following infection with VSV for 8 hours.

value: macrophages

value: OI+VSV infection


title: L_mouse1


title: H_mouse1


title: GFRa1+/Kit-, cryptorchid H3K27me3, rep03

value: Testis

value: Spermatogonia

value: Cryptorchid


title: BM_mouse1

value: eosinophil


title: GFRa1+/Kit-, control H3K27me3, rep03


title: EM, 4


title: EM, 2


title: Macrophages, OI_VSV_1

description: OI_VSV_1 FPKM


title: EM, 1


title: Macrophages, DMSO_VSV_2

description: DMSO_VSV_2 FPKM

value: DMSO+VSV infection


title: PN20_KO_M_21d

city: Philadelphia

first: Kathryn

last: Wellen

state: PA

address: 421 Curie Blvd

department: Dermatology

institute: University of Pennsylvania

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: DESeq2 output

source_name: Epidermis

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina
75bp single end reads

treatment_protocol: Mice were harvested at different timepoints post-tamoxifen induction

value: Epidermis

value: male

value: ACLY; ACSS2 dKO

value: 21 days post-tamox


title: PN19_WT_M_21d


title: C_mouse2

value: AD skin, ctrl


title: PN18_KO_M_21d


title: BM_mouse2

value: bone marrow


title: PN17_WT_M_21d


title: Macrophages, DMSO_VSV_1

description: DMSO_VSV_1 FPKM


title: Control, 4

value: control (normal)


title: PN16_KO_M_21d


title: PN15_WT_M_21d

value: WT


title: PN13_WT_M_21d


title: Mouse HSC, IC, biological rep1

city: Bronx

first: Britta

last: Will

state: NEW YORK

address: 1300 Morris Park Ave

department: Department of Cell Biology

institute: Albert Einstein College of Medicine

description: Gene expression data from mouse HSCs after 16-hours in vitro treatment with DFO

hyb_protocol: Following fragmentation, labeled cRNA of each individual sample was hybridized to Affymetrix Mouse Clariom S microarrays (Affymetrix), and stained according to the manufacturer's instructions.

scan_protocol: Hybridization signals were scanned and analyzed with GeneChip Scanner 3000 7G system (Affymetrix) according to standard protocols.

data_processing: For analysis of microarray data, intensity normalization was performed across samples with the CEL files using RMA algorithm of Oligo Bioconductor package. For analysis of differential gene expression, paired, linear modeling of Limma Bioconductor package was used to compare the treated samples versus the matched, non-treated controls.

label: Biotin

source_name: Mouse HSCs after 16-hours in vitro treatment with DFO

label_protocol: Approximately 10ng of extracted RNA was amplified and labeled using the GeneChip™ 3' IVT Pico Kit (Affymetrix, Santa Clara, CA), according to the manufacturer's instructions.

growth_protocol: Mouse HSC (Lineage−c-Kit+Sca-1+CD150+CD48−) were FACS-sorted, and cultured in Myelocult M5300 medium (Stem Cell Technologies) supplemented with 100 ng/ml rmSCF (Gemini Bio-Products, CA), 50 ng/ml rmTPO, and 200 µg/ml Primocin (InvivoGen, San Diego, CA).

extract_protocol: RNA was extracted using the RNeasy Micro kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions. Quantity and quality were assessed using Nanodrop 3300 Fluorospectrometer (Thermo Fisher Scientific, Waltham, MA) or Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mouse HSC were treated with either 10µM DFO or vehicle control (sterile H2O) in liquid culture for 16 hours. Thereafter, cells were collected and lysed with RLT plus buffer (Qiagen, Valencia, CA). Cell lysates were stored in -80 °C until use.

value: FACS-sorted HSC

value: 6-10 weeks


title: PN11_WT_M_12d

value: 12 days post-tamox


title: Control, 3

value: granulosa cells


title: Control, 2


title: PN12_KO_M_12d


title: Mouse HSC, IC, biological rep4


title: PN8_KO_F_12d


title: Control, 5


title: PN14_KO_M_21d


title: Mouse HSC, IC, biological rep3


title: PN7_WT_F_12d


title: Mouse HSC, IC, biological rep2


title: PN6_WT_M_12d


title: Control, 1


title: P79L

city: Duarte

first: Yate-Ching

last: Yuan

address: 1500 East Duarte

institute: City of Hope

description: Surgical pathology archives queried for HER2- ER+ breast cancer patients  treated with endocrine therapy, including selective estrogen receptor modulators (SERMs), selective estrogen receptor degraders (SERDs), and aromatase inhibitors (AI) following resection of the primary tumor

hyb_protocol: RNA was hybridized with codeset at 65°C for 16 hours. Samples were processed on the NanoString Prep Station and the target-probe complex was immobilized onto the analysis cartridge.

