title: P2

city: Jinan

first: Nianyu

state: ShanDong

address: 44 wenhua xi road

institute: Shandong University

data_processing:
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
High-quality mapped reads (MAPQ > 30) reads were aligned to the UCSC mm10 genome or hg19 genome using Bowtie2.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10；hg19
Supplementary files format and content: bigWig

source_name: Ovary

growth_protocol: DMEM/F12, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
The genomic DNA was extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using TruePrep Index Kit V2 for Illumina (Vazyme Biotech, China; TD202) at 11 cycles on the thermocycler. Libraries were purified with the VAHTS DNA Clean Beads (Vazyme Biotech, China; N411) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ovary

value: human primary granulosa cells


title: Endometrial samples from cows supplemented with methionine and became non pregnant after AI -Rep4

status: Public on Dec 25 2023

type: SRA

city: Bonn

first: Dessie Salilew

last: Wondim

address: Endenicher Allee 15

country: Germany

institute: University of Bonn

library_source: genomic

data_processing:
Adapter and low-quality sequences were trimmed using Trim Galore (Babraham Bioinformatics, UK) by specifying the RRBS option.
Cleaned RRBS sequences were aligned to the bovine genome using Bismark Bisulfite Mapper (Babraham Bioinformatics, UK).
The BAM files generated from mapping were sorted and the replicate libraries from the same biological group were merged using the SAMtools.
Methylation calls were obtained from merged BAM files using the Bismark methylation extractor script integrated with the Bismark Bisulfite Mapper. Bismark coverage files
Quantification of methylation calls and identification of differentially methylated CpG sites was done using SeqMonk v1.48.0 tool (Babraham Bioinformatics, UK).
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: text delimited file (Data_Geo_RRBS_2023.txt).  Column names: S12, S16. S24, S28 indicate CON_noP_1, CON_noP_2, CON_noP_3, CON_noP_4 of CON_noP  group, respectively. Column names: S14, S18, S26, S30 indicate, CON_P_1, CON_P_2, CON_P_3, CON_P_4 of CON_P  group, respectively. Column names: S13, S17, S25, S29 indicate MET_noP_1, MET_noP_2, MET_noP_3, MET_noP_4 of MET_noP group, respectively. Column names: S15,  S19,  S27,  S31 indicate MET_P_1, MET_P_2, MET_P_3, MET_P_4 of MET_P  group, respectively.

molecule: genomic DNA

organism: Bos taurus

extract_protocol:
DNA was isolated from each sample using AllPrep DNA/RNA/Protein (Qiagen).
2 µg genomic DNA was digested with MspI enzyme, end repaired, A-tailed and ligated with methylated adaptor sequences using TruSeq Nano DNA Sample Preparation kit (Illumina, San Diego, CA). Following this, 40–200 bp-sized DNA fragments were extracted using the Zyomclean™ Gel DNA Recovery Kit (Zymo Research). The samples were then treated with bisulfite using the EZ DNA Methylation-Gold Kit™ (Zymo Research).

treatment_protocol: Endometrial cytobrush samples collected from post-calving cows offered a control diet or rumen-protected methionine (RPM) were  classified based on the pregnancy. Endometrial samples collected from cows fed with control feed and that become pregnant and did not become were categorized as control pregnant (CON_P) and control non pregnant (CON_noP), respectively. Samples collected from cows supplemented with RPM and resulted in pregnancy or in no pregnancy were categorized as methionine pregnant (MET_P) and methionine non pregnant (MET_noP) groups, respectively.

tag: tissue


title: Endometrial samples from cows supplemented with methionine and became pregnant after AI -Rep2


title: Central forebrain, sleep deprived 6h & recovery 4h, rep4 [R4-4]

