title: E. coli BW25113 bacterial cells, V2, SS, GE, Bio Rep 3

city: Cambridge

first: Peter

middle: C.

last: Dedon

address: 77 Massachusetts Ave

department: Biological Engineering

institute: Massachusetts Institute of Technology

description:
Library name: D23-12995
Column name in raw_abundance_matrix.txt: V2_SS_GE_BioRep3

data_processing:
Raw sequencing reads were processed to obtain the raw abundance matrix of tRNAs using an optimized version of the custom data analytical pipeline designed for AQRNA-seq.
The raw abundance data was normalized using the median of ratios method with the DESeq2 v 1.36.0 package (Love et al., 2014) in R (R core team, 2023) to enable various downstream comparisons across results derived from different library preparation protocols while accounting for both sequencing depth and sample composition.
Assembly: Not applicable. Sequence reads were mapped to an custom E. coli BW25113 tRNA reference sequence library.
Supplementary files format and content: A tab-delimited text file containing raw abundance (i.e., read counts) across different tRNA isoacceptors.
Supplementary files format and content: A tab-delimited text file containing normalized abundance across different tRNA isoacceptors.

organism: Escherichia coli

source_name: Escherichia coli strain BW25113

growth_protocol: Overnight bacterial culture was sub-cultured (1:100) in 25 mL LB broth, followed by incubation in a shaking incubator (Shon’s Scientific Refrigeration) at 37 °C with 250 rpm until the late-exponential phase, as indicated by optical density 600 values between 0.6-0.7.

extract_protocol:
The isolation of small RNAs from bacterial cells was performed using the PureLink miRNA Isolation Kit with slight modifications. Cells were lysed using TRIzol (Sigma-Aldrich), followed by chloroform treatment and centrifugation to separate the RNA-containing aqueous phase. Total RNAs were passed through Spin Cartridges with different ethanol concentrations to selectively bind and separate large and small RNAs. Finally, the small RNAs were eluted in RNase-free water after washing and a final centrifugation step.
cDNA libraries were prepared using 75 ng of small RNAs as the input, following four variations of the AQRNA-seq library constuction protocol. Variant 1 represents the original protocol initially published by Hu et al. (2021) and later elaborated by Chen et al. (2024), while variants 2, 3, and 4 involve alternative adaptations of the original protocol with respect to the approaches for mitigating polymerase fall-off and/or primer dimers. A side-by-side comparison across the protocols represents the focus of this study.

value: Escherichia coli strain BW25113

value: bacteria


title: E. coli BW25113 bacterial cells, V3, ALKB, EXOI, Bio Rep 3

status: Public on Dec 15 2025

type: SRA

state: MA

country: USA

description:
Library name: D23-12996
Column name in raw_abundance_matrix.txt: V3_ALKB_EXOI_BioRep3

library_source: other

molecule: other

tag: cell line

tag: cell type


title: E. coli BW25113 bacterial cells, V1, ALKB, GE, Bio Rep 3

description:
Library name: D23-12994
Column name in raw_abundance_matrix.txt: V1_ALKB_GE_BioRep3


title: spt5-S1-15D , KY3594 , 8WG16 , Rep1

city: Pittsburgh

first: Karen

middle: M.

last: Arndt

state: Pennsylvania

address: 4249 Fifth Avenue

department: Biological Sciences

institute: University of Pittsburgh

description:
Library name: spt5_S1_15D_KY3594_8WG16_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D

library_source: genomic

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and the corresponding spike-in (either S. pombe or K. lactis) with bowtie2 version 2.4.5.
Mapped reads were filtered with Sambamba view and Samtools markdup to remove multi-mapped reads and PCR duplicates, respectively.
The filtered hybrid alignment was split into separate S. cerevisiae and spike-in files. Normalization factors were calculated using S. cerevisiae and spike-in read counts in the input and IP.
Spike-in normalization was applied and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: K. lactis ASM251v1
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized ChIP-seq signal

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: All yeast cultures, including spike-in cells, were grown to mid-log phase in 250 mL YPD+Trp media at 30ºC.

extract_protocol:
Cells were fixed with 1% formaldehyde for 20 minutes. After quenching and cell lysis, chromatin was sheared using a Bioruptor® (Diagenode B01060010) for 25 cycles with 30 seconds on and 30 seconds off.
ChIP-seq libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645S/L) and multiplex oligos (NEB, E6440S/L) using 0.5-1 ng of DNA input and following manufacturer's protocols. Libraries were purified using AMPure XP beads (Beckman Coulter, A63881) and verified using fragment analyzer (Fragment Analyzer, Advanced Analytics).

treatment_protocol:
For auxin inducible degron, the mid-log culture was treated with 5 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) or equivalent amount of vehicle (DMSO) for 45 minutes.
For anchor-away experiments, the mid-log culture was treated with 1 µg/mL rapamycin or equivalent amount of vehicle (DMSO) for 1 hour.

tag: strain

tag: treatment

tag: chip antibody

tag: batch


title: spt5del5 , KY4798 , 8WG16 , Rep1

description:
Library name: spt5_del5_KY4798_8WG16_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: E. coli BW25113 bacterial cells, V4, SS, EXOI, Bio Rep 3

description:
Library name: D23-12997
Column name in raw_abundance_matrix.txt: V4_SS_EXOI_BioRep3


title: WT_rep1

city: Worcester

first: GANGMING

last: ZHANG

address: 368 Plantation St, Asc5-2010

institute: RNA Therapeutics Institute, University of Massachusetts Chan Medical School

description: Library name: Sample 1

data_processing:
Sequencing adaptors were trimmed from FASTQ files using cutadapt 4.9.
Total reads with length longer than 16 nts were selected and mapped to the reporter or total reads with length between 21 nts and 23 nts were selected and mapped to the mRNA, pseudogenes and transposons with bowtie 1.3.1. Read counts were normalized to the total number of genome-mapped reads.
Assembly: WBcel235
Supplementary files format and content: merged counts.tsv

organism: Caenorhabditis elegans

source_name: wild-type

extract_protocol:
Worms were lysated and  small-RNAs were later extracted by Trizol.
Purified small-RNAs were pre-treated with PIR-1 and ligated with 3' and 5' linkers. cDNA were generated by reverse transcribed and further amplified by PCR. A size selection procedure on native PAGE were carried out.

tag: tissue

value: wild-type

value: untreated

tag: genotype

value: small RNAs

value: small-RNA seq


title: mAID-SPT5 , KY4793 , IAA , 8WG16 , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_8WG16_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

tag: time

value: 45 min


title: E. coli BW25113 bacterial cells, V4, SS, EXOI, Bio Rep 2

description:
Library name: D23-12993
Column name in raw_abundance_matrix.txt: V4_SS_EXOI_BioRep2


title: JJ03_OC

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Gene-level signal were derived from CEL files using sst-RMA algorithm implemente in Affymetrix Expression Console software

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

value: Oral Cavity


title: JF51_L

value: Larynx


title: E. coli BW25113 bacterial cells, V1, ALKB, GE, Bio Rep 2

description:
Library name: D23-12990
Column name in raw_abundance_matrix.txt: V1_ALKB_GE_BioRep2


title: JI75_L


title: E. coli BW25113 bacterial cells, V3, ALKB, EXOI, Bio Rep 2

description:
Library name: D23-12992
Column name in raw_abundance_matrix.txt: V3_ALKB_EXOI_BioRep2


title: JG08_OC


title: E. coli BW25113 bacterial cells, V4, SS, EXOI, Bio Rep 1

description:
Library name: D23-12989
Column name in raw_abundance_matrix.txt: V4_SS_EXOI_BioRep1


title: JI94_OC


title: spt5delCTR , KY4894 , Input_Sp , Rep2

description:
Library name: spt5_delCTR_KY4894_Input_Sp_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: E. coli BW25113 bacterial cells, V2, SS, GE, Bio Rep 2

description:
Library name: D23-12991
Column name in raw_abundance_matrix.txt: V2_SS_GE_BioRep2


title: JF57_L


title: rde-3 mut-16(DE6R)_rep1

description: Library name: Sample 5

source_name: rde-3 mut-16(DE6R)

value: rde-3 mut-16(DE6R)


title: lambdaN tethered MUT-14_rep2

description: Library name: Sample 8

source_name: lambdaN tethered strain

value: lambdaN tethered strain


title: spt5-S1-15A , KY4912 , Input_Sp , Rep2

description:
Library name: spt5_S1_15A_KY4912_Input_Sp_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: WT_LPS_1

city: Beijing

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

country: China

institute: University of Chinese Academy of Sciences

description: Library name: Sample 6

library_source: transcriptomic

data_processing:
Differential expressed genes were carried out byDEseq2 software. KEGG pathway enrichment was performed by KOBAS 3.0.28 (http://kobas.cbi.pku.edu.cn/). Protein and protein interaction networks were analyzed by String(https://string-db.org/) and visualized by Cytoscape.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includereads counts values for each Sample

organism: Mus musculus

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were isolated from 6-8 week-old male wild-type (WT) and TGM2KO mice and then bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days.
The total RNA of the macrophage cells were extracted using TRIzol reagent (Thermo Fisher, 15596018) and sequencing was done by the Annoroad Gene Technology Co.,Ltd. (Beijing).

value: Bone Marrow

tag: Sex

value: male

value: WT

value: WT mice bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days and then LPS (10ng/ml) for 6 hours.


title: E. coli BW25113 bacterial cells, V2, SS, GE, Bio Rep 1

description:
Library name: D23-12987
Column name in raw_abundance_matrix.txt: V2_SS_GE_BioRep1


title: E. coli BW25113 bacterial cells, V3, ALKB, EXOI, Bio Rep 1

description:
Library name: D23-12988
Column name in raw_abundance_matrix.txt: V3_ALKB_EXOI_BioRep1


title: WT , KY4803 , Input_Sp , Rep2

description:
Library name: WT_KY4803_Input_Sp_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: WT_LPS_2

description: Library name: Sample 7


title: Tgm2_KO_M0

description: Library name: Sample 3

value: Tgm2 KO

value: TGM2KO mice bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days


title: mAID-SPT5 , KY4793 , DMSO , Input_Sp , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Input_Sp_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: Tgm2_KO_LPS_2

description: Library name: Sample 2

value: TGM2KO mice bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days and then LPS (10ng/ml) for 6 hours.


title: PFC tissue, HSV-TRIM28WT, male, mouse 10

city: Richmond

first: Corinne

last: Smith

state: Virginia

address: 1217 E. Marshall St.

