title: heart_18yrs [2020_131_18_H]

description: genomic DNA from heart of 2020_131_18

value: 18 yrs

value: heart


title: brain_50yrs [2020_138_50_Br]

status: Public on Oct 22 2023

type: genomic

city: Seoul

first: Hwan Young

last: Lee

address: 103 Daehak-ro, Jongno-gu

department: Forensic Medicine

country: South Korea

institute: Seoul National University College of Medicine

description: genomic DNA from brain of 2020_138_50

hyb_protocol: Bisulfite converted DNA was amplified, fagmented and hybridised to Infinium HumanMethylation EPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were scanned with an iScan Reader (Illumina) using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v. 2011.1 (Illumina)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen DNA Mini Kit (Qiagen, Hilden, Germany) based on the manufacturers’ instructions

tag: age

value: 50 yrs

tag: gender

value: male

tag: tissue

value: brain

tag: ethnicity

value: Korean-Asian


title: heart_48yrs [2020_14_48_H]

description: genomic DNA from heart of 2020_14_48

source_name: heart

value: 48 yrs


title: heart_46yrs [2020_13_46_H]

description: genomic DNA from heart of 2020_13_46

value: 46 yrs


title: brain_18yrs [2020_131_18_Br]

description: genomic DNA from brain of 2020_131_18


title: amniotic fluid AF80882-750knsp

city: Fuzhou

first: Xiaorui

last: Xie

address: No. 18 Daoshan Road

country: China

institute: Fujian Provincial Maternity and Children’s Hospital

description:
CYCHP file was lost (disk damage)
CEL file was lost (disk damage)
Hybridized to CytoScan750K_Array

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (ChAS 4.0). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

label: Biotin

source_name: amniotic fluid AF80882

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted from uncultured amniotic fluid, fetal cord blood using a QIAGEN kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: amniotic fluid

tag: ultrasound abnormality classification

value: Isolated TE

tag: bilateral or unilateral

value: Unilateral


title: heart_50yrs [2020_138_50_H]

description: genomic DNA from heart of 2020_138_50


title: amniotic fluid AF77053-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF77053

value: Complex TE


title: amniotic fluid AF73824-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF73824

value: Bilateral


title: blood_18yrs [2020_131_18_Bl]

description: genomic DNA from blood of 2020_131_18

source_name: blood

value: blood


title: amniotic fluid AF81200-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF81200


title: amniotic fluid AF32752-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF32752


title: amniotic fluid AF75643-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF75643


title: amniotic fluid AF50177-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF50177


title: amniotic fluid AF72937-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF72937


title: amniotic fluid AF49721-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF49721


title: amniotic fluid AF120195-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF120195


title: brain_46yrs [2020_13_46_Br]

description: genomic DNA from brain of 2020_13_46


title: amniotic fluid AF122044-750knsp

source_name: amniotic fluid AF122044


title: heart_38yrs [2020_127_38_H]

description: genomic DNA from heart of 2020_127_38

value: 38 yrs


title: amniotic fluid AF45944-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF45944


title: amniotic fluid AF118438-750knsp

source_name: amniotic fluid AF118438


title: chorionic villus PC7548-750knsp

description: Hybridized to CytoScan750K_Array

source_name: chorionic villus PC7548

value: chorionic villus


title: blood_48yrs [2020_14_48_Bl]

description: genomic DNA from blood of 2020_14_48


title: amniotic fluid AF61796-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF61796


title: heart_39yrs [2020_120_39_H]

description: genomic DNA from heart of 2020_120_39

source_name: heart

value: 39 yrs


title: amniotic fluid AF110301-750knsp

source_name: amniotic fluid AF110301


title: brain_38yrs [2020_127_38_Br]

description: genomic DNA from brain of 2020_127_38

source_name: brain


title: blood_46yrs [2020_13_46_Bl]

description: genomic DNA from blood of 2020_13_46


title: amniotic fluid AF71052-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF71052


title: amniotic fluid AF101319-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF101319


title: blood_38yrs [2020_127_38_Bl]

description: genomic DNA from blood of 2020_127_38

source_name: blood


title: brain_39yrs [2020_120_39_Br]

description: genomic DNA from brain of 2020_120_39


title: amniotic fluid AF49772-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF49772


title: amniotic fluid AF106917-750knsp

source_name: amniotic fluid AF106917


title: amniotic fluid AF102411-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF102411


title: amniotic fluid AF95939-750knsp

source_name: amniotic fluid AF95939


title: amniotic fluid AF122297-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF122297


title: amniotic fluid AF102086-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF102086


title: amniotic fluid AF87059-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF87059


title: blood_39yrs [2020_120_39_Bl]

description: genomic DNA from blood of 2020_120_39


title: amniotic fluid AF109825-750knsp

source_name: amniotic fluid AF109825


title: amniotic fluid AF109836-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF109836


title: amniotic fluid AF105100-750knsp

source_name: amniotic fluid AF105100


title: cord blood BL60405-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid BL60405

value: cord blood


title: amniotic fluid AF80079-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF80079


title: amniotic fluid AF96789-750knsp

source_name: amniotic fluid AF96789


title: amniotic fluid BL40922-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood BL40922


title: chorionic villus PC4701-750knsp

description: Hybridized to CytoScan750K_Array

source_name: chorionic villus PC4701


title: heart_52yrs [2020_115_52_H]

description: genomic DNA from heart of 2020_115_52

source_name: heart

value: 52 yrs

value: heart


title: heart_77yrs [2020_118_77_H]

description: genomic DNA from heart of 2020_118_77

value: 77 yrs

value: male


title: amniotic fluid AF38434-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF38434


title: amniotic fluid AF53368-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF53368


title: amniotic fluid AF94309-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF94309


title: amniotic fluid AF116218-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF116218


title: amniotic fluid AF83475-750knsp

source_name: amniotic fluid AF83475


title: blood_52yrs [2020_115_52_Bl]

description: genomic DNA from blood of 2020_115_52

source_name: blood

value: Korean-Asian


title: amniotic fluid AF30357-750knsp

source_name: amniotic fluid AF30357


title: amniotic fluid AF36355-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF36355


title: amniotic fluid AF25079-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF25079


title: amniotic fluid AF84328-750knsp

source_name: amniotic fluid AF84328


title: amniotic fluid S246-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid S246


title: amniotic fluid S72-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid S72


title: chorionic villus C1799-750knsp

source_name: chorionic villus C1799


title: cord blood E3641-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3641


title: blood_77yrs [2020_118_77_Bl]

description: genomic DNA from blood of 2020_118_77


title: cord blood E3635-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3635


title: cord blood E3629-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3629


title: cord blood E3628-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3628


title: chorionic villus C1814-750knsp

source_name: chorionic villus C1814


title: amniotic fluid AF115814-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF115814


title: cord blood E3573-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3573


title: cord blood E3371-750knsp

description:
CEL file was lost (disk damage)
Hybridized to CytoScan750K_Array

source_name: cord blood E3371


title: cord blood E2983-750knsp

source_name: cord blood E2983


title: cord blood E2535-750knsp

source_name: cord blood E2535


title: cord blood E2242-750knsp

source_name: cord blood E2242


title: cord blood E3405-750knsp

source_name: cord blood E3405


title: cord blood E2141-750knsp

source_name: cord blood E2141


title: cord blood E1862-750knsp

source_name: cord blood E1862


title: cord blood E1825-750knsp

source_name: cord blood E1825


title: cord blood E424-750knsp

source_name: cord blood E424


title: cord blood E2363-750knsp

source_name: cord blood E2363


title: brain_52yrs [2020_109_52_Br]

description: genomic DNA from brain of 2020_109_52

source_name: brain

value: female

value: brain


title: amniotic fluid R6971-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R6971

value: amniotic fluid


title: cord blood E2634-750knsp

source_name: cord blood E2634


title: cord blood E3572-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3572


title: amniotic fluid R6798-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R6798

value: Isolated TE


title: chorionic villus C1189-750knsp

source_name: chorionic villus C1189

value: Unilateral


title: amniotic fluid R7450-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R7450


title: amniotic fluid R6826-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R6826

value: Complex TE


title: amniotic fluid AF45562-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid AF45562

value: Bilateral


title: amniotic fluid R6268-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R6268


title: heart_52yrs [2020_109_52_H]

description: genomic DNA from heart of 2020_109_52

source_name: heart


title: amniotic fluid R6783-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R6783


title: amniotic fluid R5524-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R5524


title: amniotic fluid R5786-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R5786


title: amniotic fluid R4952-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4952


title: amniotic fluid R5077-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R5077


title: blood_52yrs [2020_109_52_Bl]

description: genomic DNA from blood of 2020_109_52

source_name: blood

value: blood


title: amniotic fluid R5592-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R5592


title: amniotic fluid R4339-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4339


title: amniotic fluid R4798-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4798


title: brain_77yrs [2020_118_77_Br]

description: genomic DNA from brain of 2020_118_77

source_name: brain


title: amniotic fluid R4334-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4334


title: amniotic fluid R5863-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R5863


title: amniotic fluid R4253-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4253


title: amniotic fluid R4059-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4059


title: amniotic fluid R3730-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R3730


title: amniotic fluid R2707-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R2707


title: amniotic fluid R2553-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R2553


title: amniotic fluid R3681-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R3681


title: brain_52yrs [2020_115_52_Br]

description: genomic DNA from brain of 2020_115_52


title: amniotic fluid R3439-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R3439


title: amniotic fluid R4814-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R4814


title: amniotic fluid R3360-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R3360


title: amniotic fluid R2449-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R2449


title: amniotic fluid R1316-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R1316


title: amniotic fluid P9733-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P9733


title: amniotic fluid P9704-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P9704


title: amniotic fluid R377-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R377


title: amniotic fluid R2448-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid R2448


title: amniotic fluid P7019-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P7019


title: amniotic fluid P8279-750knsp

source_name: amniotic fluid P8279


title: amniotic fluid P7004-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P7004


title: amniotic fluid P6611-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P6611


title: amniotic fluid P7752-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P7752


title: amniotic fluid P5414-750knsp

source_name: amniotic fluid P5414


title: amniotic fluid P5625-750knsp

source_name: amniotic fluid P5625


title: amniotic fluid P4866-750knsp

source_name: amniotic fluid P4866


title: amniotic fluid P9623-750knsp

description: Hybridized to CytoScan750K_Array

source_name: amniotic fluid P9623


title: amniotic fluid P4593-750knsp

source_name: amniotic fluid P4593


title: amniotic fluid P4685-750knsp

source_name: amniotic fluid P4685


title: amniotic fluid P3689-750knsp

source_name: amniotic fluid P3689


title: amniotic fluid P4143-750knsp

source_name: amniotic fluid P4143


title: amniotic fluid P2447-750knsp

source_name: amniotic fluid P2447


title: amniotic fluid P1906-750knsp

source_name: amniotic fluid P1906


title: amniotic fluid P3053-750knsp

source_name: amniotic fluid P3053


title: amniotic fluid P1552-750knsp

source_name: amniotic fluid P1552


title: amniotic fluid P2104-750knsp

source_name: amniotic fluid P2104


title: amniotic fluid P1020-750knsp

source_name: amniotic fluid P1020


title: amniotic fluid P798-750knsp

source_name: amniotic fluid P798


title: amniotic fluid P2151-750knsp

source_name: amniotic fluid P2151


title: amniotic fluid P599-750knsp

source_name: amniotic fluid P599


title: amniotic fluid G9411-750knsp

source_name: amniotic fluid G9411


title: amniotic fluid G9832-750knsp

source_name: amniotic fluid G9832


title: amniotic fluid P554-750knsp

source_name: amniotic fluid P554


title: amniotic fluid G9930-750knsp

source_name: amniotic fluid G9930


title: amniotic fluid G8410-750knsp

source_name: amniotic fluid G8410


title: amniotic fluid G4494-750knsp

source_name: amniotic fluid G4494


title: amniotic fluid G6063-750knsp

source_name: amniotic fluid G6063


title: amniotic fluid G2249-750knsp

source_name: amniotic fluid G2249


title: amniotic fluid P321-750knsp

source_name: amniotic fluid P321


title: cord blood E3176-750knsp

description: Hybridized to CytoScan750K_Array

source_name: cord blood E3176


title: shCtrl_1

type: SRA

city: Nanjing，Zhenjiang

first: Zhicong

last: Zhao

state: Jiangsu province

address: 163 Xianlin Avenue，438 Jiefang Road

institute: School of life sciences, Nanjing university, Affiliated Hospital of Jiangsu University

library_source: transcriptomic

data_processing:
Illumina pipeline CASAVA v1.8.2 used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample …