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

country: USA

institute: Washington State Univ. Spokane

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
ZT10vR4_25016_9-3-2023_apeglm

library_source: transcriptomic

data_processing:
*library strategy: WTTS-seq (whole transcriptome termini site sequencing) targeting alternative polyA sites
Raw read processing: Raw data were obtained from 55 samples and stored in FASTQ format. We filtered raw reads with the FASTQ quality filter in the FASTX Toolkit (v0.0.13), allowing for a minimum score of ≥10 for ≥50% of bases (http://hannonlab.cshl.edu/fastx_toolkit/). We trimmed T nucleotides or T-rich sequences located at the 5’ ends of the reads using Perl scripts, as described in a previous study30. Trimmed reads of at least 16 bp in length were kept for further analysis.
Read mapping and poly(A) site clustering: For each data set, we aligned the processed reads to the Rattus norvegicus genome (mRatBN7.2/rn7) using the torrent mapping program (TMAP, v3.4.1; http://github.com/iontorrent/tmap) with the unique best hits parameter (-a 0). We then extracted raw PASs supported by the uniquely mapped reads from SAM files and obtained a polyadenylation tag (PAT) file using an in-house script. After that, we merged all the PAT files to determine the final PASs for all samples. PASs within 25 nucleotides of one another were grouped into one polyadenylation site cluster (PAC) using GetPolyaSiteCluster31. PACs with few reads were rejected according to different criteria depending on library size. For libraries that had less than 1.7M reads, clusters were retained only if a group of 5 biological replicates had at least 3 samples with ≥3 reads. For libraries with more than 1.7M reads, at least 3 samples with ≥4 reads were required.
Gene annotation and usage of poly(A) sites: We annotated all the final PACs for PAS_ID, gene symbol, functional region, and other factors, as indicated, using Cuffcompare (v2.2.1)32, Perl scripts, and annotation file (GCF_000001895.5_Rnor_6.0_genomic.gtf; https://ftp.ncbi.nlm.nih.gov/). Clusters that mapped to mitochondrial genes were removed, then the number of PAS-covered reads was normalized33 to the total number of covered reads within each library and rescaled by a factor of 107.
Circadian/ultradian PAS discovery: Based on input, unnormalized PAS read counts, rhythmic patterns were identified using the MetaCycle34 R package meta2d, which synthesizes the results of three cycle analysis algorithms (ARSER, JTK_Cycle, and Lomb-Scargle). The analysis was run 5 times with different replicates inserted into each of the appropriate ZT time slots, and the average p-value, FDR, phase, and other statistics were calculated. Only the highly corroborated PASs that were significant (p<0.05) in all 5 trials were used for all analyses.
Differential expression analysis of sleep deprivation/recovery: To evaluate the expression of PASs in sleep homeostasis experiments, PAS counts from rats recovering from 6 h SD were contrasted with time-matched controls (R0 vs ZT6, R2 vs ZT8, R4 vs ZT10, R8 vs ZT14). We removed high variation from the first principal component systematically, resulting in improved variance estimates for low read counts. Prcomp (in R) was used to perform principal component analysis (PCA) and find eigenvectors by way of singular value decomposition. DESeq-2 with "Apeglm" Shrinkage36 and the Wald Test were used to generate test statistics in R software. The FDRtool was used to determine the Local FDR
Assembly: Rattus norvegicus genome  build mRatBN7.2/rn7
Supplementary files format and content: the details in the processed_data_readme.txt

molecule: polyA RNA

organism: Rattus norvegicus

source_name: central forebrain

growth_protocol: Male Long Evans rats (7-9 weeks old) were housed in pairs at 22 ± 2 °C on a 12:12 h light-dark cycle. The rats were acclimated to this light cycle for at least 10 days prior to tissue collection, with water and chow ad libitum. Cages were cleaned weekly (between 8 and 11 AM) unless the rats were being euthanized within 24 h.