department: Anatomy and Neurobiology

institute: Virginia Commonwealth University

description: Library name: TRIM28WT_M10

data_processing:
FASTQ files were quality controlled with FASTQC (version 0.11.9)
Adapter sequences and low-quality bases removed with Trimmomatic (version 0.39). 4-base window of sequencing quality <15 and reads less than 50 bases were dropped.
High-quality reads aligned to Mus musculus GRCm39 reference genome using STAR (version 2.7.11a) with recommended parameters.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files with raw counts for each sample

source_name: brain, prefrontal cortex

extract_protocol:
RNA was extracted and purified from snap-frozen brian tissue using RNeasy kit (Qiagen) per manufacturer's instructions.
Ribosomal RNA depletion and library preparation were performed with Illumina Ribo-Zero per manufacturer's instructions.

treatment_protocol: Stereotaxic delivery of HSV-TRIM28WT, HSV-TRIM28NFD, HSV-TRIM28VPR, or HSV-GFP constructs.

value: brain, prefrontal cortex


title: JJ55_L


title: spt5-S1-15D , KY3594 , Input_Sp , Rep2

description:
Library name: spt5_S1_15D_KY3594_Input_Sp_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: JF48_OC


title: JD15_OP_HPVpos


title: JF21_L


title: spt5del5 , KY4798 , Input_Sp , Rep2

description:
Library name: spt5_del5_KY4798_Input_Sp_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: JA19_OP_HPVpos


title: WT_M0_1

description: Library name: Sample 4

value: WT mice bone marrow-derived macrophages (BMDMs) were obtained and cultured with the stimulation of M-CSF (25ng/ml) for 7 days


title: Tgm2_KO_LPS_1

description: Library name: Sample 1


title: PFC tissue, HSV-TRIM28WT, male, mouse 7

description: Library name: TRIM28WT_M7


title: JA20_HP

value: Hypopharynx


title: PFC tissue, HSV-TRIM28WT, male, mouse 6

description: Library name: TRIM28WT_M6


title: E. coli BW25113 bacterial cells, V1, ALKB, GE, Bio Rep 1

description:
Library name: D23-12986
Column name in raw_abundance_matrix.txt: V1_ALKB_GE_BioRep1

value: Escherichia coli strain BW25113

value: bacteria


title: WT_M0_2

description: Library name: Sample 5


title: spt5delCTR , KY4894 , Input_Sp , Rep1

description:
Library name: spt5_delCTR_KY4894_Input_Sp_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: PFC tissue, HSV-TRIM28WT, male, mouse 9

description: Library name: TRIM28WT_M9


title: PFC tissue, HSV-TRIM28WT, male, mouse 3

description: Library name: TRIM28WT_M3


title: PFC tissue, HSV-TRIM28WT, male, mouse 8

description: Library name: TRIM28WT_M8


title: spt5-S1-15A , KY4912 , Input_Sp , Rep1

description:
Library name: spt5_S1_15A_KY4912_Input_Sp_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: JA05_OP_HPVpos


title: IX97_OP_HPVpos


title: PFC tissue, HSV-TRIM28WT, male, mouse 4

description: Library name: TRIM28WT_M4


title: PFC tissue, HSV-TRIM28WT, male, mouse 1

description: Library name: TRIM28WT_M1


title: mAID-SPT5 , KY4793 , IAA , Input_Sp , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Input_Sp_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: PFC tissue, HSV-TRIM28WT, male, mouse 2

description: Library name: TRIM28WT_M2


title: IX94_L

value: Larynx


title: mAID-SPT5 , KY4793 , DMSO , Input_Sp , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Input_Sp_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: PFC tissue, HSV-TRIM28WT, female, mouse 10

description: Library name: TRIM28WT_F10


title: IX89_L


title: mAID-SPT5 , KY4793 , IAA , Input_Sp , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Input_Sp_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: PFC tissue, HSV-TRIM28WT, male, mouse 5

description: Library name: TRIM28WT_M5


title: PFC tissue, HSV-TRIM28WT, female, mouse 9

description: Library name: TRIM28WT_F9


title: PFC tissue, HSV-TRIM28WT, female, mouse 6

description: Library name: TRIM28WT_F6


title: PFC tissue, HSV-TRIM28WT, female, mouse 5

description: Library name: TRIM28WT_F5


title: PFC tissue, HSV-TRIM28WT, female, mouse 8

description: Library name: TRIM28WT_F8


title: spt5del5 , KY4798 , Input_Sp , Rep1

description:
Library name: spt5_del5_KY4798_Input_Sp_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: spt5-S1-15D , KY3594 , Input_Sp , Rep1

description:
Library name: spt5_S1_15D_KY3594_Input_Sp_Rep1
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: PFC tissue, HSV-TRIM28WT, female, mouse 7

description: Library name: TRIM28WT_F7


title: rtf1del , GLC7-3xHA-FRB , KY5427 , DMSO , Rep2

description:
Library name: rtf1del_GLC7_3xHA_FRB_KY5427_DMSO_Rep2
MATa his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB rtf1∆::KanMX

data_processing:
Reads were aligned to the hydrid genome of S. cerevisiae and S. pombe with HISAT2 version 2.2.1.
PCR duplicates were removed from the aligned reads using Samtools markdup.
The filtered hybrid alignment files were separated into S. cerevisiae and spike-in files.
S. pombe read counts from featureCounts were input into DESeq2 estimateSizeFactors() to get spike-in size factors.
The inverse of size factors was applied as spike-in normalization, and bigWig files were generated using bamCoverage.
Assembly: S. cerevisiae SacCer3
Assembly: S. pombe ASM294v2
Supplementary files format and content: bigWig, spike-in normalized 4tU-seq signal

growth_protocol: All yeast cultures, including spike-in cells, were grown to mid-log phase in YPD+Trp media at 30ºC.

extract_protocol:
Total RNA was extracted using hot acid phenol extraction method. From 50 µg total RNA input, 4tU-labeled RNA was biotinylated with10 µg/mL MTSEA Biotin-XX (Biotium, 90066) for 30 minutes. The biotinylated RNA was purified and bound to magnetic MyOne Streptavidin C1 beads (Invitrogen, 65001) for 15 minutes. The RNA was eluted off the beads and concenrated using RNeasy MinElute cleanup kit (Qiagen, 74204). 100 ng of RNA was used for library construction.
Libraries were prepared using Universal Plus Total RNA-seq with NuQuant kit (Tecan, 0361-A01), UPlus Total RNA AnyDeplete module (Tecan, 0370-A01) and UPlus Total AnyDeplete Custom Probe Mix for S. cerevisiae (Tecan, S02714).

treatment_protocol:
4tU was added to the mid-log culture (or after the indicated treatment) at a final concentration of 5 mM for 5 min at RT before quenching the 4tU labeling reaction by adding 1/2 volume -20 degrees cold methanol.
For auxin inducible degron, the mid-log culture was treated with 5 µM 5-phenyl-indole-3-acetic acid (5-Ph-IAA) or equivalent amount of vehicle (DMSO) for 45 minutes.
For anchor-away experiments, the mid-log culture was treated with 1 µg/mL rapamycin or equivalent amount of vehicle (DMSO) for 1 hour.

value: 1 hour


title: HS43_L


title: HT35_L


title: PFC tissue, HSV-TRIM28WT, female, mouse 3

description: Library name: TRIM28WT_F3


title: PFC tissue, HSV-TRIM28WT, female, mouse 4

description: Library name: TRIM28WT_F4


title: PFC tissue, HSV-TRIM28VPR, male, mouse 10

description: Library name: TRIM28VPR_M10


title: rtf1del , GLC7-3xHA-FRB , KY5427 , Rapa , Rep1

description:
Library name: rtf1del_GLC7_3xHA_FRB_KY5427_Rapa_Rep1
MATa his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB rtf1∆::KanMX

value: Rapamycin


title: rtf1del , GLC7-3xHA-FRB , KY5427 , DMSO , Rep1

description:
Library name: rtf1del_GLC7_3xHA_FRB_KY5427_DMSO_Rep1
MATa his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB rtf1∆::KanMX


title: rtf1del , GLC7-3xHA-FRB , KY5427 , Rapa , Rep2

description:
Library name: rtf1del_GLC7_3xHA_FRB_KY5427_Rapa_Rep2
MATa his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB rtf1∆::KanMX


title: PFC tissue, HSV-TRIM28WT, female, mouse 1

description: Library name: TRIM28WT_F1


title: WT , KY4803 , Input_Sp , Rep1

description:
Library name: WT_KY4803_Input_Sp_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: PFC tissue, HSV-TRIM28VPR, male, mouse 9

description: Library name: TRIM28VPR_M9


title: PFC tissue, HSV-TRIM28WT, female, mouse 2

description: Library name: TRIM28WT_F2


title: PFC tissue, HSV-TRIM28VPR, male, mouse 5

description: Library name: TRIM28VPR_M5


title: PFC tissue, HSV-TRIM28VPR, male, mouse 8

description: Library name: TRIM28VPR_M8


title: HR31_OP_HPVpos


title: HR06_L


title: WT , KY3454 , Rep3

description:
Library name: WT_KY3454_Rep3
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX

data_processing:
Trimmed reads to remove adaptor sequence and low-quality reads using ShortRead package in R
Aligned to the reference genome using Rbowtie2 version 2.2.0.
Collapsed nearby reads within 3 bp distance from each other to individual transposition events and saved as bed files
Counted number of transposons and number of reads per gene
Assembly: SacCer3
Supplementary files format and content: bed files containing transposition mapping
Supplementary files format and content: txt files containing number of transposons per gene

growth_protocol: Transposition in yeast cells was induced on SD-Ade agarose media supplemented with 2% galactose for 18-20 days. Harvested yeast cells were re-seeded in SD-Ade liquid media supplemented with 2% dextrose and grown to saturation to prepare cell pellets.

extract_protocol:
Genomic DNA was extracted from the yeast cell pellets using standard PCI and ethanol precipitation protocols.
The gDNA was digested with either NlaIII or DpnII restriction enzymes in parallel for 16 hours. The digested DNA was ligated with T4 ligase for 6 hours. The circularized DNA was amplified in thermocycler with custom primers to generate the DNA library. The library was purified using PCR clean-up kit and submitted for sequencing with custom primers.


