title: siTFE3.B.DK_yes_rep3

city: Giessen

first: Jochen

last: Wilhelm

state: Hessen

address: Aulweg 132

department: Institute for Lung Health

institute: Justus-Liebig University Giessen

hyb_protocol: Hybridization was performed following the Agilent protocol at 65Â°C over-night in an in-situ hybridization oven with slides mounted in Agilent hybridization chambers. Slides were rotated with 2 rpm.

scan_protocol: Slides were scanned using the InnoScan 900 scanner (Innopsys, Carbonne France) at 2 Âµm/pixel resolution and analyzed with Mapix 9.0.0

data_processing: Raw data was further processed using R (http://www.R-project.org) and limma (Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, G.K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. NAR 43(7), e47). Background correction was performed with the normexp model using negative control spots and and offset of 1. Spot intensities were quantile normalized between arrays.

source_name: Cell line, HeLa

label_protocol: Purified total RNA was amplified using the Agilent Low-Input QuickAmp Kit (Agilent, Waldbronn, Germany).

growth_protocol: HeLa cells were grown in DMEM PAN Biotech (#P04-03550) supplemented with 10 % (v/v) FBS, 100 U/ml Penicillin, 100 µg/ml Streptomycin and 2mM L-Glutamin.

extract_protocol: MACHEREY-NAGEL NucleoSpin® RNA isolation Kit

treatment_protocol: siRNA transfection (20 nM) with 1% HiPerfect  1 µg/ml IL-1α was added to the medium for 1h.

tag: sirna

value: yes


title: siRELA_yes_rep4

status: Public on Mar 05 2025

type: RNA

country: Germany

molecule: total RNA

organism: Homo sapiens

value: siRELA


title: siTFEB_no_rep3

value: siTFEB

value: no


title: siTFE3_yes_rep2


title: siTFE3_no_rep2


title: siGLIS2_no_rep2


title: siLuci_yes_rep4

value: siLuci


title: untrans_no_rep4

value: untrans


title: siTFE3.B.DK_yes_rep2


title: siGLIS2_yes_rep2


title: siTFE3.B.DK_yes_rep1


title: siTFEB_no_rep2


title: untrans_yes_rep4


title: siTFEB_yes_rep1


title: siGLIS2_yes_rep1


title: siRELA_no_rep4


title: siTFEB_yes_rep2


title: siTFEB_yes_rep3


title: siTFE3.B.DK_no_rep2


title: siGLIS2_yes_rep3


title: untrans_yes_rep3


title: siRELA_yes_rep3


title: siLuci_yes_rep3


title: siTFE3_no_rep1


title: siGLIS2_no_rep1


title: siTFE3_yes_rep1


title: siTFE3.B.DK_no_rep1


title: siTFEB_no_rep1


title: 20_H1975_DNA_2

type: SRA

city: Aarhus C

first: martin

middle: R

last: Jakobsen

address: Høegh-Guldbergs Gade 10, Bygn. 1115

department: Biomedicine

country: Denmark

institute: Aarhus University

description: Library name: 20

library_source: transcriptomic

data_processing:
The output fastq files were analyzed with R version 4.4.1 or the CLC Genomics Workbench 12 (QIAGEN) software. Using R or the RNA-seq module of the CLC Genomics Workbench 12, all reads were trimmed and mapped to the Genome Reference Consortium Human Build 38 (GRCh38/hg38). Expression values of each gene were normalized to transcripts per million (TPM).
Assembly: Genome Reference Consortium Human Build 38 (GRCh38/hg38)
Supplementary files format and content: All processed data is located in one csv file. Sheet 1 contains sample 1-12 and sheet 2 contains samle S_1, S_2, S_3, and S_4. Gene names are in the first clumn followed by samples in the next columns. Expression level is transcripts per million (TPM).

extract_protocol: RNA was purified using RNeasy mini kit (Qiagen, Cat#: 74106) or NucleoSpin RNA kit (Macherey-nagel, Cat#: 740955) and eluted in 30-40uL RNase-free water.

tag: cell line

tag: cell type

value: non-small cell lung cancer

tag: genotype

value: WT

tag: treatment

value: DNA


title: 17_H1975_UT_1

description: Library name: 17

value: Untreated


title: siLuci_no_rep3


title: 16_H596_DNA_2

description: Library name: 16


title: 18_H1975_UT_2

description: Library name: 18


title: siLuci_no_rep4


title: 19_H1975_DNA_1

description: Library name: 19


title: 13_H596_UT_1

description: Library name: 13


title: 14_H596_UT_2

description: Library name: 14


title: siRELA_no_rep3


title: 12_H1650_DNA_2

description: Library name: 12


title: 15_H596_DNA_1

description: Library name: 15


title: siRELA_yes_rep2


title: 11_H1650_DNA_1

description: Library name: 11


title: siS100A8.9.DK_yes_rep2


title: untrans_no_rep3


title: siS100A8_no_rep2


title: siZBTB5_no_rep2


title: siLuci_yes_rep2


title: untrans_yes_rep2


title: siS100A9_yes_rep2


title: siS100A8.9.DK_no_rep2


title: siLuci_no_rep2


title: siS100A9_no_rep2


title: 10_H1650_UT_2

description: Library name: 10


title: 9_H1650_UT_1

description: Library name: 9


title: 8_H2228_DNA_2

description: Library name: 8


title: siS100A8_yes_rep2


title: 7_H2228_DNA_1

description: Library name: 7


title: 6_H2228_UT_2

description: Library name: 6


title: siZBTB5_yes_rep2


title: untrans_no_rep2


title: siS100A8.9.DK_yes_rep1


title: 5_H2228_UT_1

description: Library name: 5


title: siS100A8_yes_rep1


title: untrans_yes_rep1


title: siRELA_yes_rep1


title: 4_HCC827_DNA_2

description: Library name: 4


title: 3_HCC827_DNA_1

description: Library name: 3


title: 2_HCC827_UT_2

description: Library name: 2


title: siRELA_no_rep2


title: siS100A8.9.DK_no_rep1


title: siZBTB5_yes_rep1


title: siS100A9_no_rep1


title: Paxip1_sgPaxip1_3_DON

city: Shanghai

first: Ningning

last: Niu

address: 160 Pu Jian Road, Shanghai

department: Clinical Stem Cell Research Center

country: China

institute: Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and to discard reads shorter than 50bp, then mapped to mm10 whole genome using Bowtie2 v. 2.4.2
Reads Per Kilobase of exon per Megabase of library size were calculated using homer annotatePeaks.pl
Peaks were called using MACS2 version 2.2.7.1 with the parameters -B  -t  --broad -g mm --broad-cutoff 0.1 -q 0.01
Assembly: mm10
Supplementary files format and content: peak files for each Sample.
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: KPC1201 cells

extract_protocol:
Briefly, tumor cell were generated and collected after 72 hours of glutamine starvation.CUT&Tag assay was performed following the manual of hyperactive pG-Tn5/pA-Tn5 transposase for CUT&Tag kit (TD901, Vazyme).
DNA library were prepared according to manufacturer’s instructions of Trueprep index kit v2 (TD202, Vazyme)

value: KPC1201 cells

value: pancreatic tumor cells

value: DON 1 μM


title: ileum_HFDHET6I

city: Beijing

first: ye

last: yuan

address: YiHeyuan road 5th

institute: Peking University

description: Library name: 74

data_processing:
The raw file (fastq) was processed to quality check, alignment, sorting and annotation by using viz. FastQC, Bowtie2, HISAT2, and Samtools along with imperative files containing the mouse genome reference sequence (GRCm39 from UCSC genome browser on mouse) and genes coordinate information file.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: ileum

extract_protocol:
Total RNA of duodenum, jejunum or ileum were extracted by a TRIzol Reagent (Thermo Fisher Scientific, 15596026) .
Library preparation is performed using Optimal Dual-mode mRNA Library Prep Kit (BGI-Shenzhen, China). A certain amount of RNA are denatured at suitable temperature to open the secondary structure, and mRNA is enriched by oligo (dT) attached magnetic beads. After reacting at a suitable temperature for a fixed time period, RNAs are fragmented with fragmentation reagents. Then First-strand cDNA is generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The synthesized double strand cDNA is subject to end repairment reaction. After cDNA end repairment, a single ‘A’ nucleotide is added to the 3’ ends of the blunt fragments through A tailing reaction. Then the reaction system for adaptor ligation configured to ligate adaptors with the cDNAs, and finally, the library products are amplified through PCR reaction and subjected to quality control. Next, the single-stranded library products are produced via denaturation. The reaction system for circularization is set up to get the single-stranded cyclized DNA products. Any uncyclized single stranded linear DNA molecules will be digested. The final single strand circularized library is amplified with phi29 and rolling circle amplification (RCA) to make DNA nanoball (DNB) which carries more than 300 copies of the initial single stranded circularized library molecule. The DNBs are loaded into the patterned nanoarray and PE150 bases reads are generated on T7 platform (BGI-Shenzhen, China).

tag: tissue

value: ileum


title: Paxip1_sgPaxip1_1_Cont

source_name: KPC1199 cells

value: KPC1199 cells

value: DON 0 μM


title: Paxip1_sgPaxip1_3_Cont

source_name: KPC1200 cells

value: KPC1200 cells


title: ileum_HFDHET4I

description: Library name: 72


title: Paxip1_sgPaxip1_1_DON


title: ileum_HFDHET5I

description: Library name: 73


title: ileum_HFDHET3I

description: Library name: 71


title: Paxip1_sgLacz_DON


title: Paxip1_sgLacz_Cont


title: siS100A9_yes_rep1

value: yes


title: ileum_HFDHET2I

description: Library name: 70


title: siZBTB5_no_rep1


title: siLuci_yes_rep1


title: K4me3_sgPaxip1_3_DON


title: ileum_HFDHET1I

description: Library name: 69


title: K4me3_sgPaxip1_1_DON


title: K4me3_sgPaxip1_3_Cont


title: siLuci_no_rep1


title: siS100A8_no_rep1


title: siRELA_no_rep1

value: siRELA


title: untrans_no_rep1


title: ileum_HFDWT6I

description: Library name: 67


title: ileum_HFDWT5I

description: Library name: 66


title: ileum_HFDWT7I

description: Library name: 68


title: 1_HCC827_UT_1

description: Library name: 1


title: K4me3_sgPaxip1_1_Cont


title: K4me3_sgLacz_DON


title: K4me3_sgLacz_Cont


title: ileum_HFDWT4I

description: Library name: 65


title: ileum_HFDWT1I

description: Library name: 62


title: 60485blood

type: genomic

city: New York

first: Michael

last: Corley

state: NY

address: 413 East 69th Street

department: Medicine, Division of Infectious Diseases

country: USA

institute: Weill Cornell Medicine

description: DNABlood

hyb_protocol: Samples were processed according to the Illumina Infinium HumanMethylationEPIC BeadChip (Illumina) protocol.

scan_protocol: Illumina Infinium HumanMethylationEPIC protocol. Scanned using Illumina HiScan System.

data_processing: IDAT Data loaded into R using Minfi and normalized using BMIQ method.

