title: DNA from PD52202b


title: DNA from PD52202a

status: Public on Mar 28 2025

type: genomic

city: Saffron Walden

first: Sam

last: Behjati

address: Hinxton

country: United Kingdom

institute: Wellcome Sanger Institute

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to the Human Infinium MethylationEPIC v1.0 Beadchip (Illumina) using the standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina IScan using the standard recommended scanner settings

data_processing:
Minfi in R, with funnorn normalisation method
Average Beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: Kidney

label_protocol: Standard Illumina protocol

extract_protocol: Tumour and normal kidney DNA/RNA were extracted by standard methods using the Qiagen Allprep kit/QIAmp DNA kit/RNeasy kit. Blood germline DNA was extracted with the QIAamp DNA Blood Midi Kit (Qiagen).

tag: tissue

value: Kidney


title: DNA from PD52201h

source_name: Blood

value: Blood


title: DNA from PD52201f


title: DNA from PD52201a


title: DNA from PD51622d


title: DNA from PD51622e


title: DNA from PD51622c


title: DNA from PD52201b


title: DNA from PD52201d


title: DNA from PD52201c


title: DNA from PD51622b


title: DNA from PD50734c


title: DNA from PD50734b


title: DNA from PD50733c


title: DNA from PD50733a


title: DNA from PD50730c


title: DNA from PD50730b


title: DNA from PD50726d


title: DNA from PD50726b


title: DNA from PD50728a


title: DNA from PD51622a


title: DNA from PD50726c


title: DNA from PD50724c


title: DNA from PD50724b


title: DNA from PD52211c


title: DNA from PD50733b


title: DNA from PD50720b


title: DNA from PD50720a


title: DNA from PD50728b


title: DNA from PD50719c


title: DNA from PD50719b


title: DNA from PD50717b


title: DNA from PD50717a


title: DNA from PD50716c


title: DNA from PD50717c


title: DNA from PD50724a


title: DNA from PD50715c


title: DNA from PD50716a


title: DNA from PD50716b


title: DNA from PD50734a


title: DNA from PD50730a


title: DNA from PD50715a


title: DNA from PD50715b


title: DNA from PD50713a


title: DNA from PD50711a


title: DNA from PD50709b


title: DNA from PD50726a


title: DNA from PD50713b


title: DNA from PD50711b


title: DNA from PD50708b


title: DNA from PD50707b


title: DNA from PD50707a


title: DNA from PD50699c


title: DNA from PD50719a


title: DNA from PD50707c


title: DNA from PD50699a


title: DNA from PD50697a


title: DNA from PD50699b


title: DNA from PD50698a


title: DNA from PD50696c


title: DNA from PD50697b


title: DNA from PD50695c


title: DNA from PD50695a


title: DNA from PD50696a


title: DNA from PD50686b


title: DNA from PD50683c


title: DNA from PD50686c


title: DNA from PD50686a


title: DNA from PD50683a


title: DNA from PD50682c


title: DNA from PD50695b


title: DNA from PD50683b


title: DNA from PD50709c


title: DNA from PD50708a


title: DNA from PD50709a


title: DNA from PD50678c


title: DNA from PD50682b


title: DNA from PD50678b


title: DNA from PD50678a


title: DNA from PD50675c


title: DNA from PD50675b


title: DNA from PD50675a


title: DNA from PD50698b


title: DNA from PD50696b


title: DNA from PD50669a


title: DNA from PD50665b


title: DNA from PD50665a


title: DNA from PD50667a


title: DNA from PD50663c


title: DNA from PD50663b


title: DNA from PD50682a


title: DNA from PD50662c


title: DNA from PD50663a


title: DNA from PD50662a


title: DNA from PD50643h


title: DNA from PD50643m


title: DNA from PD50662b


title: DNA from PD50643j


title: DNA from PD50643f


title: DNA from PD50643d


title: DNA from PD50602d


title: DNA from PD50600h


title: DNA from PD50602a


title: DNA from PD50602c


title: DNA from PD50600g


title: DNA from PD50669c


title: DNA from PD50669b


title: DNA from PD50667b


title: DNA from PD50600f


title: DNA from PD50667c


title: DNA from PD50600b


title: DNA from PD50599f


title: DNA from PD50643k


title: DNA from PD50596i


title: DNA from PD50596d


title: DNA from PD50596e


title: DNA from PD50596c


title: DNA from PD50643l


title: DNA from PD50596b


title: DNA from PD50596a


title: DNA from PD50594f


title: DNA from PD50643e


title: DNA from PD50594b


title: DNA from PD50593c


title: DNA from PD50594a


title: DNA from PD50602b


title: DNA from PD50591e


title: DNA from PD50591d


title: DNA from PD50591c


title: DNA from PD50593a


title: DNA from PD50590p


title: DNA from PD50591a


title: DNA from PD50590h


title: DNA from PD50590b


title: DNA from PD50599e


title: DNA from PD50599g


title: DNA from PD50599b


title: DNA from PD50590a


title: DNA from PD50589o


title: DNA from PD50594d


title: DNA from PD50589k


title: DNA from PD50589f


title: DNA from PD50589d


title: DNA from PD50589b


title: DNA from PD50589m


title: DNA from PD49348v


title: DNA from PD50589a


title: DNA from PD49348t


title: DNA from PD49348u


title: DNA from PD49348s


title: DNA from PD49348r


title: DNA from PD50593b


title: DNA from PD49348o


title: DNA from PD49348p


title: DNA from PD49348m


title: DNA from PD49348n


title: DNA from PD49348b


title: DNA from PD49223a


title: DNA from PD49223b


title: DNA from PD49217c


title: DNA from PD49219b


title: DNA from PD49217b


title: DNA from PD49219a


title: DNA from PD49217a


title: DNA from PD49216d


title: DNA from PD49216a


title: DNA from PD49216c

source_name: Unknown

value: Unknown


title: DNA from PD49216b


title: DNA from PD49215b


title: DNA from PD49215a


title: DNA from PD49214b


title: DNA from PD49214c


title: DNA from PD49213c


title: DNA from PD49214a


title: DNA from PD49213b


title: DNA from PD49211b


title: DNA from PD49211c


title: DNA from PD49211a


title: DNA from PD49210b


title: DNA from PD49210a


title: DNA from PD49210c


title: DNA from PD49213a


title: DNA from PD49209c


title: DNA from PD49209a


title: DNA from PD49204c


title: DNA from PD49204b


title: DNA from PD49204a


title: DNA from PD49209b


title: DNA from PD49203c


title: DNA from PD49203a


title: DNA from PD49200b


title: DNA from PD49200a


title: DNA from PD49200c


title: DNA from PD49215c


title: DNA from PD49199b


title: DNA from PD49199c


title: DNA from PD49199a


title: DNA from PD49198a


title: DNA from PD49198c


title: DNA from PD49197d


title: DNA from PD49197c


title: DNA from PD49195c


title: DNA from PD49193c


title: DNA from PD49195b


title: DNA from PD49193a


title: DNA from PD49198b


title: DNA from PD49197b


title: DNA from PD49197a


title: DNA from PD49191d


title: DNA from PD49195a


title: DNA from PD49191c


title: DNA from PD49193b


title: DNA from PD49203b


title: DNA from PD49191b


title: DNA from PD49189a


title: DNA from PD49187c


title: DNA from PD49189c


title: DNA from PD49191a


title: DNA from PD49189b


title: DNA from PD49186d


title: DNA from PD49186c


title: DNA from PD49186b


title: DNA from PD49186a


title: DNA from PD49185b


title: DNA from PD49187b


title: DNA from PD49187a


title: DNA from PD49185a


title: DNA from PD49184c


title: DNA from PD49184a


title: DNA from PD49184d


title: DNA from PD49183d


title: DNA from PD49183b


title: DNA from PD49177b


title: DNA from PD49183a


title: DNA from PD49176a


title: DNA from PD49176b


title: DNA from PD49174c


title: DNA from PD49177a


title: DNA from PD49174a


title: DNA from PD49174b


title: DNA from PD49173c


title: DNA from PD49173b


title: DNA from PD49173a


title: DNA from PD49171c


title: DNA from PD49171b


title: DNA from PD49171a


title: DNA from PD48726f


title: DNA from PD48726e


title: DNA from PD48726g


title: DNA from PD48726b


title: DNA from PD48725b


title: DNA from PD48725c


title: DNA from PD48726d


title: DNA from PD48725a


title: DNA from PD48724c


title: DNA from PD49184b


title: DNA from PD48724b


title: DNA from PD48724a


title: DNA from PD48723b


title: DNA from PD48723c


title: DNA from PD48722c


title: DNA from PD48722a


title: DNA from PD48722b


title: DNA from PD48721c


title: DNA from PD48721a


title: DNA from PD48721b


title: DNA from PD48720a


title: DNA from PD48720c


title: DNA from PD48719b


title: DNA from PD48719a


title: DNA from PD48718b


title: DNA from PD48718c


title: DNA from PD48720b


title: DNA from PD48718a


title: DNA from PD48715c


title: DNA from PD48717a


title: DNA from PD48714c


title: DNA from PD48715a


title: DNA from PD48715b


title: DNA from PD48717b


title: DNA from PD48714b


title: DNA from PD48714a


title: DNA from PD48713b


title: DNA from PD48723a


title: DNA from PD48712b


title: DNA from PD48712c


title: DNA from PD48719c


title: DNA from PD48712a


title: DNA from PD48713a


title: DNA from PD48713c


title: DNA from PD48710c


title: DNA from PD48710a


title: DNA from PD48709a


title: DNA from PD48708b


title: DNA from PD48709b


title: DNA from PD48708a


title: DNA from PD48706c


title: DNA from PD48706a


title: DNA from PD48706b


title: DNA from PD48710b


title: DNA from PD48705b


title: DNA from PD48717c


title: DNA from PD48705a


title: DNA from PD48701b


title: DNA from PD48705c


title: DNA from PD48700d


title: DNA from PD48700c


title: DNA from PD48701a


title: DNA from PD48701c


title: DNA from PD48700a


title: DNA from PD48700b


title: DNA from PD48699b


title: DNA from PD48699c


title: DNA from PD48696c


title: DNA from PD48709c


title: DNA from PD48696b


title: DNA from PD48699a


title: DNA from PD48696a


title: DNA from PD48696d


title: DNA from PD48696e


title: DNA from PD48692c


title: DNA from PD48692a


title: DNA from PD48690c


title: DNA from PD48691c


title: DNA from PD48691a


title: DNA from PD48691b


title: DNA from PD48692b


title: DNA from PD48690b


title: DNA from PD48690a


title: DNA from PD48688b


title: DNA from PD48687b


title: DNA from PD48688a


title: DNA from PD48688c


title: DNA from PD48687c


title: DNA from PD40713k


title: DNA from PD40713j


title: DNA from PD40713i


title: DNA from PD48687a


title: DNA from PD48686a


title: DNA from PD40713h


title: DNA from PD40713e


title: DNA from PD40713f


title: DNA from PD40713d


title: 10h rep2

type: SRA

city: Changchun

first: Wei

last: Huang

state: Jilin

address: Xinmin Street No. 1163

department: Modern biology

country: China

institute: nstitute of Frontier Medical Science, Jilin University

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
Six-to-eight week old female BALB/c mice were obtained from Changchun Yisi Experimental Animal Technology Co., Ltd (Changchun, Jilin, China). After mouse was killed by inhalation anesthesia, the spleen was harvested. The spleen was repeatedly pinched with ophthalmic forceps to free a single cell, and the cell mass was removed with a 40-μm cell screener. Red blood cells in the splenocyte suspension were removed by red blood cell lysis buffer (NH4CL2009, Tian Jin Hao Yang biological manufacturing, Tianjin, China). Dynabeads™ FlowComp™ Mouse Pan T (CD90.2) kit (11465D, Invitrogen, Carlsbad, CA, USA) was used to isolate T lymphocytes from splenocyte suspension. The isolated T lymphocytes were cultured in RPMI 1640 medium containing 2% fetal bovine serum (Biological Industries, Israel) at 37 ℃ and 5% CO2. All experimental procedures were approved by the ethics committee of School of Pharmaceutical Science of Jilin University (No. 20210056). After T lymphcytes were treated by LZ-8 with indicated time, the cells were collected by centrifugation at 200g×5min. Trizol (15596026, ThermoFihser, Waltham, MA, USA) extracted RNA from cell pellet.
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: The isolated T lymphocytes  were treated by LZ-8 for 10h before RNA extracted.