title: HR08_OP_HPVneg

value: Oropharynx


title: paf1del , GLC7-3xHA-FRB , KY5323 , Rapa , Rep2

description:
Library name: paf1del_GLC7_3xHA_FRB_KY5323_Rapa_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB paf1∆::KanMX


title: lambdaN tethered PGL-3_rep2

description: Library name: Sample 16

value: lambdaN tethered strain

value: untreated

value: small RNAs

value: small-RNA seq


title: PFC tissue, HSV-TRIM28VPR, male, mouse 7

description: Library name: TRIM28VPR_M7


title: PFC tissue, HSV-TRIM28VPR, male, mouse 4

description: Library name: TRIM28VPR_M4


title: HR05_L


title: HR27_OP_HPVneg


title: WT , KY3454 , Rep2

description:
Library name: WT_KY3454_Rep2
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX


title: paf1del , GLC7-3xHA-FRB , KY5323 , Rapa , Rep1

description:
Library name: paf1del_GLC7_3xHA_FRB_KY5323_Rapa_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB paf1∆::KanMX


title: HR29_OP_HPVpos


title: PFC tissue, HSV-TRIM28VPR, male, mouse 2

description: Library name: TRIM28VPR_M2


title: paf1del , GLC7-3xHA-FRB , KY5323 , DMSO , Rep2

description:
Library name: paf1del_GLC7_3xHA_FRB_KY5323_DMSO_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB paf1∆::KanMX


title: paf1del , GLC7-3xHA-FRB , KY5323 , DMSO , Rep1

description:
Library name: paf1del_GLC7_3xHA_FRB_KY5323_DMSO_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB paf1∆::KanMX


title: PFC tissue, HSV-TRIM28VPR, male, mouse 3

description: Library name: TRIM28VPR_M3


title: WT , KY3454 , Rep1

description:
Library name: WT_KY3454_Rep1
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX


title: Spt5-S1-15A , KY4173 , Rep2

description:
Library name: Spt5_S1_15A_KY4173_Rep2
MATalpha his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX spt5-S1-15A


title: GLC7-3xHA-FRB , KY5319 , Rapa , Rep4

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Rep4
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: HR04_HP


title: GLC7-3xHA-FRB , KY5319 , DMSO , Rep4

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Rep4
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: PFC tissue, HSV-TRIM28VPR, male, mouse 1

description: Library name: TRIM28VPR_M1


title: HQ92_HP


title: PFC tissue, HSV-TRIM28VPR, female, mouse 10

description: Library name: TRIM28VPR_F10


title: GLC7-3xHA-FRB , KY5318 , Rapa , Rep3

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Rep3
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Spt5delCTR , KY4628 , Rep3

description:
Library name: Spt5delCTR_KY4628_Rep3
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX spt5∆CTR::NatMX


title: PFC tissue, HSV-TRIM28VPR, female, mouse 9

description: Library name: TRIM28VPR_F9


title: GLC7-3xHA-FRB , KY5318 , DMSO , Rep3

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Rep3
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Spt5delCTR , KY4627 , Rep2

description:
Library name: Spt5delCTR_KY4627_Rep2
MATalpha his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX spt5∆CTR::NatMX


title: HQ90_L


title: HQ89_OP_HPVneg


title: GLC7-3xHA , KY5236 , Rapa , Rep2

description:
Library name: GLC7_3xHA_KY5236_Rapa_Rep2
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: Spt5delCTR , KY4258 , Rep1

description:
Library name: Spt5delCTR_KY4258_Rep1
MATalpha his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX spt5∆CTR::NatMX


title: HQ73_OP_HPVpos


title: HR77_OP_HPVpos


title: GLC7-3xHA , KY5235 , Rapa , Rep1

description:
Library name: GLC7_3xHA_KY5235_Rapa_Rep1
MATalpha his3∆1 lys2∆0 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA


title: PFC tissue, HSV-TRIM28VPR, female, mouse 6

description: Library name: TRIM28VPR_F6


title: PFC tissue, HSV-TRIM28VPR, female, mouse 7

description: Library name: TRIM28VPR_F7


title: HQ71_OP_HPVneg


title: GLC7-3xHA-FRB , KY5319 , Rapa , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_Rapa_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Spt5-S1-15A , KY4172 , Rep1

description:
Library name: Spt5_S1_15A_KY4172_Rep1
MATalpha his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2∆::NatMX spt5-S1-15A


title: Spt5del5 , KY3448 , Rep2

description:
Library name: Spt5del5_KY3448_Rep2
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2Δ::NatMX spt5Δ5::NatMX


title: PFC tissue, HSV-TRIM28VPR, female, mouse 5

description: Library name: TRIM28VPR_F5


title: HQ70_HP


title: PFC tissue, HSV-TRIM28VPR, female, mouse 8

description: Library name: TRIM28VPR_F8


title: PFC tissue, HSV-TRIM28VPR, female, mouse 4

description: Library name: TRIM28VPR_F4


title: mAID-SPT5 , KY4793 , DMSO , 8WG16 , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_8WG16_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: GLC7-3xHA-FRB , KY5319 , DMSO , Rep2

description:
Library name: GLC7_3xHA_FRB_KY5319_DMSO_Rep2
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: Spt5del5 , KY3450 , Rep3

description:
Library name: Spt5del5_KY3450_Rep3
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2Δ::NatMX spt5Δ5::NatMX


title: Spt5del5 , KY3449 , Rep1

description:
Library name: Spt5del5_KY3449_Rep1
MATa his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 ade2Δ::NatMX spt5Δ5::NatMX


title: GLC7-3xHA-FRB , KY5318 , Rapa , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_Rapa_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: HQ69_OC

value: Oral Cavity


title: PFC tissue, HSV-TRIM28VPR, female, mouse 3

description: Library name: TRIM28VPR_F3


title: HQ41_OP_HPVneg


title: TIG-3 cells, DXR-Sen cells, ARV825, day2

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: DXR-Sen cells_ARV825

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 sequencer in 75-base single-end mode.
Generated reads were mapped to the human (hg19) reference genome using TopHat ver. 2.0.13 in combination with Bowtie2 ver. 2.2.3.0.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using cuffdiff of Cufflinks 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: TIG-3 cells were maintained in Dulbecco's Modified Eagle's medium supplumented with 10% fetal bovine serum and 100 U ml^-1 penicillin-streptomycin.

extract_protocol:
Total RNA was extracted using miRNeasy Mini kit (QIAGEN N.V.).
Library preparation was performed using a TruSeq stranded mRNA Library Prep kit according to the manufacturer’s instructions.

treatment_protocol: For induction of cellular senescence, TIG-3 cells were incubated with doxorubicin at 250 ngper ml for 10 days. DXR-Sen TIG-3 cells were incubated with ARV825 (10 nM) for 2 days.

value: fibroblast


title: TIG-3 cells, DXR-Sen cells, Vehicle(DMSO), day2

description: Library name: DXR-Sen cells

value: DMSO


title: JD44_OP_HPVneg


title: GLC7-3xHA-FRB , KY5318 , DMSO , Rep1

description:
Library name: GLC7_3xHA_FRB_KY5318_DMSO_Rep1
MATalpha his3∆1 leu2∆0 ura3∆0 tor1-1 fpr1∆ RPL13A-2XFKBP12::TRP1 GLC7-3xHA-FRB


title: PFC tissue, HSV-TRIM28VPR, female, mouse 2

description: Library name: TRIM28VPR_F2

value: brain, prefrontal cortex


title: HQ68_OP_HPVpos


title: HP87_OC


title: WT , KY5366 , Rep2

description:
Library name: WT_KY5366_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: HP86_OP_HPVneg


title: WT , KY5366 , Rep1

description:
Library name: WT_KY5366_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 3xHA-GLC7


title: PFC tissue, HSV-TRIM28VPR, female, mouse 1

description: Library name: TRIM28VPR_F1


title: PFC tissue, HSV-TRIM28NFD, male, mouse 10

description: Library name: TRIM28NFD_M10


title: rtf1del , KY5339 , Rep2

description:
Library name: rtf1del_KY5339_Rep2
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: PFC tissue, HSV-TRIM28NFD, male, mouse 8

description: Library name: TRIM28NFD_M8


title: PFC tissue, HSV-TRIM28NFD, male, mouse 9

description: Library name: TRIM28NFD_M9


title: rtf1del , KY5339 , Rep1

description:
Library name: rtf1del_KY5339_Rep1
MATa lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 3xHA-GLC7


title: HM70_OC


title: PFC tissue, HSV-TRIM28NFD, male, mouse 7

description: Library name: TRIM28NFD_M7


title: rtf1del , ref2del , swd2del , KY5334 , Rep1

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Rep1
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: rtf1del , ref2del , swd2del , KY5334 , Rep2

description:
Library name: rtf1del_ref2del_swd2del_KY5334_Rep2
MATalpha lys2-128∂ leu2Δ1 ura3-52 rtf1Δ101::LEU2 swd2∆::hphMX ref2∆::KanMX 3xHA-GLC7


title: spt5-S1-15D , KY3594 , Rep2

description:
Library name: spt5_S1_15D_KY3594_Rep2
MATa lys2-128δ leu2Δ1 ura3-52 3xHSV-PAF1 spt5-S1-15D


title: GZ81_OP_HPVpos


title: Nutlin 3b_1

city: Kyoto City

first: Takumi

last: Mikawa

state: Kyoto

address: 54 Kawaharacho, Shogoin, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

hyb_protocol: Following fragmentation, 1.65 ug of cRNA were hybridized to the Agilent expression microarray according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Agilent Technologies G4900DA SG12494263

data_processing: Array data export processing and analysis was performed using Agilent Feature Extraction v11.0.1.1

source_name: Ras-induced senescent IMR90, 48h, 40mM, Nutlin 3b_1

label_protocol: labeled cRNA were prepared from 1~5 ug total RNA using the Agilent’s Quick Amp Labeling Kit

growth_protocol: IMR90 was cultured in MEM medium with 10% FBS.

extract_protocol: Total RNA was prepared with an RNeasy kit

treatment_protocol: senescent IMR 90 cells were treatment with 40 µM Nutlin 3b or DMSO for 48 h

tag: agent

value: Nutlin


title: control_3

source_name: Ras-induced senescent IMR90, control_3


title: Nutlin 3b_3

source_name: Ras-induced senescent IMR90, 48h, 40mM, Nutlin 3b_3


title: Nutlin 3b_2

source_name: Ras-induced senescent IMR90, 48h, 40mM, Nutlin 3b_2


title: PFC tissue, HSV-TRIM28NFD, male, mouse 6

description: Library name: TRIM28NFD_M6


title: PFC tissue, HSV-TRIM28NFD, male, mouse 5

description: Library name: TRIM28NFD_M5


title: GZ80_HP

value: Hypopharynx


title: GY88_HP


title: GY58_OC


title: GX23_HP


title: control_2

source_name: Ras-induced senescent IMR90, control_2


title: PFC tissue, HSV-TRIM28NFD, male, mouse 4

description: Library name: TRIM28NFD_M4


title: spt5delCTR , KY4894 , Rep2

description:
Library name: spt5delCTR_KY4894_Rep2
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: GX21_OP_HPVneg


title: control_1

source_name: Ras-induced senescent IMR90, control_1


title: Zebrafish retina – LIRD (biol rep 10)