label: Cy5 and Cy3

source_name: Blood

label_protocol: Illumina Infinium protocol. Cy5 and Cy3

extract_protocol: Genomic DNA was extracted using a Qiagen kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

tag: Sex

value: Male

value: Blood

tag: disease state

value: HIV

tag: chronological age


title: ileum_HFDWT2I

description: Library name: 63


title: 60480blood

description: DNABlood


title: ileum_HFDWT3I

description: Library name: 64


title: ileum_NDHET6I

description: Library name: 61


title: 60470blood

description: DNABlood


title: ileum_NDHET5I

description: Library name: 60


title: 60450blood

description: DNABlood


title: ileum_NDHET4I

description: Library name: 59


title: 60382blood

description: DNABlood

value: Female


title: ileum_NDHET2I

description: Library name: 57


title: ileum_NDHET3I

description: Library name: 58


title: ileum_NDHET1I

description: Library name: 56


title: 60333blood

description: DNABlood


title: 60438blood

description: DNABlood


title: 60491blood

description: DNABlood


title: ileum_NDWT6I

description: Library name: 55


title: 60306blood

description: DNABlood


title: ileum_NDWT4I

description: Library name: 53


title: ileum_NDWT5I

description: Library name: 54


title: 60318blood

description: DNABlood


title: 60280blood

description: DNABlood


title: 60271blood

description: DNABlood


title: ileum_NDWT2I

description: Library name: 51


title: ileum_NDWT1I

description: Library name: 50


title: 60260blood

description: DNABlood


title: jejunum_HFDHET5J

description: Library name: 49

source_name: jejunum

value: jejunum


title: 60252blood

description: DNABlood


title: 60239blood

description: DNABlood


title: 60229blood

description: DNABlood


title: jejunum_HFDHET3J

description: Library name: 47


title: 60448blood

description: DNABlood


title: jejunum_HFDHET2J

description: Library name: 46


title: jejunum_HFDHET1J

description: Library name: 45


title: 60222blood

description: DNABlood


title: 60212blood

description: DNABlood


title: 60314blood

description: DNABlood


title: jejunum_HFDWT7J

description: Library name: 44


title: 60193blood

description: DNABlood


title: jejunum_HFDWT6J

description: Library name: 43


title: jejunum_HFDWT5J

description: Library name: 42


title: 60191blood

description: DNABlood


title: 60165blood

description: DNABlood


title: 60176blood

description: DNABlood


title: 60145blood

description: DNABlood


title: jejunum_HFDWT4J

description: Library name: 41


title: ileum_NDWT3I

description: Library name: 52


title: jejunum_HFDWT1J

description: Library name: 38


title: 60126blood

description: DNABlood


title: 60143blood

description: DNABlood


title: 60121blood

description: DNABlood


title: jejunum_NDHET6J

description: Library name: 37


title: jejunum_NDHET5J

description: Library name: 36


title: jejunum_HFDHET4J

description: Library name: 48


title: jejunum_NDHET4J

description: Library name: 35


title: 60101blood

description: DNABlood


title: 60112blood

description: DNABlood


title: 60096blood

description: DNABlood


title: jejunum_NDHET3J

description: Library name: 34


title: 60089blood

description: DNABlood


title: 60076blood

description: DNABlood


title: clr4-1 cells, rep_2

first: Tomoyasu

last: Sugiyama

address: 393 Middle Huaxia Road

institute: ShanghaiTech University

data_processing:
The raw data was checked by FastQC v0.11.6
Clean reads were aligned to the Schizosaccharomyces japonicus genome using STAR (2.5.3a)
The expression of the transcript was calculated by FPKM using StringTie v1.3.1c
Assembly: S. japonicus genome sequencing data; https://www.japonicusdb.org/status/genome-overview
Supplementary files format and content: csv file containing fpkm values for each gene (a total of 5272 genes) in each sample

organism: Schizosaccharomyces japonicus

source_name: whole cell

growth_protocol: All the S. japonicus cells were grown in YES media (0.5% yeast extract, 3% glucose, and 75 mg/L of adenine, histidine, leucine, and uracil) at 30°C

extract_protocol:
Extracted total RNAs using MasterPure™ Yeast RNA Purification Kit (Lucigen)
RNA-seq libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (NR605-02, Vazyme)

value: whole cell

value: clr4-1 mutation


title: jejunum_NDHET2J

description: Library name: 33


title: 60065blood

description: DNABlood


title: clr4-1 cells, rep_1


title: jejunum_HFDWT3J

description: Library name: 40


title: jejunum_NDHET1J

description: Library name: 32


title: 60055blood

description: DNABlood


title: jejunum_HFDWT2J

description: Library name: 39


title: pab2∆ cells, rep_2

value: pab2 deletion


title: 60070blood

description: DNABlood


title: pab2∆ cells, rep_1


title: jejunum_NDWT6J

description: Library name: 31


title: 60022blood

description: DNABlood


title: NIG5572 (WT) cells, rep_2

value: WT


title: 60020blood

description: DNABlood


title: 50735blood

description: DNABlood


title: jejunum_NDWT5J

description: Library name: 30


title: jejunum_NDWT3J

description: Library name: 28


title: NIG5572 (WT) cells, rep_1


title: 50727blood

description: DNABlood


title: 50725blood

description: DNABlood


title: YG-10-3

city: GuiYang

first: Zeyang

last: Song

state: GuiZhou

address: West Campus: Jiaxiu South Road, Huaxi District.

institute: Guizhou University

data_processing:
Quality control of raw data was performed using Fastp (v 0.19.3)and transcripts were constructed from the reads through the use of StringTie (v1.3.4d).
The reference genome was utilized for comparison against clean reads with HISAT2 v2.1.0 software
Assembly: Vaccinium darrowii v1.2
Supplementary files format and content: gene.expression.count.xlsx
Supplementary files format and content: xlsx format file includes the raw counts for each  sample

organism: Vaccinium virgatum

source_name: fruit

growth_protocol: Seven-year-old rabbiteye blueberries (Menditoo × Tifblue) were cultivated in Guiyang, Guizhou, China. The cultivation region is located at 106°27′-106°52′ East longitude and 26°11′-26°34′ North latitude. The plants were grown in pots using production conventional substrate with 6.00% total nitrogen, 543.90 mg/kg hydrolysed nitrogen, 0.18% total phosphorus, 95.04 mg/kg effective phosphorus, 0.88% total potassium and 190.35 mg/kg fast-acting potassium, 1 plant in each pot with an outer diameter of 34 cm, an inner diameter of 31 cm, a diameter of 18.5 cm at the bottom, and a height of 23 cm. Randomised zonal groups were placed.  The management measures were the same except for the experimental treatments.

extract_protocol:
RNA was were extracted by Trizol method.
RNA libraries for RNA-seq were prepared using NEBNext®UltraTM RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Analytically pure potassium sulfate was dissolved in water, and 10g of potassium fertilizer was applied to each plant at the flowering stage (KH) and young fruit stage (YG), respectively. The same amount of water was applied for the CK treatment.Ninety days after flowering, the upper layer fruits were selected, and 12 to 18 fruits were sampled for each replicate. Following sampling, the fruits were frozen in liquid nitrogen and kept at -80°C for subsequent experiments.

value: fruit

tag: Stage

value: young fruit stage (YG)

value: potassium fertilizer


title: jejunum_NDWT2J

description: Library name: 27


title: 50702blood

description: DNABlood


title: YG-10-2


title: 50731blood

description: DNABlood


title: 50703blood

description: DNABlood


title: jejunum_NDWT1J

description: Library name: 26


title: 50694blood

description: DNABlood


title: 60035blood

description: DNABlood


title: 60032blood

description: DNABlood


title: 50672blood

description: DNABlood


title: duodenum_HFDHET6D

description: Library name: 25

source_name: duodenum

value: duodenum


title: 50587blood

description: DNABlood


title: 50571blood

description: DNABlood


title: KH-10-3

value: flowering stage (KH)


title: KH-10-2


title: YG-10-1


title: jejunum_NDWT4J

description: Library name: 29


title: 50572blood

description: DNABlood


title: 50514blood

description: DNABlood


title: duodenum_HFDHET5D

description: Library name: 24


title: duodenum_HFDHET4D

description: Library name: 23


title: KH-10-1


title: 50466blood

description: DNABlood


title: 50429blood

description: DNABlood


title: duodenum_HFDHET3D

description: Library name: 22


title: CK-3

value: water


title: 50427blood

description: DNABlood


title: duodenum_HFDHET2D

description: Library name: 21


title: 50366blood

description: DNABlood


title: CK-2


title: 50417blood

description: DNABlood


title: 50358blood

description: DNABlood


title: duodenum_HFDHET1D

description: Library name: 20


title: duodenum_HFDWT7D

description: Library name: 19


title: CK-1


title: 50353blood

description: DNABlood


title: 50354blood

description: DNABlood


title: 50342blood

description: DNABlood


title: 50317blood

description: DNABlood


title: CUTTag_H3K27ac_3KR_rep2

city: GuangZhou

first: meijun

last: ye

state: -- Please Select --

address: Room 418, Science and Technology Building, North Campus, Sun Yat-sen University, 74 Zhongshan 2nd Road, Guangzhou, Guangdong, China.

institute: SUN YAT-SEN UNIVERSITY

description:
Library name: CUTTag_H3K27ac_3KR_rep2
instrument model: SURFSeq 5000

data_processing:
Raw CUT&Tag reads were preprocessed using trim_galore (version 0.6.7) for adapter trimming.
These reads were then aligned to the human reference genome (hg38) using bowtie2 (v.2.5.1).
PCR duplicates were removed using sambamba (v.1.0.0).
Only the uniquely mapped reads were used in the downstream analyses. Histone modification peaks were called using MACS2 (v.2.2.7.1).
Peaks from replicates were combined using bedtools (v.2.30.0) merge.
Assembly: hg38
Supplementary files format and content: bigWig,narrowPeak
Library strategy: CUT&Tag

growth_protocol: A549 cells were grown in Ham's F-12K (Kaighn's) medium (21127030, Gibco) with 10% fetal bovine serum (F0193-500ML, Sigma), and were cultured in a humidified incubator at 37 ℃ under an atmosphere containing 5% CO2.

extract_protocol:
CUT&Tag experiments were performed by Hyperactive Universal CUT&Tag Assay Kit (TD904, Vazyme Biotech, China). Briefly, A549 cells were incubated and bound with ConA Beads Pro. Then, added 50 μl cold Antibody Buffer dilution with Anti-METTL3 (1:50, 15073-1-AP, Proteintech, China) or Anti-H3K27ac (1:100, ab4729, abcam, UK) antibodies to incubate for 12 h at 4 ℃. Next day, secondary antibodies (1:100, AS070, ABclonal, China) were added and incubated 1 h at room temperature. The unbound antibodies were removed by Dig-Wash buffer to obtain immobilize nuclei bound with antibodies.
The pA-Tn5 adaptor complex was prepared and added into the nuclei with gentle vertexing. Washed nuclei were resuspended in Tagmentation buffer and STOP buffer was used to stop tagmentation.The library DNA was purified and amplified for sequencing with the SURFSeq 5000 platform of GeneMind Biosciences Company (Shenzhen, China) on PE100 mode.

treatment_protocol: A549 cells with METTL3 stable knockdown were rescued METTL3-WT or METTL3-3KR by a doxycycline-induced lentivirus vector. Doxycycline was used to treat A549 cells for 48 h with 2 μg/ml (Sigma).

value: Human Non-Small Cell Lung Cancer Cells

value: METTL3 knockdown and rescue METTL3-3KR

tag: chip antibody

value: H3K27ac (ab4729, abcam, UK)


title: 50285blood

description: DNABlood

value: Male

value: Blood


title: CUTTag_H3K27ac_WT_rep2

description:
Library name: CUTTag_H3K27ac_WT_rep2
instrument model: SURFSeq 5000

value: METTL3 knockdown and rescue METTL3-WT


title: 50284blood

description: DNABlood

value: Female

value: HIV


title: duodenum_HFDWT6D

description: Library name: 18


title: duodenum_HFDWT4D

description: Library name: 16


title: 50261blood

description: DNABlood


title: 50434blood

description: DNABlood


title: duodenum_HFDWT5D

description: Library name: 17


title: 50242blood

description: DNABlood


title: duodenum_HFDWT3D

description: Library name: 15


title: 50239blood

description: DNABlood


title: CUTTag_H3K27ac_WT_rep1

description:
Library name: CUTTag_H3K27ac_WT_rep1
instrument model: SURFSeq 5000


title: 50232blood

description: DNABlood


title: duodenum_HFDWT2D

description: Library name: 14


title: CUTTag_METTL3_3KR_rep2

description:
Library name: CUTTag_METTL3_3KR_rep2
instrument model: SURFSeq 5000

value: METTL3 (15073-1-AP, Proteintech, China)


title: 50202blood

description: DNABlood


title: CUTTag_METTL3_3KR_rep1

description:
Library name: CUTTag_METTL3_3KR_rep1
instrument model: SURFSeq 5000


title: duodenum_HFDWT1D

description: Library name: 13


title: 50154blood

description: DNABlood


title: 50134blood

description: DNABlood


title: 50308blood

description: DNABlood


title: 50116blood

description: DNABlood


title: duodenum_NDHET6D

description: Library name: 12


title: CUTTag_METTL3_WT_rep2

description:
Library name: CUTTag_METTL3_WT_rep2
instrument model: SURFSeq 5000


title: 50112blood

description: DNABlood


title: CUTTag_METTL3_WT_rep1

description:
Library name: CUTTag_METTL3_WT_rep1
instrument model: SURFSeq 5000


title: GLORI_3KR_rep2

description: instrument model: SURFSeq 5000

library_source: other

data_processing:
The orientation of the RNA strand remained intact during the construction of the library, and the sequences obtained from reads R2 correspond to the sense strand of the original RNA. Consequently, our study exclusively utilized reads R2.
Raw reads were treated with trim_galore (v.0.6.7) for adaptor trimming.
Trimmed reads were aligned to the human reference genome (hg38) with the STAR (v.2.7.10b) and then transcriptome with bowtie (v.1.3.1). Samtools API pysam (v.0.20.0) was utilized to perform pileup.
m6A sites were called using the GLORI-tools (v.1.0) with default parameters.
When the absolute change of the m6A modification level between R-METTL3-WT and R-METTL3-3KR was greater than 15 %, it was considered to be a changed m6A site.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes m6A sites for each sample