extract_protocol:
Rats were decapitated by guillotine under normal room light (ZT2–10) or under dim red light (ZT14–22). Following decapitation, forebrains were resected (Fig. 1A), frozen in 2-methylbutane suspended in dry ice, and then stored at -80 °C until homogenization for RNA extraction. Just before RNA isolation, forebrains were removed from -80 °C storage and placed on dry ice. Prior to use, a stainless-steel mortar and pestle were cleaned with RNase Zap (Thermo Fisher) and 70% ethanol. The mortar was then partially filled with liquid nitrogen before a forebrain was added, pulverized, and placed in a conical tube. Between each sample, the mortar and pestle were cleaned with 70% ethanol. A small aliquot of sample was removed for RNA isolation using Trizol Reagent (Invitrogen), according to the manufacturer’s instructions. Purified RNA was resuspended in water, and concentration and purity were measured with a Nanodrop spectrophotometer (Thermo Fisher).
WTTS-Seq libraries were prepared as described by Zhou et al. https://doi.org/10.1534/genetics.116.188508. Briefly, total RNA (2.5 µg) was incubated at 70 °C with 10X Fragmentation buffer (Invitrogen) for 3 min. The fragmentation reaction was halted by the addition of Stop Solution and incubation on ice for at least 2 min. Next, poly(A)+ RNA was purified from the fragmented total RNA with Dynabeads Oligo (dT)25 (Invitrogen), according to the manufacturer’s directions, and used for first-strand cDNA synthesis in a 20 µL reaction mixture. First, 1.0 µL of barcode primer (100 µM) and 1.0 µL of a common SMART primer (100 µM) were annealed to the poly(A)+ RNA template by heating to 65 °C for 5 min and incubating on ice for at least 2 min. Next, 4.0 µL of 5X First-strand buffer (Invitrogen), 1.0 µL of SuperScript III reverse transcriptase (Invitrogen), 1.0 µL of 0.1 M dithiothreitol, 2.5 µL of 10 mM dNTP, and 1.0 µL of RNase OUT (Invitrogen) were added to the mixture. First-strand cDNA was synthesized by incubating the mixture at 40 °C for 90 min in the presence of library-specific adaptors. Synthesis was terminated by heating the mixture at 70 °C for 15 min. RNases I (100 U/µL; Invitrogen) and H (2 U/µL; Invitrogen) were subsequently added and incubated with the mixture at 37 °C for 30 min to hydrolyze the remaining single-stranded RNA molecules and ensure that only single-stranded cDNA remained. RNase activities were terminated by heating the samples at 70 °C for 20 min. Following purification with solid-phase reversible immobilization (SPRI) beads, second-strand cDNA was synthesized from first-strand cDNA by asymmetric PCR. In addition to the cDNA, the 50 µL PCR reaction contained 1.0 µL of Phusion Hi-Fidelity DNA polymerase, 10.0 µL of 5X HF buffer, 1.0 µL of 0.4 µM barcode primer, 1.0 µL of 0.8 µM common primer, 1.0 µL of 10 mM dNTP, and nuclease-free water. The PCR reaction was carried out by heating at 95 °C for 30 sec, followed by 20 cycles of 98 °C for 10 s, 50 °C for 30 s, and 72 °C for 30 s, with a final elongation step at 72 °C for 10 min. SPRI beads were used to purify and select 200 – 500 bp fragments from the final library.

treatment_protocol: Thirty rats were randomly assigned to one of six groups (n=5/group) that were sampled every 4 h, beginning 2 h after light onset (i.e., ZT2, 6, 10, 14, 18, and 22). For the sleep deprivation (SD) study, twenty rats were randomly assigned to 6 h SD from ZT0–6, wherein rats were kept awake by an automated bedding stir bar (Pinnacle) at the bottom of a cylindrical cage. The bar was set to rotate for 4 s, randomly changing rotation direction and stopped for a random interval ranging from 10 to 30 s28,29. Following SD, rats (n=5/time point) were euthanized immediately (R0) or were returned to their home cage for 2 h (R2), 4 h (R4), or 8 h (R8) under red light without disruption before sampling. Five additional rats were euthanized at ZT8 as undisturbed, time-matched controls.

value: central forebrain

tag: cell line

value: age 7-9 weeks

tag: cell type

value: male

tag: genotype

value: Long Evans

tag: treatment

value: sleep deprived 6h & recovery 4h


title: P1

last: Li

country: China

organism: Homo sapiens


title: C3


title: MCF7 NF1-45 E2 Rep 1

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

data_processing:
Trim reads with trim_galore v0.6.0
Reads were mapped to GRCh38 with GENCODE release 33 with STAR v2.7.8a basic two-pass mode.
The raw counts were extracted from the reverse strand alignments.
Assembly: GRCh38
Supplementary files format and content: raw_counts.tsv contains raw read counts
Supplementary files format and content: counts_per_million.tsv contains counts per million mapped reads

source_name: breast

growth_protocol: Cells were grown in MEC media (phenol red-free DMEM/F12, 10% horse serum, 20ng/mL EGF, 0.5ug/mL hydrocortisone, 100ng/mL cholera toxin, and 10ug/mL insulin) in a 37°C humidified incubator in 5% CO2.