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

institute: University of Messina

description:
Library name: mRNA-ZF-LIRD-10_S28
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

data_processing:
Raw reads were trimmed to remove adapter sequences and low-quality bases using Trimmomatic (v0.39).
Filtered reads were aligned to the Danio rerio reference genome (GRCz11, Ensembl release XX) using STAR (v2.7.9a) with default parameters.
Aligned reads were assigned to genes using featureCounts (Subread v2.0.1).
Count matrices were normalized and analyzed for differential expression using DESeq2 (v1.30.1) in R (v4.0).
Functional enrichment (GO and KEGG) was performed using clusterProfiler (v3.18).
Assembly: Danio rerio (GRCz11)
Supplementary files format and content: count_matrix.csv: rows = genes, columns = samples; raw and normalized counts.

molecule: polyA RNA

organism: Danio rerio

source_name: Retina

growth_protocol: Adult zebrafish (Danio rerio) were maintained under standard aquaculture conditions (28.5°C, 14 h light / 10 h dark cycle) in a recirculating aquatic facility. Animals were fed twice daily and monitored according to institutional guidelines.

extract_protocol:
Retinas were rapidly dissected under RNase-free conditions immediately after light exposure. Total RNA was extracted using the Qiagen RNeasy Mini Kit, following the manufacturer’s instructions, including on-column DNase I digestion. RNA integrity was assessed with the Agilent Bioanalyzer, and only samples with RIN ≥ 7 were processed further.
RNA-seq libraries were prepared using the Watchmaker RNA Library Prep Kit (Twist Bioscience). Poly(A)-selected mRNA was fragmented, reverse-transcribed, end-repaired, A-tailed, ligated to indexed adapters, and PCR-amplified according to the manufacturer’s protocol. Libraries were quantified, pooled, and sequenced on the Illumina NovaSeq 6000 platform (paired-end 150 bp).

treatment_protocol: Light-induced retinal degeneration (LIRD) was triggered by exposure to high-intensity white light (15,000 lux, 24 h). Control animals were kept under standard light conditions. No pharmacological treatments were administered to any group.

value: Retina

value: LIRD


title: Zebrafish retina – LIRD (biol rep 11)

description:
Library name: mRNA-ZF-LIRD-11_S29
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: GX22_HP


title: PFC tissue, HSV-TRIM28NFD, male, mouse 3

description: Library name: TRIM28NFD_M3


title: spt5delCTR , KY4894 , Rep1

description:
Library name: spt5delCTR_KY4894_Rep1
MATalpha lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆CTR::NatMX


title: PFC tissue, HSV-TRIM28NFD, female, mouse 9

description: Library name: TRIM28NFD_F9


title: d14, AZX, 1

city: Mölndal

first: Benjamin

last: Keith

address: Pepparedsleden 1

country: Sweden

institute: AstraZeneca

description: Library name: V11Y17-314-C1

data_processing:
FastQ files were processed using the Space Ranger 1.3.1 (10x Genomics) pipeline.
Manual alignment to the fiducial frame and identification of tissue-covered spots was performed using Loupe Browser (v.6, 10X Genomics)
Data filtering, processing, and analyses were performed in R (v.4.3.0) using semla (v. 1.2.1) and Seurat (v.4.4.0).
Coregistration with spatial metabolomics data was performed using MAGPIE and integrated analysis was performed using semla (v. 1.2.1) and MERINGUE (v1.0)
Assembly: rn6
Supplementary files format and content: Outputs from the Space Ranger processing "spatial" directory along with MEX format files are available for downstream analysis using standard spatial transcriptomics analysis packages.
Library strategy: Spatial Transcriptomics

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Agarose-inflated rat lung was cryosectioned at 10 µm.
Sequencing libraries were prepared using Visium Spatial Gene Expression Slide & Reagent Kit (Cat. No. 1000184; 10X Genomics) with Dual Index Kit TT Set A (Cat. No. 1000215; 10X Genomics) according to the Visium Spatial Gene Expression User Guide (Rev C).

treatment_protocol: The right lung lobe was inflated with 4.5mL of agarose solution via a cannula into the trachea.

value: Lung

tag: strain background

value: Wistar Han rat

value: male

value: AZX


title: PFC tissue, HSV-TRIM28NFD, female, mouse 7

description: Library name: TRIM28NFD_F7


title: spt5del5 , KY4798 , Rep2

description:
Library name: spt5del5_KY4798_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: Zebrafish retina – LIRD (biol rep 9)

description:
Library name: mRNA-ZF-LIRD-9_S27
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Zebrafish retina – LIRD (biol rep 6)

description:
Library name: mRNA-ZF-LIRD-6_S24
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Zebrafish retina – LIRD (biol rep 7)

description:
Library name: mRNA-ZF-LIRD-7_S25
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-TRIM28NFD, male, mouse 1

description: Library name: TRIM28NFD_M1


title: spt5del5 , KY4798 , Rep1

description:
Library name: spt5del5_KY4798_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5∆5::NatMX


title: PFC tissue, HSV-TRIM28NFD, female, mouse 6

description: Library name: TRIM28NFD_F6


title: GX05_HP


title: spt5-S1-15A , KY4912 , Rep1

description:
Library name: spt5_S1_15A_KY4912_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: Zebrafish retina – LIRD (biol rep 5)

description:
Library name: mRNA-ZF-LIRD-5_S23
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-TRIM28NFD, female, mouse 5

description: Library name: TRIM28NFD_F5


title: GW85_OP_HPVpos


title: Zebrafish retina – LIRD (biol rep 4)

description:
Library name: mRNA-ZF-LIRD-4_S22
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-TRIM28NFD, female, mouse 4

description: Library name: TRIM28NFD_F4


title: WT , KY4803 , Rep2

description:
Library name: WT_KY4803_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: GW87_OP_HPVpos


title: GW84_L

value: Larynx


title: Zebrafish retina – LIRD (biol rep 3)

description:
Library name: mRNA-ZF-LIRD-3_S21
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: WT , KY4803 , Rep1

description:
Library name: WT_KY4803_Rep1
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1


title: Zebrafish retina – LIRD (biol rep 2)

description:
Library name: mRNA-ZF-LIRD-2_S10
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: spt5-S1-15A , KY4912 , Rep2

description:
Library name: spt5_S1_15A_KY4912_Rep2
MATa lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 spt5-S1-15A


title: PFC tissue, HSV-TRIM28NFD, female, mouse 3

description: Library name: TRIM28NFD_F3


title: mAID-SPT5 , KY4793 , IAA , Rep1

description:
Library name: mAID_SPT5_KY4793_IAA_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: 45 min


title: GW40_HP


title: GW82_HP


title: Zebrafish retina – LIRD (biol rep 8)

description:
Library name: mRNA-ZF-LIRD-8_S26
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: GW78_OP_HPVneg

value: Oropharynx


title: PFC tissue, HSV-TRIM28NFD, female, mouse 2

description: Library name: TRIM28NFD_F2


title: Zebrafish retina – LIRD (biol rep 1)

description:
Library name: mRNA-ZF-LIRD-1_S8
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-TRIM28NFD, female, mouse 1

description: Library name: TRIM28NFD_F1


title: Zebrafish retina – Control (biol rep 11)

description:
Library name: mRNA-Zf-CTRL-11_S20
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).

value: Control


title: mAID-SPT5 , KY4793 , DMSO , Rep2

description:
Library name: mAID_SPT5_KY4793_DMSO_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: mAID-SPT5 , KY4793 , IAA , Rep2

description:
Library name: mAID_SPT5_KY4793_IAA_Rep2
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5


title: PFC tissue, HSV-GFP, male, mouse 10

description: Library name: GFP_M10

value: HSV-GFP


title: GW35_HP


title: Zebrafish retina – Control (biol rep 10)

description:
Library name: mRNA-Zf-CTRL-10_S19
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-GFP, male, mouse 8

description: Library name: GFP_M8


title: Zebrafish retina – Control (biol rep 9-rep)

description:
Library name: mRNA-Zf-CTRL-9-rep_S18
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: C9ko, knockout,R2

city: Shanghai

first: Xu

last: Pengfei

state: Shanghai

address: 800 Dongchuan RD. Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

description: Library name: C9#B

data_processing:
Without processed
Assembly: hg38
Supplementary files format and content: Without processed

source_name: cell line

extract_protocol:
TRIZOL, 2 ug of total RNA was used for the construction of sequencing libraries.
dUTP methods

treatment_protocol: without

value: cell line

value: immortalized cell line


title: C9ko, knockout,R1

description: Library name: C9#A


title: Zebrafish retina – Control (biol rep 9)

description:
Library name: mRNA-Zf-CTRL-9_S17
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: GW39_L


title: A8ko, knockout,R2

description: Library name: A8#B


title: Zebrafish retina – Control (biol rep 8)

description:
Library name: mRNA-Zf-CTRL-8_S16
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: GW20_OC

value: Oral Cavity


title: GS13_OC


title: PFC tissue, HSV-GFP, male, mouse 5

description: Library name: GFP_M5

value: brain, prefrontal cortex


title: A8ko, knockout,R1

description: Library name: A8#A


title: mAID-SPT5 , KY4793 , DMSO , Rep1

description:
Library name: mAID_SPT5_KY4793_DMSO_Rep1
MATa his3∆200::OsTIR-F74G-HIS3 lys2-128δ leu2∆1 ura3-52 3xHSV-PAF1 1xminiAID-SPT5

value: DMSO


title: A2ko, knockout,R2

description: Library name: A2#B


title: GR90_OP_HPVneg


title: Zebrafish retina – Control (biol rep 6)

description:
Library name: mRNA-Zf-CTRL-6_S14
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-GFP, male, mouse 4

description: Library name: GFP_M4


title: GS05_OC


title: GS24_OC


title: A2ko, knockout,R1

description: Library name: A2#A


title: GR91_OP_HPVneg


title: Zebrafish retina – Control (biol rep 5)

description:
Library name: mRNA-Zf-CTRL-5_S13
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-GFP, male, mouse 2

description: Library name: GFP_M2


title: PFC tissue, HSV-GFP, male, mouse 7

description: Library name: GFP_M7


title: PFC tissue, HSV-GFP, male, mouse 3

description: Library name: GFP_M3


title: Zebrafish retina – Control (biol rep 4)

description:
Library name: mRNA-Zf-CTRL-4_S12
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Zebrafish retina – Control (biol rep 7)

description:
Library name: mRNA-Zf-CTRL-7_S15
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: CAL27, Control, R3

description: Library name: WTC


title: Zebrafish retina – Control (biol rep 3)

description:
Library name: mRNA-Zf-CTRL-3_S11
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: PFC tissue, HSV-GFP, male, mouse 1

description: Library name: GFP_M1


title: PFC tissue, HSV-GFP, male, mouse 6

description: Library name: GFP_M6


title: GW33_L


title: GR88_OP_HPVneg


title: GR84_OC


title: PFC tissue, HSV-GFP, female, mouse 10

description: Library name: GFP_F10


title: CAL27, Control, R2

description: Library name: WTB


title: CAL27, Control, R1

description: Library name: WTA


title: GR81_OC


title: PFC tissue, HSV-GFP, female, mouse 9

description: Library name: GFP_F9


title: Zebrafish retina – Control (biol rep 2)

description:
Library name: mRNA-ZF-Ctrl-2_S9
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: Zebrafish retina – Control (biol rep 1)

description:
Library name: mRNA-ZF-Ctrl-1_S7
Zebrafish retina RNA-Seq; polyA selection; paired-end 150 bp; four lanes (L001–L004).