tag: stain

value: Balb/c

tag: age

value: Six-to-eight week old

tag: cell type

value: T lymphocyte

tag: treatment

value: LZ-8 for 10h

tag: group


title: 10h rep3

growth_protocol: The isolated T lymphocytes were cultured in RPMI 1640 medium containing 2% fetal bovine serum (Biological Industries, Israel) at 37 ℃ and 5% CO2.


title: 15h rep2

treatment_protocol: The isolated T lymphocytes  were treated by LZ-8 for 15h before RNA extracted.

value: LZ-8 for 15h


title: 15h rep3


title: 5h rep3

treatment_protocol: The isolated T lymphocytes  were treated by LZ-8 for 0h and 5h before RNA extracted.

value: cells were treated by LZ-8 for 5h


title: DNA from PD48686b


title: 5h rep1


title: 0h rep2

value: control

value: cells were treated by LZ-8 for 0h


title: ZA_col3_B

city: Los Angeles

first: Darian

middle: Jordan

last: Gamble

address: 1450 Biggy St Nrt 4513

country: USA

institute: University of Southern California

description: Library name: ZA_col3_B

data_processing:
Trimming was attempted but had no difference in uniquely or duplicate mapped reads. Thus, raw untrimmed reads were used.
Raw files were aligned to the Anolis Carolinensis genome (rAnoCar3.1.pri) using star 2.7.6a with default paramaters
Mapped reads were fomverten from .sam to .bam files using samtools 1.17.
Normalized counts were generated using DESeq2 version 1.45.1.
Assembly: rAnoCar3.1.pri
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

organism: Anolis carolinensis

source_name: whole tail

extract_protocol:
Total RNA was isolated using the QIAGEN RNeasy DSP FFPE Kit. TapeStation was performed on Aglient 2100 Bioanalyzer and concentration was assessed using a nanodrop.
Library was constructed using the Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus. rRNA oligo spike in was included specific to the anolis carolinensis to remove rRNA from total RNA.

treatment_protocol: ZA samples were treated with zoledronic acid (250 ul of 4ul/ml solution) via intraperitoneal injection one week prior to amputation and three times per week for three additional weeks until collected for analysis.

value: whole tail

value: Fibroblast

value: ZA


title: 0h rep3


title: PBS_col3_C

description: Library name: PBS_col3_C

value: PBS


title: ZA_col3_A

description: Library name: ZA_col3_A


title: 0h rep1


title: PBS_col3_B

description: Library name: PBS_col3_B


title: D28_col3_C

description: Library name: D28_col3_C


title: D28_col3_B

description: Library name: D28_col3_B


title: D14_col3_A

description: Library name: D14_col3_A


title: ZA_col3_C

description: Library name: ZA_col3_C


title: D14_col3_B

description: Library name: D14_col3_B


title: D28_col3_A

description: Library name: D28_col3_A


title: PBS_col3_A

description: Library name: PBS_col3_A


title: D7_col3_B

description: Library name: D7_col3_B


title: D7_col3_C

description: Library name: D7_col3_C


title: D7_col3_A

description: Library name: D7_col3_A


title: 15h rep1


title: 10h rep1


title: SNU668_shGPER3

city: JiNan

first: Dong

last: Sun

address: 440 Jiyan Road, Huaiyin District

institute: Shandong First Medical University Affiliated Cancer Hospital

description: Library name: Sample 6

data_processing:
Use fastp to filter the original data. HiSat2 was used to compare the clean data after quality control with the reference genome to obtain mapped data for subsequent transcript assembly, expression calculation, etc. RSEM was used to quantitatively analyze the expression levels of genes and transcripts.
Assembly: hg38
Supplementary files format and content: csv files include TPM values for each Sample

extract_protocol:
Total RNA was extracted using QIAzol Lysis Reagent(Qiagen).1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina Stranded Mrna Prep,Ligation following manufacturer's protocols.

tag: cell line

value: gastric signet ring cells

tag: genotype

value: GPER knockdown


title: SNU668_shGPER2

description: Library name: Sample 5


title: 5h rep2


title: SNU668_shGPER1

description: Library name: Sample 4


title: SNU668_shControl3

description: Library name: Sample 3

value: WT


title: SNU668_shControl2

description: Library name: Sample 2


title: SNU668_shControl1

description: Library name: Sample 1


title: CRC2-dCAS9-KRAB-NTC2A

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

description: Library name: Sample 11

data_processing:
Quality control assessment of raw reads was performed using FastQC, followed by Trimmomatic trimming to remove low-quality sequences. The trimmed reads were then aligned to the reference genome using STAR version 2.7.9a. To facilitate the mapping process, a genome reference index was constructed using GRCh38.108.gtf (hg38) as the reference.
Assembly: GRCh38.108.gtf (hg38)
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: colon

extract_protocol:
Total RNA from cell lines was isolated using RNAeasy mini kit (Qiagen)
RNA sequencing libraries were prepared using the Stranded mRNA Prep, Ligation Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Briefly, mRNA was purified from 1 µg total RNA using oligo(dT) beads, poly(A)+ RNA was fragmented to 150 bp and converted into cDNA, and cDNA fragments were end-repaired, adenylated on the 3’ end, adapter-ligated, and amplified with 12 cycles of PCR. The final libraries were validated using a Qubit 2.0 Fluorometer (Life Technologies) and a Bioanalyzer 2100 system. All barcoded libraries were pooled and sequenced 2x75bp paired-end on an Illumina NextSeq550 platform to obtain a minimum of 10 Mio reads per sample.

value: colon

value: colon cancer


title: CRC2-dCAS9-KRAB-KAT2A-KD3A

description: Library name: Sample 9


title: CRC2-dCAS9-KRAB-KAT2A-KD2A

description: Library name: Sample 8


title: CRC2-dCAS9-KRAB-KAT2A-KD1A

description: Library name: Sample 7


title: D14_col3_C

description: Library name: D14_col3_C


title: CRC1-dCAS9-KRAB-KAT2A-KD3A

description: Library name: Sample 3


title: CRC1-dCAS9-KRAB-NTC1A

description: Library name: Sample 4


title: CRC1-dCAS9-KRAB-NTC2A

description: Library name: Sample 5


title: CRC1-dCAS9-KRAB-KAT2A-KD1A

description: Library name: Sample 1


title: CRC1-dCAS9-KRAB-KAT2A-KD2A

description: Library name: Sample 2


title: CRC3-dCAS9-KRAB-NTC2A


title: CRC3-dCAS9-KRAB-KAT2A-KD3A


title: CRC3-dCAS9-KRAB-KAT2A-KD2A


title: CRC3-dCAS9-KRAB-KAT2A-KD1A


title: HT29-dCAS9-KRAB-NTC2A


title: HT29-dCAS9-KRAB-NTC3A


title: CRC2-dCAS9-KRAB-NTC3A

description: Library name: Sample 12


title: HT29-dCAS9-KRAB-NTC1A


title: HT29-dCAS9-KRAB-KAT2A-KD2A


title: HT29-dCAS9-KRAB-KAT2A-KD3A


title: CRC2-dCAS9-KRAB-NTC1A

description: Library name: Sample 10


title: HGC_3

city: Hohhot

first: Song

last: Yukun

state: Inner Mongolia

address: Inner Mongolia Key Laboratory of Sheep & Goat Genetics Breeding and Reproduction

institute: Inner Mongolia Agricultural University

description: Library name: HGC_3

data_processing:
High-quality clean reads were obtained using Cutadapt (v1.9) and FastQC (v0.11.9) by removing adaptor sequences, reads containing > 10% unknown nucleotides (N), and low-quality bases. Clean reads from each sample were aligned to the ovine genome sequence (Ovisaries.Oarv3.1) using HISAT2 (v2.0.4). Alignment results were sorted, analyzed, and indexed with SAMtools. Quantitative analyses of mapped reads were performed using StringTie (v2.1.6) and Ballgown
Assembly: Ovisaries.Oarv3.1
Supplementary files format and content: Alignment results were sorted, analyzed, and indexed with SAMtools
Supplementary files format and content: mRNA abundance was calculated as fragments per kilobase of transcript per million mapped reads (FPKM)

organism: Ovis aries

source_name: cell

extract_protocol:
Total RNA was extracted from granulosa cells of follicles with different statuses (three independent biological replicates per group) using TRIzol reagent
After RNA purity confirmation and rRNA removal, cDNA libraries were constructed using SuperScript™ II Reverse Transcriptase

value: cell

value: granulosa cell

value: somatic cell


title: HT29-dCAS9-KRAB-KAT2A-KD1A


title: U2OS cell line parental EZHIP Input

city: Montréal

first: Claudia

middle: L

last: Kleinman

state: Québec

address: 3999 Côte Ste-Catherine Road

department: Human Genetics

country: Canada

institute: Lady Davis Institute for Medical Research

description: Library name: U2OS_Input

library_source: genomic

data_processing:
The CUT&RUN data was processed using GenPipes (v3.6.2) ChIP Sequencing Pipeline.
This includes adapter removal and trimming with Trimmomatic (v0.39), alignment to hg19 with BWA (v0.7.17), removal of duplicated reads with Picard (v2.0.1) and generation of BigWig tracks using Homer (v4.11)
Assembly: hg19
Supplementary files format and content: Bigwig files generated with Homer v4.11, read coverage for each sample over hg19
Library strategy: CUT&Run

extract_protocol:
DNA was purified from cleaved chromatin using Qiagen minElute PCR purification kit (28004).
50 uL of purified DNA was used for library preparation using KAPA HyperPrep kit (R oche, 07962363001) using Epicypher’s CUT&RUN cycling conditions with the exception of performing 12 cycles of amplification instead of 14.

value: Osteosarcoma

tag: antibody

value: Input

value: Parental


title: MG63 cell line parental EZHIP Input

description: Library name: MG63_input


title: KHOS cell line parental EZHIP Input

description: Library name: KHOS_Input

source_name: KHOS

value: KHOS


title: HGC_2

description: Library name: HGC_2


title: CRC1-dCAS9-KRAB-NTC3A

description: Library name: Sample 6

value: control


title: U2OS cell line  EZHIP knock out rep 2 H3K27me3

description: Library name: U2OS_C54_rep2

value: EZHIP KO


title: HGC_1

description: Library name: HGC_1


title: U2OS cell line  EZHIP knock out rep 1 H3K27me3

description: Library name: U2OS_C54_rep1


title: CRC3-dCAS9-KRAB-NTC3A


title: CRC3-dCAS9-KRAB-NTC1A


title: AGC_2

description: Library name: AGC_2


title: U2OS cell line parental EZHIP rep 2 H3K27me3

description: Library name: U2OS_C1_rep2

value: EZHIP


title: U2OS cell line parental EZHIP rep 1 H3K27me3

description: Library name: U2OS_C1_rep1


title: AGC_1

description: Library name: AGC_1


title: MG63 cell line parental rep 1 H3K27me3

description: Library name: MG63_PBMN_rep1


title: MG63 cell line  EZHIP over expression  rep 2 H3K27me3

description: Library name: MG63_EZHIP_rep2


title: MG63 cell line  EZHIP over expression  rep 1 H3K27me3

description: Library name: MG63_EZHIP_rep1


title: AF-CT-siPARP12, Bio rep4

city: Richland

first: Ernesto

middle: S.