extract_protocol:
Buffer RLT (from RNeasy kit) containing betamercaptoethanol was added to each well of cells. The mix of buffer RLT and cells was then added to an MPbio lysing matrix E tube. Cells were homogenized for 20 seconds in an MPbio homogenizer, then the supernatant was added to a Qia Shredder column. An equal volume of 70% ethanol was added to the flow through, and the entire volume of liquid added to an RNeasy column. RNA was extracted according to the manufacturer’s instructions for the RNeasy kit (Qiagen).
KAPA mRNA Hyperprep kit (v7.21)

treatment_protocol: 10nM beta-estradiol for 24hr

value: breast

value: epithelial

value: beta-estradiol (10mM)


title: Endometrial samples from cows supplemented with methionine and became non pregnant after AI -Rep3


title: P3


title: Central forebrain, sleep deprived 6h & recovery 2h, rep5 [R2-5]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022

value: sleep deprived 6h & recovery 2h


title: C2


title: Endometrial samples from cows supplemented with methionine and became non pregnant after AI -Rep1


title: H1 cells, FINE, rep1

city: Haining

first: Yaqi

last: Su

state: Zhejiang

address: ZJU-UoE Institute,718 East Haizhou Rd.

institute: Zhejiang University-University of Edinburgh Institute, Zhejiang University

data_processing:
Sequence reads were mapped to GRCh38 using minimap2 (parameters: -ax splice --MD)
Read counts extraction were performed using featureCounts basd on the GRCh38.105 reference annotation (parameters: -L -M -O -g: transcript_id -t: transcript)
Assembly: human NCBI genome build 38
Supplementary files format and content: tab-delimited text files include expression raw count values for each sample

molecule: total RNA

extract_protocol:
RNA was harvested using Trizol reagent and purified.
Library was prepared according to theNanopore Ligation Sequencing Kit 1D (PM).

value: Embryonic stem cells

value: WT

value: Naïve ESCs were grown in FINE culture condition after research 50% confluency


title: Central forebrain, sleep deprived 6h & recovery 4h, rep1 [R4-1]


title: Central forebrain, sleep deprived 6h & recovery 2h, rep4 [R2-4]


title: Central forebrain, sleep deprived 6h & recovery 4h, rep2 [R4-2]


title: Central forebrain, sleep deprived 6h & recovery 2h, rep3 [R2-3]


title: C1


title: Endometrial samples from cows fed control diet and became  pregnant after AI -Rep3


title: Central forebrain, sleep deprived 6h & recovery 2h, rep2 [R2-2]


title: Endometrial samples from cows supplemented with methionine and became non pregnant after AI -Rep2


title: Endometrial samples from cows fed control diet and became  pregnant after AI -Rep4


title: Central forebrain, sleep deprived 6h & recovery 2h, rep1 [R2-1]


title: Endometrial samples from cows fed control diet and became  pregnant after AI -Rep2


title: Endometrial samples from cows fed control diet and became  pregnant after AI -Rep1


title: Endometrial samples from cows fed control diet and became non pregnant after AI -Rep4


title: Central forebrain, sleep deprived 6h & recovery 0h, rep5 [R0-5]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
ZT6vR0_25128_9-3-23_apeglm

value: sleep deprived 6h & recovery 0h


title: Cmpd-10_LPS-5_Donor2_T24

city: Spring House

first: Luvena

last: Ong

state: PA

address: 1400 McKean Rd

institute: Johnson & Johnson Innovative Medicine

description:
10x Genomics
library name: 19

library_source: transcriptomic single cell

data_processing:
The demultiplexing, processing, alignment, and gene counting were performed using Cell Ranger software
Assembly: GRCh38
Supplementary files format and content: tab separated values and matrix files

source_name: PBMC

extract_protocol:
Adherent and non-adherent cells were collected, transferred to a microcentrifuge tube, pelleted, the supernatant removed, and the pellet resuspended in 10 uL of 1X DPBS (Invitrogen).
Libraries were generated with the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to manufacturer’s directions.