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
RNA was harvested using Trizol agent (Invitrogen). ≥1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra TM RNA Library Prep Kit following manufacturer's protocols.

value: Liver

tag: genotype

value: WT

tag: treatment

value: shControl adenovirus intervention for 9 days


title: shANG8_1

value: ANGPTL8 knockdown adenovirus intervention for 9 days


title: ANG8_1

value: Intervention with ANGPTL8 overexpression adenovirus for 9 days


title: Ad_GFP_1

value: Control adenovirus intervention for 9 days


title: ANG8_2


title: shCtrl_3


title: shANG8_2


title: Ad_GFP_2


title: A549SD biol rep 1

city: Houston

first: Chaohao

last: Li

state: TX

address: 1881 East Rd

country: USA

institute: MD Anderson Cancer Center

description: Novogene

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic (v0.39).
Trimmed reads were mapped to the human reference genome assembly GRCh38 transcripts annotation using RSEM.
RSEM results normalization and differential expression analysis were performed using the R package edgeR.
Genes with log2-foldchange > log2(1.0) were identified as overexpressed in the comparison of SD vs WT (with WT as reference). Similar filtering was repeated for the comparison of WT vs SA (with SA as reference). The overlapping over-expressed genes in the two filtering were identified as satisfying the condition SD > WT > SA simultaneously.
In addition, in the comparison of SA vs V, the genes with raw p values greater than or equal to 0.05 were identified as having little difference between the two groups of comparison. So the final list will be genes with this order: SD>WT>SA=V
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text file includes genes with SD>WT>SA=V pattern using the indicated filters.

source_name: lung

growth_protocol: All cell lines were maintained in RPMI 1640 medium supplied with 10% FBS and 1% penicilin-streptomycin in 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted using Rnease Mini Kit (Qiagen) and 1ug total RNA was used for sequencing.
mRNA library preparation (poly A enrichment)

treatment_protocol: Original A549 cell line was infected with lentivirus overepxressing empty vector (pLV-EF1a-IRES-Hygro), wild-type HA-AHR, HA-AHR with S489A mutation or HA-AHR with S489D mutation and selected with 200ug/ml hygromycin for 72h.

value: lung

tag: cell line

tag: cell type

value: lung adenocarcinoma

value: SD

value: overexpression of AHR S489D


title: A549SD biol rep 3

description: Novogene


title: Ad_GFP_3


title: shANG8_3


title: A549SA biol rep 2

description: Novogene

value: SA

value: overexpression of AHR S489A


title: shCtrl_2


title: ANG8_3


title: A549SA biol rep 1

description: Novogene


title: A549SD biol rep 2

description: Novogene


title: A549WT biol rep 2

description: Novogene

value: overexpression of WT AHR


title: A549WT biol rep 3

description: Novogene


title: A549WT biol rep 1

description: Novogene


title: A549SA biol rep 3

description: Novogene


title: A549V biol rep 3

description: Novogene

value: V

value: overexpression of empty vector


title: A549V biol rep 2

description: Novogene


title: pyrop-SK56-3

city: kunming

first: Gan

last: Wang

address: jiaochang dobg lu 32#

institute: Kunming Institute of Zoology

data_processing:
Sequenced reads were mapped to human reference genome (hg38) using Hisat2 (2.0.5) with default parameters.
Aligned reads were summarized into gene counts using the StringTie (v2.1.5) command of the Subread package with default parameters in conjunction with the human gencode annotation file (hg38 release 85).
Genome_build: hg38
tab-delimited text file containing raw read counts for all samples
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: THP-1 cells were cultured in regular growth medium (1640 + 10% FBS + 1%P/S) and differentiated with phorbol 12-myristate 13-acetate (PMA) for 12 hours to get macrophage cell.

extract_protocol:
The TruSeq stranded RNA sample prep kit was used for library generation according to Illumina's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For samples 1-6, cells were treated with either 15 µM SK56 or vehicle. After 4 hours, the cells were collected for RNA-Seq.For samples 7-12, cells were treated with either 1 μg/ml LPS + 10 μM nigericin as control or 1 μg/ml LPS + 10 μM nigericin + 15 µM SK56. After 4 hours, the cells were collected for RNA-Seq.

value: PMA-differentiated THP-1

value: human macrophage cell line

tag: treated with

value: LPS and nigericin and SK56


title: pyrop-SK56-1


title: sk56-2


title: pyrop-CK1

value: LPS and nigericin


title: ck3

value: Vehicle


title: sk56-3


title: sk56-1


title: pyrop-CK3


title: ck2


title: ck1


title: S. coagulans cells, Control, biol rep 2

city: Fuchu-shi

first: Saki

last: Onishi-Sakamoto

state: Tokyo

address: 3-8-1 Harumi-cho

country: Japan

institute: Tokyo University of Agriculture and Technology

data_processing:
Bowtie2 (ver. 2.4.1) was used to read the alignment and mapping of the GCF_001792775.2 reference genomes.
After reading and writing the alignment data in the SAM and BAM formats with the SAMtools, the data were sorted and indexed.
The read counts per gene were obtained using the featureCounts (ver. 2.0.0).
The relative expression level of each gene was normalized by the RPKM (Reads per Kilobase Million) and Transcripts Per Million methods.
After normalization using the DEGES normalization method implemented in TCC (ver. 1.26.0), we performed a differential gene expression analysis using edgeR (ver. 3.28.1).
Assembly: GCF_001792775.2
Supplementary files format and content: Exeel files include RPKM and TPM  values for each Sample

organism: Staphylococcus coagulans

source_name: cell

growth_protocol: S. coagulans cultured in 802 medium with or without 5% (w/w) erythritol, 60 or 30 µL of the above seed culture was inoculated into 3 mL of 802 medium, respectively, and incubated at 30°C until OD660 = 0.8–1.0 for three independent cultures under each condition.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
After removing rRNA in samples by riboPool (siTOOLs Biotech, Planegg, Germany), the NGS library was prepared by MGIEasy RNA Directional Library Prep Set (MGI Tech, Shenzhen, China) according to the manufacturer’s protocol.

treatment_protocol: After cooling 3 mL of the culture medium on ice, the cells were collected by centrifugation at 5,000 rpm for 5 min using the centrifuge MX-107 (Tomy Seiko, Tokyo, Japan), and 800 μl of RNA later (Thermo Fisher Scientific, MA, USA) was then added to cells for RNA extraction.

value: cell

value: WT

value: without erythritol


title: S. coagulans cells, Control, biol rep 3


title: S. coagulans cells, Control, biol rep 1


title: S. coagulans cells, Erythritol added, biol rep 3

value: with erythritol


title: S. coagulans cells, Erythritol added, biol rep 2


title: NPC Pro-TGG upstream edit BRF1 ChIP-Seq rep2

city: Planegg

first: Danny

last: Nedialkova

state: Bayern

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute for Biochemistry

library_source: genomic

data_processing:
ChIP-Seq  datasets were preprocessed to remove potential 3’ adapters using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Adapter-trimmed ChIP-Seq libraries were aligned to the GRCh38 reference genome using STAR with the following settings: up to one mismatch per read, a maximum of ten alignment positions, end-to-end alignment, prohibited introns, only one alignment reported per read (--outFilterMismatchNmax 1 --outFilterMultimapNmax 10 --alignEndsType EndToEnd --alignIntronMax 1 --outSAMmultNmax 1). Reads from spike-in-containing libraries were also aligned to the D. melanogaster r6.39 genome with the same settings, except only uniquely-mapped reads were retained (--outFilterMultimapNmax 1). Read duplicates were then removed using Picard Tools MarkDuplicates v2.17.10. Peaks were called with MACS callpeak v2.2.6, supplying ChIP input samples from HPSI0214i-kucg_2 for kucg-2 hiPSC and CM datasets, HPSI0214i-wibj_2 for wibj_2 hiPSC datasets, and from HPSI0214i-kucg_2-derived NPC for NPC and neuron datasets, specifying the fragment sizes (--extsize) with shifting model building disabled (--nomodel). The small region size used to calculate dynamic lambda was reduced to 500bp (--slocal 500), and peak summits were also reported (--call-summits). Additionally, for all peak calling, signal normalized per million reads was saved in bedgraph format for visual inspection of datasets (-B and -SMPR). Finally, predicted peaks were filtered using the ENCODE project unified GRCh38 blacklist regions bed file (https://www.encodeproject.org/files/ENCFF356LFX/) by identifying overlaps using bedtools intersect v2.29.2. Blacklist-filtered peak region summits were then annotated by searching for their nearest predicted tRNA locus with bedtools closest Peaks with tRNA “hits” were then defined for each sample as those within 125 bp of an annotated tRNA gene, while tRNA hits shared by both replicates of each cell type or experimental condition were used to define consensus tRNA peaks for that condition.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, broadPeak: Peaks called with macs2

source_name: kucg-2 hiPSC

extract_protocol:
Cells were fixed with 0.8% methanol-free formaldehyde in DMEM for 10 min, followed by quenching with 0.125 M glycine for 5 min. Cells were resuspended in Farnham buffer (5 mM PIPES, pH 8; 85 mM KCl; 0.5% IGEPAL-CA 630), followed by snap freezing in liquid nitrogen. All buffers were supplemented with cOmplete™ EDTA-free Protease Inhibitor Cocktail before use. Chromatin was isolated and sheared following the NEXSON protocol. Frozen cell pellets were thawed on ice and sonicated for 2 min in 1- ml tubes on a Covaris S220 with the following settings: peak power = 75W; duty factor = 2%; cycles/burst = 200. Isolated nuclei were washed with Farnham buffer once and resuspended in shearing buffer (10 mM Tris-HCl, pH 8; 0.1% SDS; 1 mM EDTA). Chromatin was sheared on a Covaris S220 by sonication for 18 min in 1-ml tubes with the following settings: peak power = 140W; duty factor = 5%; cycles/burst = 200. Sheared chromatin was snap frozen in liquid nitrogen, aliquoted and stored at -80°C.
Sequencing libraries from ChIP eluted DNA samples were prepared with the Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (TECAN, #0344NB) and SPRIselect beads (Beckman Coulter, #B23318) according to the manufacturer’s protocol. 110-bp paired-end sequencing was performed on a NovaSeq platform (Illumina).