scan_protocol: Cartridges were scanned by the nCounter Digital Analyzer for digital counting of molecular barcodes corresponding to each target at 280 fields of view.

data_processing: All NanoString gene expression data analysis was performed using nSolver Analysis Software v3.0 (NanoString Technologies, Seattle, WA). Raw data was normalized by subtracting the mean plus one standard deviation of eight negative controls while technical variation was normalized through internal positive controls. Data was corrected for input volume via eight internal housekeeping genes using the geNorm algorithm. Clinical, tumor, and patient characteristics were analyzed in relation to recurrence status. Relative gene expression was analyzed by recurrence status. PAM50 subtype analysis was performed to identify molecular subtypes. Bioinformatics analysis was performed based on the ingenuity pathway analysis (IPA) tool (version 73620684, http://www.ingenuity.com).

source_name: Human breast cancer patient FFPE sample

label_protocol: NanoString's labeling protocol usees colo-coded probes (reporter and capture probes) to identify and detect target molecules in a sample.

extract_protocol: RNA was extracted using miRNeasy FFPE kit (Qiagen)

value: breast cancer

tag: recurrence

value: No Recurrence

tag: subtype

value: Lumi A

tag: recurrence type


title: P78R


title: bai_3

city: Chongqing

first: Zaikuan

last: Zhang

state: province

address: The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics

institute: Chongqing Medical University

description: Library name: bai_3

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample

treatment_protocol: RNA sequencing data of adipocytes treated or not treated with 200μM baicalin

tag: cell line

value: adipocyte

tag: genotype

value: baicalin


title: PN5_KO_M_12d

value: Epidermis


title: bai_2

description: Library name: bai_2


title: PN4_KO_F_12d

value: male


title: PN3_WT_M_12d


title: P77L

value: Lumi B


title: bai_1

description: Library name: bai_1


title: PN10_KO_F_12d

value: ACLY; ACSS2 dKO


title: PN10-fe-KO

data_processing:
Aligned using RNA STAR under default settings
Differential expression analysis was performed via DESeq2
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: FASTQ files, DESeq2 output

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (QIAGEN)
RNA-seq NEBNext Poly(A) mRNA magnetic isolation module, followed by NEBNext Ultra Directional RNA library prep kit for Illumina

value: female

value: AclyKO


title: PN1_WT_F_12d


title: PN2_KO_M_12d


title: CTL_3

description: Library name: CTL_3

value: DMSO


title: P75R


title: PN9_WT_F_12d

value: WT


title: L-OHP resistant gastric cancer organoid biological rep 2

hyb_protocol: Used the GeneChip Hybridization, Wash, and Stain Kit (Thermo Fisher) to hybridize 5.2 µg of single-stranded DNA to the Clariom D Array, Human (Thermo Fisher) in the GeneChip Hybridization Oven 645 (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC) ver.4.0 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: L-OHP resistant gastric cancer organoid biological rep 1

label_protocol: Utilized the GeneChip™ WT PLUS Reagent Kit (Thermo Fisher) to process 100 ng of total RNA into cRNA, followed by conversion to biotin-labeled single-stranded DNA.

growth_protocol: The organoids are cultured in frequently used medium. The medium was changed every 2‐3 days. The organoids were passaged twice a week with a split ratio of 1:3/1:6.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The organoids are collected using PBS and immidiately freezed.