title: GR82_OP_HPVneg


title: Blood neutrophil, 0h, adult SLE, replicate 8

city: Liverpool

first: Helen

middle: Louise

last: Wright

address: 6 West Derby Street

department: Institute of Life Course and Medical Sciences

country: United Kingdom

institute: University of Liverpool

description: Library name: UHC-20

data_processing:
Reads were aligned to the human genome (hg38) using HISAT2 (v2.2.0)
Counts were generated using featureCounts in R (v3.6.3) providing the hg38 GTF file (iGenomes)
Assembly: hg38
Supplementary files format and content: Raw gene counts

source_name: Neutrophil

growth_protocol: Neutrophils (purity >97%) were isolated from peripheral blood by separation of leukocytes from erythrocytes using HetaSep, then centrifugation through density-gradient reagent (Ficoll Paque). Remaining erythrocytes were removed by hypotonic lysis using ammonium chloride buffer.

extract_protocol:
Trizol:chloroform extraction followed by Qiagen RNAeasy cleanup including on-column DNase digest
100bp Paired-end reads

treatment_protocol: Neutrophils were suspended in RPMI 1640 media and processed immediately

value: Neutrophil

value: Adult healthy control

value: 0h no treatment

value: UK


title: Blood neutrophil, 0h, adult SLE, replicate 7

description: Library name: UHC-16


title: NG-A0648_36

first: Dominick

middle: J

last: Hellen

address: 32 Vassar St

description:
Library name: RNA05000033
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

data_processing:
The preparation of RNA library and whole transcriptome sequencing was performed by EuroFins. Downstream conversion of sequencing files was performed by EuroFins.
The method for differentially expressed gene (DEG) determination was edgeR using the open-source R/BioConductor software.
Assembly: GRCh38
Supplementary files format and content: CSV file with raw read data and CSV file with processed data in tpm format.

source_name: liver

growth_protocol: Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - Condition 1 - media or MASLD - Condition 2 -  media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

extract_protocol:
Scaffolds were rinsed in chilled DPBS and snap-frozen in liquid nitrogen. RNA was isolated using 1mL Trizol per scaffold. Scaffolds were sonicated for 30 seconds before adding 200µL chloroform and spun down at 18,000xg for 20 minutes. Supernatant was transferred and mixed with 500µL IPA for 10 minutes and spun at 18,000xg for 15 minutes. Pellets were rinsed twice with 75% EtOH and eluted into RNAse-free water.
The preparation of RNA library and whole transcriptome sequencing was performed by EuroFins.

treatment_protocol: 1nm of Insulin

value: liver

value: primary

value: hepatocyte

value: Condition 2 + Ins


title: PFC tissue, HSV-GFP, female, mouse 8

description: Library name: GFP_F8


title: GG78_HP

value: Hypopharynx


title: GR15_OC


title: PFC tissue, HSV-GFP, female, mouse 7

description: Library name: GFP_F7


title: NG-A0648_35

description:
Library name: RNA05000032
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: NG-A0648_34

description:
Library name: RNA05000031
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: PFC tissue, HSV-GFP, female, mouse 5

description: Library name: GFP_F5


title: NG-A0648_24

description:
Library name: RNA05000030
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric SLE, replicate 9

description: Library name: jSLE-26

value: Pediatric SLE

value: Thailand


title: PFC tissue, HSV-GFP, female, mouse 6

description: Library name: GFP_F6

value: HSV-GFP


title: Blood neutrophil, 0h, adult SLE, replicate 6

description: Library name: UHC-09


title: PFC tissue, HSV-GFP, female, mouse 3

description: Library name: GFP_F3


title: NG-A0648_23

description:
Library name: RNA05000029
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric SLE, replicate 7

description: Library name: jSLE-23


title: GG75_L

value: Larynx


title: PFC tissue, HSV-GFP, female, mouse 2

description: Library name: GFP_F2


title: Blood neutrophil, 0h, pediatric SLE, replicate 6

description: Library name: jSLE-22


title: NG-A0648_22

description:
Library name: RNA05000028
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric SLE, replicate 8

description: Library name: jSLE-24


title: GG74_OP_HPVpos


title: NG-A0648_11

description:
Library name: RNA05000027
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: PFC tissue, HSV-GFP, female, mouse 1

description: Library name: GFP_F1


title: GG61_HP


title: Blood neutrophil, 0h, pediatric SLE, replicate 4

description: Library name: jSLE-19


title: GG59_OC


title: NG-A0648_10

description:
Library name: RNA05000026
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: GG77_OC


title: Pancreatic cancer, patient 4130, whole transcriptome

city: Chapel Hill

first: Jen Jen

last: Yeh

state: NC

address: 450 West Dr, CB7295

institute: University of North Carolina at Chapel Hill

description: Library name: rnaseq_4130

data_processing:
BCL files were converted to FASTQ files using bcl2fastq2 conversion software 2.20.0
Salmon (v1.5.2) was used to derive normalized counts (TPM)
For samples sequenced at Tempus, kallisto (v0.44.0) was used to derive normalized counts (TPM)
Assembly: GENCODE Release 38 (GRCh38.p13) for whole transcriptome; GENCODE Release 37 (GRCh37) for exome capture
Supplementary files format and content: csv files include TPM values per sample

source_name: PDAC

extract_protocol:
Total RNA was extracted from FFPE samples using Rneasy FFPE Kit (Qiagen, 73504).
KAPA RNA HyperPrep Kit with RiboErase (Roche) per manufacturer protocol for whole-transcriptome RNA-seq; sequencing done at Tempus for exome capture

value: PDAC

tag: individual

value: patient 4130


title: GG54_HP


title: Blood neutrophil, 0h, pediatric SLE, replicate 2

description: Library name: jSLE-17


title: Pancreatic cancer, patient 4090, whole transcriptome

description: Library name: rnaseq_4090

value: patient 4090


title: Blood neutrophil, 0h, pediatric SLE, replicate 3

description: Library name: jSLE-18


title: GG39_L


title: NG-A0648_33

description:
Library name: RNA05000024
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 1 + Ins


title: GG37_HP


title: Pancreatic cancer, patient 3976, whole transcriptome

description: Library name: rnaseq_3976

value: patient 3976


title: NG-A0648_9

description:
Library name: RNA05000025
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric SLE, replicate 5

description: Library name: jSLE-20

value: Neutrophil


title: Pancreatic cancer, patient 4169, whole transcriptome

description: Library name: rnaseq_4169

value: patient 4169


title: Pancreatic cancer, patient 3969, whole transcriptome

description: Library name: rnaseq_3969

value: patient 3969


title: Blood neutrophil, 0h, pediatric SLE, replicate 1

description: Library name: jSLE-03

value: 0h no treatment


title: NG-A0648_31

description:
Library name: RNA05000022
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: liver

value: primary


title: Blood neutrophil, 0h, pediatric healthy control, replicate 9

description: Library name: HJ-22

value: Pediatric healthy control


title: Pancreatic cancer, patient 3924, whole transcriptome

description: Library name: rnaseq_3924

value: patient 3924


title: GG33_OP_HPVpos


title: Blood neutrophil, 0h, pediatric healthy control, replicate 8

description: Library name: HJ-21


title: GG15_OP_HPVpos


title: GG35_L


title: NG-A0648_21

description:
Library name: RNA05000021
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: hepatocyte


title: NG-A0648_32

description:
Library name: RNA05000023
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: GG14_HP

value: Hypopharynx


title: Pancreatic cancer, patient 3856, whole transcriptome

description: Library name: rnaseq_3856

value: patient 3856


title: Pancreatic cancer, patient 3917, whole transcriptome

description: Library name: rnaseq_3917

value: patient 3917


title: NG-A0648_19

description:
Library name: RNA05000019
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric healthy control, replicate 7

description: Library name: HJ-18

value: Thailand


title: NG-A0648_8

description:
Library name: RNA05000018
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric healthy control, replicate 6

description: Library name: HJ-17


title: NG-A0648_7

description:
Library name: RNA05000017
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, pediatric healthy control, replicate 4

description: Library name: HJ-15


title: GG13_OP_HPVpos


title: Blood neutrophil, 0h, pediatric healthy control, replicate 5

description: Library name: HJ-16


title: Pancreatic cancer, patient 3836, whole transcriptome

description: Library name: rnaseq_3836

value: PDAC

value: patient 3836


title: Pancreatic cancer, patient 3831, whole transcriptome

description: Library name: rnaseq_3831

value: patient 3831


title: Blood neutrophil, 0h, pediatric healthy control, replicate 3

description: Library name: HJ-14


title: NG-A0648_30

description:
Library name: RNA05000016
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 2


title: NG-A0648_20

description:
Library name: RNA05000020
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 1 + Ins


title: Pancreatic cancer, patient 3776, whole transcriptome

description: Library name: rnaseq_3776

value: patient 3776


title: GG09_OP_HPVneg

value: Oropharynx


title: NG-A0648_29

description:
Library name: RNA05000015
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: GG10_OP_HPVneg