value: kucg-2 hiPSC

value: Human neural progenitor

tag: chip antibody

value: BRF1 (Abcam, ab264191)

value: Pro-TGG-2-1 upstream edit CRISPR


title: S. coagulans cells, Erythritol added, biol rep 1


title: NPC Pro-TGG upstream edit BRF1 ChIP-Seq rep1


title: hiPSC Pro-TGG upstream edit BRF1 ChIP-Seq rep2

value: Human induced pluripotent stem cell


title: hiPSC Pro-TGG upstream edit BRF1 ChIP-Seq rep1


title: Neurons H3K9me3 ChIP-Seq rep1

value: Human mature neurons

value: Tri-Methyl-Histone H3 (Lys9) (Cell Signaling Technology, #13969)


title: A549V biol rep 1

description: Novogene

value: lung

value: lung adenocarcinoma

value: V

value: overexpression of empty vector


title: NPC H3K9me3 ChIP-Seq rep1


title: hiPSC H3K9me3 ChIP-Seq rep1


title: pyrop-CK2

value: PMA-differentiated THP-1

value: human macrophage cell line

value: LPS and nigericin


title: pyrop-SK56-2

value: LPS and nigericin and SK56


title: PC3/ELAVL3-RRM1Δ-V5 cells, V5, RIP-seq

city: Shanghai

first: Qi

state: Shanghai

address: Shanghai Pu Dong district, Dongfang Rd. No.1630

institute: Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Raw reads were filtered with Fastp (v0.20.0), an ultra-fast all-in-one FASTQ preprocessor, to obtain high-quality clean reads by removing sequencing adapters, short reads (length < 30 bp) and low-quality reads.
Then FastQC was employed to ensure high reads quality and to process data quality control.
Assembly: GRCh38

source_name: Prostate cancer cells sample

extract_protocol:
RIP assay was performed on PC3/ELAVL3-V5 and PC3/ELAVL3-RRM1Δ-V5 cells. About 1 × 107 cells in each dish were harvested and resuspended in 250 μL lysis buffer [20 mM Tris (pH 8.0), 150 mM NaCl, 1% NP-40, 10% glycerol, 2 mM EDTA, Protease inhibitor cocktail (11836145001, Roche), 0.5 mM PMSF (ST506, Beyotime, China), 2 mM Ribonucleoside Vanadyl Complexes (R0108, Beyotime, China), 2 μL RNase inhibitor (R0102, Beyotime, China)]. 10% volume of the lysates were separated into another two RNase-free tubes, labeled as input, and the rest lysates were used for RIP assay. All lysates were frozen rapidly at − 80°C overnight to gently lyse the cells. Then thawed the RIP lysates quickly and centrifuged at 15,000 rpm for 10 mins at 4°C. The supernatant was collected and incubated with V5 antibody (13202, Cell Signaling Technology) and protein A+G magnetic beads (P2108, Beyotime, China) at 4°C for 4 hours with rotation. The V5-Beads were washed with 500 μL lysis buffer for 5 times, rigorously. After the last washing, thawed the input lysates and added 1 mL Trizol reagent to the input lysates and the V5-Beads to extract total RNA. RNA was extracted using Trizol reagent according to the manufacturer's instructions. rRNAs were removed by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA library was constructedusing rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Sequencing was performed on the illumina NovaseqTM 6000 system (Illumina, San Diego, CA) at high out-put model according to the manufacturer’s instruction.
RIP-seq libraries were prepared following the SMARTseq protocol

value: Prostate cancer cells sample

value: Prostate cancer cells

tag: antibody


title: PC3/ELAVL3-V5 cells, V5, RIP-seq


title: PLC/PRF/5 cells, PF429242, 24 h

city: New Taipei City

first: Pei-Ming

last: Yang

address: No. 301, Yuantong Rd., Zhonghe Dist.

department: Graduate Institute of Cancer Biology and Drug Discovery

country: Taiwan

institute: Taipei Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.
Algorithm for mapping sequences: TopHat2
Assembly: GRCh38
Supplementary files format and content: A matrix table includes FPKM values for each Sample.

growth_protocol: HepG2 and PLC/PRF/5 cells were maintained in MEM supplemented with 2 mM L-glutamine, Earle's balanced salt solution (BSS), 1.5 g/L sodium bicarbonate, 0.1 mM non-essential amino acids (NEAAs), 1.0 mM sodium pyruvate, and 10% FBS in a 37℃ humidified incubator.

extract_protocol:
RNA was prepared using the GENEzol TriRNA Pure Kit following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 20 uM PF429242 for 24 h.

value: Liver cancer cells

value: WT


title: PC3/ELAVL3-RRM1Δ-V5 cells, Input, RIP-seq

value: input


title: Hulunbuir Short-tail Sheep embryo (D1)

city: Inner Mongolia

first: Hong

last: Su

state: Inner Mongolia

address: No. 306, Zhaowuda Road, Saihan District, Hohhot, Inner Mongolia Autonomous Region

institute: Inner MongoliaAgricultural University

data_processing:
A cDNA library constructed by technology from the pooled RNA from samples was sequenced run with Illumina Novaseq TM 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. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis．
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Genome_build: Oar_v3.1
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample

organism: Ovis aries

source_name: Hulunbuir Short-tail Sheep embryo

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Hulunbuir Short-tail Sheep

tag: developmental  stage

value: embryo


title: Hulunbuir Short-tail Sheep embryo (D3)


title: Ujumqin sheep embryo (C3)

source_name: Ujumqin sheep embryo

value: Ujumqin sheep


title: PLC/PRF/5 cells, control, 24 h

value: untreated control at 24 h


title: Ujumqin sheep embryo (B3)


title: Ujumqin sheep embryo (C1)


title: hiPSC wibj-2 ChIP-Seq Input

data_processing:
ChIP-Seq  datasets were preprocessed to remove potential 3’ adapters using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Adapter-trimmed ChIP-Seq libraries were aligned to the GRCh38 reference genome using STAR with the following settings: up to one mismatch per read, a maximum of ten alignment positions, end-to-end alignment, prohibited introns, only one alignment reported per read (--outFilterMismatchNmax 1 --outFilterMultimapNmax 10 --alignEndsType EndToEnd --alignIntronMax 1 --outSAMmultNmax 1). Reads from spike-in-containing libraries were also aligned to the D. melanogaster r6.39 genome with the same settings, except only uniquely-mapped reads were retained (--outFilterMultimapNmax 1). Read duplicates were then removed using Picard Tools MarkDuplicates v2.17.10. Peaks were called with MACS callpeak v2.2.6, supplying ChIP input samples from HPSI0214i-kucg_2 for kucg-2 hiPSC and CM datasets, HPSI0214i-wibj_2 for wibj_2 hiPSC datasets, and from HPSI0214i-kucg_2-derived NPC for NPC and neuron datasets, specifying the fragment sizes (--extsize) with shifting model building disabled (--nomodel). The small region size used to calculate dynamic lambda was reduced to 500bp (--slocal 500), and peak summits were also reported (--call-summits). Additionally, for all peak calling, signal normalized per million reads was saved in bedgraph format for visual inspection of datasets (-B and -SMPR). Finally, predicted peaks were filtered using the ENCODE project unified GRCh38 blacklist regions bed file (https://www.encodeproject.org/files/ENCFF356LFX/) by identifying overlaps using bedtools intersect v2.29.2. Blacklist-filtered peak region summits were then annotated by searching for their nearest predicted tRNA locus with bedtools closest Peaks with tRNA “hits” were then defined for each sample as those within 125 bp of an annotated tRNA gene, while tRNA hits shared by both replicates of each cell type or experimental condition were used to define consensus tRNA peaks for that condition.
Assembly: GRCh38
Supplementary files format and content: narrowPeak, broadPeak: Peaks called with macs2 (except input samples)
Supplementary files format and content: control lambda bedGraph for (Input control samples only)

source_name: wibj-2 hiPSC

value: wibj-2 hiPSC

value: Human induced pluripotent stem cell


title: Ujumqin sheep embryo (C2)


title: CM ChIP-Seq Input

value: kucg-2 hiPSC

value: Human cardiomyocytes


title: HEK293T ChIP-Seq Input

value: Human embryonic kidney


title: HepG2 cells, PF429242, 24 h


title: HepG2 cells, control, 24 h


title: NPC ChIP-Seq Input

value: Human neural progenitor


title: Ujumqin sheep embryo (B2)


title: Hulunbuir Short-tail Sheep embryo (D2)


title: cord blood E1790-750knsp

source_name: cord blood E1790

value: cord blood

value: Isolated TE

value: Bilateral


title: hiPSC RPC7a KD RPC1 ChIP-Seq rep2

value: RPC1 (Cell Signaling Technology, #12825)

value: RPC7a KD CRIPSRi


title: cord blood E1880-750knsp

source_name: cord blood E1880

value: Complex TE


title: PC3/ELAVL3-V5 cells, Input, RIP-seq

value: Prostate cancer cells sample

value: Prostate cancer cells

value: input


title: hiPSC RPC7a KD RPC1 ChIP-Seq rep1


title: hiPSC RPC7a ctrl RPC1 ChIP-Seq rep2

value: WT


title: Hulunbuir Short-tail Sheep embryo (A2)

value: Hulunbuir Short-tail Sheep

value: embryo


title: hiPSC RPC7a ctrl RPC1 ChIP-Seq rep1

value: Human induced pluripotent stem cell


title: Hulunbuir Short-tail Sheep embryo (A1)


title: Hulunbuir Short-tail Sheep embryo (A3)


title: hiPSC RPC7a ChIP-Seq rep2

value: kucg-2 hiPSC

value: RPC7α/POLR3G antibody (Santa Cruz, #sc21754)


title: Ujumqin sheep embryo (B1)

value: Ujumqin sheep


title: F3 STING 3

city: Cardiff

first: Van Dien

last: Nguyen

address: Heath Park

department: School of Medicine

country: United Kingdom

institute: Cardiff University

data_processing:
Sequencing reads of all samples were first quality controlled using FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), followed by a trimming process using trimmomatic v0.38 (PMID: 24695404) to obtain high-quality reads
Qualified reads were then mapped to GRCh38 with STAR v.2.5.2b
subsequently went through an indexing process with samtools v1.10
Finally, the aligned files were used for generating gene counts by featureCounts programme under subread v.1.5.2
Assembly: GRCh38
Supplementary files format and content: rawCounts_all.csv