value: L-OHP resistant gastric cancer organoid

tag: Sex

tag: age


title: L-OHP resistant gastric cancer organoid biological rep 3


title: PN7-fe-WT

tag: gender


title: CTL_2

description: Library name: CTL_2


title: parental gastric cancer organoid

source_name: parental gastric cancer organoid

value: gastric cancer organoid


title: normal gastric organoid

source_name: normal gastric organoid

value: normal gastric organoid


title: CTL_1

description: Library name: CTL_1


title: PN6-fe-WT


title: PN5-male-KO


title: PN2-male-WT


title: P76L


title: SchizosaccharomycesPombe,ZT,repeat3

city: nanjing

first: Guangchun

last: Lu

address: wenyuan road

institute: Nanjing Normal University

data_processing:
First, the descending raw reads was quality-controlled using the fastp
clean reads were aligned to the ribosome database of this species using the short reads alignment tool bowtie2[2], the reads on the upper ribosomes were removed without mismatch allowed, and the retained unmapped reads was used for subsequent transcriptome analysis.
Using the HISAT2 software, a reference genome-based alignment analysis was performed.
Based on the alignment results of the HISAT2, we reconstructed the transcripts using the Stringtie and calculated the expression levels of all the genes in each sample using the RSEM
Input data for gene differential expression analysis are the reads count data obtained from gene expression level analysis and were analyzed using DESeq2[6] software
Assembly: Using the STRING protein interaction database (http://string-db.org).
Supplementary files format and content: Ensembl_release45
Supplementary files format and content: Each Excel corresponds to the information of one sample, with a total of two tables, namely all gene expression and significant gene expression.

organism: Schizosaccharomyces pombe

source_name: whole cell

extract_protocol:
Total RNA was extracted using Trizol reagent kit.The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT), reverse transcribed to cDNA, after PCR amplification, and then sequenced.
The RNA libraries of RNA-Seq were enriched for mRNA using Oligo (dT),following manufacturer's protocols.

value: whole cell


title: SchizosaccharomycesPombe,ZT,repeat2


title: PN8-fe-KO


title: P73R

value: breast cancer


title: P74R

value: No Recurrence


title: P72L


title: PN9-fe-KO


title: SchizosaccharomycesPombe,dsk1,repeat3

value: dsk1  knockdown


title: Treg from Foxp3YFP-Cre rep3

city: Bethesda

first: Peng

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
Library name: Sample7
Treg from Foxp3YFP-Cre rep3

data_processing:
Sequenced reads were aligned to the mm10 genome assembly using Bowtie 2.2.6 and Tophat 2.2.1
Aligned reads are converted to BAM files using samtools v0.1.8. BAM files are subsequently converted to BED files using bedtools v2.25.0. Unpublished python scripts were used to calculate RPKM (reads per kilobase per million reads) to normalize gene expression values for RNA-Seq data. R package edgeR was used to identify differentially expressed genes.
Assembly: mm10/GRCm38
Supplementary files format and content: Gene expression in text format, content include gene name, symbol, chromosome, length of transcripts, and raw reads

source_name: allergic lung tissue

growth_protocol: For nTregs cultured without TCR stimulation, the sequencing libraries were constructed from 10 ng of total RNA using the Takara Bio’s SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Cat# 634888) following the manufacturer’s instruction. For TCR-stimulated nTregs, Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero was used.

extract_protocol:
Cells were harvested and the RNA-seq libraries were prepared with 100 -500 ng of total RNA according to the manufacturer’s instructions.
The fragment size of RNA-seq libraries was verified using the Agilent 2100 Bioanalyzer (Agilent) and the concentration were determined using Qubit (LifeTech). The libraries were loaded onto the Illumina’s NovaSeq 6000 to generate 50 bp single end sequencing reads.

treatment_protocol: nTregs were stimulated with TCR (anti-CD3 + anti-CD28) in the absence versus presence of TSLP. Foxp3YFP-Cre/YCrlf2fl/fl and Foxp3YFP-Cre Tregs were isolated from allergic lung tissue