molecule: other

extract_protocol:
The cells were collected, washed with 1 ml cold PBS buffer containing 1 mM EDTA, and centrifugated at 500 g and room temperature for 5 min. Added 200uL ice-cold cytoplasmic lysis buffer (10 mM Tris-HCl pH=7.5, 0.1% IGEPAL®CA-630, 150 mM NaCl) to the cell pellet and incubated on ice for 5 min, then added 2.5 volumes of chilled sucrose cushion (24% RNAse-free sucrose in cytoplasmic lysis buffer). Subsequently, centrifuge at 15,000g and 4 ℃ for 10 min. The supernatant was collected as the cytoplasmic fraction. Added 100uL of prechilled glycerol buffer (20 mM Tris-HCl pH=7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) to resuspend the nuclei pellet, then added an equal volume of cold nuclei lysis buffer (10 mM HEPES pH=7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M UREA, 1% IGEPAL®CA-630) and vigorously vortexed. The mixtures of nuclei pellets were incubated on ice for 2 min, then centrifuged at 4°C with 15,000 g for 2 min. The supernatant is soluble nucleoplasm, and the pellet is chromatin fraction. The chromatin fraction was dissolved  in 1ml of TRI Reagent™ (AM9738, Invitrogen, USA), and was heated at 50 °C with shaking at 1,000 rpm for 20 minutes until the pellet completely dissolved. Then, caRNAs were extracted according to the manufacturer’s instructions for TRI Reagent™.  For GLORI reaction,genomic DNA is removed from caRNAs by using DNase Ⅰ (EN401, Vazyme). Subsequently, non-ribosomal caRNAs were further enriched by using the Ribo-MagOff rRNA Depletion Kit (N420-01, Vazyme Biotech, ChinaVazyme). Then, GLORI was carried out according to previously published. Briefly, caRNAs were fragmented at 94 °C for 30 s. Then, guanosine of fragmented caRNAs was protected in a protection buffer (1.32 M glyoxal, 50% DMSO) at 50 °C for 30 min. Subsequently, add 10 μl saturated H3BO3 solution and incubate at 50 °C for 30min. Next, add deamination buffer (750 mM NaNO2, 40 mM MES buffer, and 2.08 M glyoxal) and incubate at 16 °C for 8 h to deaminize adenine. Finally, add deprotection buffer (0.25 M TEAA and 25% deionized formamide) and incubate at 95 °C for 10 minutes.
For the library construction of GLORI products, SMARTer Stranded Total RNA-Seq Kit v2 (Takara) was used according to the manufacturer’s protocols. Sequencing was performed at GeneMind Biosciences Company (Shenzhen, China) through the SURFSeq 5000 platform on PE100 mode.

value: Doxycycline was used to treat A549 cells for 48 h with 2 ug/ml (Sigma)


title: 50093blood

description: DNABlood


title: 50106blood

description: DNABlood


title: 50061blood

description: DNABlood


title: duodenum_NDHET3D

description: Library name: 9


title: GLORI_3KR_rep1

description: instrument model: SURFSeq 5000


title: 50045blood

description: DNABlood


title: GLORI_WT_rep2

description: instrument model: SURFSeq 5000


title: 50087blood

description: DNABlood


title: 50012blood

description: DNABlood


title: 50038blood

description: DNABlood


title: duodenum_NDHET2D

description: Library name: 8


title: 50057blood

description: DNABlood


title: duodenum_NDHET4D

description: Library name: 10


title: 50153blood

description: DNABlood


title: duodenum_NDHET1D

description: Library name: 7


title: CUTTag_H3K27ac_3KR_rep1

description:
Library name: CUTTag_H3K27ac_3KR_rep1
instrument model: SURFSeq 5000


title: 60461blood

description: DNABlood


title: 60454blood

description: DNABlood


title: duodenum_NDWT6D

description: Library name: 6


title: 60434blood

description: DNABlood


title: OE rep 2

city: Seoul

first: Keon Wook

last: Kang

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: seoul national university

data_processing:
Trimmomatic v0.38 was used to remove adapter sequences and trim bases with poor base quality.
The cleaned reads were aligned to the Homo sapiens(GRCh38) using HISAT v2.1.0 (KIM et al, 2015), based on the HISAT and Bowtie2 implementations.
The reference genome sequence and gene annotation data were downloaded from NCBI Genome assembly and NCBI RefSeq database respectively.
Aligned data (SAM file format) were sorted and indexed using SAMtools v 1.9. After alignment, the transcripts were assembled and quantified using StringTie v2.1.3b (Pertea, Mihaela, et al., 2015, 2016).
Gene-level and Transcript-level quantification were calculated as raw read count, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) and TPM (Transcripts Per Million)
Assembly: GRCh38
Supplementary files format and content: Expression_Profile.GRCh38.gene.xlsx

extract_protocol:
Total RNA was extracted using Trizol reagent.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #20020595)

value: treated with supernatant of HCC827-DKK1 OE


title: OE rep 3


title: duodenum_NDWT5D

description: Library name: 5


title: 60399blood

description: DNABlood


title: duodenum_NDHET5D

description: Library name: 11


title: 60420blood

description: DNABlood


title: OE rep 1


title: 60369blood

description: DNABlood


title: duodenum_NDWT4D

description: Library name: 4


title: Con rep 3

value: treated with supernatant of HCC827-LV-con


title: 60362blood

description: DNABlood


title: duodenum_NDWT3D

description: Library name: 3


title: 60326blood

description: DNABlood


title: Con rep 2


title: GLORI_WT_rep1

description: instrument model: SURFSeq 5000


title: 60475blood

description: DNABlood


title: 60301blood

description: DNABlood


title: duodenum_NDWT2D

description: Library name: 2


title: 60295blood

description: DNABlood


title: duodenum_NDWT1D

description: Library name: 1


title: 60267blood

description: DNABlood


title: Aged_LT-HSC_IL4_3

city: Boston

first: Jingfei

last: Yao

state: Massachusetts

address: 300 Longwood Ave

institute: Boston Children's Hospital

description: Library name: Aged_LT-HSC_IL4_3

data_processing:
bcl2fq used for basecalling.
Sequenced reads were trimmed by Trimmomatic, then mapped to mm10 whole genome using HISAT2 (v2.0.4)
Reads Per Kilobase of exon model per Million mapped reads (RPKM) and Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated by StringTie (v1.3.6)
Assembly: mm10
Supplementary files format and content: csv files include raw counts for each treatment

source_name: bone marrow

extract_protocol:
Cells were sorted by flow sorting based on their surface markers, then directly add lysis buffer provided in SMART-Seq v4 Ultra Low Input RNA Kit
Bulk RNA-seq libraries were prepared using the Smart-seq2 method with the SMART-Seq v4 Ultra Low Input RNA Kit following the manufacturer’s instructions.

value: bone marrow

value: LT-HSC

value: WT


title: 60270blood

description: DNABlood


title: Con rep 1


title: Aged_LT-HSC_IL4_2

description: Library name: Aged_LT-HSC_IL4_2


title: Slide2

type: other

city: Phoenix

first: Nicholas

last: Banovich

state: AZ

address: 445 North Fifth Street

department: Integrated Cancer Genomics

institute: TGen - Translational Genomics Research Institute

hyb_protocol: A total of 477 unique genes were included in the analysis of this dataset. 377 genes came from a predesigned panel (Human Multi-Tissue and Cancer) and 100 genes from a custom designed panel. The custom panel was curated based on published single-nuclear RNA-seq, bulk RNA-seq and microarray studies. Gene panel probe hybridization occurred overnight for 18 hours at 50°C (Bio-Rad DNA Engine Tetrad 2). Subsequent washes the next day removed unbound probes. Ligase was added to circularize the paired ends of bound probes (2 hours at 37°C) and followed by enzymatic rolling circle amplification (2 hours at 30°C). Slides were washed in TE buffer before background fluorescence was chemically quenched; autofluorescence is a known issue in lung tissue as well as a byproduct of formalin-fixation. Following PBS and PBS-T washes, DAPI was used to stain sample nuclei. Finalized slides were stored in PBS-T in the dark at 4°C for ≤5 days until being loaded onto the Xenium Analyzer instrument. Stepwise Xenium FFPE preparation guidelines and buffer recipes can be found in 10X Genomics Demonstrated Protocol CG000578.

scan_protocol: Xenium Analyzer is fully automated. The user marks regions for analysis by manually selecting sample location on an initial low-resolution image. After loading consumable reagents and slides, internal sample and liquid handling mechanics control experiment progression. Data collection occurs in cycles of fluorescently labeled probe binding, image acquisition, and probe stripping. Localized points of fluorescence intensity detected during the rounds of imaging are then defined as potential RNA puncta. Each gene on the panel has a unique fluorescence pattern across the image channels. Puncta that match a specific pattern are then decoded and labeled according to the gene ID. All image FOVs (4240 x 2960 pixels) and associated detected transcripts are computationally stitched together via the DAPI-stained image. The data in this paper was acquired on instrument software version 1.1.2.4 and analysis version xenium-1.1.0.2. Detailed instructions on instrument operation and consumable preparation can be found in 10X Genomics’ Demonstrated Protocol CG000582.

data_processing: heart_spatial_obj.rds contains a Seurat object of spatial transcriptomics data measuring expression of 477 genes across 195 0.6 um diameter heart tissue cores from 49 adult   and 13 pediatric heart transplant recipients using the 10X Genomics Xenium platform.

source_name: Heart

label_protocol: Deparaffinization and decrosslinking was performed to make subcellular RNA targets accessible (10X Genomics Demonstrated Protocol CG000580).

growth_protocol: A 5um section of each FFPE EMB block was H&E stained for clinical diagnosis and presented to a cardiovascular pathologist (R.D.H.) who identified two areas of interest for each sample.

extract_protocol: Sectioning was performed at 5um. Sections were placed on Xenium slides (10X Genomics) and left to dry overnight. Slides were then stored in a sealed dessicator at room temperature for ≤7 days.

treatment_protocol: All protocol workstations and equipment were cleaned using RNase Away (RPI 147002) followed by 70% Isopropanol. All reagents, including water, were molecular grade nuclease-free.

value: heart


title: 60248blood

description: DNABlood


title: 60244blood

description: DNABlood


title: 60217blood

description: DNABlood


title: Slide1


title: 60218blood

description: DNABlood


title: 60208blood

description: DNABlood


title: 60203blood

description: DNABlood


title: Aged_LT-HSC_Sal_3

description: Library name: Aged_LT-HSC_Sal_3

value: Saline


title: 60338blood

description: DNABlood


title: Aged_LT-HSC_Sal_2

description: Library name: Aged_LT-HSC_Sal_2


title: 60164blood

description: DNABlood


title: 60156blood

description: DNABlood


title: Aged_MPP_IL4_3

description: Library name: Aged_MPP_IL4_3

value: MPP


title: Aged_MPP_IL4_2

description: Library name: Aged_MPP_IL4_2


title: 60091blood

description: DNABlood


title: Tumor, TCR

city: Minneapolis

first: Ingunn

last: Stromnes

state: Minnesota

address: 2-186 Wallin Medical Biosciences Building, 2101 6th St SE

department: Medical School

institute: University of Minnesota

description: Library name: Tumor_TCR

data_processing:
The raw data of were preprocessed and demultiplexed using Cell Ranger (v7.0.0). The GEX and FB raw fastq files containing multiple cell multiplexing oligo (CMO) references (cmo.csv) and sample information file (config_cd8.csv) were mapped to a reference genome (mm10 Ensembl mouse v98) with default multi parameter (10x Genomics) for each of the tissue sample. The mapped output files were subsequently processed with Cell Ranger function (bamtofastq) for further gene expression profiling. To construct TCR receptors and preserve the cell identity matching the gene expression data, the outputs of bamtofastq along with feature reference information (feature_reference.csv) and VDJ genome reference (preprocessed GRCm38 ensembl v5.0.0) were further processed by using Cell Ranger with multi parameter (config.csv). Further aggregated investigation uses the default cellranger aggr parameter (aggregation.csv)
Assembly: mm10 Ensembl mouse v98
Supplementary files format and content: RAW_counts.tar TAR (of csv) containing ADT & RNA counts for aggregate, CD8, UE, & Tumor integrated in csv.gz
Supplementary files format and content: RAW_vdj_t.tar TAR (of csv) containing VDJ T clonotypes and filtered contig annotation for aggregate, each subsample of CD8, UE, & Tumor in csv.gz
Library strategy: CITE-Seq

source_name: Tumor

extract_protocol:
Immune cells were isolated from splenocytes using magnetic enrichment or orthotopic KPC2a PDA tumors using collagenase digestion and percoll enrichment. Samples were uniquely barcoded with oligo tagged antibodies prior to capture and single cell RNA sequencing.
Cells were captured and the library was constructed with the 10X Genomics Chromium Next GEM Single Cell 5' Reagent Kits v2 (Dual Index) according to the manufacturer's instructions.
scRNAseq. Libraries were generated for feature barcoding, TCR, and gene expression.