title: Pancreatic cancer, patient 3837, whole transcriptome

description: Library name: rnaseq_3837

value: patient 3837


title: Pancreatic cancer, patient 3770, whole transcriptome

description: Library name: rnaseq_3770

value: patient 3770


title: Blood neutrophil, 0h, pediatric healthy control, replicate 1

description: Library name: HJ-11

value: Neutrophil

value: 0h no treatment


title: GG11_OC

value: Oral Cavity


title: Pancreatic cancer, patient 3766, whole transcriptome

description: Library name: rnaseq_3766

value: patient 3766


title: FY55_OP_HPVneg


title: NG-A0648_28

description:
Library name: RNA05000014
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: liver

value: primary

value: hepatocyte


title: FY54_OP_HPVneg


title: Pancreatic cancer, patient 3730, whole transcriptome

description: Library name: rnaseq_3730

value: patient 3730


title: siLRP1-3

first: Chuqing

last: He

address: No. 910, Hengshan Rd

department: Department of Obstetrics and Gynecology

institute: School of Medicine, Shanghai Jiaotong University

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to human genome (GRCh38,Ensembl104) using the Star.
Gene ontology (GO) analysis was performed to facilitate elucidating the biological implications of the differentially expressed genes in the experiment.
Pathway analysis was used to find out the significant pathway of the differentially expressed genes according to KEGG database. We turn to the Fisher’s exact test to select the significant pathway, and the threshold of significance was defined by P-value< 0.05.
Assembly: hg38

source_name: primary human uterine fibroblast

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately.
The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction. The cDNA libraries were constructed for each RNA sample using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (vazyme, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand. The cDNA fragments were end repaired, A-tailed and ligated with indexed adapters. The ligated cDNA products were purified and treated with uracil DNA glycosylase to remove the second-strand cDNA. Purified first-strand cDNA was enriched by PCR to create the cDNA libraries. The libraries were quality controlled with Agilent 2200 and sequenced by DNBSEQ-T7 on a 150 bp paired-end run.

value: primary human uterine fibroblast

value: primary human uterine fibroblasts were  transfected with  LRP1 siRNA for 48 hours,  subsequently incubated with CTGF for 48 hours.


title: Blood neutrophil, 0h, adult healthy control, replicate 9

description: Library name: HC-10

value: Adult healthy control

value: Thailand


title: NG-A0648_17

description:
Library name: RNA05000012
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 2


title: NG-A0648_18

description:
Library name: RNA05000013
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: FX78_OP_HPVneg


title: Blood neutrophil, 0h, adult healthy control, replicate 8

description: Library name: HC-09


title: FX74_OP_HPVneg


title: siLRP1-2


title: FY52_OP_HPVpos


title: FX67_HP

value: Hypopharynx


title: Pancreatic cancer, patient 3689, whole transcriptome

description: Library name: rnaseq_3689

value: PDAC

value: patient 3689


title: NG-A0648_6

description:
Library name: RNA05000010
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, adult healthy control, replicate 6

description: Library name: HC-07


title: Blood neutrophil, 0h, adult healthy control, replicate 5

description: Library name: HC-06


title: Pancreatic cancer, patient 3665, whole transcriptome

description: Library name: rnaseq_3665

value: patient 3665


title: NG-A0648_16

description:
Library name: RNA05000011
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: siLRP1-1


title: siNC-2

value: primary human uterine fibroblasts were  transfected with negative-control siRNA for 48 hours,  subsequently incubated with CTGF for 48 hours.


title: Blood neutrophil, 0h, adult healthy control, replicate 4

description: Library name: HC-05

value: Neutrophil

value: 0h no treatment


title: Pancreatic cancer, patient 3676, whole transcriptome

description: Library name: rnaseq_3676

value: patient 3676


title: D36_GA-AFUC IMs

first: Michael

middle: S.

last: Diamond

state: MO

address: 425 S. Euclid Ave

department: Immunology and Pathology

institute: Washington University School of Medicine

description: Library name: D36

data_processing:
RNA-seq reads were aligned to the Mus musculus reference genome (GRCm39) using HISAT2 (v2.2.1). Gene-level quantification was performed with featureCounts from the Subread package (v2.0.6) using Ensembl annotations (Mus_musculus_Ensemble_107_new). Across samples, the median mapping rate was ~94%. Raw counts were imported into R (v4.4.0) for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: tsv files include raw gene counts for all samples

source_name: interstitial macrophages

extract_protocol:
Three days after MA30 infection, mice were anesthetized with ketamine/xylazine (100 and 10 mg/kg via intraperitoneal injection, respectively), and 100 μL of CD45.2 antibody (APC; clone 104; Biolegend) was administered at a 1:10 dilution in PBS by retroorbital injection to identify intravascular cells. Two min later, mice were euthanized and then perfused with sterile PBS. Lungs were digested in 50 μL of Liberase Tm (5 mg/mL, Roche) and 12.5 μl of DNase I (10 mg/mL, Sigma-Aldrich) in 5 mL of HBSS at 37°C for 35 min. Single-cell suspensions were pre-incubated with Fc block antibody (BioLegend) in PBS + 2% heat-inactivated FBS + 1 mM EDTA for 20 min at 4°C. Cells were then divided into two groups for sorting. For interstitial macrophages, cells were stained with antibodies against CD45 (PE-Cy7; clone 30-F11; Biolegend), MHCII (BV421; clone M5; Biolegend), CD88 (PE; clone 20/70; Biolegend), and CX3CR1 (BV510; clone SA011F11; Biolegend). For classical monocytes, cells were stained with antibodies against CD45 (PE-Cy7; clone 30-F11; Biolegend), Ly6G (BV510; clone 1A8; Biolegend), Ly6C (PE; clone HK1.4; Biolegend), and CD115 (BV421; clone AFS98; Biolegend). All samples were stained with fixable viability dye (zombie green), True-Stain Monocyte Blocker (5 μL per sample), and Brilliant Stain Buffer Plus (10 μL per sample). All antibodies were used at a dilution of 1:200, with the exceptions of MHCII BV421, CD88 PE, and Ly6C, which were used at 1:100, and the viability dye, which was used at 1:2,000. Following incubation in PBS + 2% heat-inactivated FBS + 1 mM EDTA for 20 min at 4°C, cells were sorted on a MACSQuant Tyto instrument (Miltenyi Biotec).
Following cell sorting, RNA was extracted using the Arcturus PicoPure RNA isolation kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. RNA purity was confirmed using a NanoPhotometer® spectrophotometer (IMPLEN). RNA concentration and quality were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies). One µg of 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 the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using a random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. To select cDNA fragments of 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then, 3 µL of USER Enzyme (NEB) was added with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR with Phusion High-Fidelity DNA polymerase, Universal PCR primers and an Index Primer. Finally, PCR products were purified (AMPure XP system), and the library quality was assessed on an Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform, and paired-end reads were generated.

treatment_protocol: For MA30 challenge experiments, 24-week-old Hu-FcgR Tg male mice were administered different doses of S309, S309-GA-AFUC, or isotype control by intraperitoneal injection depending on the experimental question. To assess for differences in virological protection, mice were administered 6 mg/kg of antibody -24 h and then harvested at 4 dpi. The antibody dose was increased to account for the enhanced viral infection in the MA30 model compared to B.1.351. For evaluation of lung ventilatory function and histopathology, mice were administered a lower 1 mg/kg dose of antibody at -24 h and then harvested at 7 dpi, which facilitated differences in disease progression between treatment groups. At day 0 (one day after mAb treatment), mice were inoculated intranasally with 6 x 105 FFU of SARS-CoV-2 MA30 in a final volume of 50 μL. Lungs, nasal turbinates and nasal washes (collected in 1 mL of 0.5% bovine serum albumin in PBS) were collected at 4 dpi for virological and flow cytometric analyses.

value: interstitial macrophages

value: Hu-FcgR Tg

tag: infection status

value: low infection


title: Pancreatic cancer, patient 3656, whole transcriptome

description: Library name: rnaseq_3656

value: patient 3656


title: Blood neutrophil, 0h, adult healthy control, replicate 2

description: Library name: HC-02


title: siNC-3

value: primary human uterine fibroblast


title: Blood neutrophil, 0h, adult healthy control, replicate 7

description: Library name: HC-08


title: Pancreatic cancer, patient 3659, whole transcriptome

description: Library name: rnaseq_3659

value: patient 3659


title: NG-A0648_5

description:
Library name: RNA05000009
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: liver

value: primary

value: hepatocyte


title: NG-A0648_26

description:
Library name: RNA05000007
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 1


title: Blood neutrophil, 0h, pediatric healthy control, replicate 2

description: Library name: HJ-12

value: Pediatric healthy control

value: Thailand


title: siNC-1


title: D35_GA-AFUC IMs

description: Library name: D35


title: Pancreatic cancer, patient 3620, whole transcriptome

description: Library name: rnaseq_3620

value: PDAC

value: patient 3620


title: Pancreatic cancer, patient 3613, whole transcriptome

description: Library name: rnaseq_3613

value: patient 3613


title: NG-A0648_14

description:
Library name: RNA05000005
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, adult healthy control, replicate 1

description: Library name: HC-01

value: Neutrophil

value: Adult healthy control

value: 0h no treatment


title: NG-A0648_13

description:
Library name: RNA05000004
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: Blood neutrophil, 0h, adult healthy control, replicate 3

description: Library name: HC-04


title: Blood neutrophil, 0h, adult SLE, replicate 5

description: Library name: aSLE-UOL-5

value: Adult SLE

value: UK


title: Blood neutrophil, 0h, adult SLE, replicate 4

description: Library name: aSLE-UOL-4


title: Pancreatic cancer, patient 3594, whole transcriptome

description: Library name: rnaseq_3594

value: patient 3594


title: Pancreatic cancer, patient 3599, whole transcriptome

description: Library name: rnaseq_3599

value: patient 3599


title: D32_GA-AFUC monocytes

description: Library name: D32

source_name: infiltrating monocytes

value: infiltrating monocytes

value: Hu-FcgR Tg

value: low infection


title: NG-A0648_3

description:
Library name: RNA05000003
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: liver

value: primary

value: hepatocyte


title: Blood neutrophil, 0h, adult SLE, replicate 3

description: Library name: aSLE-UOL-3


title: NG-A0648_4

description:
Library name: RNA05000008
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 2


title: NG-A0648_2

description:
Library name: RNA05000002
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.

value: Condition 1


title: NG-A0648_1

description:
Library name: RNA05000001
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: NG-A0648_25

description:
Library name: RNA05000006
Primary human hepatocytes were culture in vitro in the CnBio MPS model in normal - maintenance - media or insulin resistance media for 14 days. Then accutely stimulated or not with 1 nM human insulin for the last 24h before harvesting the cell.