source_name: PMA-differentiated THP-1 cells

extract_protocol:
RNASeq was performed by GENEWIZ, comprising total RNA isolation, library preparation with poly(A) selection and 150 bp paired-end sequencing using an HiSeq 2500 (Illumina)
Pre-made library
Samples were sequenced using an Illumina HiSeq 2500 with 150 bp paired-end reads

value: PMA-differentiated THP-1 cells

tag: cell line_name

value: C5aR2 KO

value: STING


title: F3 STING 2


title: NPC Pro-TGG upstream edit RPC1 ChIP-Seq rep2

value: Human neural progenitor

value: Pro-TGG-1-1 upstream edit CRISPR


title: NPC Pro-TGG upstream edit RPC1 ChIP-Seq rep1

value: RPC1 (Cell Signaling Technology, #12825)


title: C3 STING 2

value: C5aR1 KO


title: hiPSC Pro-TGG upstream edit RPC1 ChIP-Seq rep1


title: NPC Pro-TGG body edit RPC1 ChIP-Seq rep1

value: Pro-TGG-1-1 edit CRISPR


title: C3 STING 1


title: C3 STING 3


title: NPC Pro-TGG body edit RPC1 ChIP-Seq rep2


title: hiPSC Pro-TGG body edit RPC1 ChIP-Seq rep2


title: NPC derived MAF1 KD RPC1 ChIP-Seq rep2

value: MAF1 KD CRISPRi


title: F3 C5a 2


title: hiPSC Pro-TGG body edit RPC1 ChIP-Seq rep1


title: C3 C5a 1


title: F3 Untreated 3

value: Untreated


title: F3 C5a 3


title: C3 C5a 3


title: NPC derived MAF1 ctrl RPC1 ChIP-Seq rep1

value: WT


title: NPC derived MAF1 ctrl RPC1 ChIP-Seq rep2


title: NPC derived MAF1 KD RPC1 ChIP-Seq rep1


title: NPC MAF1 KD RPC1 ChIP-Seq rep1


title: F3 Untreated 2


title: hiPSC Pro-TGG upstream edit RPC1 ChIP-Seq rep2


title: F3 Untreated 1


title: F3 STING 1


title: NPC MAF1 KD RPC1 ChIP-Seq rep2


title: NPC MAF1 ctrl RPC1 ChIP-Seq rep2


title: NPC MAF1 ctrl RPC1 ChIP-Seq rep1


title: hiPSC MAF1 KD RPC1 ChIP-Seq rep1


title: C3 C5a 2


title: C3 Untreated 2


title: hiPSC MAF1 ctrl RPC1 ChIP-Seq rep2


title: F3 C5a 1


title: hiPSC MAF1 KD RPC1 ChIP-Seq rep2


title: F7 STING 2


title: F7 STING 3


title: hiPSC MAF1 ctrl RPC1 ChIP-Seq rep1


title: D3 STING 3


title: hiPSC RPC7a ChIP-Seq rep1


title: F7 STING 1


title: Neurons H3K27me3 ChIP-Seq rep1

value: Human mature neurons


title: CM H3K27me3 ChIP-Seq rep1

value: Human cardiomyocytes


title: D3 STING 1


title: D3 STING 2


title: hiPSC H3K27me3 ChIP-Seq rep1

value: Human induced pluripotent stem cell

value: H3K4me3 (Active Motif, #39159)


title: G8 STING 3


title: CM H3K4me3 ChIP-Seq rep2

value: kucg-2 hiPSC


title: G8 STING 2


title: B6 STING 3


title: G8 STING 1


title: C3 Untreated 3


title: C3 Untreated 1


title: Neurons H3K4me3 ChIP-Seq rep2


title: Neurons H3K4me3 ChIP-Seq rep1


title: CM H3K4me3 ChIP-Seq rep1


title: NPC H3K4me3 ChIP-Seq rep1


title: WT STING 3


title: WT STING 2


title: WT STING 1


title: hiPSC H3K4me3 ChIP-Seq rep1


title: B6 STING 1


title: F7 C5a 3


title: NPC H3K27me3 ChIP-Seq rep1


title: CM BRF1 ChIP-Seq rep2

value: BRF1 (Abcam, ab264191)


title: hiPSC H3K4me3 ChIP-Seq rep2


title: B6 STING 2

value: PMA-differentiated THP-1 cells


title: Neurons BRF1 ChIP-Seq rep2


title: Neorons BRF1 ChIP-Seq rep1


title: F7 C5a 2

value: C5aR2 KO


title: NPC BRF1 ChIP-Seq rep2


title: F7 C5a 1


title: NPC BRF1 ChIP-Seq rep1


title: D3 C5a 3


title: D3 C5a 2


title: hiPSC BRF1 ChIP-Seq rep1


title: G8 C5a 3


title: HEK293T RPC1 ChIP-Seq rep2

value: Human embryonic kidney


title: HEK293T RPC1 ChIP-Seq rep1


title: G8 C5a 2


title: CM RPC1 ChIP-Seq rep2


title: G8 C5a 1


title: B6 C5a 3


title: CM BRF1 ChIP-Seq rep1


title: CM RPC1 ChIP-Seq rep1


title: B6 C5a 2


title: Neurons RPC1 ChIP-Seq rep1


title: NPC RPC1 ChIP-Seq rep2

value: Human neural progenitor


title: Neurons RPC1 ChIP-Seq rep2


title: RM1_PR3_3

city: San Francisco

first: Deepak

middle: A

last: Lamba

state: CA

address: 35 Medical Center Way, Rm1024

institute: University of California, San Francisco

data_processing:
Following QC, alignments were using Salmon (V1.5.1) using GRCh37 - hg19 reference sequence
Differential expressions were determined through DESeq2 R package (v1.14.1 ).81 Genes with an adjusted p-value <0.05 (Benjamini and Hochberg’s approach) found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias was corrected.
Assembly: GRCH38
Supplementary files format and content: CSV file of readcounts from various conditions

source_name: RM-iPSC line

growth_protocol: iPSC-derived retinal organoids were generated using our previously described protocol (Chirco et al Stem Cell Reports 2021)

extract_protocol:
RNA was harvested using TriReagent and Chloroform-Ethanol extraction.
Library preparation and Illumina-based transcriptome sequencing was carried out at Novogene

treatment_protocol: On treatment day for PR3 studies, organoids were treated with PR3 (0.25uM) for 7 days prior to collection for RNA isolation.

value: RM-iPSC line

value: retinal organoids

value: RHO-CNV

tag: time

value: 7-days post-treatment


title: B6 C5a 1

value: C5aR1 KO


title: NPC RPC1 ChIP-Seq rep1

value: RPC1 (Cell Signaling Technology, #12825)


title: WT C5a 3

value: WT


title: RM1_PR3_2


title: RM1_PR3_1


title: hiPSC wibj-2 RPC1 ChIP-Seq rep1

value: wibj-2 hiPSC


title: WT C5a 1


title: DU145/ELAVL3-V5 cells, V5, RIP-seq

data_processing:
Raw reads were filtered with Fastp (v0.20.0), an ultra-fast all-in-one FASTQ preprocessor, to obtain high-quality clean reads by removing sequencing adapters, short reads (length < 30 bp) and low-quality reads.
Then FastQC was employed to ensure high reads quality and to process data quality control.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RIP assay was performed on PC3/ELAVL3-V5 and DU145/ELAVL3-V5 cells. About 1 × 107 cells in each dish were harvested and resuspended in 250 μL lysis buffer [20 mM Tris (pH 8.0), 150 mM NaCl, 1% NP-40, 10% glycerol, 2 mM EDTA, Protease inhibitor cocktail (11836145001, Roche), 0.5 mM PMSF (ST506, Beyotime, China), 2 mM Ribonucleoside Vanadyl Complexes (R0108, Beyotime, China), 2 μL RNase inhibitor (R0102, Beyotime, China)]. 10% volume of the lysates were separated into another two RNase-free tubes, labeled as input, and the rest lysates were used for RIP assay. All lysates were frozen rapidly at − 80°C overnight to gently lyse the cells. Then thawed the RIP lysates quickly and centrifuged at 15,000 rpm for 10 mins at 4°C. The supernatant was collected and incubated with V5 antibody (13202, Cell Signaling Technology) and protein A+G magnetic beads (P2108, Beyotime, China) at 4°C for 4 hours with rotation. The V5-Beads were washed with 500 μL lysis buffer for 5 times, rigorously. After the last washing, thawed the input lysates and added 1 mL Trizol reagent to the input lysates and the V5-Beads to extract total RNA. RNA was extracted using Trizol reagent according to the manufacturer's instructions. rRNAs were removed by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA, USA). RNA library was constructedusing rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.
Sequencing was performed on the illumina NovaseqTM 6000 system (Illumina, San Diego, CA) at high out-put model according to the manufacturer’s instruction.
RIP-seq libraries were prepared following the SMARTseq protocol

value: Prostate cancer cells sample

value: Prostate cancer cells


title: D3 C5a 1


title: hiPSC kucg-2 RPC1 ChIP-Seq rep2

value: Human induced pluripotent stem cell


title: hiPSC kucg-2 RPC1 ChIP-Seq rep1

value: kucg-2 hiPSC


title: RM1-D

value: Vehicle

value: disease


title: F7 Untreated 3

value: PMA-differentiated THP-1 cells

value: C5aR2 KO

value: Untreated


title: F7 Untreated 2


title: RM1-B

value: RM-iPSC line


title: RC1-D

source_name: RC-iPSC line

value: RC-iPSC line

value: retinal organoids

value: Ctrl


title: DU145/ELAVL3-V5 cells, Input, RIP-seq


title: DU145/ELAVL3-V5 cells, IgG, RIP-seq


title: RM1-A

value: RHO-CNV


title: PC3/ELAVL3-V5 cells, IgG, RIP-seq


title: PC3/ELAVL3-V5 cells, Input, RIP-seq


title: LNCaP/AR/shTP53/shRB1/shELAVL3 cells,  Day7_2

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina HiSeq X Ten platform and 150 bp paired-end reads were generated.

value: LNCaP

value: PBS


title: hiPSC BRF1 ChIP-Seq rep2

value: BRF1 (Abcam, ab264191)

value: WT


title: RC1-C


title: LNCaP/AR/shTP53/shRB1/shELAVL3 cells,  Day7_1

value: Prostate cancer cells sample

value: Prostate cancer cells


title: F7 Untreated 1


title: RC1-A


title: D3 Untreated 2


title: WT C5a 2


title: hiPSC wibj-2 RPC1 ChIP-Seq rep2

value: wibj-2 hiPSC

value: Human induced pluripotent stem cell

value: RPC1 (Cell Signaling Technology, #12825)


title: hAoSMCs treated with PDGF-BB 24h rep3

type: RNA

city: shanghai

first: Xian

last: Guo

address: changhai road 168

institute: Changhai hospital

description: Gene expression data from hAoSMCs treated with PDGF-BB 24h

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

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000 (Affymetrix).