value: Tumor

value: Pooled sample (untreated (Untx), aCD40, aPD-L1, Both aPD-L1 & aCD40 (Dual))

tag: library type

value: T-cell receptor (TCR)

tag: tcr

value: TotalSeq-C0961 PE Streptavidin as TETRA_PE, TotalSeq-C0001 anti-mouse CD4 Antibody, TotalSeq-C0004 anti-mouse CD279 (PD-1) Antibody, TotalSeq-C0097 anti-mouse CD25 Antibody, TotalSeq-C0193 anti-mouse CD357 (GITR) Antibody, TotalSeq-C0378 anti-mouse CD223 (LAG-3) Antibody, TotalSeq-C0250 anti-mouse/human KLRG1 (MAFA) Antibody, TotalSeq-C0002 anti-mouse CD8a Antibody


title: 60102blood

description: DNABlood

value: Male

value: Blood


title: 60086blood

description: DNABlood

value: HIV


title: Tumor, GEX

description: Library name: Tumor_GEX

molecule: polyA RNA

value: Gene Expression (GEX)


title: 60259blood

description: DNABlood

value: Female


title: Aged_MPP_IL4_1

description: Library name: Aged_MPP_IL4_1


title: Aged_LT-HSC_IL4_1

description: Library name: Aged_LT-HSC_IL4_1


title: 60071blood

description: DNABlood


title: Tumor, FB

description: Library name: Tumor_FB

molecule: protein

value: Feature Barcode (FB) Multiplexing capture

tag: fb

value: TotalSeq-C0306 anti-mouse Tumor-Untx, TotalSeq-C0308 anti-mouse Tumor-aPD-L1, TotalSeq-C0309 anti-mouse Tumor-aCD-40, TotalSeq-C0310 anti-mouse Tumor-Dual


title: 60061blood

description: DNABlood


title: 60060blood

description: DNABlood


title: 60014blood

description: DNABlood


title: 60034blood

description: DNABlood


title: CD8, Spleen CD8 T cell enriched, TCR

description: Library name: CD8_TCR

source_name: Spleen

value: Spleen


title: Aged_MPP_Sal_3

description: Library name: Aged_MPP_Sal_3

value: bone marrow


title: 60200blood

description: DNABlood


title: Aged_LT-HSC_Sal_1

description: Library name: Aged_LT-HSC_Sal_1

value: LT-HSC

value: WT


title: 50734blood

description: DNABlood


title: Aged_MPP_Sal_2

description: Library name: Aged_MPP_Sal_2

value: Saline


title: 50682blood

description: DNABlood


title: CD8, Spleen CD8 T cell enriched, GEX

description: Library name: CD8_GEX


title: CD8, Spleen CD8 T cell enriched, FB

description: Library name: CD8_FB

value: TotalSeq-C0306 anti-mouse CD8-Untx, TotalSeq-C0308 anti-mouse  CD8-aPD-L1, TotalSeq-C0309 anti-mouse  CD8-aCD-40, TotalSeq-C0310 anti-mouse  CD8-Dual


title: LT-HSC_IL4_3

description: Library name: LT-HSC_IL4_3


title: Aged_MPP_Sal_1

description: Library name: Aged_MPP_Sal_1

value: MPP


title: 50665blood

description: DNABlood


title: 60110blood

description: DNABlood


title: UE, Spleen Unenriched, TCR

description: Library name: UE_TCR

value: Unenriched (bulk splenocytes)

value: Pooled sample (untreated (Untx), aCD40, aPD-L1, Both aPD-L1 & aCD40 (Dual))


title: 50668blood

description: DNABlood


title: 50606blood

description: DNABlood


title: UE, Spleen Unenriched GEX

description: Library name: UE_GEX


title: LT-HSC_IL4_1

description: Library name: LT-HSC_IL4_1


title: 50596blood

description: DNABlood


title: 50595blood

description: DNABlood


title: UE, Spleen Unenriched, FB

description: Library name: UE_FB

value: TotalSeq-C0306 anti-mouse UE-Untx, TotalSeq-C0308 anti-mouse UE-aPD-L1, TotalSeq-C0309 anti-mouse UE-aCD-40, TotalSeq-C0310 anti-mouse UE-Dual


title: 50589blood

description: DNABlood

value: Male


title: LT-HSC_Sal_3

description: Library name: LT-HSC_Sal_3


title: 50739blood

description: DNABlood

value: Blood


title: 50611blood

description: DNABlood

value: HIV


title: LT-HSC_IL4_2

description: Library name: LT-HSC_IL4_2


title: 50535blood

description: DNABlood


title: RNAseq_3KR_rep2

description: Library name: RNAseq_3KR_rep2

data_processing:
Raw sequencing reads were preprocessed using trim_galore (version 0.6.7) for adapter trimming.
Trimmed sequencing reads were aligned to the human reference genome (hg38) with the STAR aligner (version 2.7.1a) with default parameters.
The expression for each GENCODE annotated gene was calculated using Stringtie (version 2.2.1) with the '--rf' parameter.
Differentially expressed genes were determined using DESeq2 (v.1.42.1) by requiring at least 10 average read counts of all samples with adjusted P value < 0.05.
Pathway and gene ontology enrichment analysis of down-regulated genes was performed using the clusterProfiler R package (v.4.10.1). Enrichment terms were determined using MSigDB C2 gene sets and C5 gene sets.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each gene in each sample

extract_protocol:
The total RNA was extracted from cells using FastPure Cell/Tissue Total RNA Isolation Kit V2 (RC112-01, Vazyme Biotech, China).Total RNA was captured mRNA by using VAHTS mRNA Capture Beads (N401, Vazyme).
library preparation was performed by using VAHTS Universal V10 RNA-seq Library Prep Kit for MGI (NRM606-01, Vazyme). After the quality control, Sequencing was performed at BGI Company (Shenzhen, China) through the MGISEQ-2000 platform on PE150 mode.

value: Human Non-Small Cell Lung Cancer Cells

value: METTL3 knockdown and rescue METTL3-3KR

value: Doxycycline was used to treat A549 cells for 48 h with 2 μg/ml (Sigma)


title: 50522blood

description: DNABlood

value: Female


title: 50503blood

description: DNABlood


title: LT-HSC_Sal_1

description: Library name: LT-HSC_Sal_1


title: 50499blood

description: DNABlood


title: RNAseq_3KR_rep1

description: Library name: RNAseq_3KR_rep1


title: 50497blood

description: DNABlood


title: 50491blood

description: DNABlood


title: RNAseq_WT_rep3

description: Library name: RNAseq_WT_rep3

value: METTL3 knockdown and rescue METTL3-WT


title: 50662blood

description: DNABlood


title: 50484blood

description: DNABlood


title: MPP_STAT6KO_2

description: Library name: MPP_STAT6KO_2

value: bone marrow


title: 50481blood

description: DNABlood


title: RNAseq_WT_rep2

description: Library name: RNAseq_WT_rep2


title: MPP_STAT6KO_1

description: Library name: MPP_STAT6KO_1


title: 50463blood

description: DNABlood


title: 50467blood

description: DNABlood


title: RNAseq_WT_rep1

description: Library name: RNAseq_WT_rep1


title: 50450blood

description: DNABlood


title: RNAseq_3KR_rep3

description: Library name: RNAseq_3KR_rep3


title: MPP_IL4_3

description: Library name: MPP_IL4_3


title: caRNAseq_3KR_rep3

description: Library name: caRNAseq_3KR_rep3

data_processing:
Raw sequencing reads were preprocessed using trim_galore (version 0.6.7) for adapter trimming.
Trimmed sequencing reads were aligned to the human reference genome (hg38) with the STAR aligner (version 2.7.1a) with default parameters.
Promoter regions were determined as the regions located from 1 kb upstream to 100 bp downstream of the transcription start site (TSS). The enhancer regions were determined as the H3K27ac peaks within -50 kb to -5 kb upstream and 5 kb to 50 kb downstream of the TSS. We categorized the RNAs derived from enhancers as enhancer RNA (eRNA) and the RNA derived from promoters as promoter-associated RNA (paRNA). To ensure the exclusion of potential noise from nascent pre-mRNA, we further classified paRNAs into sense (paRNA [+], coding strand) and antisense paRNAs (paRNA [-], template strand) based on the transcript origins.
The read count for each eRNA and paRNA region was calculated using HTSeq (v.2.0.5)
The transcript abundance for each eRNA and paRNA region was normalized using DESeq2 (v.1.42.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each eRNA and paRNA [-] region in each sample

extract_protocol:
The cells were collected, washed with 1 ml cold PBS buffer containing 1 mM EDTA, and centrifugated at 500 g and room temperature for 5 min. Added 200uL ice-cold cytoplasmic lysis buffer (10 mM Tris-HCl pH=7.5, 0.1% IGEPAL®CA-630, 150 mM NaCl) to the cell pellet and incubated on ice for 5 min, then added 2.5 volumes of chilled sucrose cushion (24% RNAse-free sucrose in cytoplasmic lysis buffer). Subsequently, centrifuge at 15,000g and 4 ℃ for 10 min. The supernatant was collected as the cytoplasmic fraction. Added 100uL of prechilled glycerol buffer (20 mM Tris-HCl pH=7.9, 75 mM NaCl, 0.5 mM EDTA, 0.85 mM DTT, 0.125 mM PMSF, 50% glycerol) to resuspend the nuclei pellet, then added an equal volume of cold nuclei lysis buffer (10 mM HEPES pH=7.6, 1 mM DTT, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M UREA, 1% IGEPAL®CA-630) and vigorously vortexed. The mixtures of nuclei pellets were incubated on ice for 2 min, then centrifuged at 4°C with 15,000 g for 2 min. The supernatant is soluble nucleoplasm, and the pellet is chromatin fraction. The chromatin fraction was dissolved  in 1ml of TRI Reagent™ (AM9738, Invitrogen, USA), and was heated at 50 °C with shaking at 1,000 rpm for 20 minutes until the pellet completely dissolved. Then, caRNAs were extracted according to the manufacturer’s instructions for TRI Reagent™.
For library construction of caRNA, SMARTer Stranded Total RNA-Seq Kit v2 (Takara) was used according to the manufacturer’s protocols. Sequencing was performed at BGI Company (Shenzhen, China) through the MGISEQ-2000 platform on PE150 mode.


title: 50372blood

description: DNABlood


title: LT-HSC_Sal_2

description: Library name: LT-HSC_Sal_2

value: LT-HSC


title: 50345blood

description: DNABlood


title: MPP_IL4_2

description: Library name: MPP_IL4_2

value: WT


title: 50347blood

description: DNABlood


title: caRNAseq_3KR_rep2

description: Library name: caRNAseq_3KR_rep2


title: 50330blood

description: DNABlood


title: MPP_IL4_1

description: Library name: MPP_IL4_1


title: caRNAseq_3KR_rep1

description: Library name: caRNAseq_3KR_rep1


title: MPP_STAT6KO_3

description: Library name: MPP_STAT6KO_3


title: PBMCs of SPF chicken 14 days after vaccination of live IBV vaccine

city: Xi'an

first: Hai

last: Li

address: No.76 Yanta West Road

department: Department of Pathogenic Microbiology and Immunology

institute: Xi'an Jiaotong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://github.com/10XGenomics/cellranger)
Assembly: GRCg6a
Supplementary files format and content: Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

organism: Gallus gallus

source_name: blood

extract_protocol:
Seperated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols (single cell 3’ v3 protocol, 10x Genomics).