value: allergic lung tissue

value: Treg

value: wild-type

value: OVA-immunized


title: Treg from Crlf2fl/fl Foxp3YFP-Cre rep2

description:
Library name: Sample9
Treg from Crlf2fl/fl Foxp3YFP-Cre rep2

value: conditional Knock-out


title: Treg from Crlf2fl/fl Foxp3YFP-Cre rep3

description:
Library name: Sample10
Treg from Crlf2fl/fl Foxp3YFP-Cre rep3


title: L-OHP resistant gastric cancer organoid biological rep 1

first: Kenji

address: 6-5-1 Kashiwanoha

institute: National Cancer Center


title: P70L

value: Lumi A


title: P71R


title: SchizosaccharomycesPombe,dsk1,repeat1


title: SchizosaccharomycesPombe,dsk1,repeat2


title: P69R


title: PN1-male-WT

value: Epidermis

value: male


title: Treg from Foxp3YFP-Cre rep2

description:
Library name: Sample6
Treg from Foxp3YFP-Cre rep2


title: P68R


title: Crep5

city: Birmingham

first: Matthew

middle: S

last: Alexander

state: AL

address: 1900 University Blvd. THT 929 Box# 96

department: Pediatrics

institute: University of Alabama at Birmingham

description: Library name: Crep5

data_processing:
Basecalls were performed using bcl2fastq
Raw sequence FASTQ files were trimmed with Trim Galore version 0.6.10 using parameters --paired --trim-n --trim1 --nextseq 20
Trimmed sequence FASTQ files were aligned with STAR version 2.7.10b_alpha_230301 using parameters --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All
Transcript abundances were calculated from STAR aligned BAMs with HTSeq-count version 2.0.2 using parameters -m union -r pos -t exon -i gene_id -a 10 -s no -f bam
Assembly: Gencode GRCm39 Release M32
Supplementary files format and content: tab-delimited text file containing Ensembl IDs with raw transcript abundances for each sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from tibialis anterior (TA) muscle using Trizol reagent. Quality of RNA was assessed by Nanodrop and Bioanalyzer.
The library was amplified and purified using AMPure beads. The library size and mass were evaluated and quantititative PCR was performed to validate the libraries. Barcoded samples were pooled equimolarly for simultanoeus sequencing. The quality of RNA-sequencing data was assessed for downstream analysis. Low-quality sequences and reads were removed.

value: skeletal muscle

value: TA muscle

value: Dmd flox52/Y:HSA mKO

value: 4-6 months


title: Treg from Foxp3YFP-Cre rep1

description:
Library name: Sample5
Treg from Foxp3YFP-Cre rep1


title: XG1_KD

city: Nanjing

first: Pinggang

last: Ding

address: 138 Xianlin Road

institute: Nanjing University of Chinese Medicine

description: Library name: sample2

data_processing:
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each Sample
Supplementary files format and content: XG1_KDVSXG1_Ctrl_Gene_differential_expression.xlsx

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511)
We aligned reads of all samples to the < research species > reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.

value: multiple myeloma

value: CHD4 KD


description:
Library name: Sample4
nTregs cultured for 24h with TCR+TSLP rep2

source_name: spleen

value: spleen

value: nTreg

value: TCR (anti-CD3 + anti-CD28) + TSLP


title: XG1_Ctrl

description: Library name: sample1

value: control


title: U251MG cells, Radioresistant, ATAC-seq

first: Zhou

address: No.2094 Xie-Tu Road

institute: Fudan University

data_processing:
The library was sequenced using NovaSeq 6000 (Illumina, San Diego, CA, USA) or Illumina HiSeq 2500 (Illumina, San Diego, CA, USA)
Reads containing adapters, poly-N, and low-quality reads were removed with Trim Galore software (v0.6.6)
Clean reads were mapped to the human reference genome (hg38) using TopHat soft-ware and Cufflinks software (v2.2.1)
featureCount software was used to obtain read counts/fragments per kilobase of transcript per million fragments mapped (FPKM)/transcripts per million (TPM) for each noticed gene.
Alignment files were sorted and indexed using Bowtie2 software (v2.2.5) and Samtools software (v1.10). Peaks were defined using MACS2 software (v2.1.4).
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes TPM values for each Sample
Supplementary files format and content: BED (ATAC-seq)

extract_protocol:
RNA-seq: Total cellular RNA was extracted using Trizol reagent (Invitrogen, San Diego, CA, USA). ATAC-seq: Cells were used for ATAC-seq analysis following the manufacturer's protocol (Active motif Inc., Shanghai, China).
RNA-seq: The NEBNext Ultra mRNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was used for RNA library construction. ATAC-seq: Chromatin was extracted and processed for Tn5-mediated labeling and adapter incorporation using the Nextera DNA Sample Preparation Kit (Illumina, San Diego, CA).