last: Nakayasu

state: WA

address: 902 Battelle Blvd

institute: Pacific northwest national laboratory

description: Library name: r3_A16_S32_R1_001

data_processing:
RNAs eluted post-incubation with AF1521 and Control (mutant AF1521) beads were processed for cDNA synthesis using SMARTer® Universal Low Input RNA Kit (Takara, cat#634938) according to instruction manual, followed by template library prep using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat#E7805S). Single-read sequencing of the barcoded cDNA libraries with a read length of 150 were performed on NextSeq 550 plateform using NextSeq500/550 High Output v2.5 150 cycles (cat#20024907). Quality control of RNA-seq data was performed using FastQC (Version 0.12.0) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Read trimming was performed using BBDuk (https://github.com/BioInfoTools/BBMap/blob/master/sh/bbduk.sh). Reads were aligned to the mouse genome GRCm39 using STAR and mapped to genome features using the featureCounts program from the subread package (https://subread.sourceforge.net/). To account for technical variability raw counts were batch corrected with ComBat-Seq with default parameters prior to differential expression analysis with DESeq2.
Assembly: GRCm39
Supplementary files format and content: .txt file represents number of raw read counts mapping to each gene

extract_protocol:
MIN6 cells were a gift from the Yamagata lab and were grown in DMEM containing 4.5 g/L each of D-glucose and L-glutamine, 10% FBS, 100 units/mL penicillin, 100 μg/mL streptomycin, and 50 mM 2-mercaptoethanol maintained at 37 ºC in a 5% CO2 atmosphere. For PARP12 knockdown experiments, cells were treated at 80% confluency using Lipofectamine RNAiMAX (Invitrogen, Cat# 13778150) with SMARTpool ON-TARGETplus non-targeting siRNA (Dharmacon, cat#D-001810-10-20) or siRNA targeting Parp12 (Dharmacon, cat# L-065127-01-0020), with concomitant treatment with CT2 (100 ng/mL IFN-γ: R&D, cat#485-MI-100, 10 ng/mL TNF-α: R&D, Cat#410-MT-010, and 5 ng/mL IL-1β: R&D, cat #401-ML-005) for 24 h.
MIN6 cells were harvested using Tri reagent (Zymo Research, R2050-1-200) and the RNA was extracted using RNA Clean & Concentrator™-5 kit (Zymo Research, R1014), following manufacturer instructions. To test the specificity of the ADP-ribosylation-binding AF1521 macrodomain, an RNA aliquot was pre-treated with 2 nM SARS-CoV2 macrodomain MAC1 at room temp for 1 h in hydrolase reaction buffer (250 mM HEPES, 750 mM NaCl, 10 mM β-mercaptoethanol, 0.05 mM Triton X100, 5 mM MgCl2, 1X RNAsecure) to remove ADP-ribosylation. Equal amount of total RNA from each sample was incubated with either 20 µL of Af1521 macrodomain conjugated to magnetic beads (Tulip Biolabs, 2426) or control (naked or mutated Af1521) beads in 600 µL RNA pulldown buffer (10 mM Tris-HCl, 0.6 M NaCl, 0.1% NP40, 1X RNA secure) overnight at 4 C. After overnight incubation, the beads were gently washed with RNA pulldown buffer three times, and 50 µL of Tri reagent was added to elute RNA from the beads, followed by RNA Clean & Concentrator™-5 extraction.
RNAs eluted post-incubation with AF1521 and Control (mutant AF1521) beads were processed for cDNA synthesis using SMARTer® Universal Low Input RNA Kit (Takara, cat#634938) according to instruction manual, followed by template library prep using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (NEB, cat#E7805S). Single-read sequencing of the barcoded cDNA libraries with a read length of 150 were performed on NextSeq 550 plateform using NextSeq500/550 High Output v2.5 150 cycles (cat#20024907).

value: Islet Beta Cell

value: PARP12 knockdown

value: Cytokine cocktail

tag: batch

value: AF1521 bead


title: LAD_LEC_wt_rep3

type: RNA

city: Chapel Hill

first: Kathleen

middle: M

last: Caron

state: NC

address: 111 Mason Farm Rd

institute: University of North Carolina at Chapel Hill

hyb_protocol: The Thermo Fisher® GeneChip™ 3’ IVT Pico Kit Manual Workflow User Guide was followed to prepare the samples. The GeneChip™ Hybridization, Wash, and Stain Kit was used to prepare the ds-cDNA samples for hybridization. Fragmented and labeled ds-cDNA was added to a hybridization cocktail (50 ng/µl fragmented and labeled ds-cDNA final concentration, 50 pM control oligonucleotide B2, BioB, BioC, BioD and cre hybridization controls, 7 % DMSO, 100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20). Thermo FisherClariom S Mouse arrays were hybridized for 16 hours at 45°C in the GeneChip Hybridization Oven 645 (Affymetrix). The arrays were washed and stained with R-phycoerythrin streptavidin in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G Plus with autoloader. GeneChip Command Console Software (AGCC) was used for washing, staining and scanning control of the instrumentation.

data_processing: Transcriptome Analysis Console Software v 4.0 was used for basic data analysis and quality control. Microarray data was evaluated using the Partek Genomics Suite (Partek) software program. For statistical analysis of the data, one-way ANOVA was performed, and false discovery rate-adjusted p values ≤0.01 were considered significant.

label: biotin

source_name: LAD, LEC, WT

label_protocol: The Thermo Fisher® GeneChip™ 3’ IVT Pico Kit Manual Workflow User Guide was followed to prepare the samples. Following synthesis of ds-cDNA, the cDNA is converted to biotinylated ds-cDNA hybridization targets for unbiased coverage of the transcriptome.

growth_protocol: Mice had ad libitum access to normal laboratory diet and water. The mice were provided with environmental enrichment in the form of nesting material and lofts. The mice had a 12h:12h light-dark cycle, with a temperature range between 68-74°F and humidity between 30-70%.

extract_protocol: RNA was extracted using the Qiagen Rneasy Plus kit. Total RNA (10 ng) was used to synthesize fragmented and labeled double-stranded cDNA (ds-cDNA) using the GeneChip™ Pico Kit (Thermo Fisher).

treatment_protocol: LAD ligation was performed 7 days prior to sample collection in the case of LAD ligated mice.

value: LAD

value: LEC

value: WT


title: KHOS cell line parental rep 2 H3K27me3

description: Library name: KHOS_PBMN_rep2


title: KHOS cell line parental rep 1 H3K27me3

description: Library name: KHOS_PBMN_rep1


title: AF-CT-NT, Bio rep4

description: Library name: r3_A15_S31_R1_001

value: Nontarget siRNA


title: AF-NoCT-siPARP12, Bio rep4

description: Library name: r3_A14_S30_R1_001

value: No Cytokine cocktail


title: KHOS cell line  EZHIP over expression  rep 1 H3K27me3

description: Library name: KHOS_EZHIP_rep1


title: LAD_LEC_wt_rep2


title: AGC_3

description: Library name: AGC_3

value: cell

value: granulosa cell

value: somatic cell


title: AF-NoCT-NT, Bio rep4

description: Library name: r3_A13_S29_R1_001


title: U2OS cell line  EZHIP over expression rep 2 H3K27me3

description: Library name: U2OS_C54_EZHIP_OE_rep2

value: Osteosarcoma

value: EZHIP OE


title: U2OS cell line  EZHIP over expression rep 1 H3K27me3

description: Library name: U2OS_C54_EZHIP_OE_rep1


title: LAD_LEC_Cre_rep1

source_name: LAD, LEC, Cre

value: Cre


title: MG63 cell line parental rep 2 H3K27me3

description: Library name: MG63_PBMN_rep2


title: LAD_LEC_Cre_rep2


title: LAD_LEC_Cre_rep3


title: AF-CT-NT, Bio rep3

description: Library name: r3_A11_S27_R1_001


title: baseline_LEC_wt_rep3

source_name: baseline, LEC, WT

value: baseline


title: baseline_LEC_Cre_rep3

source_name: baseline, LEC, Cre


title: AF-CT-siPARP12, Bio rep2

description: Library name: r3_A8_S24_R1_001


title: LAD_LEC_wt_rep1


title: rs2305089 wild type MSC cell line 3 at 72 hours, replicate 3

city: London

first: Lucia

last: Cottone

address: 72 Huntley Street

institute: UCL Cancer Institute

data_processing:
Aligned to GRCh38 using the default options of the Salmon aligner and post alignment QC with FastQC and MultiQC.
Differential gene expression analysis was performed using DESeq2 v1.36.0 using cell line/genotype as the factor in the model.
Assembly: GRCh38
Supplementary files format and content: norm_matrix_48and72hrs.csv

molecule: polyA RNA

source_name: MSC

growth_protocol: The human episomal line of induced pluripotent stem cells (A18945, Gibco; Thermo Fisher Scientific, Inc, Waltham, MA, United States ) was maintained in feeder-free culture on Geltrex (A1413202, Invitrogen, Thermo Fisher Scientific) and Essential 8 Flex (E8 Flex) medium (A28585, Gibco, Thermo Fisher Scientific) supplemented with 0.5% of Penicillin (10,000 U/ml). Cells were cultured at 37 °C in a humidified atmosphere with 5% CO2. Cells were passaged by incubation for 5 min at 37 °C with Dulbecco’s phosphate buffered saline (DPBS)-EDTA 0.5 mM pH 8.00 (Invitrogen, Thermo Fisher Scientific, 14190250 and 15575020)

extract_protocol:
Direct-zol kit (Zymo Research, CA, USA) including an on-column DNA
TruSeq Stranded mRNA Library Prep kit.

treatment_protocol: iPSC were subcultured in a 1:25 split using PBS-EDTA into 24 well plates coated with Geltrex and grown for 12 hours ensuring sufficient space for colonies to grow from single cells. Colonies were recovered overnight in Essential 8 medium (E8) without Revitacell then the medium was changed to 500μl Cardiomyocyte Differentiation Medium A (ThermoFisher Scientific, A29209-01).