value: blood

value: male

value: peripheral blood mononuclear cells

tag: age

value: 35-day old

value: live IBV vaccine


title: caRNAseq_WT_rep3

description: Library name: caRNAseq_WT_rep3


title: 50311blood

description: DNABlood


title: PBMCs of SPF chicken 35 days after vaccination of inactivated IBV vaccine

description: 10x Genomics

value: inactivated IBV vaccine


title: PBMCs of SPF chicken 14 days after vaccination of inactivated IBV vaccine

description: 10x Genomics


title: MPP_Sal(WT)_2

description: Library name: MPP_Sal(WT)_2

value: MPP

value: Saline


title: 50306blood

description: DNABlood

value: Male

value: Blood

value: HIV


title: caRNAseq_WT_rep2

description: Library name: caRNAseq_WT_rep2

value: Human Non-Small Cell Lung Cancer Cells

value: Doxycycline was used to treat A549 cells for 48 h with 2 μg/ml (Sigma)


title: 50299blood

description: DNABlood

value: Female


title: MPP_Sal(WT)_1

description: Library name: MPP_Sal(WT)_1

value: bone marrow


title: HSPC_STAT6KO_3

description: Library name: HSPC_STAT6KO_3

value: HSPC


title: 50267blood

description: DNABlood


title: PBMCs of SPF chicken 7 days after vaccination of inactivated IBV vaccine

description: 10x Genomics


title: HSPC_STAT6KO_2

description: Library name: HSPC_STAT6KO_2


title: 50246blood

description: DNABlood


title: 50240blood

description: DNABlood


title: PBMCs of SPF chicken 4 days after vaccination of inactivated IBV vaccine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://github.com/10XGenomics/cellranger).
Assembly: GRCg6a
Supplementary files format and content: Matrix file containing the transcription profiles of all single cells could be loaded to Seurat for further analysis.

extract_protocol:
Separated single_cell samples were treated by Smart_Seq2 protocol to get amplified cDNA.
RNA libraries were prepared for sequencing using standard Illumina scRNA-seq and 10 × Chromium platform protocols (single cell 3’ v3 protocol, 10x Genomics).

value: 35 days


title: HSPC_STAT6KO_1

description: Library name: HSPC_STAT6KO_1


title: 50235blood

description: DNABlood


title: HSPC_IL4_3

description: Library name: HSPC_IL4_3

value: WT


title: MPP_Sal(WT)_3

description: Library name: MPP_Sal(WT)_3


title: Motor neurons under microgravity

city: 武汉市

first: yang

last: fei

address: 狮子山街道

institute: 无

data_processing:
dlo hic toolsl were modified and used for linker filtering
Two end of interacted fragments were seperated by the command awk
Two end of interacted fragments were separately mapped to hg19 by bwa v0.7.12-r1039 with the parameter -n 0, and then unique mapping reads were kept
Samtools v1.2 was used to transfer the sam format to bed format
Two end bed format files were combined to bedpe file by a perl script
The bedpe format file sorted by the command sort
The sorted file transferred to matrix by a python script
The interactions were convered to .hic files by Juicer tools and loops were called with default paremeters
Assembly: hg19
Supplementary files format and content: a .hic file

growth_protocol: Moter neuron progenitors were cultured in neural culture medium added with 0.01μM RA and 0.1μM SAG to differentiate to motor neurons.

extract_protocol:
DNA was precipitated at room temperature with 10µl of Dr. GenTLE Precipitation Carrier (Takara), 100µl of 3 M sodium acetate (pH 5.2), and an equal volume of isopropanol
In situ DLO Hi-C library construction strategies refer to previously published articles: “Lin, D. et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature genetics 50, 754 (2018).”
DLO Hi-C

treatment_protocol: Two-dimensional (2D) clinostat was used to simulate microgravity (SMG).

value: Motor neurons derived from embryonic stem cells

value: microgravity


title: MyD88KO-Fib_DSS_5

city: Hershey

first: Marina

last: Chulkina

state: Pennsylvania

address: 500 University dr department of medicine

department: Medicine

institute: Penn State Health Medical Center

description:
Library name: B23
Column name in MyD88KODSS_Counts.csv B23

data_processing:
Raw data were aligned to mouse genome (mm39) using STAR (v2.7.3a).
Assembly: mm39
Supplementary files format and content: MyD88KODSS_Counts.csv file includes raw data counts for each sample

source_name: colonic mucosa

extract_protocol:
RNA was harvested using Rnaeasy kit (Qiagen).
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 will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: colonic mucosa

value: DSS


title: Ze2_ZT7_20-3

city: St. Paul

first: kathleen

last: Greenham

state: MN

address: 1445 Gortner Avenue

data_processing:
Raw reads were mapped to a concatenated reference consisting of B. rapa R500 v1.2 (Lou et al., 2020) and B. olerarcea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77)  genomes.
The reads were trimmed and filtered by quality using Trimmomatic v0.33, and alignment was performed using HISAT2 2.1.0.
Raw counts were normalized using the R package edgeR
Genes with no variance in expression across the time series were removed and are referred to as 'Processed Genes' which are available on the GreenhamLab GitHub.
We further filtered out lowly expressed genes by retaining those with a mean log2 FPKM greater than zero in at least one time point.
Gene expression for any missing replicate (See MetaData table) was imputed as the median of the two remaining replicates for that time point.
Assembly: We used a concatenated genome consisting of B. rapa R500 v1.2 (Lou, P. et al. (2020). Genetic and genomic resources to study natural variation in Brassica rapa. Plant Direct 4: e00285) and B. oleracea TO1000 (Parkin, I.A.P. et al. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biol. 15: R77.) genomes.
Supplementary files format and content: Raw counts for each gene (rows) at every timepoint and treatment (columns). ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.
Supplementary files format and content: Normalized counts for each gene (rows) at every timepoint and treatment (columns). We require at least one sample (where a sample is a full time course for a single plant) to have mean FPKM greater than zero to be kept as a "processed gene". ZT refers to number of hours since lights on. Well watered plants are described as 100 and water limited plants are described at 20. Column names identify the 'accession'_'ZT'_'well watered/water limited'-'biological replicate'.

organism: Brassica napus

source_name: leaf

growth_protocol: Seeds were inbibed on wet whatman paper for five days before sowing into 4inch wide pots filled with MetroMix360. Growth conditions were 28C/22C day/night temperatures, 14 hour day lengths with 400 umol/m2/s light intensity and 40% relative humidity for the duration of the four week experiment.

extract_protocol:
Leaf tissue from the apex of the youngest leaf from three individual plants was collected at_ZT (Zeitgeber; hours after dawn) 1, 7, 13, and 19. RNA was isolated using the MagMAX Plant RNA Isolation Kit (Thermo Fisher Scientific, Waltham MA).
Illumina TruSeq Stranded mRNA HT

treatment_protocol: Plants were equally separated into two treatments for the duration of the experiment: 100% watering (well-watered) and 20% watering (water limited). The target watering weights were determined as described in Fahlgren et al. (Fahlgren et al., 2015). All pots were watered once to 100% capacity on the first day of the experiment, and then weighed twice per day to maintain a target water weight through day seven on the Bellwether phenotyping platform. Starting on day eight, water limited plants were allowed to dry down to 20% capacity and maintained at 20% capacity until day 14 (seven days after water limitation treatment began). At this point all watering amounts were increased by 10% for the rest of the experiment.

value: leaf

tag: temperature

tag: photoperiod

tag: timepoint (zt_=_hours_after_dawn)

value: Water limited, 20% full capacity


title: 50184blood

description: DNABlood


title: Ze2_ZT1_100-3

value: Well watered, 100% full capacity


title: PBMCs of SPF chicken 4 days after vaccination of live IBV vaccine

description: 10x Genomics

value: blood

value: male

value: peripheral blood mononuclear cells

value: live IBV vaccine


title: HSPC_IL4_2

description: Library name: HSPC_IL4_2


title: Motor neurons under normal gravity

tag: cell line

value: normal gravity


title: Ze2_ZT19_100-1


title: 50159blood

description: DNABlood

value: Female

tag: cell type

value: Blood

value: HIV


title: PBMCs of SPF chicken at the onset of vaccination

description: 10x Genomics

value: 35 days

value: Mock


title: Ze2_ZT19_20-2

tag: genotype


title: caRNAseq_WT_rep1

description: Library name: caRNAseq_WT_rep1

value: Human Non-Small Cell Lung Cancer Cells

value: METTL3 knockdown and rescue METTL3-WT

tag: treatment

value: Doxycycline was used to treat A549 cells for 48 h with 2 μg/ml (Sigma)


title: MyD88KO-Fib_DSS_4

description:
Library name: B22
Column name in MyD88KODSS_Counts.csv B22

tag: tissue

value: colonic mucosa

value: DSS


title: Control_DSS_5

description:
Library name: B12
Column name in MyD88KODSS_Counts.csv B12


title: PBMCs of SPF chicken 7 days after vaccination of live IBV vaccine

description: 10x Genomics

tag: Sex

value: 35-day old


title: HSPC_IL4_1

description: Library name: HSPC_IL4_1

value: bone marrow

value: HSPC

value: WT


title: 50144blood

description: DNABlood

value: Male

tag: disease state


title: HSPC_Sal(WT)_3

description: Library name: HSPC_Sal(WT)_3

value: Saline


title: HSPC_Sal(WT)_2

description: Library name: HSPC_Sal(WT)_2


title: Ze2_ZT13_20-3

value: leaf

value: Water limited, 20% full capacity


title: Control_DSS_4

description:
Library name: B11
Column name in MyD88KODSS_Counts.csv B11


title: Ze2_ZT19_20-1


title: MyD88KO-Fib_DSS_3

description:
Library name: A24
Column name in MyD88KODSS_Counts.csv A24


title: HSPC_Sal(WT)_1

description: Library name: HSPC_Sal(WT)_1


title: Noc_Untreated_Control

city: Irvine

first: Annie

last: Trinh

state: CA

address: 419 S. Circle View Drive

department: Microbiology & Molecular Genetics

institute: University of California, Irvine

description: Library name: Noc_Untreated_Control

data_processing:
For BrdU-labeled samples loaded on R9.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN106D), basecalling on raw current signals was performed using Guppy v6.5.7. DNA sequences were aligned to the hg19 human reference genome using Minimap2 v2.24 and chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v3.1.254 was used to detect the BrdU base analog within individual reads. CpG methylation was called using nanopolish v0.13.255. For BrdU-labeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and unlabeled samples loaded on R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M), basecalling and alignment to the hg19 human reference genome were performed using Dorado v0.6.2. Chimeric reads were removed using samtools v1.15.1. To identify BrdU-containing reads, DNAscent v4.0.1 was used to detect the nucleoside analog within individual reads. CpG methylation was called using Dorado v0.6.2. Nanoplot v1.41.6 was used to assess and visualize read-level statistics such as number of reads, read length N50, mean and median read length, and mean and median read quality.
Assembly: GRCh37 (hg19)
Supplementary files format and content: For nanopore long-read samples, processed data are available in bedMethyl files (.bed) and read-level calls (.tsv). For Repli-ATAC samples, processed data are provided as .bigWig files.

growth_protocol: HUES64 hESCs were cultured on Geltrex (Thermo Fisher Scientific, A1413302) coated tissue culture plates with mTeSR (STEMCELL Technologies) media. Cells were incubated at 37°C with 5% CO2. Media was changed daily and cells were passaged upon reaching 80% confluency using ReleSR (STEMCELL Technologies).

extract_protocol:
For samples labeled with 50 µM BrdU or nocodazole, cells were lysed via incubation in SDS-PK buffer (0.5% wt/vol) sodium dodecyl sulfate (SDS), 50mM Tris-HCl, 0.01M EDTA, 1M NaCl and 0.2mg/ml proteinase K) at 56°C for 2h. Genomic DNA was isolated using phenol-chloroform extraction and isopropanol precipitation. For samples labeled with 500 µM BrdU, genomic DNA was isolated using the Puregene Cell Kit (8 x 10^8) (Qiagen, 158043) or Monarch® Genomic DNA Purification Kit (NEB, T3010S) according to the manufacturer’s instructions.
For samples labeled with 50 µM BrdU or nocodazole, libraries were prepared from purified and fragmented genomic DNA using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK110) according to the manufacturer’s instructions. Briefly, DNA repair and end-prep were performed using NEBNext® FFPE DNA Repair Mix (NEB, M6630) and NEBNext® Ultra II End Repair/dA-tailing Module (NEB, E7546). Adapter ligation and clean-up were performed using the NEBNext® Quick Ligation Module (NEB, E6056). Long Fragment Buffer from the Ligation Sequencing Kit was used in the clean-up step to enrich for DNA fragments of >3 kb. Libraries were loaded onto R9.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN106D) and sequenced using a MinION Mk1b device (Oxford Nanopore Technologies) for 16 hours. Minimum read length was set to 200 bp. For samples labeled with 500 µM BrdU and samples not labeled with BrdU, libraries were prepared using a Ligation Sequencing Kit (Oxford Nanopore Technologies, SQK-LSK114) according to the manufacturer’s instructions, similarly to previously described. Libraries for samples labeled with 500 µM BrdU were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-MIN114) and sequenced using a MinION Mk1b device for 32 hours. Libraries generated from unlabeled samples were loaded onto R10.4.1 flow cells (Oxford Nanopore Technologies, FLO-PRO114M) and sequenced on a PromethION P2 solo device (Oxford Nanopore Technologies) for 72 hours. Minimum read length was set to 1000 bp. All sequencing data was collected using MinKNOW v23.07.5.