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: hAoSMCs treated with PDGF-BB 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The hAoSMCs were purchased from ScienCell and cultured in Smooth Muscle Cell Medium supplemented with 2% FBS and smooth muscle growth supplement in a humidified 5% CO2 incubator. hAoSMCs used for GeneChips detection were passage 5.

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

treatment_protocol: Human AoSMCs were seeded in 6-well plates at an appropriate concentration, when the cell density reached 60-70%, hAoVSMCs were starved with serum-free medium for 24 hrs and then treated with vehicle or PDGF-BB for 24 hrs.

tag: sample type

value: cell


title: LNCaP/AR/shTP53/shRB1/shCtrl cells,  Day7_2


title: hAoSMCs treated with PDGF-BB 24h rep2


title: hAoSMCs treated with vehicle 24h rep3

description: Gene expression data from hAoSMCs treated with vehicle 24h

source_name: hAoSMCs treated with vehicle 24h


title: D3 Untreated 1

value: PMA-differentiated THP-1 cells

value: C5aR2 KO


title: G8 Untreated 3

value: C5aR1 KO

value: Untreated


title: NCI-H660 cells, PP, Day3_3

source_name: NEPC cells sample

value: NEPC cells sample

value: NEPC cells

value: PP


title: PC3/ELAVL3-V5 cells, V5, RIP-seq


title: NCI-H660 cells, PP, Day3_2


title: hAoSMCs treated with PDGF-BB 24h rep1


title: G8 Untreated 2


title: G8 Untreated 1


title: hAoSMCs treated with vehicle 24h rep2


title: NCI-H660 cells, PP, Day3_1


title: D3 Untreated 3


title: LNCaP/AR/shTP53/shRB1/shCtrl cells,  Day7_1

value: LNCaP


title: hAoSMCs treated with vehicle 24h rep1


title: NCI-H660 cells, PBS, Day3_2

value: PBS


title: B6 Untreated 2


title: NCI-H660 cells, PBS, Day3_3


title: buried at T48 biological replicate 2

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: Gene expression data from concealment simulation (mouse in sealed bags with soil)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45ºC on GeneChip™ Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G

data_processing: Microarray data were normalized with the R suite using the RMA normalization. The identification of differentially expressed genes, enrichment and cluster analyses were performed with the AltAnalyze platform. Searching analysis for the most likely cell types and tissues represented in our RNA samples was performed using the lineage profile analysis implemented in the AltAnalyze platform. Microarray gene expression was also used to identify specific markers for each condition (Marker-Finder in the AltAnalyzer platform). Parameters used for the identification of differentially expressed genes are the following: genes expressed below 1 were filtered out, comparison groups with moderate t-test corrected for the p-value with Benjamini-Hochberg. Gene enrichment analyses were performed on genes having 1.5 as the minimum gene expression fold change and 0.05 as the maximum gene expression t-test p-value. Gene enrichment parameters were: z-score cut off 1.96, p-value based on 2000 permutations lower than 0.05, minimum number of genes in a gene set was 3.

source_name: Brain of mouse buried in soil 48h after death

label_protocol: Biotinylated cRNA were prepared according to the standard Affymentrix protocol from 100ng of RNA (GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript Expression Arrays, 2017, Affymetrix)

growth_protocol: 16 weeks-old male C57BL/6jn mice were used for experiments in triplicate.

extract_protocol: Illustra RNAspin Mini Isolation Kit (GE Healthcare) according to the manufacturer's guidelines

treatment_protocol: All animals were euthanized by CO2 exposure and distributed into the groups: control (0h after death); air exposed (48h after death), submerged in water (48h after death); buried in soil (48h after death). Our experiments were carried out in a room with controlled temperature (23 ºC) and humidity (55 %).

tag: strain

tag: gender

value: male

tag: age

value: 16 weeks

value: brain


title: B6 Untreated 1


title: NCI-H660 cells, PBS, Day3_1

tag: tissue

value: WT


title: WT Untreated 3


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 24h, r2

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

description: Sequencing performed by Novogene Co., Ltd.

data_processing:
Sequenced reads of mRNA were aligned against the human transcriptome using HISAT2 [D. Kim, B. Langmead and S.L. Salzberg, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, vol. 12, no. 4, pp. 357–360, 2015.]
Gene and transcript annotations were used from RefSeq (GCF_000001405.38_GRCh38.p12_genomic.fna from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference)
Aligned sequence counts were then aggregated for genes using RSEM [B. Li and C.N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol. 12, p. 323, Aug. 2011.]
Assembly: GRCh38.p12
Supplementary files format and content: RSEM aggregation results on gene level are provided as text files with 7 columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, and FPKM.

source_name: diffuse large B-cell lymphoma

growth_protocol: RPMI-1640, 20% FCS, Pen/Strep, beta-Mercaptoethanol, sodium pyruvate

extract_protocol:
NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs)
RNA library was prepared for sequencing on the Illumina platform according to the manufacturers’ protocol

treatment_protocol: Solvent (control); 5 nM tafasitamab; 5 nM rituixmab; 5 nM tafasitamab + 5 nM rituixmab

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like

value: 5nM tafasitamab and 5nM rituximab

tag: time [hours]

tag: replicate


title: MPC-Dif.2

city: Beijing

first: Jianyong

last: Han

address: 2rd, Yuanmingyuan West Road

department: State Key Laboratory of Agrobiotechnology

institute: China Agricultural University

data_processing:
For the all paired-end libraries from public data and our data, trim_garole(Martin, 2011) (v-0.6.6) software was used for quality control with the parameters: “-q 25 -j 8 --phred33 --length (reads length)/2 -e 0.1 --stringency 4 --paired”. Then, high quality reads from 12 RNA-seq libraries of our data were mapped to the reference pig genome(Sscrofa 11.1) using HISAT2(Pertea et al., 2016) (v-2.1.0) with default parameters. Expression levels of all genes were quantified as reads counts using FeatureCounts(Liao et al., 2014) (v-2.0.1) and only genes containing exons were counted, with the reference annotation Sus_scrofa.Sscrofa11.1.105.gtf downloaded from Ensembl (http://dec2021.archive.ensembl.org/index.html) that mitochondrial genes were removed.
Assembly: Sscrofa 11.1
Supplementary files format and content: Excel file includes genes TPM for each Sample

organism: Sus scrofa

source_name: pMuSCs (porcine muscle stem cells)

growth_protocol: (1) pgEpiSCs (pgEpiSCs-Low, pgEpiSCs-high) were maintained on MEF feeder layers in 3i/LAF culture medium under 20% O2 and 5% CO2 at 37℃. Basic culture medium:227.5 mL DMEM/F12, 227.5 mL neurobasal, 2.5 mL N2 supplement, 5 mL B27 supplement, 0.5% GlutaMAX, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin–streptomycin, 5% knockout serum replacement, and 50 μg/mL ascorbic acid. 3i/LAF medium: small molecules and cytokines were added to BM to the following final concentrations, 1 μM CHIR99021, 2.5 μM IWR-1-endo, 1 μM WH-4-023, 10 ng/mL recombinant human LIF, 25 ng/mL recombinant human activin A, 10 ng/mL recombinant human FGF2.   (2) pgEpiSCs-dervied muscle cells (pgEpiSCs-MPCs, pgEpiSCs-MCs) were differentiated under  5% CO2 at 37℃. The culture medium as follow: ①MDM basic medium (MDM BM): DMEM/F12 supplemented with 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin–streptomycin, 15% knockout serum replacement, 200 μM ascorbic acid; ② MDM BM supplemented with 1% B27,   3 μM CHIR99021 and 2 μM SB431542 for 3 days; ③The culture was replaced with MDM IIII (MDM BM supplemented with 10 ng/ml HGF, 10 ng/ml IGF-1, 20 ng/ml FGF2 and 0.5 μM LDN193189) for 2 days； ④MDM IV (MDM BM supplemented with 10 ng/ml IGF-1) was supplied and maintained for 4 days；⑤ Incubate for 20-25 days in MDM V ( MDM BM supplemented with 10 ng/ml HGF and 10 ng/ml IGF-1)；⑥  Replaced V with N2 differentiation medium (DMEM/F12 supplemented with 15% KOSR, 1% N2, 1% penicillin–streptomycin, and 1% nonessential amino acids).  (3)The porcine muscle stem cells were cultured under DMEM/F12 supplemented with 1% penicillin-streptomycin, 1% MEM Non-Essential Amino Acids Solution, 10% FBS, and 5 ng/mL FGF2.While cell fusion reached 90%, the cultured medium was changed to MuSCs differentiation medium (DMEM supplemented with 1% penicillin-streptomycin and 2% Horse serum  for 4 days .

extract_protocol:
Around 1×10^6 cells of samples were collected per replicate. The cells were lysed in Trizol (Invitrogen). RNA-seq library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, NR604-02). PCR production was purified using VAHTSTM DNA Clean Beads (Vazyme, N411-03).
RNA-seq library was constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme, NR604-02) following manufacturer's protocols.

value: MPC-Dif

tag: genotype

tag: treatment

value: myogenic lineage differentiation

value: Day 4


title: buried at T48 biological replicate 1


title: MPC-Dif.1

tag: cell type


title: submerged at T48 biological replicate 3

description: Gene expression data from concealment simulation (mouse in sealed bags with water)

source_name: Brain of mouse submerged in water 48h after death


title: buried at T48 biological replicate 3


title: MPC-Dif.3


title: submerged at T48 biological replicate 2


title: submerged at T48 biological replicate 1


title: air exposed at T48 biological replicate 3

description: Gene expression data from concealment simulation (mouse in sealed bags)

source_name: Brain of mouse in a air esposed container 48h after death


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 24h, r1

tag: cell line


title: WT Untreated 2

value: PMA-differentiated THP-1 cells


title: pgEpiSCs-MCs.3

source_name: pgEpiSCs (porcine pre-gastrulation epiblast stem cells)

value: pgEpiSCs-MCs

value: myogenic lineage differentiation derivatives

value: Day 44


title: WT Untreated 1

value: Untreated


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 18h, r2


title: B6 Untreated 3

value: C5aR1 KO


title: pgEpiSCs-MCs.2


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 18h, r1


title: WT Untreated 0h 3


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 12h, r2


title: pgEpiSCs-MPCs.2

value: pgEpiSCs-MPCs

value: Day 8


title: pgEpiSCs-MCs.1


title: CM tRNA-Seq rep2

data_processing:
Read demultiplexing and adapter trimming performed with cutadapt v3.5, where bases were quality trimmed from 5' and 3' ends using a phred score cutoff of 30. Only trimmed reads were retained, and reads sorter than 10 bases were discarded. An additional round of trimming was performed to remove 5’-RN nucleotides introduced by circularization from the RT primer.
Reads were processed with the mim-tRNAseq computational pipeline (v1.2) using the parameters --species Hsap --cluster-id 0.97 --min-cov 0.0005 --max-mismatches 0.075 --control-condition kiPSC --deconv-cov-ratio 0.4 --remap-mismatches 0.05. Additional DESeq2 analysis was performed by excluding unsplit tRNA clusters, and on read counts summed by isotype.
Assembly: hg38
Supplementary files format and content: csv; mim-tRNAseq generated tRNA transcript resad counts
Library strategy: mim-tRNAseq

source_name: kucg-2 hiPSC

extract_protocol:
Cells were lysed in LiDS/LET buffer (5% LiDS in 20 mM Tris, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH7.4, 100 μg/ml Proteinase K). Lysates were incubated at 60°C for 10 minutes, pushed 10 times through a 1-ml syringe with a 26G needle, and mixed by vortexing. Two volumes of cold acid phenol (pH 4.3), 1/10 volume 1-Bromo-3-chloropropane and 50 µg glycogen were added. Samples were mixed vigorously by vortexing, followed by centrifuging at 10,000 g, 4°C. The aqueous phase was transferred to a new tube and the phenol/BCP extraction was repeated. RNA was by the addition of 3 volumes of 100% ethanol and incubation at -20°C for 30 min. Pellets were washed with 80% ethanol, air-dried, and resuspended in RNase-free water.
tRNA-seq libraries were prepared using the mim-tRNAseq workflow (Behrens 2021, 2022) and sequenced on an Illumina NextSeq 500 platform.