value: MSC

value: Induced pluripotent stem cells

value: Wild type

value: MSC differentation


title: baseline_LEC_wt_rep2


title: rs2305089 wild type MSC cell line 3 at 72 hours, replicate 1


title: rs2305089 wild type MSC cell line 2 at 72 hours, replicate 2


title: AF-NoCT-siPARP12, Bio rep2

description: Library name: r3_A6_S22_R1_001

value: Islet Beta Cell

value: PARP12 knockdown

value: AF1521 bead


title: AF-CT-siPARP12, Bio rep3

description: Library name: r3_A12_S28_R1_001

value: Cytokine cocktail


title: rs2305089 wild type MSC cell line 2 at 72 hours, replicate 1


title: rs2305089 wild type MSC cell line 1 at 72 hours, replicate 3


title: AF-NoCT-NT, Bio rep2

description: Library name: r3_A5_S21_R1_001

value: Nontarget siRNA


title: LAD_macrophage_Cre_rep3

source_name: LAD, macrophage, Cre

value: LAD

value: macrophage


title: AF-NoCT-siPARP12, Bio rep3

description: Library name: r3_A10_S26_R1_001

value: No Cytokine cocktail


title: AF-NoCT-NT, Bio rep3

description: Library name: r3_A9_S25_R1_001


title: rs2305089 wild type MSC cell line 1 at 72 hours, replicate 2


title: rs2305089 wild type MSC cell line 1 at 72 hours, replicate 1


title: baseline_LEC_Cre_rep2

value: LEC


title: LAD_macrophage_wt_rep2

source_name: LAD, macrophage, WT

value: WT


title: AF-CT-siPARP12, Bio rep1

description: Library name: r3_A4_S20_R1_001


title: AF-CT-NT, Bio rep1

description: Library name: r3_A3_S19_R1_001


title: rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 3


title: rs2305089 wild type MSC cell line 3 at 72 hours, replicate 2


title: baseline_LEC_Cre_rep1


title: LAD_macrophage_Cre_rep1


title: baseline_LEC_wt_rep1


title: AF-CT-NT, Bio rep2

description: Library name: r3_A7_S23_R1_001


title: rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 2


title: LAD_macrophage_Cre_rep2


title: LAD_macrophage_wt_rep1


title: LAD_macrophage_wt_rep3


title: rs2305089 wild type MSC cell line 2 at 72 hours, replicate 3


title: AF-NoCT-siPARP12, Bio rep1

description: Library name: r3_A2_S18_R1_001


title: rs2305089 heterozygous MSC cell line 3 at 72 hours, replicate 1


title: rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 2


title: rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 3


title: AF-NoCT-NT, Bio rep1

description: Library name: r3_A1_S17_R1_001


title: rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 3


title: rs2305089 heterozygous MSC cell line 2 at 72 hours, replicate 1


title: Ctr-CT-siPARP12, Bio rep4

description: Library name: r3_c16_S16_R1_001

value: Control bead


title: rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 2


title: baseline_macrophage_wt_rep3

source_name: baseline, macrophage, WT


title: Ctr-CT-NT, Bio rep4

description: Library name: r3_c15_S15_R1_001


title: Ctr-NoCT-siPARP12, Bio rep4

description: Library name: r3_c14_S14_R1_001


title: rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 2

source_name: Mesoderm

value: Mesoderm

value: Heterozygous

value: Mesoderm differentation


title: rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 3

value: Induced pluripotent stem cells


title: rs2305089 heterozygous MSC cell line 1 at 72 hours, replicate 1

value: MSC

value: Wild type


title: baseline_macrophage_Cre_rep3

source_name: baseline, macrophage, Cre

value: baseline

value: Cre


title: baseline_macrophage_wt_rep2


title: baseline_macrophage_Cre_rep2


title: rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 3


title: Ctr-NoCT-NT, Bio rep4

description: Library name: r3_c13_S13_R1_001

value: Islet Beta Cell


title: Liver, Placebo, d28, patient 673

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Base call data generated by Illumina NextSeq 2000
Read quality assessed using FastQC and MultiQC (v.1.3.dev0)
Adapter, poly-G and low-quality base trimming with Cutadapt (v.1.16)
Read alignment with STAR (v.2.7.1a)
Read counting with RSEM (v.1.2.28)
Differential expression computed using DESeq2 (v.1.26.0)
Assembly: GRCh38
Supplementary files format and content: Tab separated matrix table with raw gene counts for all genes and samples

source_name: liver

growth_protocol: Transjugular paired liver biopses from alcohol-associated hepatitis (AH) patients were extracted and flashfrozen at baseline (day 0) and 28 days post treatment.

extract_protocol:
Total RNA from transjugular liver biopsies was extracted using QIAzol lysis reagent protocol (Qiagen). RNA samples were treated with Turbo DNA-free Kit (Thermo Fisher) to remove genomic DNA following manufacturer’s guidelines.
Where possible 10ng of each total RNA sample was fragmented to a size appropriate for sequencing on an Illumina platform and first-strand cDNA was generated using the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian kit (Clontech Laboratories, Inc. #634411). Samples were grouped for library prep based on the amount of fragmentation required, as recommended in the protocol. [n=8 samples were subject to 4 minutes fragmentation time; n=15 samples were subject to 3 minutes of fragmentation; remaining samples required no fragmentation.] Illumina-compatible adapters and indexes were then added via 5 cycles of PCR. AMPure XP beads (Beckman Coulter, #A63881) were then used to purify the cDNA library. Depletion of ribosomal cDNA was performed using ZapR v2 and R-probes v2 specific to mammalian ribosomal RNA and human mitochondrial rRNA. Uncleaved fragments were enriched by 13 cycles of PCR before a final library purification using AMPure XP beads.

treatment_protocol: AH patients were administered with either placebo (5% dextrose) or canakinumab (a blocking IL-1B antibody) at baseline.

value: liver

tag: time

value: day 28

value: Placebo


title: rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 2


title: rs2305089 wild type mesoderm cell line 2 at 48 hours, replicate 1


title: rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 3


title: Ctr-CT-siPARP12, Bio rep3

description: Library name: r3_c12_S12_R1_001

value: PARP12 knockdown

value: Cytokine cocktail


title: Liver, Placebo, d0, patient 673

value: day 0


title: rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 1


title: Ctr-CT-NT, Bio rep3

description: Library name: r3_c11_S11_R1_001

value: Nontarget siRNA


title: rs2305089 wild type mesoderm cell line 1 at 48 hours, replicate 2


title: rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 3


title: baseline_macrophage_Cre_rep1

value: macrophage


title: rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 2

value: Mesoderm


title: rs2305089 wild type mesoderm cell line 3 at 48 hours, replicate 1

value: Heterozygous


title: Ctr-NoCT-siPARP12, Bio rep3

description: Library name: r3_c10_S10_R1_001

value: No Cytokine cocktail

value: Control bead


title: baseline_macrophage_wt_rep1

value: WT


title: Ctr-NoCT-NT, Bio rep3

description: Library name: r3_c9_S9_R1_001


title: Liver, Canakinumab, d28, patient 668

value: Canakinumab


title: rs2305089 heterozygous mesoderm cell line 3 at 48 hours, replicate 1

value: Induced pluripotent stem cells

value: Mesoderm differentation


title: rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 3


title: Liver, Canakinumab, d28, patient 620


title: rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 1


title: Ctr-CT-siPARP12, Bio rep2

description: Library name: r3_c8_S8_R1_001

value: Islet Beta Cell


title: rs2305089 heterozygous mesoderm cell line 2 at 48 hours, replicate 2


title: Liver, Canakinumab, d0, patient 620

value: liver


title: rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 2


title: Ctr-CT-NT, Bio rep2

description: Library name: r3_c7_S7_R1_001


title: Olig2, D13, AA

city: Amsterdam

first: Jeen

last: Engelenburg

address: Meibergdreef 47

country: Netherlands

institute: Netherlands Institute for Neuroscience

data_processing:
Reads were first clipped for adapters using fastp (v0.23.4), and subsequently mapped using STAR2 (v0.23.4) using the following settings: --outFilterMismatchNmax 2 --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 60. Separate fastq-files from the same sample were merged after mapping using samtools (v1.20). Quality control was performed using FastQC (v0.12.1). Counts were obtained using featureCounts (v2.0.6) with the ‘gencode.v45.primary_assambly.annotation.gtf’ file.
Assembly: hg38
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample

molecule: nuclear RNA

source_name: Brain

extract_protocol:
RNA from isolated nuclei was extracted using the RNeasy Micro kit (Qiagen, Hilden, Germany), according to the manufacturer’s instructions.
Samples were  library prepped using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian Library Prep Kit according to the manufacturer's instructions.

value: Brain

tag: donor

value: AA

tag: nucnr

tag: isolation batch


title: Liver, Placebo, d28, patient 605

value: day 28

value: Placebo


title: Olig2, D12, CC

value: CC


title: Ctr-NoCT-siPARP12, Bio rep2

description: Library name: r3_c6_S6_R1_001

value: PARP12 knockdown


title: Olig2, D11, CC


title: Liver, Canakinumab, d0, patient 668

value: day 0


title: Ctr-NoCT-NT, Bio rep2

description: Library name: r3_c5_S5_R1_001

value: Nontarget siRNA


title: Olig2, D10, AA


title: Liver, Canakinumab, d0, patient 376


title: Liver, Placebo, d0, patient 605


title: Olig2, D9, CC


title: Ctr-CT-NT, Bio rep1

description: Library name: r3_c3_S3_R1_001

value: Cytokine cocktail


title: rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 1

value: Mesoderm

value: Heterozygous


title: Olig2, D7, CC


title: Olig2, D8, AA


title: Liver, Canakinumab, d28, patient 376


title: Ctr-NoCT-siPARP12, Bio rep1

description: Library name: r3_c2_S2_R1_001

value: No Cytokine cocktail

value: Control bead


title: Ctr-CT-siPARP12, Bio rep1

description: Library name: r3_c4_S4_R1_001


title: Olig2, D6, AA


title: Olig2, D5, CC


title: Liver, Canakinumab, d0, patient 375

value: Canakinumab


title: Liver, Canakinumab, d28, patient 375


title: Olig2, D4, CC


title: Ctr-NoCT-NT, Bio rep1

description: Library name: r3_c1_S1_R1_001


title: rs2305089 heterozygous mesoderm cell line 1 at 48 hours, replicate 3

value: Induced pluripotent stem cells

value: Mesoderm differentation


title: Olig2, D3, CC


title: Liver, Canakinumab, d28, patient 370

value: liver


title: Olig2, D2, CC

value: Brain


title: Olig2, D1, AA

value: AA


title: Liver, Canakinumab, d0, patient 370


title: endosperm, ros1-3xC24, 7DAP, rep3

city: Cambridge

first: Elizabeth

middle: A

last: Hemenway

state: MA

address: 455 Main St

institute: Whitehead Institute for Biomedical Research

data_processing:
*library strategy: EM-seq
Data processing was preformed based on the Bismark pipeline (https://felixkrueger.github.io/Bismark/). Reads were trimmed and filtered using Trimgalore using standard settings for phred33 quality control and paired-end Illumina reads. Trimmed reads were then mapped to TAIR10 genome containing the pUC19 methylated control sequence using Bismark alignment. We set the number of mismatches allowed in a seed alignment (--N) to 1 and the maximum insert size (--X) to 600. Bismark deduplicate was used to remove PCR duplicates using default settings. Methylation information was extracted from deduplicated reads using Bismark Methylation Extractor using default settings for paired-end reads. Initial conversion and protection quality checks, and analysis of whole-genome methylation status were performed.
Reads were trimmed and filtered using Trimgalore using standard settings for phred33 quality control and paired-end Illumina reads. Trimmed reads were then mapped to TAIR10 genome containing the pUC19 methylated control sequence using Bismark alignment. We set the number of mismatches allowed in a seed alignment (--N) to 1 and the maximum insert size (--X) to 600. Bismark deduplicate was used to remove PCR duplicates using default settings. Methylation information was extracted from deduplicated reads using Bismark Methylation Extractor using default settings for paired-end reads. Initial conversion and protection quality checks, and analysis of whole-genome methylation status were performed at this stage. Remaining reads that did not map to TAIR10-pUC19 were then mapped to a pseudo-C24 genome and deduplicated. Mapped reads from both mapping runs were assigned to a parent-of-origin using the SNPs identified between Col-0 and C24 by Jiao et al 2020, accounting for C-T or G-A SNPs, using assign_to_allele.py36. Methylation information was then extracted from each parental genome individually using Bismark Methylation Extractor, before combining outputs from the same parental genomes from the two mapping runs.
Assembly: TAIR10/Araport11 annotation, TAIR10-C24 pseudogenome. To facilitate mapping reads from C24 ecotype genomes, we generated a TAIR10 genome with substituted SNPs for the C24 variant (Jiao et al 2020). We then prepared this genome for mapping using Bismark genome preparation with default settings.
Supplementary files format and content: Tab-deliniated .bed files containing position and methylation status for analyzed cytosines in CG, CHG, and CHH sequence contexts. For samples generated by crossing Col-0 and C24 ecotypes for allelic information, there are tab-deliniated .bed files containing position and methylation status for analyzed cytosines in CG, CHG, and CHH sequence contexts that were extracted from mapped reads assigned to Col-0 or C24 using SNPs.

organism: Arabidopsis thaliana

source_name: seed, 7DAP

growth_protocol: Plants for the non-allelic methylation profiling in endosperm and leaf were grown in a Conviron growth chamber at 22 C using 22 hr light/2hr dark cycles with 120 uM fluorescent light. Plants for allele-specific methylation profiling were grown using 16 hr light/8hr dark cycles; set-point for temperature was 22C. The mutants ros1-3 and ros1-3; dml2-1; dml3-1 were originally described in Penterman et al., 2007. The ros1-7 allele was described in Williams et al 2015. In the C24 background, the ros1-1 mutant allele was described in Gong et al 2002 and was obtained from ABRC (CS66099). Genotypes for all plants were PCR-verified.