treatment_protocol: For the nocodazole experiment, hESCs were treated with 2 µg/ml nocodazole for 16h prior to DNA extraction. For the BrdU pulse-chase experiments, BrdU pulses are conducted by adding BrdU to the culture medium at the desired final concentration and incubating for the specified durations (10 minutes, 20 minutes, 30 minutes, or 1 hour). Cells are then either collected immediately (0h chase) or washed three times with DPBS and incubated in fresh mTeSR medium for 16 hours (16h chase). For mock treatments, BrdU is replaced with an equivalent volume of Ultrapure H2O. Cells subjected to mock treatments undergo the same incubation times as their BrdU-treated counterparts, with samples collected at 0h or following a 16h incubation.

value: human embryonic stem cells

value: DMSO vehicle control


title: MyD88KO-Fib_DSS_2

description:
Library name: A22
Column name in MyD88KODSS_Counts.csv A22


title: Ze2_ZT7_100-3

value: Well watered, 100% full capacity


title: 50046blood

description: DNABlood

data_processing: IDAT Data loaded into R using Minfi and normalized using BMIQ method.

extract_protocol: Genomic DNA was extracted using a Qiagen kit according to manufacturer's instructions. DNA was bisulfite converted using the Zymo EZ DNA methylation kit.

value: Blood

value: HIV

tag: chronological age


title: 50041blood

description: DNABlood

value: Female


title: Nocodazole

description: Library name: Nocodazole

value: 2 µg/ml nocodazole


title: Ze2_ZT7_20-2


title: BioRep2, BrdU 500 uM 16h

description: Library name: BioRep2, BrdU 500 uM 16h

value: 500 µM BrdU, 10m pulse, 16h chase


title: MyD88KO-Fib_DSS_1

description:
Library name: A21
Column name in MyD88KODSS_Counts.csv A21

value: colonic mucosa

value: DSS


title: Control_DSS_3

description:
Library name: A13
Column name in MyD88KODSS_Counts.csv A13


title: Ze2_ZT13_20-1


title: 50020blood

description: DNABlood


title: 50036blood

description: DNABlood


title: BioRep2, BrdU 500 uM 0h

description: Library name: BioRep2, BrdU 500 uM 0h

value: 500 µM BrdU, 10m pulse, 0h chase


title: Ze2_ZT7_20-1


title: Control_DSS_2

description:
Library name: A12
Column name in MyD88KODSS_Counts.csv A12


title: RNA-Seq_Embryo cortex_E18.5 HFD rep 2

city: Al Ain

first: Suraiya

last: Ansari

address: Tawam

country: United Arab Emirates

institute: United Arab Emirates University

description: E18.5 HFD rep 2

data_processing:
Quality Cotrol (FastQC), genome alignment (bowtie2), read counts (HTSeq-count ) and Differentially expressed genes (DESEq2)
Assembly: rn6
Supplementary files format and content: .xlsx raw read counts

organism: Rattus norvegicus

source_name: Embryo brain cortex

extract_protocol:
Total RNA was isolated from E14.5, E16.5, and E18.5 rat embryo cortex using the MasterPure™ RNA Purification Kit from Epicentre (Cat. #MCR 85102) following the manufacturer's guidelines.
RNA libraries for sequencing were then prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7775) according to the provided instructions. During library preparation, 1 µg of total RNA was depleted of ribosomal RNAs using NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) (E7400L) and purified with AMPure XP beads.

value: Embryo brain cortex

tag: strain

value: Wistar-rat

value: E18.5 HFD Set 2

value: HFD


title: BioRep1, Mock 500uM 0h

description: Library name: BioRep1, Mock 500uM 0h

value: Mock 500 µM, 10m pulse, 0h chase


title: Control_DSS_1

description:
Library name: A11
Column name in MyD88KODSS_Counts.csv A11


title: RNA-Seq_Embryo cortex_E18.5 HFD rep 1

description: E18.5 HFD rep 1

value: E18.5 HFD Set 1


title: 50048blood

description: DNABlood

value: Male


title: Ze2_ZT1_100-1

value: leaf


title: EGFR_KO_mono_AREG_KO_tumor_rep3

city: Chicago

first: Andras

last: Piffko

state: IL

address: 900 E 57th St

institute: University of Chicago

description: Library name: EGFR_KO_mono_AREG_KO_tumor_3

data_processing:
Sequence quality control was performed using Fastqc 0.12.1
Sequence alignment was performed using STAR 2.7.10b
Samtools 1.17 was used to filter sequences with a quality score lower than 30 post-alignment.
Subread 2.0.5 was used to generate raw counts
Read normalization and further analysis was performed using DESeq2 in Rstudio using R version 4.3.1 (2023-06-16)
Gene Set Enrichment Analysis was performed using GSEA 4.3.2
Assembly: mm10
Supplementary files format and content: tumor_raw_counts_all.csv and monocytes_raw_counts_all.csv contain raw counts for all Samples called by Subread
Supplementary files format and content: tumor_normalized_counts_all.csv and monocytes_normalized_counts_all.csv contain normalized counts for each Sample (normalization method - median of ratios utilized by DESeq2)

source_name: Ly6C+ MNPs from EGFR- cKO mice (LysM cre Egfr -/-) co-cultured with LLC-AR- cells

growth_protocol: Tumor cells were cultured in 5% CO2 and were maintained in DMEM medium (Corning, Manassas, VA), supplemented with 10% heat-inactivated fetal bovine serum (Sigma, St Louis, MO), 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
RNA was extracted using Qiagen Kit (Life Technologies) according to manufacturer’s instructions
cDNA library preparation and RNA sequencing were performed by the genomics core facility at The University of Chicago using NovaSeqX Plus (Illumina)

treatment_protocol: WT_IR samples were treated with 4Gy irradation in vitro.

value: bone marrow

value: isolated from conditional EGFR KO (LysMcre Egfr -/-) mice

value: Ly6C+ mononuclear phagocytes

value: EGFR- (LysmCre Egfr-/-)

value: co-cultured for 24 hours with LLC-AR- tumor cells

tag: batch


title: BioRep1, BrdU 500 uM 0h

description: Library name: BioRep1, BrdU 500 uM 0h

value: human embryonic stem cells


title: RNA-Seq_Embryo cortex_E18.5 Control rep 3

description: E18.5 Control rep 3

value: E18.5 Control Set 3

value: Control


title: EGFR_KO_mono_AREG_KO_tumor_rep2

description: Library name: EGFR_KO_mono_AREG_KO_tumor_2


title: Ze2_ZT19_100-3

value: Well watered, 100% full capacity


title: EGFR_KO_mono_AREG_KO_tumor_rep1

description: Library name: EGFR_KO_mono_AREG_KO_tumor_1


title: RNA-Seq_Embryo cortex_E18.5 Control rep 2

description: E18.5 Control rep 2

value: Embryo brain cortex

value: E18.5 Control Set 2


title: Ze2_ZT13_100-3


title: RNA-Seq_Embryo cortex_E18.5 Control rep 1

description: E18.5 Control rep 1

value: Wistar-rat

value: E18.5 Control Set 1


title: Mock 16h

description: Library name: Mock 16h

value: Mock 50 µM, 10m pulse, 16h chase


title: EGFR_KO_mono_WT_tumor_rep3

description: Library name: EGFR_KO_mono_WT_tumor_3

source_name: Ly6C+ MNPs from EGFR- cKO mice (LysM cre Egfr -/-) co-cultured with LLC-AR+ cells

value: co-cultured for 24 hours with LLC-AR+ tumor cells


title: Mock 0h

description: Library name: Mock 0h

value: Mock 50 µM, 10m pulse, 0h chase


title: RNA-Seq_Embryo cortex_E16.5 HFD rep 2

description: E16.5 HFD rep 2

value: E16.5 HFD Set 2

value: HFD


title: Ze2_ZT1_20-2

value: leaf

value: Water limited, 20% full capacity


title: EGFR_KO_mono_WT_tumor_rep1

description: Library name: EGFR_KO_mono_WT_tumor_1

value: bone marrow

value: isolated from conditional EGFR KO (LysMcre Egfr -/-) mice

value: Ly6C+ mononuclear phagocytes

value: EGFR- (LysmCre Egfr-/-)


title: BrdU 1h pulse 16h chase

description: Library name: BrdU 1h pulse 16h chase

value: human embryonic stem cells

value: 50 µM BrdU, 1h pulse, 16h chase


title: BrdU 1h pulse 0h chase

description: Library name: BrdU 1h pulse 0h chase

value: 50 µM BrdU, 1h pulse, 0h chase


title: Ze2_ZT13_20-2


title: WT_mono_AREG_KO_tumor_rep3

description: Library name: WT_mono_AREG_KO_tumor_3

source_name: Ly6C+ MNPs from EGFR+ WT mice co-cultured with LLC-AR- cells

value: isolated from EGFR+ (Egfr flx/flx) mice

value: EGFR+ (WT)

value: co-cultured for 24 hours with LLC-AR- tumor cells


title: BioRep1, BrdU 500 uM 16h

description: Library name: BioRep1, BrdU 500 uM 16h

value: 500 µM BrdU, 10m pulse, 16h chase


title: Ze2_ZT7_100-2

value: Well watered, 100% full capacity


title: RNA-Seq_Embryo cortex_E16.5 Control rep 2

description: E16.5 Control rep 2

value: Embryo brain cortex

value: Wistar-rat

value: E16.5 Control Set 2

value: Control


title: RNA-Seq_Embryo cortex_E16.5 HFD rep 1

description: E16.5 HFD rep 1

value: E16.5 HFD Set 1

value: HFD


title: RNA-Seq_Embryo cortex_E16.5 Control rep 3

description: E16.5 Control rep 3

value: E16.5 Control Set 3


title: Ze2_ZT19_20-3

value: leaf

value: Water limited, 20% full capacity


title: EGFR_KO_mono_WT_tumor_rep2

description: Library name: EGFR_KO_mono_WT_tumor_2

value: bone marrow

value: isolated from conditional EGFR KO (LysMcre Egfr -/-) mice

value: Ly6C+ mononuclear phagocytes

value: EGFR- (LysmCre Egfr-/-)

value: co-cultured for 24 hours with LLC-AR+ tumor cells


title: Ze2_ZT13_100-2


title: WT_mono_AREG_KO_tumor_rep2

description: Library name: WT_mono_AREG_KO_tumor_2

value: isolated from EGFR+ (Egfr flx/flx) mice

value: EGFR+ (WT)

value: co-cultured for 24 hours with LLC-AR- tumor cells


title: BrdU 30m pulse 16h chase

description: Library name: BrdU 30m pulse 16h chase

value: human embryonic stem cells

value: 50 µM BrdU, 30m pulse, 16h chase


title: Ze2_ZT7_100-1

value: Well watered, 100% full capacity


title: RNA-Seq_Embryo cortex_E16.5 Control rep 1

description: E16.5 Control rep 1

value: Embryo brain cortex

value: Wistar-rat

value: E16.5 Control Set 1

value: Control


title: BrdU 20m pulse 16h chase

description: Library name: BrdU 20m pulse 16h chase

value: 50 µM BrdU, 20m pulse, 16h chase


title: RNA-Seq_Embryo cortex_E14.5 HFD rep 2

description: E14.5 HFD rep 2

value: E14.5 HFD Set 2

value: HFD


title: BrdU 20m pulse 0h chase

description: Library name: BrdU 20m pulse 0h chase

value: 50 µM BrdU, 20m pulse, 0h chase


title: Ze2_ZT19_100-2

value: leaf


title: WT_mono_WT_tumor_rep3

description: Library name: WT_mono_WT_tumor_3

source_name: Ly6C+ MNPs from EGFR+ WT mice co-cultured with LLC-AR+ cells

value: bone marrow

value: Ly6C+ mononuclear phagocytes


title: Ze2_ZT1_100-2


title: Ze2_ZT1_20-1

value: Water limited, 20% full capacity


title: WT_mono_WT_tumor_rep2

description: Library name: WT_mono_WT_tumor_2

value: isolated from EGFR+ (Egfr flx/flx) mice

value: EGFR+ (WT)