treatment_protocol: PBMCs were isolated from heparinized whole blood collected from de-identified and fully consented healthy donors using density gradient centrifugation and cryopreserved. On the day of the experiment, thawed cells were plated in a tissue culture dish and either JRD-SIK1/2i-3 or DMSO was added to a final concentration of 1 or 10 micromolar and incubated at 37°C for 1 hr. LPS (Sigma) was added at a final concentration of 5 ng/mL and incubated for additional 1, 4, or 24 hr at 37°C. Adherent and non-adherent cells were collected and transferred to a microcentrifuge tube and pelleted. After removing the supernatant and resuspending the cell pellet in 10 uL of 1X DPBS (Invitrogen), libraries were generated with the Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) according to manufacturer’s directions.

value: PBMC

value: 10 uM SIKi, 5 ng/mL LPS

tag: compound concentration

tag: lps

tag: time

tag: donor


title: Cmpd-10_LPS-5_Donor2_T04

description:
10x Genomics
library name: 16


title: Endometrial samples from cows fed control diet and became non pregnant after AI -Rep3


title: Cmpd-10_LPS-5_Donor2_T01

description:
10x Genomics
library name: 17


title: Central forebrain, sleep deprived 6h & recovery 0h, rep4 [R0-4]


title: Endometrial samples from cows fed control diet and became non pregnant after AI -Rep1


title: Central forebrain, sleep deprived 6h & recovery 0h, rep3 [R0-3]


title: Cmpd-10_LPS-5_Donor1_T24

description:
10x Genomics
library name: 1


title: FS109-BY4742-rnh201-null

city: Atlanta

first: Francesca

last: Storici

state: GA

address: 950 State Street Nw, Krone Engineering Biosystems Building

department: Biological Sciences

institute: Georgia Institute of Technology

description: ribose-seq

library_source: other

data_processing:
trimming with Cutadapt to trim adapter sequence "AGTTGCGACACGGATCTATCA" with filteration of reads with less than 62 bases and quality 15
deduplication and alignment to sacCer2 using Alignment module of Ribose-Map toolkit (bam files)
subtraction of rNMPs with restriction enzyme sites and filteration of mismatches with the reference genome (bedgraph files)
Assembly: sacCer2
Supplementary files format and content: bedgraph format
Library strategy: ribose-seq

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Standard yeast growth protocol till stationary phase

extract_protocol:
ribose-seq and WGS with KAPA Hyper Prep library preparation kitdna-seq
PCR and size fractionation

treatment_protocol: creating AGS ortholgous mutations using diletto perfecto method


title: FS138-BY4742-rnh201-null

description: ribose-seq


title: Central forebrain, sleep deprived 6h & recovery 0h, rep1 [R0-1]


title: Cmpd-10_LPS-5_Donor1_T04

description:
10x Genomics
library name: 13


title: FS213-BY4742-WT

description: ribose-seq

value: wildtype


title: FS208-BY4742-rnh201-G42S

description: ribose-seq


title: Cmpd-10_LPS-5_Donor1_T01

description:
10x Genomics
library name: 14


title: FS142-BY4742-WT

description: ribose-seq


title: FS210-BY4742-rnh201-G42S

description: ribose-seq


title: FS215-BY4742-WT

description: ribose-seq


title: FS106-BY4742-WT

description: ribose-seq


title: Cmpd-1_LPS-5_Donor2_T24

description:
10x Genomics
library name: 2

value: 1 uM SIKi, 5 ng/mL LPS


title: FS214-BY4742-WT

description: ribose-seq


title: Central forebrain, ZT22 undesturbed, rep3 [ZT22-3]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
meta2d_12h_no_mito_WTTS
meta2d_24h_no_mito_WTTS

value: central forebrain

value: ZT22 undesturbed


title: Cmpd-1_LPS-5_Donor2_T04

description:
10x Genomics
library name: 15


title: Endometrial samples from cows fed control diet and became non pregnant after AI -Rep2