title: D31_GA-AFUC monocytes

description: Library name: D31


title: Pancreatic cancer, patient 3577, whole transcriptome

description: Library name: rnaseq_3577

value: PDAC

value: patient 3577


title: E2 Donor 3

city: Scottsdale

first: Elizabeth

middle: A.

last: Jacobsen

state: AZ

address: 13400 E. Shea Blvd.

institute: Mayo Clinic

data_processing:
Samples were sequenced using a 2x150bp Paired End (PE) configuration with Illumina HiSeq instrument (4000)
Image analysis and base calling were conducted by the HiSeq Control Software (HCS)
Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Sequence read was trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts  were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fall within exon regions were counted.
Assembly: GrCh38
Supplementary files format and content: raw counts

source_name: blood

growth_protocol: Peripheral blood was isolated from 3 otherwise normal donors. Eosinophils were immediately isolated using Miltenyi's MACSxpress Whole Blood Eosinophil Isolation kit ( 130-104-446), verified by cytospin and HE for 99% purity. 2 million/ml cells were plated in RPMI-1640+10% FBS + 1X streptomycin-penacllin-glutamine in different conditions.

extract_protocol:
Trizol Extraction and rRNA was removed with Ribozero rRNA removalkit (illumina). Quantified with Quibit 2.0 and RIN by 4200 TapeStation
NEBNext UltraRNA Library Prep Kit

treatment_protocol: Culture conditions include E0: [IL-5 (1ng/mL)], E1: [IL-5 (1ng/mL)+ TNF-alpha (15ng/mL) + IFN-gamma (15ng/,L);  E2: [ Il-5 (1ng/mL) +IL-4 (10ng/mL )+ GM-CSF (10ng/mL) + IL-33 (50ng/mL) for 18 hrs and then isolated for RNA and RNA sequencing.

value: blood

value: eosinophil

tag: genetic modification

value: IL-5, IL-4, GM-CSF, IL-33

value: 18 hrs


title: Blood neutrophil, 0h, adult SLE, replicate 1

description: Library name: aSLE-UOL-1

value: Neutrophil

value: Adult SLE

value: 0h no treatment

value: UK


title: D29_GA-AFUC monocytes

description: Library name: D29

value: infiltrating monocytes

value: Hu-FcgR Tg


title: Blood neutrophil, 0h, adult SLE, replicate 2

description: Library name: aSLE-UOL-2


title: Pancreatic cancer, patient 3571, whole transcriptome

description: Library name: rnaseq_3571

value: patient 3571


title: E2 Donor 2


title: D34_GA-AFUC IMs

description: Library name: D34

value: interstitial macrophages

value: low infection


title: Pancreatic cancer, patient 3562, whole transcriptome

description: Library name: rnaseq_3562

value: patient 3562


title: C28_S309 IMs

description: Library name: C28

value: moderate infection


title: patient7, T-cells, nat, ATAC

city: New York

first: Sneha

last: Mitra

state: NY

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description:
Library name: patient7_nat_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

library_source: genomic single cell

data_processing:
Multiome files we demultiplexed using cellranger mkfastq
Demultiplexed data was processed using the cellranger aggr pipeline
Assembly: mm10
Supplementary files format and content: Cellranger output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz

source_name: nat

extract_protocol:
Immediately following sorting, cells were washed and nuclei were isolated by lysing cell membranes. Nuclei were then used for 10X multi-ome for sc ATAC and sc nuclear RNA following manufacturer protocols.
Libaries construction for both scATAC and snRNA followed manufacturer protocols (10X genomics) for single cell Multi-omic protocols.

value: nat

value: T-cell

tag: library type

value: ATAC


title: C27_S309 IMs

description: Library name: C27


title: D33_GA-AFUC IMs

description: Library name: D33


title: Pancreatic cancer, patient 3559, whole transcriptome

description: Library name: rnaseq_3559

value: PDAC

value: patient 3559


title: E2 Donor 1

value: blood

value: eosinophil

value: IL-5, IL-4, GM-CSF, IL-33

value: 18 hrs


title: patient7, T-cells, tumor, ATAC

description:
Library name: patient7_tumor_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

source_name: tumor

value: tumor


title: Pancreatic cancer, patient 3549, whole transcriptome

description: Library name: rnaseq_3549

value: patient 3549


title: patient7, T-cells, tumor, GEX

description:
Library name: patient7_tumor_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

library_source: transcriptomic single cell

molecule: nuclear RNA

value: mRNA


title: patient7, T-cells, nat, GEX

description:
Library name: patient7_nat_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Pancreatic cancer, patient 3592, whole transcriptome

description: Library name: rnaseq_3592

value: patient 3592


title: E1 Donor 3

value: IL-5, TNF, IFNG


title: E1 Donor 2


title: C25_S309 IMs

description: Library name: C25

value: interstitial macrophages

value: Hu-FcgR Tg


title: Pancreatic cancer, patient 3544, whole transcriptome

description: Library name: rnaseq_3544

value: patient 3544


title: D30_GA-AFUC monocytes

description: Library name: D30

value: infiltrating monocytes

value: low infection


title: patient4, T-cells, nat, ATAC

description:
Library name: patient4_nat_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: nat

value: T-cell

value: ATAC


title: Pancreatic cancer, patient 3515, whole transcriptome

description: Library name: rnaseq_3515

value: PDAC

value: patient 3515


title: C24_S309 monocytes

description: Library name: C24

value: moderate infection


title: patient4, T-cells, nat, GEX

description:
Library name: patient4_nat_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: Pancreatic cancer, patient 3606, whole transcriptome

description: Library name: rnaseq_3606

value: patient 3606


title: IL-5 Donor 3

value: blood

value: eosinophil

value: 18 hrs


title: E1 Donor 1


title: C23_S309 monocytes

description: Library name: C23


title: Pancreatic cancer, patient 3510, whole transcriptome

description: Library name: rnaseq_3510

value: patient 3510


title: patient4, T-cells, tumor, ATAC

description:
Library name: patient4_tumor_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: tumor


title: IL-5 Donor 2


title: patient4, T-cells, tumor, GEX

description:
Library name: patient4_tumor_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: mRNA


title: Pancreatic cancer, patient 3497, whole transcriptome

description: Library name: rnaseq_3497

value: patient 3497


title: IL-5 Donor 1


title: C26_S309 IMs

description: Library name: C26

value: interstitial macrophages

value: Hu-FcgR Tg


title: patient2, T-cells, nat, ATAC

description:
Library name: patient2_nat_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences


title: C21_S309 monocytes

description: Library name: C21

value: infiltrating monocytes


title: Pancreatic cancer, patient 3496, whole transcriptome

description: Library name: rnaseq_3496

value: patient 3496


title: Pancreatic cancer, patient 3495, whole transcriptome

description: Library name: rnaseq_3495

value: patient 3495


title: B20_hE16 resident IMs

description: Library name: B20

value: high infection


title: patient2, T-cells, nat, GEX

description:
Library name: patient2_nat_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence

value: nat

value: T-cell


title: Yellow 1

city: Chuncheon

first: Beom-Soon

last: Choi

address: Kangwondaehak-gil 1

country: South Korea

institute: NBIT

description: Library name: Sample 2

data_processing:
Trimmomatic v0.36
Trimmomatic sliding window (4:20)
HITSAT2 v2.1.0
String Tie v1.3.4d
DESeq V1.36.0 (for DEGs analysis)
Assembly: Williams 82 v6
Supplementary files format and content: tab-delimited text files include FPKM anf TPM values for each sample

organism: Glycine max

source_name: Seeds

growth_protocol: Soybean F9 (Black and Yellow) seeds were gwron under normal condition

extract_protocol:
Kit using Genall Hybrid plant
RNA-Seq and cDNA library

treatment_protocol: No treatments

value: Seeds

tag: developmental stage

value: Matured stage


title: Black 1

description: Library name: Sample 1


title: B19_hE16 resident IMs

description: Library name: B19


title: Pancreatic cancer, patient 3493, whole transcriptome

description: Library name: rnaseq_3493

value: PDAC

value: patient 3493


title: patient2, T-cells, tumor, ATAC

description:
Library name: patient2_tumor_T_ATAC
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences

value: ATAC


title: patient2, T-cells, tumor, GEX

description:
Library name: patient2_tumor_T_mRNA
3' mRNA: read1 contains cell barcode and UMI; read2 contains transcript sequence


title: B17_hE16 resident IMs

description: Library name: B17


title: Pancreatic cancer, patient 3487, whole transcriptome

description: Library name: rnaseq_3487

value: patient 3487


title: B18_hE16 resident IMs

description: Library name: B18


title: Pancreatic cancer, patient 3454, whole transcriptome

description: Library name: rnaseq_3454

value: patient 3454


title: apocrine gland anal sac adenocarcinoma (AGASAC), 26

city: Berlin

first: Alexander

middle: F. H.

last: Haake

address: Robert-von-Ostertag-Straße 15

department: Department of Veterinary Medicine

country: Germany

institute: Freie Universität Berlin

hyb_protocol: 150 to 250 ng of total RNA was hybridised to the nCounter Canine IO Panel XT CodeSets (NanoString Technologies, Inc., Seattle, WA, USA). Hybridised samples were processed following the manufacturer’s protocols (protocol ID: MAN-10023-11, MAN-10056-06) and loaded onto the nCounter MAX Analysis System’s (NanoString) Prep Station for purification and immobilization on sample cartridges.

scan_protocol: Samples were transferred to the nCounter MAX Digital Analyzer (NanoString) for data collection following the manufacturer’s user manual (protocol ID: MAN-C0035-08).

data_processing: Following the workflow described in the manufacturer’s user manuals (MAN-C0019-08, MAN-C0011-04), the reporter library files (RLF) and reporter code count (RCC) files were imported into the nSolverTM 4.0 Analysis Software. Quality control and normalisation followed default settings.

organism: Canis lupus familiaris

source_name: archival FFPE tumour tissue

extract_protocol: Total RNA was extracted utilising the PureLinkTM FFPE Total RNA Isolation Kit (Thermo Fisher Scientific Inc., Waltham, MA, USA).