value: co-cultured for 24 hours with LLC-AR+ tumor cells


title: BrdU 10m pulse 16h chase

description: Library name: BrdU 10m pulse 16h chase

value: human embryonic stem cells

value: 50 µM BrdU, 10m pulse, 16h chase


title: RNA-Seq_Embryo cortex_E14.5 Control rep 3

description: E14.5 Control rep 3

value: Embryo brain cortex

value: E14.5 Control Set 3


title: BrdU 10m pulse 0h chase

description: Library name: BrdU 10m pulse 0h chase

value: 50 µM BrdU, 10m pulse, 0h chase


title: Ze2_ZT1_20-3


title: WT_mono_WT_tumor_rep1

description: Library name: WT_mono_WT_tumor_1


title: RNA-Seq_Embryo cortex_E14.5 Control rep 2

description: E14.5 Control rep 2

value: Wistar-rat

value: E14.5 Control Set 2

value: Control


title: Ze2_ZT13_100-1

value: Well watered, 100% full capacity


title: BrdU 30m pulse 0h chase

description: Library name: BrdU 30m pulse 0h chase

value: 50 µM BrdU, 30m pulse, 0h chase


title: WT_IR_rep2

description: Library name: WT_IR_2

source_name: LLC tumor cells expressing RFP treated with 4Gy irradiation

value: tumor cells

value: LLC-AR+

value: LLC tumor cells expressing RFP

value: WT

value: 4 Gy irradiation in vitro


title: HFD_Total H3_ChIP_3

description:
rat embryo cortex  HFD Total H3 pulldown
Total_H3_HFD_narrow_peaks.narrowPeak
Total_H3_HFD.bw

data_processing:
Raw data checked for quality and aligned against rn6 genome using bowtie2 then peaks were called using macs2, visualised enriched regiongs with the help of deeptools
Assembly: rn6
Supplementary files format and content: .bw, narrowpeaks, broadpeaks

source_name: rat embryo brain cortex

extract_protocol:
The ChIP (Chromatin Immunoprecipitation) assay was carried following established protocols with minor modifications. Briefly, cells were crosslinked using 1% formaldehyde, and chromatin was fragmented by sonication. Immunoprecipitation was performed using specific antibodies (list of antibodies with catalogues) against H3K27me3, H3K4me3, H4K16Ac, total H3 and pan H4. Protein-DNA complexes were captured using protein A/G magnetic beads, washed, and eluted.
ChIP-seq libraries were prepared using NEBNext® Ultra™ II for DNA Library Prep (NEB #E7645) as per the manufacturer’s instructions. A final cleanup step was carried out using AMPure XP beads to ensure the library's quality. The DNA was then eluted from the beads and then subjected to quality control using a bioanalyzer before proceeding with the Next-Generation Sequencing (NGS

value: rat embryo brain cortex

tag: chip antibody

value: Total H3

value: HFD


title: Barcode 5 Calu-6 siDelta2-4

city: Ann Arbor

first: Andrew

last: Ludlow

state: Education

address: 830 N University Ave

institute: University of Michigan

data_processing:
Base-calling was performed by Guppy (v 3.1.5). Fastq files which were classified as passed (Phred score of 8) by the MinKNOW software were subsequently processed and analyzed.
Passed fastq files were aligned to human genome (GRCh38.p14) using minimap2 (v 2.14; [19, 20]) in SAM MD-tag aware mode. Sam files were sorted with SAMtools (v 1.13; [21]) followed by transcriptClean (v 2.0.3; [22]) for correction of read microindels (< 5 bp), mismatches, and noncanonical splice junctions (< 5 bp). Read annotation was performed with TALON (v 5.0; [23]), using the human Gencode v.44 reference annotation gtf with minimum alignment identity = 0.6 and coverage = 0.8. Identified transcripts were subsequently filtered using a minimum count threshold of N = 5 reads in K = 3 samples.
Assembly: human genome (GRCh38.p14)
Supplementary files format and content: siDelta2-4_CountMatrix.tsv

source_name: lung cancer

extract_protocol:
RNA was extracted from frozen cell pellets using RNeasy® Plus Universal Mini Kit (Qiagen, 73404) according to manufacturer’s protocol.
Barcoded libraries were prepared following ONT PCR-cDNA kit (SQK-PCB111.24), pooled libraries were prepared by equal molar loading and loaded onto ONT flow cell (FLO-MIN106D) and sequenced for 72 hrs on a MinION Mk1c.

treatment_protocol: Non-silencing control (siControl) or a siRNA targeting TERT Delta2-4 (siDelta 2-4; junction of exon 1 and exon 5) were transfected using RNAiMAX (invitrogen) in 10 nM concentration for 48h.

value: lung cancer

value: Lung cancer


title: WT_IR_rep3

description: Library name: WT_IR_3


title: Barcode 6 Calu-6 siDelta2-4


title: Barcode 4 Calu-6 siDelta2-4


title: Yu1-42_ZT7_20-3

value: leaf

value: Water limited, 20% full capacity


title: Yu1-42_ZT13_100-2


title: WT_rep3

description: Library name: WT_3

source_name: LLC tumor cells expressing RFP

value: no treatment


title: WT_mono_AREG_KO_tumor_rep1

description: Library name: WT_mono_AREG_KO_tumor_1

value: bone marrow

value: isolated from EGFR+ (Egfr flx/flx) mice

value: Ly6C+ mononuclear phagocytes

value: EGFR+ (WT)

value: co-cultured for 24 hours with LLC-AR- tumor cells


title: RNA-Seq_Embryo cortex_E14.5 HFD rep 1

description: E14.5 HFD rep 1

value: Embryo brain cortex

value: Wistar-rat

value: E14.5 HFD Set 1


title: WT_IR_rep1

description: Library name: WT_IR_1

value: tumor cells

value: LLC-AR+

value: LLC tumor cells expressing RFP

value: WT

value: 4 Gy irradiation in vitro


title: HFD_Total H3_ChIP_1

value: rat embryo brain cortex

value: Total H3

value: HFD


title: Yu1-42_ZT13_20-2

value: leaf

value: Water limited, 20% full capacity


title: WT_rep2

description: Library name: WT_2

value: no treatment


title: Barcode 3 Calu-6 siControl

value: lung cancer

value: Lung cancer

value: siControl


title: Barcode 2 Calu-6 siControl


title: Yu1-42_ZT13_20-3


title: HFD_Pan H4_ChIP_3

description:
rat embryo cortex  HFD Pan H4 pulldown
Pan_H4_HFD_narrow_peaks.narrowPeak
Pan_H4_HFD.bw

value: Pan H4


title: WT_rep1

description: Library name: WT_1


title: Barcode 1 Calu-6 siControl


title: lowerbands barcode 12 iPSCs

data_processing:
Base-calling was performed by Guppy (v 3.1.5). Fastq files which were classified as passed (Phred score of 8) by the MinKNOW software were subsequently processed and analyzed.
Passed fastq files were aligned to human genome (GRCh38.p13) using minimap2 (v 2.14; [19, 20]) in SAM MD-tag aware mode. Sam files were sorted with SAMtools (v 1.13; [21]) followed by transcriptClean (v 2.0.2; [22]) for correction of read microindels (< 5 bp), mismatches, and noncanonical splice junctions (< 5 bp). Read annotation was performed with TALON (v 5.0; [23]), using the human Gencode v.38 reference annotation gtf with minimum alignment identity = 0.5 and coverage = 0.5. Identified transcripts were subsequently filtered using a minimum count threshold of N = 35 reads in K = 2 samples.
Assembly: human genome (GRCh38.p13)
Supplementary files format and content: The processed data files are .tsv count matrix files generated by TALON (Talon abundance)

source_name: iPSCs

extract_protocol:
RNA was extracted (Qiazol) from four human cell lines (iPSCs CHiPs 22 Takara, H1299, Calu-6, A549).
cDNAs were synthesized (SuperScript IV Thermo Fisher). Sequencing libraries were prepared following ONT kit instructions with TERT specific primers and ONT sequences with a total 30 cycles. DNA bands in the 2.5 kb – 4 kb range (upper bands; upper TERT) and bands below 2.5 kb to 0.5 kb (lower bands; lower TERT) were excised and purified via gel extraction (Qiagen). Next, size binned fractions were amplified with ONT barcoded primers 1-12 (4 cells lines by 3 replicates by 2 size bins) for 20 cycles. Barcoded libraries from each cell line were pooled at equal molar ratios for each size bin (upper bands or lower bands). The pooled libraries for each size bin were sequenced on its own flow cell (two R9.4.1 flowcells). Sequencing was performed with the standard 72 h sequencing protocol run on the MinION Mk1C, using the MinKNOW software (v 3.3.2). From lower TERT, 21.8 million reads were obtained and 16.4 million reads passed from all 12 samples. From upper TERT, 14.1 million reads were obtained, and 12.2 million reads were passed from all 12 samples. Base-calling was performed by Guppy (v 3.1.5). Fastq files which were classified as passed (Phred score of 8) by the MinKNOW software were subsequently processed and analyzed.

value: iPSCs

value: untreated


title: RNA-Seq_Embryo cortex_E14.5 Control rep 1

description: E14.5 Control rep 1

value: Embryo brain cortex

value: Wistar-rat

value: E14.5 Control Set 1

value: Control


title: Yu1-42_ZT19_20-1


title: HFD_Pan H4_ChIP_1


title: whole-cell RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_N3L]

city: Palo Alto

first: Maria

last: Barna

address: 240 Pasteur Dr, BMI 4500

department: Genetics

institute: Stanford University

description: Library name: ALIBi_Nmd3_Gnl3_KD_N3L

data_processing:
For all RNA-seq analysis, the reference genome was generated using STAR/2.7.9a on the Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27 and --sjdbOverhang 149. Alignment was performed with adapter sequences AGATCGGAAGAGCACA CGTCTGAACTCCAGTCAC and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAG ATCTCGGTGGTCGCCGTATCATT, and --clip3pAdapterMMp 0.1 0.1. Read counting was performed with htseq-count from htseq/0.11.2 -m intersection-nonempty -s reverse -i gene_id with annotations from GENCODE vM27. Genes were included in downstream analysis if the mean raw count across all samples was at least 5.  For RNA-seq analysis comparing cytosolic and ER ALIBi, differential abundance of read counts was performed using DESeq2 with a design matrix of “~ organelle + fraction + replicate + organelle:fraction” where “organelle” has values of “cytoplasm” or “endoplasmic reticulum” and “fraction” has values of “lysate” (whole-cell RNA fraction) or “eluate” (ribosome-bound RNA fraction). GO-Slim Cellular Component gene ontology terms were mapped using the PANTHER database. For comparison to existing ER transcriptome and translatome datasets from HEK293 cells, mouse gene IDs were converted based on the corresponding ENSEMBL gene ID or UCSC ID in each species, and mouse genes with no human homologs were excluded.  For RNA-seq analysis of ER ALIBi with Lsg1, Nmd3, or Gnl3 siRNA knockdown, differential abundance of read counts was analyzed separately for the whole-cell RNA fractions and for the ER ribosome-bound RNA fractions from cells transfected with ER-ALIBi using DESeq2 with a design matrix of “~replicate + sirna” where “sirna” has values representing either the siRNA-targeted gene or “scramble” (non-targeting control siRNA). For the Nmd3 and Gnl3 whole-cell RNA fractions, one out of three replicates for each condition was excluded from analysis because it appeared as an outlier in principle component analysis (PCA). Uniprot subcellular location codes were used to identify genes encoding membrane proteins or secreted/lumenal proteins.  For all RNA-seq analysis, adjusted p-values reflect multiple comparison correction using the Benjamini-Hochberg method, as implemented in DESeq2.
Assembly: Mus musculus GRCm39 primary assembly with annotations from GENCODE vM27
Supplementary files format and content: Tab-delimited HTSeq output files containing raw counts

source_name: Rpl31-FTA E14Tg2a.4 mESCs

growth_protocol: E14Tg2a.4 mESCs were a gift from Thom Saunder’s lab (University of Michigan). Cell line identity was verified via short tandem repeat profiling performed by the American Type Culture Collection (ATCC, 137-XV, Manassas, VA). Cells were cultured in Knockout DMEM (ThermoFisher 10829-018) supplemented to a final concentration of 15% ES-qualified fetal bovine serum (MilliporeSigma ES-009-B), 1% non-essential amino acids (MilliporeSigma TMS-001-C), 2 mM L-glutamine (MilliporeSigma TMS-002-C), 1% penicillin/streptomycin (ThermoFisher 15140-122), 55 μM beta-mercaptoethanol (ThermoFisher 21985-023), and 1000 U/mL mouse leukemia inhibitory factor (mLIF, Gemini 400-495 10^7). Media was changed daily and cells were passaged every two days. Mycoplasma testing was performed according to the manufacturer’s instructions using the PromoKine PCR Mycoplasma Test Kit (PK-CA91-1096, Heidelberg, Germany).