title: Central forebrain, ZT22 undesturbed, rep2 [ZT22-2]

value: age 7-9 weeks

value: male


title: LNCaP_shPRMT5-3

city: Changsha

first: Dingxiao

last: Zhang

state: Hunan

address: Yuelushan

department: School of BioMedical Sciences

institute: Hunan University

description: growth condition: RPMI+FBS

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to human genome (GRCh38.p7) by STAR (version 2.5.2).
The number of fragments in each known gene from GENCODE (version 25) was enumerated using STAR QuantMode (GeneCounts) function.
The normalized fragment count for each gene was calculated by R/Bioconductor package DESeq2 (version 1.18.1).
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are normalized expression values (estimated by DESeq2) for all the samples.

source_name: Prostate cancer cell line

growth_protocol: Early passage of PC3 and LNCaP cells (obtained from ATCC) were grown in RPMI1640 mediun supplemented with 7% serum.

extract_protocol:
Puromycin-resistant prostate cancer cells treated with shRNAs are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected with lentiviral shRNAs (shNC, shPRMT5-1, shPRMT5-3) for 48hrs and then sellected by puromycin (1ug/ml) for 7 days.

value: Prostate cancer cell line

value: Prostate cancer

value: LNCaP

tag: ar status

value: AR+


title: LNCaP_shPRMT5-1

description: growth condition: RPMI+FBS


title: LNCaP_shNC

description: growth condition: RPMI+FBS


title: PC3_shPRMT5-3

description: growth condition: RPMI+FBS

value: AR-


title: Cmpd-1_LPS-5_Donor1_T24

description:
10x Genomics
library name: 9


title: Central forebrain, sleep deprived 6h & recovery 0h, rep2 [R0-2]

value: Long Evans


title: PC3_shPRMT5-1

description: growth condition: RPMI+FBS


title: Central forebrain, ZT22 undesturbed, rep1 [ZT22-1]


title: Central forebrain, ZT22 undesturbed, rep4 [ZT22-4]


title: Central forebrain, ZT22 undesturbed, rep5 [ZT22-5]


title: PC3_shNC

description: growth condition: RPMI+FBS


title: Cmpd-1_LPS-5_Donor1_T04

description:
10x Genomics
library name: 6


title: Central forebrain, ZT18 undesturbed, rep5 [ZT18-5]

value: ZT18 undesturbed


title: Cmpd-0_LPS-5_Donor2_T24

description:
10x Genomics
library name: 18

value: 0 uM SIKi, 5 ng/mL LPS


title: Cmpd-1_LPS-5_Donor2_T01

description:
10x Genomics
library name: 3


title: Central forebrain, ZT18 undesturbed, rep3 [ZT18-3]


title: Central forebrain, ZT18 undesturbed, rep2 [ZT18-2]


title: Cmpd-0_LPS-5_Donor2_T01

description:
10x Genomics
library name: 20


title: LNCaP_Ctrl_rep1

description: Sample 5

extract_protocol:
Prostate cancer cells treated with PRMT5i are subject to total RNA extraction by RNeasy mini kit (Qiagen, Valencia, CA). Illumina TruSeq Stranded Total RNA Preparation Kit (Illumina, cat#: RS-122-2301) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with or without PRMT5i at 4uM for 4 days.

tag: cancer type

tag: growth condition

value: FBS+DMSO


title: PC3_Ctrl_rep1

description: Sample 1


title: LNCaP_PRMT5i_rep1

description: Sample 7


title: LNCaP_PRMT5i_rep2

description: Sample 8


title: PC3_Ctrl_rep2

description: Sample 2


title: PC3_PRMT5i_rep1

description: Sample 3


title: PC3_PRMT5i_rep2

description: Sample 4


title: LNCaP_Ctrl_rep2

description: Sample 6


title: Cmpd-0_LPS-5_Donor1_T24

description:
10x Genomics
library name: 11

value: PBMC


title: Central forebrain, ZT18 undesturbed, rep1 [ZT18-1]


title: Central forebrain, ZT14 undesturbed, rep4 [ZT14-4]