value: female

tag: breed

value: Retriever-mix

tag: age (years)


title: B16_hE16 resident IMs

description: Library name: B16

tag: cell type

value: interstitial macrophages


title: apocrine gland anal sac adenocarcinoma (AGASAC), 28

value: n/s

value: Mixed-breed


title: C22_S309 monocytes

description: Library name: C22

value: infiltrating monocytes

value: Hu-FcgR Tg

tag: treatment

value: moderate infection


title: Pancreatic cancer, patient 3469, whole transcriptome

description: Library name: rnaseq_3469

value: patient 3469


title: ZNF626_Human_Unbound_2

city: Palo Alto

first: Zheng

last: Zuo

state: CA

address: Stanford

department: Genetics

institute: Stanford university

description:
Library name: Spec_seq_sample_ZNF626_Human_Unbound_2
ZNF626(Human).rep2.csv

data_processing:
Counting the number of Bound and Unbound reads for each sample. The negative logarithmic ratio of Bound and Unbound reads can be calculated as the relative binding energy for each binding sites.
Cross comparison between replicate samples reveals the resolution of each sample, usually around 0.2kT for individual site.
The motif or specificity profile can be constructed by regression of binding energy values of select sequences, e.g., some reference site and all of its single/double variants. TFCookbook package, which contains all necessary codes to analyze the TF-DNA motif profile, can be accessed through https://github.com/zeropin/zeropin/TFCookbook.
Assembly: human genome hg38
Supplementary files format and content: For each sample, the associated csv file (linked to the corresponding *bound sample records) contains the bound and unbound reads, calculated relative bindng energy, library type, and the number of mismatches to some reference site for individual binding site. The data analysis protocol for each ZFP can be accessed through Github https://github.com/zeropin/ZFPCookbook

source_name: Recombinant protein

growth_protocol: We used the NEB PURExpress or E. coli(BL21) system to produce N-terminal HALO tagged ZFP constructs and noticed better success rates than previously used SUMO-tagged constructs.

extract_protocol:
The bound and unbound fractions of each sample were cut separately as thin gel slice, extracted by acrylamide gel extraction buffer (soaking a 55C for more than 30mins). Each fraction of DNA pool was purified and further amplified by uniquely indexed Illumina primers set for at least 12 cycles (annealing temperature 52C, extension time 30s). All samples were pooled together for Illumina Novaseq.
Synthetic DNA library was prepared by ordering 20 degenrate ologos containing triply randomized sites within the putative ZNF626 binding site (54bp long). Reversed PE2 primer was used to anneal and extend the ssDNA library to make dsDNA library.

treatment_protocol: We ran EMSA to physically separate DNA bound by ZNF626(Human) or ZNF626(Macaque) from unbound DNA. The EMSA condition is 10% Tris-glycine gel, 170V for 1h in cold room.

value: Recombinant protein

tag: fraction

value: unbound


title: ZNF626_Human_Bound_2

description:
Library name: Spec_seq_sample_ZNF626_Human_Bound_2
ZNF626(Human).rep2.csv

tag: cell line

value: bound


title: B15_hE16 monocytes

description: Library name: B15

value: high infection


title: apocrine gland anal sac adenocarcinoma (AGASAC), 25

value: male

value: Labrador Retriever


title: ZNF626_Human_Bound_1

description:
Library name: Spec_seq_sample_ZNF626_Human_Bound_1
ZNF626(Human).rep1.csv

tag: tissue


title: B14_hE16 monocytes

description: Library name: B14

tag: genotype


title: Pancreatic cancer, patient 3444, whole transcriptome

description: Library name: rnaseq_3444

value: PDAC

value: patient 3444


title: B13_hE16 monocytes

description: Library name: B13


title: apocrine gland anal sac adenocarcinoma (AGASAC), 24

value: Boxer-mix


title: Pancreatic cancer, patient 3408, whole transcriptome

description: Library name: rnaseq_3408

value: patient 3408


title: Pancreatic cancer, patient 3434, whole transcriptome

description: Library name: rnaseq_3434

value: patient 3434


title: AnR-SS-3

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

description:
Library name: S63
AR_SS#3

data_processing:
RNA-Seq
Indexed sequences were checked quality by Fastqc
Indexed sequences were trimmed adaptor sequence by cutadapt (v 2.8) with parameters -m 75 -q 30
Reads were aligned to genome human GRCh38.p13 primary assembly genome , utilizing STAR (v 2.7.10a) with parameter --outFilterMismatchNoverReadLmax 0.01 --outFilterMultimapNmax 1
Read counts over annotated genes were obtained using featureCount (subreads | version: 2.0.3) with parameters -T 12 -B -O --fraction -s 2 -p --countReadPairs -d 50 -D 800 -g gene_id
Assembly: GRCh38.p13
Supplementary files format and content: comma-delimited text files include human gene counts for each sample

growth_protocol: Cells were frown either in 2D ( standard) culture conditions or in suspension cultures on poly hema coated plates

extract_protocol:
RNA extraction using Qiagen's RNeasy plus mini kit , cat# 74134
Sequencing libraries were generated using NEBNext UltraExpress® RNA Library Prep Kit

treatment_protocol: OV90 parental ( anoikis sensitive) and adapted resistant lines were treated with vehicle ( DMSO) or 500nM SNX631 for 4 days in attached cultures. Adapted resistant OV90 cells were also either treated for 4 days in attached 2D culture followed by switch to suspension culture on polyhema coated plates for 24 hrs. Cells were either treated with vehicle or SNX631 ( 500nM) in attached culture, followed, by either  treatmet with DMSO or SNX631 ( 500nM) in suspension alone or continued treatment of SNX631 in both attached and suspension culture. DMSO serves as control everywhere.

value: cell line

value: OV90 adapted anoikis resistant

value: ovarian cancer

value: WT


title: B11_hE16 monocytes

description: Library name: B11

value: infiltrating monocytes

value: Hu-FcgR Tg


title: Pancreatic cancer, patient 3428, whole transcriptome

description: Library name: rnaseq_3428

value: patient 3428


title: Pancreatic cancer, patient 3402, whole transcriptome

description: Library name: rnaseq_3402

value: patient 3402


title: AnR-SS-2

description:
Library name: S62
AR_SS#2


title: hepatoid gland adenoma (HGA), 8

description: re-analysis of GSM8152092

value: Hunting dog-mix


title: hepatoid gland adenoma (HGA), 10

description: re-analysis of GSM8152094

value: female, neutered

value: Australian Shepherd


title: Pancreatic cancer, patient 3362, whole transcriptome

description: Library name: rnaseq_3362

value: patient 3362


title: hepatoid gland adenoma (HGA), 9

description: re-analysis of GSM8152093

value: male

value: Golden Retriever


title: AnR-SS-4

description:
Library name: S64
AR_SS#4


title: hepatoid gland adenoma (HGA), 7

value: Entlebucher Sennenhund


title: hepatoid gland adenoma (HGA), 11

description: re-analysis of GSM8152095

value: Mixed-breed


title: A9_Naïve resident IMs

description: Library name: A9

value: interstitial macrophages

value: naive


title: Pancreatic cancer, patient 3554, whole transcriptome

description: Library name: rnaseq_3354

value: PDAC

value: patient 3554


title: hepatoid gland adenoma (HGA), 6


title: ZNF626_Human_Unbound_1

description:
Library name: Spec_seq_sample_ZNF626_Human_Unbound_1
ZNF626(Human).rep1.csv

value: Recombinant protein

value: unbound


title: AnR SD-4

description:
Library name: S60
AR_SD#4

value: cell line

value: OV90 adapted anoikis resistant

value: ovarian cancer

value: WT


title: Pancreatic cancer, patient 3353, whole transcriptome

description: Library name: rnaseq_3353

value: patient 3353


title: A8_Naïve resident IMs

description: Library name: A8

value: Hu-FcgR Tg


title: AnR SD-3

description:
Library name: S59
AR_SD#3


title: Pancreatic cancer, patient 3343, whole transcriptome

description: Library name: rnaseq_3343

value: patient 3343


title: B12_hE16 monocytes

description: Library name: B12

value: infiltrating monocytes

value: high infection


title: apocrine gland anal sac adenocarcinoma (AGASAC), 23

value: female, neutered


title: AnR SD-2

description:
Library name: S58
AR_SD#2


title: AnR-SS-1

description:
Library name: S61
AR_SS#1


title: apocrine gland anal sac adenocarcinoma (AGASAC), 22

value: German Shepherd


title: Pancreatic cancer, patient 3337, whole transcriptome

description: Library name: rnaseq_3337

value: patient 3337


title: A6_Naïve resident IMs

description: Library name: A6

value: interstitial macrophages

value: naive


title: A5_Naïve monocytes

description: Library name: A5


title: Pancreatic cancer, patient 3328, whole transcriptome

description: Library name: rnaseq_3328

value: PDAC

value: patient 3328


title: apocrine gland anal sac adenocarcinoma (AGASAC), 21

value: female

value: Cocker Spaniel


title: A4_Naïve monocytes

description: Library name: A4


title: AnR DS-4

description:
Library name: S56
AR_DS#4

value: cell line

value: OV90 adapted anoikis resistant


title: Pancreatic cancer, patient 3282, whole transcriptome

description: Library name: rnaseq_3282

value: patient 3282


title: A3_Naïve monocytes

description: Library name: A3


title: apocrine gland anal sac adenocarcinoma (AGASAC), 19

value: Husky


title: AnR DS-3

description:
Library name: S55
AR_DS#3

value: ovarian cancer

value: WT


title: Pancreatic cancer, patient 3275, whole transcriptome

description: Library name: rnaseq_3275

value: patient 3275


title: apocrine gland anal sac adenocarcinoma (AGASAC), 20

value: male

value: Poodle


title: AnR DS-2

description:
Library name: S54
AR_DS#2


title: Pancreatic cancer, patient 3253, whole transcriptome

description: Library name: rnaseq_3253

value: patient 3253


title: A7_Naïve resident IMs

description: Library name: A7

value: Hu-FcgR Tg


title: A10_Naïve resident IMs

description: Library name: A10

value: interstitial macrophages


title: AnR DS-1

description:
Library name: S53
AR_DS#1


title: apocrine gland anal sac adenocarcinoma (AGASAC), 18

value: Cavalier King Charles Spaniel


title: Pancreatic cancer, patient 3252, whole transcriptome

description: Library name: rnaseq_3252

value: PDAC

value: patient 3252


title: AnR DD-4

description:
Library name: S52
AR_DD#4

value: DMSO


title: A2_Naïve monocytes

description: Library name: A2

value: infiltrating monocytes

value: naive


title: apocrine gland anal sac adenocarcinoma (AGASAC), 17

value: male, neutered

value: Shepherd-Mix


title: Pancreatic cancer, patient 3250, whole transcriptome

description: Library name: rnaseq_3250

value: patient 3250