value: Glioblastoma cells

value: WT

value: Radioresistance


title: cren973

description: Library name: cren973

value: Dmd flox52/Y


title: U251MG cells, Radioresistant, shIFI16, replicate 3

data_processing:
The library was sequenced using NovaSeq 6000 (Illumina, San Diego, CA, USA)
Reads containing adapters, poly-N, and low-quality reads were removed with Trim Galore software (v0.6.6)
Clean reads were mapped to the human reference genome (hg38) using TopHat soft-ware and Cufflinks software (v2.2.1)
featureCount software was used to obtain read counts/fragments per kilobase of transcript per million fragments mapped (FPKM)/transcripts per million (TPM) for each noticed gene.
Assembly: hg38
Supplementary files format and content: Tab-delimited text includes TPM values for each Sample

extract_protocol:
Total cellular RNA was extracted using Trizol reagent (Invitrogen, San Diego, CA, USA)
The NEBNext Ultra mRNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) was used for RNA library construction.


title: Crep1

description: Library name: Crep1


title: U251MG cells, Control, ATAC-seq

value: Control


title: nTregs cultured for 24h with TCR rep2

description:
Library name: Sample2
nTregs cultured for 24h with TCR rep2

value: wild-type

value: TCR (anti-CD3 + anti-CD28)


description:
Library name: Sample3
nTregs cultured for 24h with TCR+TSLP rep1


title: cren972

description: Library name: cren972

value: skeletal muscle


title: SchizosaccharomycesPombe,ZT,repeat1

value: whole cell


title: P66R

value: breast cancer

value: Distant Recurrence

value: Lumi A

value: Recurrence


title: Crep2

description: Library name: Crep2

value: TA muscle

value: Dmd flox52/Y:HSA mKO

value: 4-6 months


title: P64L

value: Local Regional Recurrence


title: U251MG cells, Radioresistant, shIFI16, replicate 2

value: Glioblastoma cells


title: P63R

value: No Recurrence

value: Lumi B


title: nTregs cultured for 24h with TCR rep1

description:
Library name: Sample1
nTregs cultured for 24h with TCR rep1

value: spleen

value: nTreg


title: P62L


title: U251MG cells, Radioresistant, shIFI16, replicate 1

value: WT


title: Crep3

description: Library name: Crep3


title: P67R


title: High Avidity TCR

city: Farmington

first: Summit

last: Singhaviranon

state: Connecticut

address: 263 Farmington Ave

institute: University of Connecticut School of Medicine

description: TCR sequencing of High Avidity TIL

data_processing:
fastQ files were processed and aggregated using the CellRanger multi function to run aggr, count, vdj leading to a composite output.
Assembly: mm10
Supplementary files format and content: *barcodes.tsv.gz, *features.tsv.gz, *matrix.mtx.gz,  *all_contig_annotations.csv

molecule: cytoplasmic RNA

source_name: TIL

extract_protocol:
Sorted low, medium, and high avidity PDPRMUT specific CD8 TIL from MethA bearing mice were subject to 5' 10x genomic sequencing, feature bar code sequencing, and VDJ sequencing.
Three libraries were generated for each condition using the Library Construction Kit, 5’ Feature Barcode Kit, and Single Cell Mouse TCR Amplification Kit (10X Genomics) using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (Dual Index) CG000330 Rev D protocol before Next Generation Sequencing with NovaSeq (Illumina Inc.).

value: TIL

value: High Avidity

tag: library type

value: VDJ

value: Untreated


title: Med Avidity TCR

description: TCR sequencing of Med Avidity TIL

value: Med Avidity


title: cren784

description: Library name: cren784

value: skeletal muscle

value: Dmd flox52/Y


title: P61L

value: breast cancer

value: Lumi A


title: cren781

description: Library name: cren781

value: TA muscle

value: 4-6 months


title: P60L


title: U251MG cells, Radioresistant, shNC, replicate 3

value: Glioblastoma cells

value: shNC


title: P65R

value: No Recurrence


title: cren970

description: Library name: cren970


title: Low Avidity TCR

description: TCR sequencing of Low Avidity TIL

value: Low Avidity


title: siHIF1B_1

city: GuangZhou

first: qianqian

last: wang

address: college of pharmacy in Sun Yat-Sen University

institute: Sun Yat-Sen University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: stomach

growth_protocol: The gastric cancer cell lines in this study were grown in RPMI1640 supplemented with 10% FBS.

extract_protocol:
Cells were harvested, and RNA was extracted using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 mg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: AGS cells were transfected with siCont, siRORC, siHIF1A or siHIF1B for 24 h and cultured under hypoxia for additional 24 h.