extract_protocol:
Flowers were emasculated and pollinations were preformed 2 days after emasculation. Seven days after pollination (DAP), seeds were removed from 3-6 siliques and placed into 120 ml of Nuclei Extraction Buffer, available as part of CyStain UV Precise P kit (Partec North America #055002) on ice. Seeds were ground manually using a sterile pestle. 800ul of companion Nuclei Staining Buffer was added to ground seeds, and mixture was filtered 1-2 times through sterile Cell Trics 30um filters and kept on ice. 3C and 6C nuclei were then sorted into 200ul of Buffer ATL from Qiagen QIAamp DNA micro kit (#56304) with BD FACSAria SORP equipped with an 100mW UV laser using a nozzle size = 100 microns, Sheath pressure = 20 psi. 20ul of Proteinase K solution was added to nuclei mixture and incubated overnight at 56C. The next day, remaining steps for QIAamp DNA micro kit were followed, using the tissue protocol. DNA was eluted in 20ul of nuclease-free water and kept at -20C until all samples were prepared. Rosette leaf tissue from 4-week-old plants was collected and ground manually in Nuclei extraction buffer using a razor blade. All following nuclei preparation steps were the same as for seeds. For leaf tissue, 2C and 4C nuclei were collected using the FACSAria conditions described above. DNA extraction steps were the same as for seed nuclei.
To prepare converted libraries for whole-genome sequencing of DNA methylation, we used the EM-seq kit from NEB (#E7120S). 1ul diluted 1:100 pUC19 control DNA per 10-30 ng sample DNA was spiked in as per kit instructions.  Using a Covaris, DNA samples for the non-allelic seed and leaf were sheared in 130ul of 1x TE buffer, 6x16mm tubed using conditions: [Peak power = 175 W, Duty factor = 10% Cycles/burst = 200 Time = 180 sec]. TE buffer was then exchanged for 50 ul nuclease free water using a 1X Ampure bead clean up before continuing the EM-seq protocol. Conditions were later optimized, and for the allelic endosperm experiments DNA was sheared in 50ul of 1x TE buffer, 6x16mm tubes under conditions [Peak power = 175W Duty factor = 10% Cycles/burst = 200 Time = 80 sec]. All remaining library prep steps were then performed as written in the EM-seq manual; we used 7-8 cycles of PCR amplification to amplify libraries. Libraries were pooled at approximately equimolar using library quantity quantified from Fragment Analyzer readouts prior to a final bead clean-up of remaining adapter fragments, and sequenced on a NovaSeq S4.

value: seed, 7DAP

value: 3C and 6C nuclei, endosperm

value: ros1-3xC24 F1

tag: growth conditions

value: 16hr light, 8hr dark; Set-point 22C, 50% relative humidity


title: NeuN, D13, AA

value: NeuN


title: NeuN, D12, CC

value: CC


title: Liver, Placebo, d28, patient 363

value: day 28

value: Placebo


title: NeuN, D11, CC


title: endosperm, ros1-3xC24, 7DAP, rep2


title: NeuN, D9, CC


title: endosperm, ros1-3xC24, 7DAP, rep1


title: NeuN, D10, AA


title: Liver, Placebo, d0, patient 363

value: day 0


title: Liver, Canakinumab, d28, patient 360


title: NeuN, D8, AA


title: NeuN, D7, CC


title: endosperm, C24xros1-3 F1, 7DAP, rep3

value: C24xros1-3 F1


title: NeuN, D6, AA


title: NeuN, D5, CC


title: Liver, Canakinumab, d0, patient 360


title: endosperm, C24xros1-3 F1, 7DAP, rep2


title: Liver, Placebo, d0, patient 358


title: Liver, Placebo, d28, patient 358


title: NeuN, D4, CC


title: NeuN, D3, CC


title: endosperm, ros1-1xros1-3 F1, 7DAP, rep2

value: ros1-1xros1-3 F1

value: 16hr light, 8hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: endosperm, ros1-1xros1-3 F1, 7DAP, rep3


title: NeuN, D2, CC


title: endosperm, C24xros1-3 F1, 7DAP, rep1


title: Liver, Canakinumab, d28, patient 355

value: Canakinumab


title: endosperm, ros1-1xros1-3 F1, 7DAP, rep1


title: Liver, Canakinumab, d0, patient 355


title: NeuN, D1, AA


title: endosperm, ros1-3xros1-1 F1, 7DAP, rep3

value: ros1-3xros1-1 F1


title: PL05

city: PARIS

first: Juliette

last: LEON

address: 149 rue de Sèvres

country: France

institute: APHP

description: fromFFPE, three sections of approximately 20 μm for each sample were deparaffinized and the mRNA was extracted using a column according to the manufacturer’s instructions (RNeasy FFPE kit, Qiagen®). The total mRNA from each sample was then hybridized with the nCounter Banff Human Organ Transplant panel (B-HOT, NanoString Technologies, Seattle, WA, USA), which evaluates mRNA expression of 758 target genes, covering core pathways associated with innate and adaptive immunity, as well as rejection in solid organ transplants

data_processing: The raw data files (.rcc files) were processed through RStudio via the NanoTube R package (https://www.bioconductor.org/packages/NanoTube/ <https://www.bioconductor.org/packages/NanoTube/>) for positive control normalization, background correction, and housekeeping normalization, in order to get the normalized read counts table.

source_name: placenta

extract_protocol: Three sections of approximately 20 μm for each FFPE sample were deparaffinized and the mRNA was extracted using a column according to the manufacturer’s instructions (RNeasy FFPE kit, Qiagen®).

value: PLACENTA

tag: status

value: Control

tag: experimental batch

tag: age at event years

tag: term issue

tag: grade ihc

tag: tissue preparation

value: FFPE


title: PL06

hyb_protocol: The total mRNA from each sample was then hybridized with the nCounter Banff Human Organ Transplant panel (B-HOT, NanoString Technologies, Seattle, WA, USA), which evaluates mRNA expression of 758 target genes, covering core pathways associated with innate and adaptive immunity, as well as rejection in solid organ transplants

tag: tissue


title: PL04

label_protocol: nCounter Banff Human Organ Transplant panel (B-HOT, NanoString Technologies, Seattle, WA, USA)


title: PL07


title: Liver, Placebo, d28, patient 341

value: liver

tag: treatment


title: PL03


title: endosperm, ros1-3xros1-1 F1, 7DAP, rep2

value: seed, 7DAP

tag: cell type

value: 3C and 6C nuclei, endosperm


title: Liver, Placebo, d0, patient 341


title: PDX1_Eltanexor2

city: Halle

first: Razif

last: Gabdoulline

state: Sachsen-Anhalt

address: Ernst-Grube-Straße 40

department: Innere Medizin IV Haematologie und Onkologie

institute: Universitätsklinikum Halle

data_processing:
Sequencing quality check with MultiQC (passed)
Alignment with STAR version 2.7.10b
Feature count/Read summarisation with Rsubread on Homo_sapiens.GRCh38.79.gtf
Zero count features removed; other than protein_coding features removed
Count-per-million (CPM) values were normalized using trimmed mean of M-values (TMM) method
Assembly: hg38
Supplementary files format and content: Excel worksheet with gene expression values (TMM normalised CPM, log2 transformed) on columns for all samples

source_name: bone marrow

growth_protocol: FKH-1 cells were grown in vitro in RPM1 supplemented with 20% FCS. PDX cells were freshly isolated from mice bone marrow

extract_protocol:
Rneasy mini kit (Qiagen)
Illumina

treatment_protocol: Treatment was carried out for the FKH-1 cell line in vitro, with vehicle (DMSO) and 400 nM of eltanexor for 24h. PDX1 mice were treated with vehicle (1% Tween-80, 0.5% methyl cellulose and water) or eltanexor 12.5 mg/kg daily for 11 days

tag: cell line

value: Human CD45+ cells from bone marrow of PDX mouse

tag: genotype

value: 11 days

value: bone marrow


title: Liver, Canakinumab, d28, patient 332

value: day 28


title: PDX1_Vehicle2


title: endosperm, C24xCol F1, 7DAP, rep3

value: C24xCol-0 F1


title: PL20

value: Case


title: PDX1_Vehicle1


title: endosperm, ros1-3xros1-1 F1, 7DAP, rep1


title: PL21


title: endosperm, C24xCol F1, 7DAP, rep2


title: Liver, Canakinumab, d0, patient 332

value: day 0


title: Liver, Canakinumab, d28, patient 313


title: PL19


title: FKH-1_eltanexor400nM_c

value: acute myelocytic leukemia

value: wt

value: eltanexor


title: endosperm, C24xCol F1, 7DAP, rep1

value: 16hr light, 8hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: FKH-1_eltanexor400nM_b


title: PL18

value: PLACENTA


title: Liver, Canakinumab, d0, patient 313

value: Canakinumab


title: PL17

value: FFPE


title: PDX1_Eltanexor1


title: FKH-1_eltanexor400nM_a


title: FKH-1_DMSO-c

value: DMSO


title: Liver, Placebo, d28, patient 311

value: liver

value: Placebo


title: endosperm, ColxC24 F1, 7DAP, rep3

value: seed, 7DAP

value: 3C and 6C nuclei, endosperm

value: Col-0xC24 F1


title: endosperm, ColxC24 F1, 7DAP, rep2


title: PL16


title: Liver, Canakinumab, d28, patient 310

value: day 28


title: endosperm, ColxC24 F1, 7DAP, rep1


title: FKH-1_DMSO-b


title: endosperm, ros1-1, 7DAP, rep3


title: PL15


title: endosperm, ros1-1, 7DAP, rep2


title: PL12


title: FKH-1_DMSO-a


title: Patient11B, scRNA-seq

city: Houston

first: Hussein

last: Abbas

state: Texas

address: 1515 Holcombe Blvd

institute: The University of Texas at MD Anderson Cancer cent

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq data were demultiplexed and aligned and read count matrix was generated using the Cell Ranger Single Cell Software Suite provided by 10x Genomics. The Seurat v4 (version 4.2.1) R package77 was used to analyze the scRNA-seq data.
Genes detected in fewer than 3 cells and cells with fewer than 250 genes, or 500 transcripts were excluded from subsequent analysis. Cells with more than 10% of reads mapping to mitochondrial genes were removed as well.
Possible doublets were identified and removed
Batch effects were removed using the Harmony package
Assembly: GRCh38
Supplementary files format and content: Seurat object with expression matrix and metadata

source_name: Bone Marrow

extract_protocol:
Samples were freshly frozen with freezing medium containing 20% fetal calf serum (FCS) and 10% dimethyl sulfoxide (DMSO) in Dulbecco’s modified Eagle medium (DMEM) and stored in liquid nitrogen. All frozen BM samples were retrieved immediately before sample processing. To maximize the recovery of the cellular viability, samples were processed in batches according to a thawing protocol.
The 5’ gene expression libraries were prepared using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 5′ V5.1 reagent kits (10x Genomics).