value: kucg-2 hiPSC

value: Human cardiomyocytes


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 12h, r1


title: air exposed at T48 biological replicate 1

value: male

value: 16 weeks

value: brain


title: WT Untreated 0h 2

value: WT


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 06h, r2

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like

value: 5nM tafasitamab and 5nM rituximab


title: CM tRNA-Seq rep1


title: pgEpiSCs-MPCs.1


title: MCF7 cell, Day 45, replicate3

first: Wenze

last: Huang

address: Tsinghua street

institute: Tsinghua University

description:
MCF7_D45_3
MCF7.count.txt

data_processing:
The raw reads in FASTQ files were trimmed using cutadapt to remove flanking sequences.
The clean reads of each sample were subsampled to 8 million reads using vsearch.
The clean reads were mapped to the reference library we designed using Bowtie2.
The MAGeCK tool was used to obtain read count tables for all samples from the SAM files of mapping results.
Assembly: The design pair crRNA library
Supplementary files format and content: Tap-separated values files
Library strategy: CRISPR screens

growth_protocol: All cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco) supplemented with 10% FBS (Dox-free, BI) and 1 × antibiotic-antimycotic (Gibco), and were grown at 37 °C in a 5% CO2 cell culture incubator.

extract_protocol:
The genomic DNA was isolated from 4 × 106 cells using the Genomic DNA Kit (TianGen Biotech) for each replicated sample, and a total of 32 μg of the recovered products, representing at least 200 × coverage of the initial library size, were used as amplification templates in 16 independent PCR tubes (50 μl system each).
The genomic barcode regions encoding paired crRNAs introduced by lentivirus infection were PCR amplified using Q5 High Fidelity Polymerase (NEB) with 22 cycles using two primers targeting the upstream U6 promoter and the downstream CMV promoter. In a second round of PCR, adaptors for sequencing purposes with different barcodes were added for different samples (replicates and time points). Finally, the PCR products of all samples were pooled and purified with DNA Clean & Concentrator-5 kit (Zymo Research).

tag: time point

value: Day 45


title: SU-DHL-6, TAFA@5nM+RTX@5nM, 06h, r1


title: air exposed at T48 biological replicate 2


title: pgEpiSCs-high.2

value: pgEpiSCs-high

value: No treatment

value: Day 0


title: pgEpiSCs-high.3


title: Neurons tRNA-Seq rep2

value: Human mature neurons


title: control at T0 biological replicate 2

description: Gene expression data from non-concealed mouse

source_name: Brain of mouse immediately after death


title: MCF7 cell, Day 45, replicate2

description:
MCF7_D45_2
MCF7.count.txt


title: control at T0 biological replicate 3


title: SU-DHL-6, TAFA@5nM, 24h, r2

value: 5nM tafasitamab


title: Neurons tRNA-Seq rep1


title: pgEpiSCs-high.1


title: control at T0 biological replicate 1


title: WT Untreated 0h 1

value: PMA-differentiated THP-1 cells

value: Untreated


title: pgEpiSCs-Low.3

value: pgEpiSCs-Low


title: MCF7 cell, Day 45, replicate1

description:
MCF7_D45_1
MCF7.count.txt


title: SU-DHL-6, TAFA@5nM, 24h, r1


title: NPC tRNA-Seq rep2

value: kucg-2 hiPSC

value: Human neural progenitor


title: MCF7 cell, Day 30, replicate3

description:
MCF7_D30_3
MCF7.count.txt

value: Day 30


title: NPC tRNA-Seq rep1


title: MCF7 cell, Day 30, replicate2

description:
MCF7_D30_2
MCF7.count.txt


title: SU-DHL-6, TAFA@5nM, 18h, r2


title: SU-DHL-6, TAFA@5nM, 18h, r1


title: pgEpiSCs-Low.1


title: hiPSC kucg-2 tRNA-Seq rep1

value: Human induced pluripotent stem cell


title: SU-DHL-6, TAFA@5nM, 12h, r2


title: SU-DHL-6, TAFA@5nM, 12h, r1


title: MCF7 cell, Day 15, replicate3

description:
MCF7_D15_3
MCF7.count.txt

value: Day 15


title: MCF7 cell, Day 30, replicate1

description:
MCF7_D30_1
MCF7.count.txt


title: hiPSC kucg-2 Ribo-Seq CHX rep1

data_processing:
Sequencing libraries were demultiplexed and adapter-trimmed with Cutadapt v2.5 [Martin 2011]. Indels in the alignment to the adapter sequence were disabled with --no-indels and low-quality bases were removed from both 5’ and 3’ ends with -q 30,30. Reads without adapters were discarded with --trimmed-only. Following demultiplexing, reads were further trimmed to remove the two 5′-RN nucleotides introduced by circularization from the RT primer with -u 2. Trimmed reads longer than 10 nt were aligned to a human ribosomal RNA reference using Bowtie v1.2.2 [Langmead et al. 2009] with the following options: -p 40 -S --best.
rRNA-filtered reads were aligned to GRCh38.p13 using STAR v2.6.1c [Dobin et al., 2013] the following options: --outFilterMultimapNmax 1 --outSAMtype BAM SortedByCoordinate --outFilterMismatchNmax 0 --outFilterMatchNmin 20 --alignEndsType Local --seedSearchStartLmax 14 --alignIntronMax 10000 --sjdbOverhang 28 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --quantMode TranscriptomeSAM --outSAMattributes NH HI AS nM NM MD.
We identified the A site location in each mapped read with Scikit-ribo [Fang et al. 2018], which uses a random forest with recursive feature selection and a generalized linear model for accurate A-site prediction based on matched ribosome profiling and RNA-Seq datasets. Kallisto 0.44.0 with parameters -b 100 --single -l 180 -s 20 -t 40 was used to quantify transcript abundances in Transcripts Per Million (TPM) from RNA-Seq data based on the reference set of MANE-annotated transcripts (see Codon usage analysis for description of this annotation). To avoid memory errors due to the large size of the human genome and the presence of multiple transcript isoforms, all RNAfold dependencies in Scikit-ribo were omitted, and the index was built separately for each chromosome. To make the hg38 GTF compatible with Scikit-ribo, transcript/UTR annotations were removed. For each transcript, the start codon in the first exon and the stop codon in the last exon were adjusted to represent transcript start and end coordinates, taking into account the gene strand. To estimate codon dwell times, short (20-23 nt) and long (28-33 nt) ribosome footprints were analyzed separately.
Assembly: GRCh38
Supplementary files format and content: csv; codon dwell times from scikit-ribo for all samples
Library strategy: Ribo-Seq

extract_protocol:
Cells were quickly washed with ice cold PBS supplemented with 100 µg/ml cycloheximide (CHX) and snap-frozen in liquid nitrogen. For libraries prepared with cycloheximide in the lysis buffer, plates were thawed on ice and cells were scraped off the plate in 400 µl polysome lysis buffer (20 mM Tris pH=7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100, 1 mM DTT, 100 µg/ml CHX, 25 U/ml Turbo DNase), 0.1% NP-40, 10 µg/ml aprotinin, 20 µM leupeptin, 2.5 µM pepstatin A, 0.5 mM AEBSF and 1x Phosphatase Inhibitor Cocktail. Samples were vortexed vigorously, triturated through a 26G gauge needle, and spun down for 7 minutes at 16,000xg/ 4°C. Supernatant was transferred to a new tube. 20 µg RNA in 200 µl polysome lysis buffer were digested with 50 U RNase I for 45 minutes at 2,000 rpm/22°C. For libraries prepared with cycloheximide/tigecycline (CHX/TIG) in the lysis buffer, plates were thawed and cells from a 10-cm dish were lysed in 15 ml polysome lysis buffer supplemented with 0.1% NP-40 and 100 µg/ml tigecycline (TIG). After incubation on ice for 5 minutes, extracts were pre-cleared by centrifugation for 5 minutes at 3,000 g/ 4°C. Ribosomes were pelleted through 3 ml of a sucrose cushion (1 M sucrose, 20 mM Tris pH=8.0, 140 mM KCl, 5 mM MgCl2, 1 mM DTT) by spinning the layered solutions in the Type 70 Ti rotor for 120 minutes at 50,000 rpm/ 4°C. Ribosome pellets were rinsed once, dissolved in 200 µl drug-free polysome lysis buffer, and incubated with 200 U (hiPSC) or 300 U (NPC) RNase I for 45 minutes at 2,000 rpm/22°C.
Ribosome footprint libraries were prepared essentially as described (McGlincy and Ingolia, 2017; Wu 2019) with minor modifications. RNase I digestion was stopped by addition of 100 U Superase In and extracts were loaded on a sucrose cushion. The pellet was dissolved in 400 µl LiDS/LET lysis buffer and RNA was extracted with the acid phenol protocol. Fragments in the range of 19 to 32 nucleotides were isolated by gel size selection, with T4 PNK and ligated to pre-adenylated adapters containing 5 random nucleotides at their 5’ ends (McGlinzy 2017) with T4 RNA Ligase 2, truncated KQ. Adapter-ligated RNA was subjected to rRNA depletion using the Ribo-Seq riboPOOL h/m/r depletion kit (siTOOLs) for CHX-only samples, and legacy RiboZero Gold kit (Illumina) for CHX+TIG samples The rRNA-depleted footprints were reverse-transcribed with Protoscript II and cDNA was circularized with recombinant TS2126 RNA ligase 1 (commercially available as CircLigase). Libraries were constructed from circularized cDNA with KAPA HiFi DNA Polymerase and single-end sequencing was performed on a NextSeq 550 platform (Illumina).