value: ZT14 undesturbed


title: spleen, Cy3+HA+, Smart-seq, cell 94

city: Stanford

first: Yueh-hsiu

last: Chien

state: CA

address: Stanford University

department: Microbiology and Immunology

institute: Stanford University

data_processing:
FASTQ files for each cell were extracted and generated, distinguished by the unique dual index adaptors. Reads were aligned to the mm10 genome using STAR v2.6.1d. Transcript abundance was quantified using HTSeq v0.5.4p5.
Assembly: mm10
Supplementary files format and content: csv file including counts for each cell

organism: Mus musculus

source_name: spleen

extract_protocol:
Spleen Cy3+HA+ gdT cells (Live Cy3+HA+CD3+TCRgd+TCRb-CD19-F4/80-CD11b-CD11c-TER119- cells) were sorted into 96-well plates and cDNA synthesis was performed using the Smart-seq protocol.
Illumina sequencing libraries were prepared as described previously using a Mosquito HTS liquid handler (TTP Labtech). In brief, the tagmentation was carried out on 0.4 μl double-stranded cDNA using the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Amplicon Tagment Mix (Illumina), then incubated at 55 °C for 10 min. The reaction was stopped by adding 0.4 μl Neutralize Tagment Buffer (Illumina) and centrifuging at room temperature at 3,000 g for 5 min. Indexing PCR reactions were performed by adding 0.8 μl of pre-mixed 5 μM i5 and i7 unique dual indexing primers (IDT, customized) and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a C1000 Touch™ Thermal Cycler with 384-Well Reaction Module (Bio-rad) using the following program: 1) 72 °C for 3 min, 2) 95 °C for 30 s, 3) 12 cycles of 95 °C for 10 s, 55 °C for 30 s and 72 °C for 1 min, and 4) 72 °C for 5 min.

value: spleen

tag: strain

value: Cy3+HA+ gdT

tag: Sex

value: female

value: No (wild-type, naive)


title: spleen, Cy3+HA+, Smart-seq, cell 100


title: spleen, Cy3+HA+, Smart-seq, cell 105


title: Cmpd-0_LPS-5_Donor1_T04

description:
10x Genomics
library name: 7


title: spleen, Cy3+HA+, Smart-seq, cell 104


title: spleen, Cy3+HA+, Smart-seq, cell 102


title: Cmpd-1_LPS-5_Donor1_T01

description:
10x Genomics
library name: 24

value: 1 uM SIKi, 5 ng/mL LPS


title: Central forebrain, ZT14 undesturbed, rep3 [ZT14-3]

value: central forebrain

value: age 7-9 weeks

value: male


title: Central forebrain, ZT18 undesturbed, rep4 [ZT18-4]


title: Central forebrain, ZT14 undesturbed, rep5 [ZT14-5]


title: spleen, Cy3+HA+, Smart-seq, cell 101


title: spleen, Cy3+HA+, Smart-seq, cell 93


title: Cmpd-0_LPS-0_Donor2_T24

description:
10x Genomics
library name: 4


title: spleen, Cy3+HA+, Smart-seq, cell 91


title: Central forebrain, ZT14 undesturbed, rep2 [ZT14-2]


title: spleen, Cy3+HA+, Smart-seq, cell 87


title: spleen, Cy3+HA+, Smart-seq, cell 90


title: Cmpd-0_LPS-5_Donor2_T04

description:
10x Genomics
library name: 22


title: Central forebrain, ZT14 undesturbed, rep1 [ZT14-1]


title: Central forebrain, ZT10 undesturbed, rep5 [ZT10-5]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
meta2d_12h_no_mito_WTTS
meta2d_24h_no_mito_WTTS
ZT10vR4_25016_9-3-2023_apeglm