value: Bone Marrow

value: Hematopoietic

value: Aza+Ven+Margo


title: endosperm, ros1-1, 7DAP, rep1


title: Patient11A, scRNA-seq

value: Pre-treatment


title: PL11

value: Case


title: PL10


title: endosperm, C24, 7DAP, rep3

value: C24 wild-type


title: Patient10C, scRNA-seq


title: PL09


title: Liver, Placebo, d0, patient 307

value: day 0


title: PL08

value: PLACENTA


title: endosperm, C24, 7DAP, rep2

value: 16hr light, 8hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: Liver, Placebo, d0, patient 311


title: Patient10B, scRNA-seq


title: Liver, Placebo, d0, patient 303


title: vcDNA_76509_75569_C_2

city: Shenzhen

first: SHAO

middle: MIN

last: YANG

state: guangdong

address: Nanshan

department: Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center

institute: Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine

data_processing:
Gene expression quantification: After removing low-quality, adapter-polluted, and high content of unknown base (N) read, the clean reads data were aligned to the human genome hg38 using STAR. The counts of mapped reads for each gene were calculated using FeatureCounts from the sorted BAM files.
Assembly: hg38
Supplementary files format and content: counts

extract_protocol: RNA samples were used for library preparation and subsequently sequenced using BGI DNBseq platform in PE150

treatment_protocol: HEK293T cells were seeded at a density of 10^6 in 12-well plate and than transfected with 1μg vcDNA


title: vcDNA_76509_75569_C_3


title: Liver, Canakinumab, d28, patient 302

value: Canakinumab


title: endosperm, C24, 7DAP, rep1


title: Liver, Canakinumab, d0, patient 310


title: leaf, ros1-7, rep3

source_name: young leaf

value: young leaf

value: 2C and 4C nuclei

value: 22hr light, 2hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: vcDNA_76509_75569_C_1


title: Liver, Placebo, d28, patient 307

value: liver

value: Placebo


title: Patient10A, scRNA-seq


title: vcDNA_76509_75569_L_3

value: VZV linear 75569-76509 DNA


title: Liver, Placebo, d28, patient 180

value: day 28


title: leaf, ros1-7, rep2


title: Patient9B, scRNA-seq

value: Bone Marrow


title: Patient9A, scRNA-seq

value: Hematopoietic


title: Liver, Canakinumab, d0, patient 302


title: leaf, ros1-7, rep1


title: Liver, Placebo, d28, patient 303


title: vcDNA_76509_75569_L_2


title: vcDNA_76509_75569_L_1


title: Patient8B, scRNA-seq

value: Aza+Ven+Margo


title: leaf, ros1-3, rep3


title: Liver, Canakinumab, d28, patient 179


title: Liver, Placebo, d0, patient 180


title: Patient8A, scRNA-seq

value: Pre-treatment


title: Liver, Canakinumab, d0, patient 179


title: GFP_CMV_C1_3

value: Circular GFP_CMV DNA


title: Patient7C, scRNA-seq


title: leaf, ros1-3, rep2


title: Liver, Placebo, d28, patient 1672


title: GFP_CMV_C1_2


title: GFP_CMV_C1_1


title: Patient7B, scRNA-seq


title: Liver, Placebo, d0, patient 1672


title: Patient7A, scRNA-seq


title: leaf, Col-0, rep2

value: Col-0 wild-type


title: GFP_CMV_L_3

value: Linear GFP_CMV DNA


title: leaf, Col-0, rep3


title: Liver, Placebo, d28, patient 156


title: Patient6B, scRNA-seq


title: leaf, Col-0, rep1


title: GFP_CMV_L_2


title: endosperm, rdd, 7DAP, rep3

value: seed, 7DAP

value: 3C and 6C nuclei, endosperm


title: Liver, Canakinumab, d28, patient 146

value: Canakinumab


title: Patient5B, scRNA-seq


title: GFP_CMV_L_1


title: endosperm, rdd, 7DAP, rep2


title: Control_3

value: Control


title: Liver, Canakinumab, d0, patient 146

value: day 0


title: Control_2


title: Liver, Placebo, d28, patient 133


title: Patient4C, scRNA-seq


title: endosperm, ros1-7, 7DAP, rep3

value: 22hr light, 2hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: Control_1


title: leaf, ros1-3, rep1

value: young leaf

value: 2C and 4C nuclei


title: Patient5A, scRNA-seq


title: endosperm, rdd, 7DAP, rep1


title: Liver, Placebo, d0, patient 133

value: liver

value: Placebo


title: Liver, Placebo, d28, patient 116

value: day 28


title: Patient4A, scRNA-seq

value: Bone Marrow

value: Hematopoietic


title: endosperm, ros1-7, 7DAP, rep2


title: endosperm, ros1-7, 7DAP, rep1


title: Liver, Placebo, d0, patient 156


title: Patient6A, scRNA-seq

value: Pre-treatment


title: Patient4B, scRNA-seq

value: Aza+Ven+Margo


title: Patient3C, scRNA-seq


title: Liver, Placebo, d0, patient 116


title: Liver, Placebo, d28, patient 1143


title: Patient3B, scRNA-seq


title: endosperm, ros1-3, 7DAP, rep3


title: Patient3A, scRNA-seq


title: endosperm, ros1-3, 7DAP, rep2


title: Liver, Placebo, d0, patient 1143


title: endosperm, ros1-3, 7DAP, rep1


title: Patient2B, scRNA-seq


title: endosperm, Col-0, 7DAP, rep3

value: Col-0 wild-type


title: Liver, Placebo, d0, patient 108


title: Patient2A, scRNA-seq


title: endosperm, Col-0, 7DAP, rep2


title: Liver, Placebo, d28, patient 1077


title: Patient1C, scRNA-seq


title: Patient1B, scRNA-seq


title: Patient1A, scRNA-seq


title: MI_NOC_NO_rep5

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

data_processing:
The fastq files were aligned on the UCSC rn6 genome using STAR (2.7.1a) [PMID:23104886] to produce bam files.
Bam files were counted using HTSeq framework (0.11.2) [PMID:25260700] with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none
Normalization and differential analysis were performed using the R software [R Core Team. R: A language and environment for statistical computing. Vienna, Austria : R Foundation for Statistical Computing, 2017], DESeq2 (1.22.2) [PMID:20979621, PMID:25516281] and SARTools [PMID:27280887] packages.
Assembly: rn6
Supplementary files format and content: fastq,counts

organism: Rattus norvegicus

source_name: Heart / Left ventricle

extract_protocol:
After euthanasia, heart were rinced in PBS, and snap-frozen. Total mRNA from remote areas were extracted from crushed snap-frozen heart tissue using Tri-Reagent RNA isolation reagent (Sigma Aldrich). RNA quality was monitored for quality control using Agilent Bioanalyzer Nano RNA chip and Nanodrop absorbance ratios of 260/280 nm and 260/230 nm.
Library construction was performed according to the Illumina kit protocol (TruSeq stranded mRNA sample preparation). mRNA was enriched using oligo dT magnetic beads and chemically fragmented. The libraries were validated by qPCR and sized by Agilent Bioanalyzer DNA high sensitivity chip. The concentrations for the libraries were normalized and then multiplexed together. The concentration used for clustering the flowcell SP was 300 pM. The multiplexed libraries were sequenced on one lane using single-end 100 cycle chemistry for the NovaSeq 6000 (Illumina).

treatment_protocol: Following a left thoracotomy, left middle cervical and stellate ganglion were removed, then the pericardium was dissected, and the left anterior coronary artery was ligated using a non-absorbable braided silk suture. Sham-operated rats were subjected to the same surgical procedure, except for the CSD. Echocardiography (2D, B and M-mode) was performed 3 days after surgery to confirm MI and exclude animals with limited reduction of left ventricle (LV) ejection fraction (> 45%). Rats were randomly exposed to intermittent hypoxia (IH) or normoxia (N) for 14 weeks. Randomization was adjusted to form homogeneous groups based on baseline ejection fraction. Animals were exposed daily to 8 consecutive hours of IH or N during their daytime sleep period. The IH stimulus was performed using a specifically designed device (HypE platform Grenoble), with alternating 30 s of hypoxia (5% fraction of inspired O2 (FiO2)) and 30 s of normoxia (21% FiO2). Normoxic rats were exposed to similar air streams to reproduce equivalent levels of noise and turbulence related to gas circulation.

value: Heart / Left ventricle

tag: exposure

value: Normoxia

tag: surgery

value: Myocardial Infarction + Sham

value: wistar rat (RjHan:WI)


title: Liver, Canakinumab, d0, patient 106

tag: time

value: Canakinumab


title: MI_NOC_NO_rep4


title: WT Lig5 D10 ligature model

city: Iowa City

first: Shaoping

last: Zhang

address: 801 Newton Rd

department: Periodontics, College of Dentistry

institute: University of Iowa

description:
Library name: WT_Lig5
10x Genomics

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the homo sapiens reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: hg38
Supplementary files format and content: Gene expression text file includes raw counts and FPKM values for each Sample

source_name: Gingiva tissues

extract_protocol:
RNA was isolated with a miRNeasy minikit (QIAgen) from the mouse gingiva where the ligature was placed. Then the RNA was quantified using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

value: Gingiva tissues

value: WT

value: Ligature model (Day 10)

tag: batch


title: Liver, Placebo, d28, patient 108


title: MI_NOC_NO_rep3


title: blood_PRYA301

city: Los Angeles

first: Suhas

middle: G

last: Kallapur

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
For each sample 100 ng of total RNA were used for library preparation with the Illumina RNA Prep with Enrichment (L) Tagmentation kit (Illumina, cat # 20040536) following manufacturer’s instructions. Briefly, after the first and second strand cDNA synthesis, double-stranded DNA was subject to tagmentation, where the Transposomes simultaneously tagmented and added adapters to the double-stranded cDNA. After tagmentation, the fragments were purified and amplified to add index adapter sequences (IDT for Illumina DNA/RNA UD Indexes Set B, cat # 20027214) for dual indexing and P7 and P5 sequences for clustering. 200 ng of library were hybridized to enrichment oligos (Illumina Exome Panel cat # 20020183) with an overnight incubation at 58°C. The enriched libraries were amplified with 14 PCR cycles and cleaned up with Agencourt AMPure XP beads (Beckman Coulter cat # A63880). The libraries quality control was performed using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, cat # Q32850) and the Agilent D1000 ScreenTape assay (Agilent, cat # 5067-5582).
Demultiplexed .fastq files were trimmed using fastp (v0.23.1) with the following options: -w 8 -l 30 --trim_front1 10 --trim_front2 10, and specifying the Nextera adapter (CTGTCTCTTATACACATCT), followed by alignment to the human genome (GRCh38) and gene counts (to the Homo sapiens GRCh38.p10 gtf annotation) using STAR (2.7.9a) with default options. Counts were processed with DESeq2 (v1.40.2) to determine the differentially expressed genes (abs(log2FC) > 1 and adjusted p-value <0.05), with the following design formula: ~ Labor + Delivery + GestWeek + COVID19_positivity. Principal Component Analysis was performed using PCAtools (v2.12.0), correlation with the rcorr function in the Hmisc package (v5.1-0) and RcmdrMisc package (v2.7-2). Plots were generated in R with ggplot2 (v3.4.2) or ggpubr (v0.6.0), while volcano plots were generated using the R package EnhancedVolcano (v1.18.0).
Assembly: Homo sapiens GRCh38
Supplementary files format and content: raw counts matrix for blood samples obtained with STAR RNA --quantMode GeneCounts option. Tab-separated values.
Supplementary files format and content: raw counts matrix for placenta samples obtained with STAR RNA --quantMode GeneCounts option. Tab-separated values.

source_name: whole blood

extract_protocol:
Total RNA was extracted from placenta samples using the Qiagen Rneasy Mini kit cat #74104 and from blood samples using the Ribo kit Invitrogen AM1928
For each sample 100 ng of total RNA were used for library preparation with the Illumina RNA Prep with Enrichment (L) Tagmentation kit (Illumina, cat # 20040536) following manufacturer’s instructions. Briefly, after the first and second strand cDNA synthesis, double-stranded DNA was subject to tagmentation, where the Transposomes simultaneously tagmented and added adapters to the double-stranded cDNA. After tagmentation, the fragments were purified and amplified to add index adapter sequences (IDT for Illumina DNA/RNA UD Indexes Set B, cat # 20027214) for dual indexing and P7 and P5 sequences for clustering. 200 ng of library were hybridized to enrichment oligos (Illumina Exome Panel cat # 20020183) with an overnight incubation at 58°C. The enriched libraries were amplified with 14 PCR cycles and cleaned up with Agencourt AMPure XP beads (Beckman Coulter cat # A63880). The libraries quality control was performed using the Qubit dsDNA BR assay kit (Thermo Fisher Scientific, cat # Q32850) and the Agilent D1000 ScreenTape assay (Agilent, cat # 5067-5582). The libraries were pooled after quality control followed by sequencing on a NovaSeq 6000 SP lane as paired-end 100 bases.