extract_protocol:
Prior to affinity purification, an aliquot of cell lysate was reserved and mixed at a volume ratio of 1:9 with TRIzol (Thermo 15596-018) in an RNA non-stick tube. After affinity purification, eluate was mixed at a volume of 1:3 with TRIzol LS (Thermo 10296010) in an RNA non-stick tube. RNA was extracted using the DirectZol kit (R2060), following the manufacturer protocol without the on-column DNAse treatment. Extracted RNA was treated with Turbo DNAse (AM2239) per the manufacturer protocol and re-purified with an RNA Clean & Concentrator-5 column (R1016) per the manufacturer protocol. RNA concentration was estimated by Nanodrop 2000 (Thermo), and RNA integrity number (RIN) was assessed on an Agilent 2100 Bioanalyzer (total RNA pico) at the Stanford Protein and Nucleic Acid Facility.
For each sample, 750 ng of RNA was used as input for the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs E7760S) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs E7490) and indices from the NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (New England Biolabs E7335S, E7500S), per the manufacturer protocol with 9 cycles of PCR amplification. Libraries were assessed on an Agilent 2100 Bioanalyzer (DNA 1000) to have an amplicon size of ~300 bp. Libraries were sequenced by Novogene on a Novaseq X or X Plus with paired-end 150 bp reads to a total target depth of 20 - 26 million read pairs per sample.

treatment_protocol: Lysis buffer: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 2% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide, 1X Halt EDTA-Free Protease Inhibitor (ThermoFisher 78425), 0.1 U/µL Superase RNAse Inhibitor (ThermoFisher AM2696), 0.014 U/µL Turbo DNAse (ThermoFisher AM2239), 1 U/mL apyrase (New England Biolabs M0398L) in Ultrapure distilled water (ThermoFisher 10977-015).  RNAse removal buffer: 100 mM NaOH (MilliporeSigma 72068), 50 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Salt wash: 100 mM NaCl (ThermoFisher AM9760G) in Ultrapure distilled water (ThermoFisher 10977-015).  Wash I: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 150 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Wash II: 20 mM Tris pH 7.5 (ThermoFisher 15567027), 15 mM MgCl2 (ThermoFisher AM9530G), 300 mM NaCl (ThermoFisher AM9760G), 0.5 mM DTT (MilliporeSigma 43815), 0.05% n-dodecyl b-d-maltoside (MilliporeSigma W53094), 100 µg/mL cycloheximide in Ultrapure distilled water (ThermoFisher 10977-015).  Elution buffer (ThermoFisher 12575015): 1X AcTEV buffer, 1 mM DTT, 1% v/v AcTEV protease in Ultrapure distilled water (ThermoFisher 10977-015).  General precautions: once cells were transfected, exposure to ambient light and temperatures below 37 °C was minimized. Lysis, centrifugation, pulldown, and wash steps were carried out in a dark room with samples and buffers chilled to 4 C. Protein low-binding microcentrifuge tubes were used unless otherwise specified.  For samples not treated with siRNA, Rpl31-FTA mESCs were transfected with plasmids encoding the appropriate N- and C-terminal ALIBi fragments. 1.5 µg of each ALIBi plasmid was diluted in 100 µL Opti-MEM. In parallel, 7.5 µL of Lipofectamine 2000 was diluted in 100 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 3 million trypsinized cells were resuspended in 300 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 2 minutes at room temperature, and plated into one well of a 6-well plate containing 1.5 mL warmed media. Plates were incubated at 37 °C for 4 hours to allow reattachment before changing to fresh media. Media was changed 24 hours after transfection. At 48 hours after transfection, cells were changed to media containing 100 µg/mL cycloheximide and 50 uM biotin. Plates were immediately placed on a blue light transilluminator inside a 37 °C incubator for 15 minutes. Plates were washed once with ice-cold DPBS containing 100 µg/mL CHX, before adding 500 µL ice-cold lysis buffer per well. After incubating plates with lysis buffer on ice for 5 minutes, lysate was pipetted up and down six times in the plate with a P1000 pipet to fully dislodge cells and transferred to a 1.5 mL microcentrifuge tube. The lysate was further incubated for 15 minutes on ice, then clarified by centrifuging at 17,000 g for 3 minutes at 4 C. A 300 µL aliquot of the clarified lysate was added to pre-washed beads for affinity purification. For each sample, a 150 µL aliquot of beads was pre-washed as follows: the storage buffer was removed and the beads were washed twice with 500 µL of RNAse removal buffer, once with 500 µL of salt wash, and twice with 500 µL of Wash I. After adding clarified lysate, beads were rotated at 4 °C for 1 h, then washed once with a double bead volume of Wash I and twice with a double bead volume of Wash II. The beads were then incubated in one bead volume of elution buffer at room temperature for 1 h on a thermomixer at 800 rpm.  For samples with Lsg1, Nmd3, or Gnl3 siRNA knockdown and subsequent RNA-seq, a modified transfection was performed: 0.625 µg of each ALIBi plasmid and 26.7 pmol of Lsg1 siRNA (Horizon Discovery M-057491-01-0005), Nmd3 siRNA (Horizon Discovery M-051297-01-0005), Gnl3 siRNA (Horizon Discovery M-051664-01-0005), or control siRNA (Horizon Discovery D-001206-14-05) were diluted in 41.7 µL Opti-MEM. In parallel, 3.13 µL of Lipofectamine 2000 was diluted in 41.7 µL Opti-MEM. The plasmid/Opti-MEM and Lipofectamine/Opti-MEM mixes were combined and incubated for 20 minutes at room temperature. For each condition, 1.25 million trypsinized cells were resuspended in 125 µL Opti-MEM, mixed with the plasmid-Lipofectamine complexes for 10 minutes at room temperature, and plated into one well of a 6-well plate containing 2 mL warmed media. The remaining steps were performed as described above, with the modification that ALIBi activation, cell lysis, and affinity purification were performed 24 h after transfection.

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells

tag: organelle

value: endoplasmic reticulum

tag: fraction

value: whole-cell

tag: sirna

tag: replicate

value: biol rep 3


title: Yu1-42_ZT7_20-2

value: leaf

tag: temperature

tag: photoperiod

value: Water limited, 20% full capacity


title: Yu1-42_ZT19_20-2

tag: timepoint (zt_=_hours_after_dawn)


title: Yu1-42_ZT7_20-1


title: HFD_Total H3_ChIP_2

value: rat embryo brain cortex

value: Total H3

value: HFD


title: whole-cell RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_N2L]

description:
Library name: ALIBi_Nmd3_Gnl3_KD_N2L
sample excluded from analysis because outlier on PCA

tag: cell line

tag: cell type

value: biol rep 2


title: lowerbands barcode 10 iPSCs

value: iPSCs

value: Lung cancer

tag: genotype

value: WT

tag: treatment


title: ribosome-bound RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_N3E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_N3E

value: ribosome-bound


title: HFD_H4K16ac_ChIP_3

description:
rat embryo cortex  HFD H4K16ac pulldown
H4K16Ac_HFD_broad_peaks.broadPeak
H4K16Ac_HFD.bw

tag: tissue

value: Wistar-rat


title: lowerbands barcode 11 iPSCs

value: untreated


title: ribosome-bound RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_N2E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_N2E

value: Rpl31-FTA E14Tg2a.4 mESCs


title: HFD_H4K16ac_ChIP_1


title: Yu1-42_ZT1_100-3

value: Well watered, 100% full capacity


title: whole-cell RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 1 [ALIBi_Nmd3_Gnl3_KD_N1L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_N1L

value: mouse embryonic stem cells

value: endoplasmic reticulum

value: biol rep 1


title: HFD_H4K16ac_ChIP_2


title: lowerbands barcode 9 calu-6 cells

value: lung cancer


title: lowerbands barcode 8 calu-6 cells


title: lowerbands barcode 7 calu-6 cells


title: HFD_Pan H4_ChIP_2

value: Pan H4


title: ribosome-bound RNA, endoplasmic reticulum, Nmd3 siRNA, biol rep 1 [ALIBi_Nmd3_Gnl3_KD_N1E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_N1E


title: HFD_H3K4me3_ChIP_2

description:
rat embryo cortex  HFD H3K4me3 pulldown
H3K4me3_HFD_narrow_peaks.narrowPeak
H3K4me3_HFD.bw

value: rat embryo brain cortex


title: Yu1-42_ZT19_20-3

value: leaf

value: Water limited, 20% full capacity


title: Yu1-42_ZT7_100-2


title: HFD_H3K4me3_ChIP_3

value: HFD


title: whole-cell RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_G3L]

description:
Library name: ALIBi_Nmd3_Gnl3_KD_G3L
sample excluded from analysis because outlier on PCA

value: whole-cell

value: biol rep 3


title: HFD_H3K4me3_ChIP_1


title: lowerbands barcode 6 H1299 cells

value: Lung cancer

value: WT


title: Yu1-42_ZT13_20-1


title: lowerbands barcode 5 H1299 cells


title: Yu1-42_ZT13_100-3


title: ribosome-bound RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_G3E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_G3E

value: ribosome-bound


title: HFD_H3K27me3_ChIP_3

description:
rat embryo cortex  HFD H3K27me3 pulldown
H3K27me3_HFD_broad_peaks.broadPeak
H3K27me3_HFD.bw

value: Wistar-rat


title: Yu1-42_ZT1_100-2


title: whole-cell RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_G2L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_G2L

value: Rpl31-FTA E14Tg2a.4 mESCs

value: biol rep 2


title: lowerbands barcode 4 H1299 cells

value: untreated


title: ribosome-bound RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_G2E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_G2E

value: mouse embryonic stem cells

value: endoplasmic reticulum


title: HFD_H3K27me3_ChIP_2


title: lowerbands barcode 3 A549 cells

value: lung cancer


title: Yu1-42_ZT19_100-2

value: Well watered, 100% full capacity


title: HFD_H3K27me3_ChIP_1

value: rat embryo brain cortex


title: Yu1-42_ZT1_20-3

value: leaf


title: lowerbands barcode 2 A549 cells


title: Control_Total H3_ChIP_3

description:
rat embryo cortex  HFD Total H3 pulldown
Total_H3_CTRL_narrow_peaks.narrowPeak
Total_H3_CTRL.bw

value: Total H3


title: ribosome-bound RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 1 [ALIBi_Nmd3_Gnl3_KD_G1E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_G1E

value: biol rep 1


title: whole-cell RNA, endoplasmic reticulum, Gnl3 siRNA, biol rep 1 [ALIBi_Nmd3_Gnl3_KD_G1L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_G1L

value: whole-cell


title: Yu1-42_ZT19_100-3


title: lowerbands barcode 1 A549 cells


title: Control_Total H3_ChIP_2

description:
rat embryo cortex  Control Total H3 pulldown
Total_H3_CTRL_narrow_peaks.narrowPeak
Total_H3_CTRL.bw

value: Control


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_C3L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_C3L

value: scramble

value: biol rep 3


title: Yu1-42_ZT1_20-2

value: Water limited, 20% full capacity


title: upperbands barcode 12 iPSCs

value: iPSCs

value: iPS

value: WT


title: Control_Total H3_ChIP_1

value: Wistar-rat


title: Yu1-42_ZT19_100-1


title: Control_Pan H4_ChIP_3

description:
rat embryo cortex  Control Pan H4 pulldown
Pan_H4_CTRL_narrow_peaks.narrowPeak
Pan_H4_CTRL.bw

value: Pan H4


title: ribosome-bound RNA, endoplasmic reticulum, scramble siRNA, biol rep 3 [ALIBi_Nmd3_Gnl3_KD_C3E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_C3E

value: Rpl31-FTA E14Tg2a.4 mESCs

value: mouse embryonic stem cells

value: endoplasmic reticulum

value: ribosome-bound


title: Yu1-42_ZT7_100-1

value: leaf

value: Well watered, 100% full capacity


title: upperbands barcode 10 iPSCs

value: untreated


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_C2L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_C2L

value: whole-cell

value: biol rep 2


title: Control_Pan H4_ChIP_2

value: rat embryo brain cortex

value: Control


title: Yu1-42_ZT1_100-1


title: ribosome-bound RNA, endoplasmic reticulum, scramble siRNA, biol rep 2 [ALIBi_Nmd3_Gnl3_KD_C2E]

description: Library name: ALIBi_Nmd3_Gnl3_KD_C2E

value: scramble


title: Control_Pan H4_ChIP_1


title: whole-cell RNA, endoplasmic reticulum, scramble siRNA, biol rep 1 [ALIBi_Nmd3_Gnl3_KD_C1L]

description: Library name: ALIBi_Nmd3_Gnl3_KD_C1L

value: biol rep 1


title: Yu1-42_ZT7_100-3


title: upperbands barcode 8 calu-6

value: lung cancer

value: Lung cancer


title: Yu1-42_ZT13_100-1


title: Control_H4K16ac_ChIP_3

description:
rat embryo cortex  Control H4K16ac pulldown
H4K16Ac_CTRL_broad_peaks.broadPeak
H4K16Ac_CTRL.bw

value: Wistar-rat