value: stomach

value: AGS

value: cancer cells


title: U251MG cells, Radioresistant, shNC, replicate 1

city: Shanghai

last: Yuchuan

value: WT


title: siRORC_1

value: siRORC

value: cultured under hypoxia for additional 24 h


title: Low Avidity FBC

description: feature bar code sequencing

value: TIL

value: feature bar code sequencing

value: Untreated


title: Med Avidity FBC

description: feature bar code sequencing

value: Med Avidity


title: High Avidity FBC

description: feature bar code sequencing

value: High Avidity


title: 40 Gy Radioresistant Tumorospheroids (RRsp2) Second experimental replicate

city: Mumbai

first: Murali

middle: MS

last: Balla

state: Maharashtra

address: Trombay

department: Radiation Biology and Health Sciences Division

country: India

institute: Bhabha Atomic Research Centre

data_processing:
Galaxy
Sequence reads werechecked for quality by using FASTQC and were mapped with human reference genome GRCh38.106 (hg19) using splice aware aligner RNA STAR Galaxy Version 2.7.8a
The number of raw reads and number of reads successfully aligned for each of the samples. Gene counts from the aligned BAM files were estimated using feature counts.
DESeq2 was run on the counts data of RR versus CC and RRsp versus
Read count extraction and normalization were performed using DESeq2 in galaxy
Assembly: human reference genome GRCh38.106 (hg19)
Supplementary files format and content: Tab-delimited text files include raw files estimated using feature counts

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted from two experimental replicates of A549 parental control, RR, Spheroids of A549 cells and RR cells using RNeasy mini kit (Qiagen, Hilden, Germany)
Libraries were prepared using the Truseq RNA sample prep kit V2 as per the manufacturer’s protocol (Illumina, San Diego, CA, USA)

treatment_protocol: Radio-resistant (40 Gy and 20 Gy RR) A549 cells were generated by clonogenic assay. Five hundred cells per 100 mm plate and were exposed to 5Gy dose of 60Co γ-radiation using  Bhabhatron (RSCB, BARC Mumbai, India; dose rate: 1 Gy/min), BARC) after attachment to the surface. Irradiated cells were cultured for 10–14 days. Colonies produced by surviving cells were trypsinized and again seeded for next dose of ionizing radiation.Procedure was continued until a cumulative dose of 40Gy radio resistance (RR) was reached. Sham treatment to parental A549 cells was maintained for equal passage number as that of RR A549 cells and these cells were used as control (CC)

value: Lung Adenocarcinoma cells

value: Spheroids of Radiation treated Epithelial cancer cell line

value: Radioresistant (40 Gy) Spheroids (RRsp)


title: 40 Gy Radioresistant Tumorospheroids (RRsp1) First experimental replicate


title: A549 Tumorospheroids (CCsp2) Second experimental replicate

value: Spheroids of Epithelial cancer cell line

value: A549 Spheroids (CCsp)


title: siCont_1

value: siCont


title: P59L

value: breast cancer

value: No Recurrence

value: Lumi B


title: P58L


title: P56R

value: Lumi A


title: P57R


title: Med Avidity CD8 TIL GEX

description: Gene Expression of Med Avidity CD8 TIL

value: mRNA + ADT


title: HGC27_RORC_7

description: HGC27_Vector_RORC_genes_fpkm_expression.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome Reference Consortium Human Build 38 patch release 12 (GRCh38.p12)
Supplementary files format and content: tab-delimited text files include FPKM, TPM, and read counts values for each Sample

treatment_protocol: MKN45 cells were cultured in a normoxic incubator for 24 h or in a hypoxic incubator with certified gas containning 94% N2, 1%O2 and 5%CO2 for 24 h. AGS  cells were cultured in growth medium containing Vehicel control (DMSO) or GSK805 (5 μM) for 48 h. For HGC27,  cells transfected with Vector plasmid (HGC27-Vector) and RORγ overexpressing HGC27 stable transfectants (HGC27-RORC) were cultured in growth medium.