value: 100 ug/ml CHX


title: hiPSC kucg-2 tRNA-Seq rep2

value: WT


title: MCF7 cell, Day 15, replicate2

description:
MCF7_D15_2
MCF7.count.txt


title: NPC kucg-2 Ribo-Seq CHX+TIG rep2

value: 100 ug/ml CHX, 100 ug/ml TIG


title: SU-DHL-6, TAFA@5nM, 06h, r1

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like


title: MCF7 cell, Day 15, replicate1

description:
MCF7_D15_1
MCF7.count.txt


title: KO_HFD

city: Kraków

first: Monika

middle: Marta

last: Stefanska

state: malopolska

address: Medical College, Wielicka 265

department: Department of Clinical Immunology

country: Poland

institute: Jagiellonian University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Output fastq files were uploaded to 10x Genomics Cell Ranger Software (cellranger-6.1.2). Data were demultiplexed, pre-analyzed and mapped to the mouse reference genome (mm10-3.0.0) with a provided by 10x Genomics cellranger mkref pipeline.
Assembly: mm10-3.0.0
Supplementary files format and content: count matrix files

source_name: Aorta

extract_protocol:
The aortas of each group of mice were pooled, cut into small pieces, and digested in 2.5 ml enzyme mix from Multi Tissue Dissociation Kit 2 (Miltenyi Biotec) prepared as described in the protocol provided by the vendor. The samples were placed at 37oC for 30 min with shaking (250 RPM). The suspension was gently pipetted every 15 min. Then the cells were filtered through a 70 μm strainer, centrifuged at 500 × g for 5 min, and resuspended in red blood cells lysis buffer (BioLegend). After 5 min, the cells were centrifuged at 500 × g for 5 min, washed with PBS, and resuspended in 300 µl of PBS containing 2% FBS and 200 ng/ml DAPI. To exclude dead cells and collect only the viable ones, the DAPI-negative cells were sorted with MoFlo XPD (Beckman Coulter) cell sorter.
Cells isolated from meniscal zones were subjected to library construction with the use of Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics, #PN-1000269). Samples were processed according to the manufacturer's protocol. Firstly cell suspensions were divided into the single-cell format with a Chromium X Series controller (10x Genomics) that encapsulates single cells within nanoliter-scale Gel Beads-in-emulsion (GEMs), where all generated cDNA share a common barcode. Incubation of the GEMs produced barcoded full-length cDNA from polyadenylated mRNA. After incubation, the GEMs were ruptured and the pooled fractions were recovered. Silane magnetic beads were used to purify the first-strand cDNA from the reaction mixture. Barcoded, full-length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the size of the cDNA amplicons. Samples` indexes and TruSeq Read 2 were added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final librarieswere used in Illumina bridge amplification.

value: Aorta


title: Lox_HFD

description: 10x Genomics


title: KO_CTR

description: 10x Genomics


title: pgEpiSCs-Low.2

value: No treatment

value: Day 0


title: NPC kucg-2 Ribo-Seq CHX+TIG rep1


title: MCF7 cell, Day 00, replicate1

description:
MCF7_D00_1
MCF7.count.txt

value: Day 00


title: Lox_CTR

description: 10x Genomics


title: hiPSC kucg-2 Ribo-Seq CHX+TIG rep1


title: SU-DHL-6, RTX@5nM, 24h, r1

value: 5nM rituximab


title: WT fast proliferating CD8 T cells

city: Xiamen

first: Guo

last: Fu

address: No. 422, Siming South Road, Xiamen, Fujian, China.

institute: Xiamen University

description: 10x Genomics

data_processing:
The sample demultiplexing, barcode processing, single cell 3' gene counting, and the ability to process data was from Targeted Gene Expression and Feature Barcode technology.
Supplementary files format and content: mm-10
Supplementary files format and content: 10x Genomics Cloud, tar archive with *.bed, *.csv, *json and vloupe files
Library strategy: scTCR-seq

source_name: spleen

extract_protocol:
Naïve CD8 T cells were isolated from WT or MHC II-/- mice, labeled with CTV, adoptively transferred into 15 irradiated B6 mice respectively, with one million CD8 T cells per mouse. Splenocytes were isolated and CTV- fast-proliferating cells were sorted. All 0.02 million CTV- WT CD8 T cells sorted and 0.15 million out of 1.2 million CTV- MHC II-/- CD8 T cells sorted were subjected to 10x genomics TCR sequencing.After filtering with a 30-micron MACS SmartStrainer (Miltenyi Biotec), single cells were resuspended in PBS (calcium and magnesium free) containing 0.04% weight/volume BSA, and further diluted to 300 cells/µl after cell count (Countess II FL, Life Technologies).
Library preparation was performed following the 10x Genomics Single Cell V(D)J Reagent kit v1.1 protocol

value: spleen

value: WT fast proliferating CD8 T cells

value: CTV labeled naive CD8 T cells were adoptive transfer into irradited CD45.1 mice for 6 Days, CTV- CD8 T cells were sorted for sequencing.

tag: batch


title: MHC II-/- fast proliferating CD8 T cells, replicate5

description: 10x Genomics

value: MHC II-/-


title: SU-DHL-6, RTX@5nM, 24h, r2


title: Huh7 cell, Day 45, replicate3

description:
Huh7_D45_3
Huh7.count.txt

value: Day 45


title: CM RNA-Seq rep2

data_processing:
3’ adapters were trimmed using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Reads were aligned to the GRCh38 human genome using STAR v2.6.1c with the following parameters: --outSAMtype BAM SortedByCoordinate --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --quantMode TranscriptomeSAM GeneCounts. featureCounts v1.6.2 was used to count reads overlapping a filtered set of protein coding gene annotations from the GENCODE basic gene annotation. Differential gene expression analysis was performed using DESEq2 v1.38.1 with default settings and gene counts from featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv; transcripts-per-million (TPM) counts per transcript in MANE annotation

extract_protocol:
Cells were lysed in LiDS/LET buffer (5% LiDS in 20 mM Tris, 100 mM LiCl, 2 mM EDTA, 5 mM DTT, pH7.4, 100 μg/ml Proteinase K). Lysates were incubated at 60°C for 10 minutes, pushed 10 times through a 1-ml syringe with a 26G needle, and mixed by vortexing. Two volumes of cold acid phenol (pH 4.3), 1/10 volume 1-Bromo-3-chloropropane and 50 µg glycogen were added. Samples were mixed vigorously by vortexing, followed by centrifuging at 10,000 g, 4°C. The aqueous phase was transferred to a new tube and the phenol/BCP extraction was repeated. RNA was by the addition of 3 volumes of 100% ethanol and incubation at -20°C for 30 min. Pellets were washed with 80% ethanol, air-dried, and resuspended in RNase-free water.
250 ng of the same total RNA used for mim-tRNAseq library preparation were used for mRNA-Seq library construction with the Zymo-Seq RiboFree Total RNA Library Kit (Zymo Research, #R3000). Libraries were sequenced on a NextSeq 500 platform.

value: kucg-2 hiPSC

value: Human cardiomyocytes


title: SU-DHL-6, RTX@5nM, 18h, r2


title: Huh7 cell, Day 45, replicate2

description:
Huh7_D45_2
Huh7.count.txt


title: hiPSC kucg-2 Ribo-Seq CHX+TIG rep2

value: Human induced pluripotent stem cell


title: SU-DHL-6, TAFA@5nM, 06h, r2

value: 5nM tafasitamab


title: MHC II-/- fast proliferating CD8 T cells, replicate4

description: 10x Genomics


title: Huh7 cell, Day 45, replicate1

description:
Huh7_D45_1
Huh7.count.txt


title: Neurons RNA-Seq rep2

value: Human mature neurons

value: WT


title: MHC II-/- fast proliferating CD8 T cells, replicate3

description: 10x Genomics


title: SU-DHL-6, RTX@5nM, 18h, r1

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like


title: MHC II-/- fast proliferating CD8 T cells, replicate2

description: 10x Genomics


title: SU-DHL-6, RTX@5nM, 12h, r2


title: Huh7 cell, Day 30, replicate2

description:
Huh7_D30_2
Huh7.count.txt

value: Day 30


title: SU-DHL-6, RTX@5nM, 12h, r1


title: MHC II-/- activated CD8 T cells, replicate3

description: 10x Genomics

value: MHC II-/-  activated CD8 T cells

value: naive CD8 T cells were treated with anti-CD3/CD28 for 3 days


title: NPC RNA-Seq rep2

value: Human neural progenitor


title: NPC RNA-Seq rep1


title: Huh7 cell, Day 15, replicate3

description:
Huh7_D15_3
Huh7.count.txt

value: Day 15


title: SU-DHL-6, RTX@5nM, 06h, r1

value: 5nM rituximab


title: MHC II-/- activated CD8 T cells, replicate2

description: 10x Genomics

value: spleen


title: Huh7 cell, Day 30, replicate3

description:
Huh7_D30_3
Huh7.count.txt


title: CM RNA-Seq rep1


title: Huh7 cell, Day 15, replicate2

description:
Huh7_D15_2
Huh7.count.txt


title: SU-DHL-6, solvent, 24h, r2

value: control (solvent only)


title: hiPSC kucg-2 RNA-Seq rep2


title: SU-DHL-6, solvent, 24h, r1


title: hiPSC kucg-2 RNA-Seq rep1


title: MHC II-/- fast proliferating CD8 T cells, replicate1

description: 10x Genomics

value: MHC II-/-

value: CTV labeled naive CD8 T cells were adoptive transfer into irradited CD45.1 mice for 6 Days, CTV- CD8 T cells were sorted for sequencing.


title: WT activated CD8 T cells, replicate3

description: 10x Genomics

value: WT activated CD8 T cells


title: Huh7 cell, Day 00, replicate1

description:
Huh7_D00_1
Huh7.count.txt

value: Day 00


title: SU-DHL-6, solvent, 18h, r2


title: Huh7 cell, Day 30, replicate1

description:
Huh7_D30_1
Huh7.count.txt


title: HeLa cell, Day 45, replicate3

description:
HeLa_D45_3
HeLa.count.txt

source_name: HeLa

value: HeLa

value: Day 45


title: WT activated CD8 T cells, replicate2

description: 10x Genomics

value: WT


title: SU-DHL-6, solvent, 18h, r1

value: diffuse large B-cell lymphoma


title: CM ATAC-Seq rep1

data_processing:
ATAC-Seq  datasets were preprocessed to remove potential 3’ adapters using Trim Galore v0.6.4 with default settings, retaining reads of length ≥20.
Adapter-trimmed ATAC-Seq libraries were aligned to the GRCh38 reference genome using STAR with the following settings: up to one mismatch per read, a maximum of ten alignment positions, end-to-end alignment, prohibited introns, only one alignment reported per read (--outFilterMismatchNmax 1 --outFilterMultimapNmax 10 --alignEndsType EndToEnd --alignIntronMax 1 --outSAMmultNmax 1). Read duplicates were then removed using Picard Tools MarkDuplicates v2.17.10 as described above, and alignments to the mitochondrial genome were also filtered. To account for dimerisation of the transposon before insertion (Buenrostro et al., 2013 Nat Methods), filtered ATAC-Seq reads were additionally shifted by +4 bp and -5 bp for positive and negative strand alignments, respectively, using deepTools alignmentSieve v3.4.0. Simultaneously, alignmentSieve was used to split fragments with a maximum length of 100 nt representing nucleosome-free regions (NFRs). Both operations were performed simultaneously using the --ATACshift and --maxFragmentLength 100 parameters. ATAC-Seq NFR alignments were then converted to BEDPE format for peak calling using alignmentSieve --BED. MACS peak calling was performed on all reads without duplicate removal (--keep-dup all), as these had previously been filtered for duplicates with Picard Tools. BEDPE files generated above were used (-f BEDPE) without corresponding control input samples, shifting model building was not disabled, and fragment sizes were not specified. Additionally, for all peak calling, signal normalized per million reads was saved in bedgraph format for visual inspection of datasets (-B and -SMPR). Finally, predicted peaks were filtered using the ENCODE project unified GRCh38 blacklist regions bed file (https://www.encodeproject.org/files/ENCFF356LFX/) by identifying overlaps using bedtools intersect v2.29.2.
Assembly: hg38
Supplementary files format and content: narrowPeak; peaks called with macs2
Supplementary files format and content: csv; ATAC-Seq NFR read counts at hg38 tRNA genes (+-125 bp)

extract_protocol:
Cells were collected from plates by trypsinization.
ATAC-Seq libraries were generated  with the ATAC-Seq Kit from Active Motif (#53150) according to the manufacturer's instructions and sequenced in a 75-bp paired-end run on an Illimina NextSeq 500 platform.