treatment_protocol: Samples were preserved in RNA later solution right after delivery

value: whole blood

value: blood cells

tag: patient

value: control


title: WT Lig4 D10 ligature model

description:
Library name: WT_Lig4
10x Genomics


title: blood_PRYA298


title: Liver, Canakinumab, d0, patient 1029

value: liver

value: day 0


title: Liver, Placebo, d28, patient 1023

value: day 28

value: Placebo


title: blood_PRYA297


title: N.vSTING, biological rep3

city: Hangzhou

first: Meng

last: Lou

address: 88 Jiefang Road, The Second Affiliated Hospital, School of Medicine

institute: Zhejiang University

description: Gene expression data from up-regulated genes activated by H.s STING ΔCTT and N.v STING in HEK293T cells

hyb_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols (Shanghai OE Biotech Co., Ltd). Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray.

data_processing: After washing and staining, the arrays were scanned by the Affymetrix Scanner 3000(Affymetrix) by Shanghai OE Biotech Co., Ltd.Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis. Then the gene expression analysis and alternative splice analysis proceeded separately.

source_name: HEK293T cells

growth_protocol: HEK293T (CRL-3216, ATCC) cells were cultured in Dulbecco's modified Eagle’s medium (DMEM) with 10% fetal bovine serum and maintained at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol: Total RNAs was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNAs integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies) by Shanghai OE Biotech Co., Ltd.

treatment_protocol: HEK293T cells were transfected cGAS with H.sSTING ΔCTT or N.vSTING or its control vector. 20 h later, samples were prepared by Shanghai OE Biotech Co., Ltd.

tag: cells

value: HEK293T cells were transfected cGAS with N.vSTING


title: H.sSTING ΔCTT, biological rep2

scan_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols (Shanghai OE Biotech Co., Ltd). Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray.

value: HEK293T cells were transfected cGAS with H.sSTING ΔCTT


title: Liver, Placebo, d0, patient 1077


title: endosperm, Col-0, 7DAP, rep1

value: seed, 7DAP

value: 3C and 6C nuclei, endosperm

value: Col-0 wild-type

tag: growth conditions

value: 22hr light, 2hr dark; 120 uM fluor light; Set-point 22C, 50% relative humidity


title: H.sSTING ΔCTT, biological rep3

label_protocol: The sample labeling, microarray hybridization and washing were performed based on the manufacturer’s standard protocols (Shanghai OE Biotech Co., Ltd). Briefly, total RNAs were transcribed to double strand cDNAs and then synthesized cRNAs. Next, 2nd cycle cDNAs were synthesized from cRNAs. Followed fragmentation and biotin labeling, the 2nd cycle cDNAs were hybridized onto the microarray.


title: MI_NOC_NO_rep1

value: Heart / Left ventricle

value: Normoxia

value: Myocardial Infarction + Sham

value: wistar rat (RjHan:WI)


title: Empty vector as control, biological rep1

value: HEK293T cells were transfected cGAS with control vector


title: N.vSTING, biological rep1


title: N.vSTING, biological rep2


title: H.sSTING ΔCTT, biological rep1


title: Empty vector as control, biological rep2


title: WT Lig2 D10 ligature model

description:
Library name: WT_Lig2
10x Genomics

value: Gingiva tissues

value: WT

value: Ligature model (Day 10)


title: Liver, Placebo, d0, patient 1023

value: liver

value: day 0


title: Liver, Canakinumab, d28, patient 1029

value: day 28

value: Canakinumab


title: Empty vector as control, biological rep3


title: MI_NOC_IH_rep5

value: Intermittent Hypoxia


title: blood_PRYA290

value: whole blood

value: blood cells

value: control


title: Liver, Placebo, d28, patient 1019

value: Placebo


title: MI_NOC_IH_rep4

value: Heart / Left ventricle


title: IFNAR1 KO Lig5 D10 ligature model

description:
Library name: Ifnar1KO_Lig5
10x Genomics

value: IFNAR1 KO


title: blood_PRYA286


title: WT Lig1 D10 ligature model

description:
Library name: WT_Lig1
10x Genomics


title: MI_NOC_NO_rep2

value: Normoxia

value: Myocardial Infarction + Sham


title: IFNAR1 KO Lig4 D10 ligature model

description:
Library name: Ifnar1KO_Lig4
10x Genomics


title: VL-17A cells, ethanol treated, rep 4

growth_protocol: VL-17A cells were cultured in VL-17A complete media: Dulbecco’s modified Eagle medium (DMEM), high glucose, GlutaMAX™ Supplement, pyruvate (Thermo Fisher Scientific) supplemented with 10% Fetal Calf Serum (FCS; Life Technologies), 50 µg/ml Gentamicin (Gibco), 1% Penicillin/Streptomycin (Invitrogen), 400 µg/mL zeocin (Thermo Fisher Scientific) and 400 µg/mL geneticin (Gibco).

extract_protocol:
Cells were collected at the end of the experiment in RLT buffer (Qiagen) for RNA extraction. RNA was extracted using RNeasy mini kit (Qiagen) following manufacturer's instructions. DNase treatment was performed to remove genomic DNA.
Libraries were prepared from 500ng of each total-RNA sample using the NEBNEXT Ultra II Directional RNA Library Prep kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the provided protocol. Poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads. Following purification, the mRNA was fragmented using divalent cations under elevated temperature and primed with random hexamers. Primed RNA fragments were reverse transcribed into first strand cDNA using reverse transcriptase and random primers. RNA templates were removed and a replacement strand synthesised incorporating dUTP in place of dTTP to generate ds cDNA. AMPure XP beads (Beckman Coulter, #A63881) were used to separate the ds cDNA from the second strand reaction mix, providing blunt-ended cDNA. Multiple indexing adapters were then ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 10 cycles of PCR were used to selectively enrich DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing. Libraries were purified using AMPure XP beads, quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with DNA HS Kit (#5067-4626).

treatment_protocol: When cells were cultured in the presence of ethanol, 25mM of HEPES (Life Technologies) was added to the VL-17A complete media. Cells were cultured in 25 cm2 flasks, in VL-17A complete media containing 0.5% FCS in the presence/absence of ethanol (VWR chemicals, 437433T) at 100 mM for 48 hours. Flasks were paraffin wrapped to minimise ethanol evaporation.

value: modified human hepatocellular HepG2 cells

value: EtOH


title: MI_NOC_IH_rep2

value: wistar rat (RjHan:WI)


title: WT Lig3 D10 ligature model

description:
Library name: WT_Lig3
10x Genomics

value: Gingiva tissues

value: WT

value: Ligature model (Day 10)


title: blood_PRYA141

value: asymptomatic COVID-19


title: MI_NOC_IH_rep1


title: IFNAR1 KO Lig1 D10 ligature model

description:
Library name: Ifnar1KO_Lig1
10x Genomics


title: VL-17A cells, ethanol treated, rep 1


title: blood_PRYA288


title: MI_CSD_NO_rep5

value: Myocardial Infarction + Cardiac Sympathetic Denervation


title: MI_CSD_NO_rep4


title: VL-17A cells, control, rep 4

value: Ctrl


title: Liver, Placebo, d0, patient 1019

value: liver

value: day 0


title: IFNAR1 KO Lig3 D10 ligature model

description:
Library name: Ifnar1KO_Lig3
10x Genomics


title: VL-17A cells, ethanol treated, rep 3


title: blood_PRYA190

value: whole blood

value: blood cells

value: mild/moderate COVID-19


title: VL-17A cells, control, rep 3


title: VL-17A cells, control, rep 2


title: MI_NOC_IH_rep3

value: Heart / Left ventricle

value: Intermittent Hypoxia


title: blood_PRYA146


title: WT D3 ligature model

description:
Library name: WTS1
10x Genomics

data_processing:
Illumina NovaSeq 6000 was used for basecalling. CellRanger software package (v7.1.0) used for demultiplexing, barcoded processing, alignmentm and filtering prior to post processing with Seurat in R.
Assembly: mm10
Supplementary files format and content: 1) barcodes file (.tsv.gz); 2) features.tsv; 3) matrix.mtx

source_name: Gingival tissue

extract_protocol:
3 days after ligature placement, the gingival tissue was harvested and incubated with RPMI 1640 medium containing 0.15 mg/ml DNase and 3.2 mg/ml type IV collagenase for 25 minutes at 37°C in a shaker. 0.5M EDTA (pH8) was added to the suspension to stop the enzymatic digestion. After homogenization, the dissociated suspension was passed through a 70mm cell strainer, washed, and incubated with an anti-mouse CD45 antibody-Alexa Fluor 700 for half an hour. After washing, Hoechst was added to the cell suspension. Then, live CD45+ cells were immediately sorted by a Cytek Aurora CS cells sorter and counted under a microscope. Samples with a viability above 85% and more than 990 live cells/µl were proceeded with scRAN-seq.
Library was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Reagent Kits v3.1 protocol, 10X genomics) Briefly, sorted CD45+ gingival cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse-transcribed to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10X Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified with PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Ligature was placed between the first and second maxillary molars of wildtype and Ifnar1 knockout mice for 3 days.

value: Gingival tissue

value: Ligature model (Day 3)


title: blood_PRYA187


title: MI_CSD_NO_rep1

value: Normoxia


title: VL-17A cells, control, rep 1

value: modified human hepatocellular HepG2 cells


title: IFNAR1 KO Lig2 D10 ligature model

description:
Library name: Ifnar1KO_Lig2
10x Genomics

value: Gingiva tissues

value: IFNAR1 KO


title: blood_PRYA2000


title: VL-17A cells, ethanol treated, rep 2

value: EtOH


title: MI_CSD_IH_rep5

value: wistar rat (RjHan:WI)


title: blood_PRYA175-1

value: critical/severe COVID-19


title: Mouse lung tissue, LPS, 48hr

city: Seoul

first: dongryul

last: oh

address: Samsung Medical Center

country: South Korea

institute: Department of Radiation Oncology

description:
Library name: LPS
10× Genomics

data_processing:
Sequencing data were processed using CellRanger version 7 and aligned to the mouse reference genome (mm10). R version 4.2.2 and Seurat Version 4.3.0 were used to process CellRanger output files. Cells with less than 250 or more than 2500 expressed genes were removed, and doublets were removed using DoubletFinder.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: Cellranger output file: barcodes.tsv,features.tsv, matrix.mtx, Raw data file:fastq

source_name: Lung

extract_protocol:
Mouse lung tissues were isolated and digested using a gentleMACSTM Dissociator and MACS Lung Dissociation Kit (Miltenyi Biotec, Gladbach, Germany). To separate mononuclear cells, the dissociated lung cells were slowly added to Ficoll-Paque™ PREMIUM 1.084 sterile solution (Cytiva, Wilmington, DE, USA) (Ficoll: cells = 3:4 mL). The solution was centrifuged at 400× g for 30 min (20 ℃, decel = 0), the intermediate zone (layer between Ficoll and plasma) was collected and DMEM (Gibco, Thermo Fisher Scientific, Waltham, MA, USA) was added. The solution was centrifuged at 400× g for 5 min (25 ℃, decel = 9), the supernatant was removed, and the cells were resuspended in PBS.
Mouse cell samples were prepared for scRNA-seq using the Chromium Single-Cell 3′ Reagent version 3.1 kit (PN 1000121) and Chromium Single-Cell Controller (10× Genomics, Pleasanton, CA, USA). Subsequently, the cells were loaded onto a Single-Cell G Chip (PN 1000127) for gel bead-in-emulsion generation and barcoding, targeting a recovery of 10,000 cells per sample. Reverse transcription, clean-up, and cDNA amplification were performed to isolate and amplify cDNA or a ligated sequencing adaptor for Illumina library construction, according to the manufacturer’s protocol. The libraries were constructed using the Chromium Single-Cell 3′ reagent kit v3.1 (PN 1000121), 3′ Library Construction Kit (PN-1000157) according to the manufacturer’s protocol. For sequencing, the library concentration was assessed using a Qubit 2.0 Fluorometer and dsDNA HS Assay Kit (Thermo Fisher Scientific) according to the manufacturer’s protocol. Single-Cell 3′ gene expression libraries were run on an Illumina NovaSeq 6000 system with 2×100 bp read length.