value: stomach

value: cancer cells

value: RORgamma overexpressed

value: overexpressed RORγ


title: siHIF1A_1

value: AGS

value: cultured under hypoxia for additional 24 h


title: U251MG cells, Radioresistant, shNC, replicate 2

value: Glioblastoma cells

value: WT

value: shNC


title: A549 Tumorospheroids (CCsp1) First experimental replicate

value: Lung Adenocarcinoma cells

value: Spheroids of Epithelial cancer cell line


title: P55L


title: P54R


title: Low Avidity CD8 TIL GEX

description: Gene Expression of Low Avidity CD8 TIL

value: TIL

value: Low Avidity

value: Untreated


title: 40 Gy Radioresistant A549 cells (RR2) Second experimental replicate

value: Radiation treated Epithelial cancer cell line

value: Radiation treated A549 cells (5 Gy/fraction eight times)


title: Ms-PDL1scfv-IL15_3

first: Mei

last: Yi

state: Jiangsu

address: 321 Zhongshan Road

institute: Nanjing Drum Tower Hospital

description: replicate biosample 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp (version 0.23.4) (parameter arsg: -l 39 --dont_eval_duplication  --qualified_quality_phred 20 --unqualified_percent_limit 8 --adapter_sequence  --adapter_sequence_r2  --fix_mgi_id) contaminated with adaptor sequences were trimmed.
Trimmed reads were mapped to GRCh38 using STAR software (version 2.5.3a) (parameters- --outSAMtype BAM SortedByCoordinate)
Read count extraction and normalization were performed using featureCounts（Version 1.5.1）（parameter -T 10 -d 30 -D 1000  were calculated.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include all reads count for each Sample

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026）. 2 ug of total RNA was used for the construction of sequencing libraries. electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit（Life Technologies，Q10210）
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO.

value: Subcutaneous tissue


title: HGC27_Vector_1

value: stomach

value: overexpressed Vector


title: Ms-PDL1scfv-IL15_2

description: replicate biosample 2


title: 40 Gy Radioresistant A549 cells (RR1) First experimental replicate

value: Radiation treated A549 cells(5 Gy/fraction eight times)


title: P52L

value: breast cancer

value: No Recurrence

value: Lumi A


title: AGS_GSK805_1

description: AGS_DMSO_GSK805_genes_fpkm_expression.txt

value: AGS

value: cancer cells

value: GSK805-5 microM-48 h


title: P53L


title: High Avidity CD8 TIL GEX

description: Gene Expression of Med Avidity CD8 TIL

value: High Avidity

value: mRNA + ADT


title: A549 Lung Adenocarcinoma cells (CC2) Second experimental replicate

value: Lung Adenocarcinoma cells

value: Epithelial cancer cell line

value: A549 cells


title: AGS_DMSO_1

value: WT

value: DMSO


title: Ms-PDL1scfv-IL15_1

description: replicate biosample 1

value: Subcutaneous tissue


title: PBS_3

description: control group, replicate biosample 3

value: PBS


title: A549 Lung Adenocarcinoma cells (CC1) First experimental replicate


title: MKN45 _normoxia_1

description: MKN45_normoxia_hypoxia_genes_fpkm_expression.txt

value: stomach

value: normoxia


title: PBS_2

description: control group, replicate biosample 2


title: MKN45_hypoxia_1

value: hypoxia


title: P50R

value: breast cancer

value: No Recurrence


title: P51L

value: Distant Recurrence

value: Lumi A

value: Recurrence


title: PBS_1

description: control group, replicate biosample 1


title: DNMT1/L1TD1-3_repeat

city: Vienna

first: Christian

last: Seiser

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description:
sample name:
52685