value: kucg-2 hiPSC

value: Human cardiomyocytes


title: SU-DHL-6, RTX@5nM, 06h, r2

value: germinal center B-cell-like


title: HeLa cell, Day 45, replicate2

description:
HeLa_D45_2
HeLa.count.txt


title: Neurons RNA-Seq rep1

value: Human mature neurons


title: WT activated CD8 T cells, replicate1

description: 10x Genomics

value: naive CD8 T cells were treated with anti-CD3/CD28 for 3 days


title: SU-DHL-6, solvent, 12h, r2


title: Neurons ATAC-Seq rep2


title: Huh7 cell, Day 15, replicate1

description:
Huh7_D15_1
Huh7.count.txt

value: Day 15


title: HeLa cell, Day 45, replicate1

description:
HeLa_D45_1
HeLa.count.txt


title: HeLa cell, Day 30, replicate3

description:
HeLa_D30_3
HeLa.count.txt

value: Day 30


title: HeLa cell, Day 30, replicate2

description:
HeLa_D30_2
HeLa.count.txt


title: NPC ATAC-Seq rep2

value: Human neural progenitor


title: SU-DHL-6, solvent, 06h, r2

value: control (solvent only)


title: Neurons ATAC-Seq rep1


title: SU-DHL-6, solvent, 12h, r1


title: SU-DHL-6, solvent, 06h, r1


title: klf2neg_stim_polya3

city: Cincinnati

first: Sing Sing

last: Way

state: Ohio

address: 3333 Burnet Avenue, MLC 7017

department: Pediatrics

institute: Cincinnati Children's

description: Library 07

data_processing:
FASTQ files were mapped with STAR (version 2.7.9) to the mm10 genome as follows: STAR --runThreadN 16 --genomeDir <path> --readFilesCommand zcat --readFilesIn <read1.fastq.gz> <read2..fastq.gz> --outSAMtype BAM SortedByCoordinate
Mapped data was converted into HOMER tag directory format using HOMER (v4.11) and samtools with the following command: makeTagDirectory <directory_output_path>  <path to aligned BAM file> -genome mm10 -checkGC -format sam
Sequencing counts were quantified using HOMER (v4.11) using the rnaQuan.R wrapper script ((https://github.com/z5ouyang/A.C.Rsuite) using).
Pairwise differential expression was determined using HOMER (v4.11) and DeSeq2 using the rnaDiff.R wrapper script (https://github.com/z5ouyang/A.C.Rsuite).
Assembly: GRCm38
Supplementary files format and content: rawCount
Supplementary files format and content: rawTPM

molecule: polyA RNA

source_name: CD4 T-cells

extract_protocol:
RNA extraction was performed using the manufacter (Qiagen RNeasy) instructions
SMARTeR stranded mammalian pico protocol

treatment_protocol: FACS purified FOXP3-negative KLF2+ CD44hi and FOXP3-negative KLF2-negative CD44hi CD4 cells were stimulated with anti-CD3 (2.5 micrograms/mL) plus anti-CD28 antibody (1.25 micrograms/mL ) compared with no stimulation controls for 48 hours prior to RNA harvest

value: CD4 T-cells

value: KLF2 negative

value: Stimulated


title: klf2neg_stim_polya 4

description: Library 08


title: CM ATAC-Seq rep2


title: NPC ATAC-Seq rep1


title: klf2neg_nostim_polya4

description: Library 06

value: Unstimulated


title: klf2neg_nostim_polya3

description: Library 05


title: hiPSC kucg-2 ATAC-Seq rep1

value: Human induced pluripotent stem cell


title: Untreated AsPC-1 cells

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads are filtered to remove reads containing adapters or reads of low quality, so that downstream analyses are based on clean reads.
Algorithm for mapping sequences: TopHat2
Genome_build: GRCh37.90
Supplementary_files_format_and_content: A matrix table includes FPKM values for each Sample.

source_name: Pancreatic cancer cell line

extract_protocol:
RNA was prepared using the GENEzol TriRNA Pure Kit following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: untreated


title: klf2pos_stim_polya2

description: Library 04

value: KLF2 positive


title: hiPSC kucg-2 ATAC-Seq rep2

value: WT


title: VU-0365114-treated AsPC-1 cells


title: HeLa cell, Day 15, replicate3

description:
HeLa_D15_3
HeLa.count.txt

value: HeLa


title: MHC II-/-  activated CD8 T cells, replicate1

description: 10x Genomics

value: spleen

value: MHC II-/-  activated CD8 T cells

value: MHC II-/-


title: HeLa cell, Day 15, replicate2

description:
HeLa_D15_2
HeLa.count.txt


title: VU-0365114-treated PANC-1 cells


title: klf2pos_stim_polya1

description: Library 03


title: HeLa cell, Day 15, replicate1

description:
HeLa_D15_1
HeLa.count.txt


title: klf2pos_nostim_polya2

description: Library 02


title: Untreated PANC-1 cells


title: purifed 2W1S specific CD4 cell from Ca-2W1S colonized mice (April 2016)

data_processing:
Mapping was performed using AltAnalyze (https://www.altanalyze.org)
Assembly: mm10
Supplementary files format and content: comma separated file includes log-normalized counts

source_name: spleen and peripheral lymph nodes

extract_protocol:
For the initial cell capture, cDNA synthesis and amplification, and harvest step, the Core Staff uses the SMART-Seq® v4 Ultra Low Input RNA Kit for the Fluidigm® C1™ System, IFCs User Manual and follows all manufacturer’s instructions.
For the Library Preparation, Pooling and Cleanup, again the Core Staff follows the manufacturer’s instructions from the SMART-Seq® v4 Ultra Low Input RNA Kit for the Fluidigm® C1™ System, IFCs User Manual. The only change is the time of the tagmentation reaction. The Core staff using the following Tagmentation Step: 55 C – for 20 minutes.

value: spleen and peripheral lymph nodes

value: CD4 T cell

value: CA-2W1S colonization


title: klf2pos_nostim_polya 1

description: Library 01


title: purifed 2W1S specific CD4 cell from Ca-2W1S colonized mice (March 2016)


title: Frontal bone, biological replicate 3

status: Public on Oct 21 2023

city: Pittsburgh

first: Matthew

middle: Brian

last: Rogera

state: Pennsylvania

address: 325 Sutherland Drive

department: Oral and craniofacial sciences

institute: University of Pittsburgh

data_processing:
Reads were mapped using TopHat, and transcripts were assembled using Cufflinks. Differential abundances were calculated using EdgeR with counts fitted to a generalized linear model and tested using a likelihood ratio test (GLMLRT).
Genes with counts per million of less than 1, in two biological replicates were excluded from the analysis. Genes were considered significant with a FDR (false discovery rate) of <0.05.
Assembly: mm38
Supplementary files format and content: genes.count_tracking

source_name: microdissected frontal bones including metopic suture

growth_protocol: Timed-pregnant CD-1 females were purchased from Charles River Laboratory. We collected embryos via C-section after CO2 euthanasia of the pregnant dam on the appropriate day and we confirmed embryo staging by morphology. All animal husbandry, procedures and protocols were approved by and performed under the oversight of the University of Pittsburgh Institutional Animal Care and Use Committee.

extract_protocol:
The tissues were lysed with the Trizol reagent, followed by further disruption with QiaShredder followed by RNA extraction with Qiagen RNAeasy kit.
Axeq generated and sequenced the libraries as 100 bp paired end reads on an Illumina HiSeq2000 sequencer

treatment_protocol: To perform frontal and parietal bone-derived calvarial osteoblast cultures we dissected the skull cap off, removed the overlying tissue and dissected the bones out along the naso-frontal, coronal and lambdoidal sutures (Fig 1A). The dissection included the interfrontal suture between the frontal bones and the sagittal suture joining the parietal bones. We pooled 3 pairs of frontal bones and 3 pairs of parietal bones to make one biological replicate for RNASeq analysis.

value: embryonic organ

value: wildtype


title: Frontal bone, biological replicate 2

value: microdissected frontal bones including metopic suture


title: Parietal bone, biological replicate 2

source_name: microdissected parietal bones including sagittal suture


title: Parietal bone, biological replicate 3

value: microdissected parietal bones including sagittal suture


title: Parietal bone, biological replicate 1


title: HeLa cell, Day 00, replicate1

description:
HeLa_D00_1
HeLa.count.txt

value: Day 00


title: HEK293 cells, PKA Cα, doxycycline, biol rep 2

city: La Jolla

first: Valeria

last: Burghi

address: 3855 Health Sciences Drive, Room 2345

department: Pharmacology

institute: University of California San Diego

data_processing:
The quantification of transcripts was calculated using Salmon (version 1.7.0), which provides accurate expression estimates.
The differential gene expression analysis including quality control, model fitting, and hypothesis testing was conducted using DESeq2.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) from Genome Reference Consortium
Supplementary files format and content: SF files containing count values of each sample generated by Salmon (version 1.7.0).

growth_protocol: HEK293 parental and PKA Cα cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (D6429, Sigma) supplemented with 10% fetal bovine serum (FBS) (F2442, Sigma) and 1% penicillin/streptomycin (A5955, Sigma) and maintained in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
After treatment, the cells were washed with PBS, total RNA was isolated with a RNeasy Mini Kit (74104, Qiagen) including an on-column DNase I digestion and quantified using a Nanodrop ND-1000 (Thermo Scientific).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.

treatment_protocol: HEK293 wild type and PKA Cα cells were seeded in poly-D-lysine coated 6 well-plates and treated with 1 μg/ml doxycycline for 48 hours.

value: embryonic

value: PKA Calpha subunit overexpression

value: incubation with doxycycline

value: 48 hours


title: HEK293 cells, PKA Cα, doxycycline, biol rep 3


title: HEK293 cells, PKA Cα, doxycycline, biol rep 1


title: HEK293 cells, parental, doxycycline, biol rep 2

value: wild type


title: HEK293 cells, parental, doxycycline, biol rep 1