treatment_protocol: Mice were then intratracheally injected with 100 μL phosphate-buffered saline (PBS) or 200 μg LPS (extracted from E. coli O55:B5, Sigma-Aldrich, St. Louis, MO, USA) per mouse using a 22-gauge catheter. Additionally, 0.4 mL air was injected to evenly spread the solution throughout the lungs. The day after intratracheal injection, the mice were anesthetized and irradiated with 1 Gy X-rays using a VitalBeam linear accelerator (Varian Medical Systems, Palo Alto, CA, USA). To avoid radiation exposure of other vital organs, the thorax of each mouse was placed inside a radiation field. 6 MV X-ray beams were delivered at 4 Gy/min with a source-to-surface distance of 100 cm.

value: Lung

value: tissue cell

tag: strain

value: WT

tag: Sex

value: male

tag: age

value: 6-7 weeks

value: LPS


title: Mouse lung tissue, PBS, 48hr, LDRT 24hr

description:
Library name: PBS+RT
10× Genomics

value: PBS, LDRT


title: MI_CSD_IH_rep4

value: Heart / Left ventricle

value: Intermittent Hypoxia

value: Myocardial Infarction + Cardiac Sympathetic Denervation


title: MTBVAC CellSurfaceProtein

city: Madrid

first: Álvaro

middle: Fernando

last: García-Jiménez

state: Madrid

address: Darwin st, 3

department: Immunology and Oncology

country: Spain

institute: CNB-CSIC

description: SC5P-R2 with sample multiplexing

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2
Sequence read quality was evaluated from FastQC
Human Total-Seq C Hashtag antibodies [1, 2 and 3] (Biolegend) were used for individual multiplexing
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
After co-culture of PBMCs with MTBVAC, for 7 days in RPMI complete medium, high viability single-cell suspensions were obtained using the Dead Cell Remove Kit (Miltenyi Biotec), and cells were pooled and resuspended in PBS + 0.04% BSA prior to sequencing
Library was generated according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). PBMCs were resuspended in the master mix and loaded together with partitioning oil and gel beads to generate partitioned cells (GEMs, Gel beads-in-Emulsion). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, incorporating an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: PBMCs were cultured in vitro with MTBVAC vaccine, and then plated in 96-well U bottom plates during 7 days

value: Blood

value: PBMCs

value: MTBVAC


title: MI_CSD_NO_rep3

value: Normoxia


title: IFNAR1 KO D3 ligature model

description:
Library name: IFNKOS1
10x Genomics

value: Gingival tissue

value: IFNAR1 KO

value: Ligature model (Day 3)


title: blood_PRYA110/YA248

value: whole blood

value: blood cells

value: control


title: Mouse lung tissue, PBS, 48hr

description:
Library name: PBS
10× Genomics

value: Lung

value: tissue cell

value: WT

value: male

value: PBS


title: MTBVAC GeneExpression

description: SC5P-R2 with sample multiplexing


title: MI_CSD_NO_rep2

value: Heart / Left ventricle

value: wistar rat (RjHan:WI)


title: blood_PRYA148

value: asymptomatic COVID-19


title: Mouse lung tissue, LPS, 48hr, LDRT 24hr

description:
Library name: LPS+RT
10× Genomics

value: 6-7 weeks

value: LPS , LDRT


title: MI_CSD_IH_rep2

value: Intermittent Hypoxia

value: Myocardial Infarction + Cardiac Sympathetic Denervation


title: blood_PRYA207

value: mild/moderate COVID-19


title: blood_PRYA211


title: RBM25_Mut5

city: Cleveland

first: Soon Yeul

last: Yi

state: OH

address: CWRU Wood Research Building W127A, 2109 Adelbert Rd,

department: Biochemistry

institute: Case Western Reserve University

description: Library name: RBM25_Mut5

data_processing:
Raw fastq files were used as an input for CLIPittyClip processing pipeline (PMID: 38658162)
Assembly: GRCh38. p14
Supplementary files format and content: tab-delimited text file containing peak coordinates
Library strategy: CLIP-seq

growth_protocol: HEK293 cell lines were grown and maintained at 37'C in DMEM media containing 5% FBS and 1% NEAA.

extract_protocol:
Cell pellets were lysed with PBS lysis buffer (1x PBS, 0.1% SDS, 0.5% NaDoc, 0.5% NP-40, 1 protease inhibitor tablet (Roche)) for 10 minutes on ice. Lysate was then treated with RQ1 DNase (Promega) for 5 minutes at 37'C with shaking at 1100RPM.  The lysates were then briefly treated with RNase I at 1:100 or 1:5000 dilutions at the same condition as DNase treatment. Lysates were clarified by centrifuging on tabletop 4'C centrifuge for 10 minutes. V5 IP was performed overnight at 4'C with nutation. Immunoprecipitated samples were labeled with radioactivity (gamma-32P-ATP (Revity)) and ran on SDS-PAGE. The SDS-PAGE was run in non-reducing conditions for hnRNPC and in reducing conditions for RBM25. The gels were transferred to a nitrocellulose membrane, and bands 10-30kDa above the hnRNPC (32kDa) and RBM25 (100kDa) were excised. The excised membranes were treated with proteinase K (Roche) to release the protein-bound RNAs from the membrane.
CLIP footprints were reverse-transcribed using the BrdU incorporation and bead-capture strategy described previously (PMID: 24613350).

treatment_protocol: Expression of the exogenous proteins were induced by treating the cells with 1mg/mL doxycycline for 24 hours. Then, cellular media was replaced with ice-cold PBS for crosslinking using 254nm UV light, on ice, for a dose of 400mJ/cm^2 and a dose of 200mJ/cm^2. Samples were scraped into tubes, centrifuged and cell pellets stored at -80C until use.

value: Human Embryonic Kidney


title: RBM25_Mut4

description: Library name: RBM25_Mut4


title: 4T1 PD-L1 overexpressed tumor treated with anti-PD-L1 (Sample 3)

first: Ju Hee

last: Kim

address: 71, Daehak-ro

institute: Seoul National University Hospital

description:
Library name: PP4_TR
Raw counts and FPKM data for PP4_TR

data_processing:
Raw sequencing reads were quality-checked using FastQC (v0.11.7) to assess read quality. Adapter trimming and quality filtering were performed using Trimmomatic (v0.38) with the following parameters: ILLUMINACLIP, SLIDINGWINDOW, LEADING, TRAILING, CROP, HEADCROP, and MINLEN.
Trimmed reads were mapped to the Mus musculus reference genome (mm10) using HISAT2 (v2.1.0) or Bowtie2 (v2.3.4.1) with default parameters. Transcript assembly and quantification were performed using StringTie (v2.1.3b).
Normalized expression values (FPKM) were generated using StringTie.
Assembly: mm10
Supplementary files format and content: cvs files include raw counts for each sample
Supplementary files format and content: cvs files include FPKM values for each sample

source_name: Mammary tumor

growth_protocol: 4T1 control or PD-L1-overexpressing 4T1 cells were cultured in RPMI-1640 supplemented 10% fetal bovine serum and antiiotics at 37℃ CO2. For in vivo studies, syngeneic BALB/C mouse models were established by injecting 1×105 cells into the mammary fatpad.

extract_protocol:
Total RNA was extracted from the tumors using the Tri-RNA reagent (FAVORGEN, Kaohsiung, Taiwan) according to the manufacturer's instructions.
RNA libraries for RNA-seq were prepared using SureSelectXT RNA Direct Library Preparation kit following manufacturer's protocols.

treatment_protocol: Mice bearing 4T1 tumors were randomized into treatment groups and administered either anti-PD-L1 antibody (BP0101, 150 µg/100 µL) or IgG control (BP0090, 150 µg/100 µL) via intraperitoneal injection twice weekly. The treatment lasted for three sessions (total 17 days).

value: Mammary tumor

value: Tumor cells

value: PD-L1 overexpressed


title: 4T1 PD-L1 overexpressed tumor treated with anti-PD-L1 (Sample 2)

description:
Library name: PP3_TR
Raw counts and FPKM data for PP3_TR


title: blood_PRYA206/184-1

value: whole blood

value: blood cells

value: critical/severe COVID-19


title: 4T1 PD-L1 overexpressed tumor treated with anti-PD-L1 (Sample 1)

description:
Library name: PP1_TR
Raw counts and FPKM data for PP1_TR


title: RBM25_Mut3

description: Library name: RBM25_Mut3


title: blood_PRYA108/YA252

value: control


title: MI_CSD_IH_rep1


title: 4T1 PD-L1 overexpressed tumor treated with IgG (Sample 3)

description:
Library name: PC3_TR
Raw counts and FPKM data for PC3_TR

value: IgG


title: RBM25_Mut2

description: Library name: RBM25_Mut2


title: blood_PRYA176


title: MI_CSD_IH_rep3

value: Heart / Left ventricle


title: RBM25_Mut1

description: Library name: RBM25_Mut1


title: 4T1 PD-L1 overexpressed tumor treated with IgG (Sample 2)

description:
Library name: PC2_TR
Raw counts and FPKM data for PC2_TR


title: blood_PRYA167-1


title: 4T1 PD-L1 overexpressed tumor treated with IgG (Sample 1)

description:
Library name: PC1_TR
Raw counts and FPKM data for PC1_TR


title: RBM25_WT5

description: Library name: RBM25_WT5


title: RBM25_WT4

description: Library name: RBM25_WT4


title: blood_PRYA132


title: blood_PRYA209/133-1


title: 4T1 control tumor treated with anti-PD-L1 (Sample 3)

description:
Library name: CP3_TR
Raw counts and FPKM data for CP3_TR

value: Control


title: RBM25_WT3

description: Library name: RBM25_WT3


title: 4T1 control tumor treated with anti-PD-L1 (Sample 2)

description:
Library name: CP2_TR
Raw counts and FPKM data for CP2_TR


title: blood_PRYA186


title: RBM25_WT2

description: Library name: RBM25_WT2


title: 4T1 control tumor treated with anti-PD-L1 (Sample 1)

description:
Library name: CP1_TR
Raw counts and FPKM data for CP1_TR


title: blood_PRYA215


title: 4T1 control tumor treated with IgG (Sample 3)

description:
Library name: CC3_TR
Raw counts and FPKM data for CC3_TR


title: blood_PRYA144-1


title: RBM25_WT1

description: Library name: RBM25_WT1


title: 4T1 control tumor treated with IgG (Sample 2)

description:
Library name: CC2_TR
Raw counts and FPKM data for CC2_TR


title: placenta_PRYA301

value: placenta

value: placenta cells


title: hnRNPC_Mut5

description: Library name: hnRNPC_Mut5


title: 4T1 control tumor treated with IgG (Sample 1)

description:
Library name: CC1_TR
Raw counts and FPKM data for CC1_TR


title: placenta_PRYA298


title: R1881_48h, rep1

city: Vancouver

first: Anne

last: Haegert

state: BC

address: 2660 Oak Street

department: Genomics Core

institute: Vancouver Prostate Centre

description: DHT-treated 48h sample rep1

hyb_protocol: Samples were hybridized on Agilent SurePrint G3 Human GE v3 8x60K Microarray (Design ID 072363)

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution

data_processing: Data was processed with Agilent Feature Extraction 11.0.1.1.  Processed signal was quantile normalized with Agilent GeneSpring 11.5.1.

source_name: LNCaP cells

label_protocol: Samples were prepared following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0. An input of 100ng of total RNA was used to generate Cyanine-3 labeled cRNA

extract_protocol: Mirvana total RNA isolation kit from Ambion

value: Immortalized cell line LNCaP

tag: silac

value: heavy amino acid-labeled

value: DHT-treated 48h


title: hnRNPC_Mut3

description: Library name: hnRNPC_Mut3


title: R1881_24h, rep1

description: DHT-treated 24h sample rep1

value: medium animo acid-labeled

value: DHT-treated 24h


title: placenta_PRYA297


title: R1881_24h, rep3

description: DHT-treated 24h sample rep3