data_processing:
SCS: PN:HiSeq Control Software,VN:2.2.58,Controlling software on instrument
basecalling: PN:RTA,VN:1.18.64.0,Basecalling Package
bcl2fastq: PN:bcl2fastq,VN:2.16.0,bcl2fastq
fastq2bam: PN:fastq2bam,VN:0.3,conversion to unaligned bam files
BamIndexDecoder: PN:BamIndexDecoder,VN:V1.16-1-g590b59e-dirty,demultiplexging
bam2fastq: PN:samtools,VN:1.3.1,conversion to fastq
zcat: PN:zcat,VN:unknown,merging of fastq files of the same sampleid
cutadapt: PN:cutadapt,VN:v1.4.2,adapter trimming,--match-read-wildcards -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
bowtie2: PN:bowtie2,VN:2.1.0 ,rRNA removal by alignment to rDNA,--very-sensitive-local,KY962518.1, NR_023363.1 and the ERCC.fa
star: PN:STAR,VN:v2.4.2a,mRNA alignment,--outSAMstrandField None --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 10 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterMatchNmin 30 --chimSegmentMin 15 --quantMode TranscriptomeSAM --chimJunctionOverhangMin 15 --twopassMode Basic --outSAMtype SAM --outSAMattributes All --outReadsUnmapped Fastx intronMotif --alignIntronMax 200000  --outSJfilterIntronMaxVsReadN 10000 20000 30000 50000 --outSJfilterOverhangMin 20 12 12 12 --outFilterType BySJout --alignMatesGapMax 0  --outFilterMultimapNmax 20,
htseq: PN:htseq-count ,VN:0.6.0,read counting,--mode union --stranded reverse
combine: PN:combine.py,VN:0.3.0,combines counts to table
repenrich: PN:RepEnrich,VN:commit 0e9228149b2aff06874ed7ff0c8836aefa864c9e,repeat enrichment. Citation: Criscione, S.W., Zhang, Y., Thompson, W. et al. Transcriptional landscape of repetitive elements in normal and cancer human cells. BMC Genomics 15, 583 (2014). https://doi.org/10.1186/1471-2164-15-583
diff: PN:deseq2,VN:1.10.1,differential expression
transcriptome annotation: ENSEMBL Homo_sapiens.GRCh38.78
Genome_build: GRCh38
Supplementary_files_format_and_content: *htseq.counts.tab: counts of reads per gene, combined reads from both sequencing runs
Supplementary_files_format_and_content: repeats_counts.tab: containing the reads aligned against repeats with RepEnrich also the combined reads from both sequencing runs
Supplementary_files_format_and_content: DNMT1_vs_Control.tab: differential expression of genes DNMT1 vs Control
Supplementary_files_format_and_content: DNMT1_L1TD1_vs_Control.tab: differential expression of genes DNMT1 L1TD1 vs Control
Supplementary_files_format_and_content: DNMT1_L1TD1_vs_DNMT1.tab: differential expression of genes DNMT1 L1TD1 vs DNMT1

source_name: HAP1 cells

extract_protocol:
Total RNA was isolated following the manufacturer’s instructions (TRIzol, Invitrogen) and then used for RNA sequencing.
For transcriptome sequencing (RNA-seq) experiments, RNA was subjected to poly(A) selection with a Dynabeads mRNA purification kit (Invitrogen), followed by reverse transcription using a NEB RNA Ultra kit and library generation using a TruSeq library generation kit (Illumina).

treatment_protocol:
HAP1 cells were cultured then harvested for RNA isolation.
HAP1 is a near-haploid cell line derived from the KBM-7 cell line. KBM-7 was found in a patient with chronic myeloid leukemia (CML). This cell line has a haploid karyotype except for chromosomes 8 and 15. It also possesses a reciprocal chromosomal translocation of Chromosomes 9 and 22 which created a Philadelphia chromosome.

value: male

value: HAP1 cells


title: DNMT1/L1TD1-2_repeat

description:
sample name:
52684


title: HGC27_RORC_1

value: cancer cells

value: RORgamma overexpressed

value: overexpressed RORγ


title: P48R


title: OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep3

city: Beijing

first: Zexian (Davis)

last: Zeng

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
RNA-Seq immune analysis pipeline (RIMA)
sequencing reads were aligned to the mouse reference genome (GRCm38/mm10) using STAR v2.6.1d
Salmon v0.13.1 was utilized to map transcripts to genes and generate a gene count matrix.
Differentially expressed genes were identified using DESeq2 v1.34.0, with an adjusted P-value (FDR) threshold of <0.05 for determining significance. The replicates of RNA-Seq from each condition were considered as a covariate in DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized abundance measurements generated by DESeq2

extract_protocol:
RNA was harvested using the Rneasy mini plus kit by Qiagen. A total of 1.3 micrograms (μg) of RNA was utilized for the construction of sequencing libraries, which is a process for preparing RNA samples for next-generation sequencing.
The libraries for RNA-seq were prepared using the SMARTer mRNA-Seq Library Prep Kit, adhering strictly to the protocols provided by the manufacturer. This step involves converting RNA into a library of cDNA fragments with adaptors attached to each end, a prerequisite for sequencing.

value: CD8+ T cell

value: Tnfaip3 knockout