value: ZT10 undesturbed


title: spleen, Cy3+HA+, Smart-seq, cell 84


title: spleen, Cy3+HA+, Smart-seq, cell 89


title: Cmpd-0_LPS-0_Donor2_T01

description:
10x Genomics
library name: 8


title: Cmpd-0_LPS-0_Donor2_T04

description:
10x Genomics
library name: 10


title: Cmpd-0_LPS-0_Donor1_T24

description:
10x Genomics
library name: 21


title: Cmpd-0_LPS-5_Donor1_T01

description:
10x Genomics
library name: 12


title: spleen, Cy3+HA+, Smart-seq, cell 82


title: spleen, Cy3+HA+, Smart-seq, cell 81


title: Cmpd-0_LPS-0_Donor1_T01

description:
10x Genomics
library name: 23


title: Cmpd-0_LPS-0_Donor1_T04

description:
10x Genomics
library name: 5


title: spleen, Cy3+HA+, Smart-seq, cell 79


title: spleen, Cy3+HA+, Smart-seq, cell 83


title: Central forebrain, ZT10 undesturbed, rep4 [ZT10-4]


title: Central forebrain, ZT10 undesturbed, rep3 [ZT10-3]


title: spleen, Cy3+HA+, Smart-seq, cell 80


title: RH4_dCBP1_6h

city: Cleveland

first: Hyunmin

last: Kim

state: Ohio

address: 10900 Euclid Ave.

department: Department of Genetics and Genome Sciences

institute: Case Western Reserve University

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.17
The ChIP-seq peaks were called by MACS3 version 3.0.0a6. Duplicates were allowed.
Enrichment of known and de novo motifs were found using HOMER version 4.9.1
Assembly: Hg38
Supplementary files format and content: peak files are tab delimited text files (BED coordinates) for each sample.

growth_protocol: Cell lines were grown in DMEM supplemented with 10%FBS and 1% Pen/Strep/Glut.

extract_protocol:
For ChIP-seq, the NEB MNase (Catalogue #M0247S) was used. Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-RNA Pol2 antibody (Santa Cruz Biotechnology, Mouse mAb #sc-47701 X) or anti-H3K27ac antibody (Millipore, Rabbit mAb #MABE647  RM172). This was followed by reversal of crosslinks, proteinase K treatment, and DNA purification. Drosophile spike-in was added to the samples for normalization.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For ChIP-seq experiments, adenine base edited RH4 cells with wt P3F or C793R mutant P3F or RH4 cells treated with DMSO or dCBP1 for six hours were used.


title: spleen, Cy3+HA+, Smart-seq, cell 76


title: spleen, Cy3+HA+, Smart-seq, cell 78


title: RH4_DMSO_6h

value: DMSO


title: spleen, Cy3+HA+, Smart-seq, cell 86


title: spleen, Cy3+HA+, Smart-seq, cell 88


title: Central forebrain, ZT10 undesturbed, rep2 [ZT10-2]


title: Central forebrain, ZT10 undesturbed, rep1 [ZT10-1]


title: spleen, Cy3+HA+, Smart-seq, cell 74


title: spleen, Cy3+HA+, Smart-seq, cell 72


title: RH4-ABE_P3FC793R

value: ABE P3F C793R


title: RH4-ABE_NT

value: ABE NT


title: spleen, Cy3+HA+, Smart-seq, cell 73


title: RH4_P3F_FKBP12_dTAG-47_6h

data_processing:
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: hic files are provided at the chromosome-level.
Library strategy: HiChIP

extract_protocol:
For HiChIP, the Dovetail MNase HiChIP kit (Catalogue #21007) was used. Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-RNA Pol2 antibody (Santa Cruz Biotechnology, Mouse mAb #sc-47701 X). On-bead bridge incorporation and religation was performed, followed by reversal of crosslinks, proteinase K treatment, and DNA purification. Mouse C2C12 spike-in was added to the samples for normalization.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For HiChIP experiment, RH4-P3F-FKBP12 cells were treated with DMSO or dTAG-47 for six hours.


title: spleen, Cy3+HA+, Smart-seq, cell 71


title: Central forebrain, ZT08 undesturbed, rep4 [ZT08-4]

value: Long Evans

value: ZT08 undesturbed


title: Central forebrain, ZT08 undesturbed, rep3 [ZT08-3]


title: spleen, Cy3+HA+, Smart-seq, cell 69


title: spleen, Cy3+HA+, Smart-seq, cell 70


title: spleen, Cy3+HA+, Smart-seq, cell 68


title: Central forebrain, ZT08 undesturbed, rep2 [ZT08-2]


title: RH4_P3F_FKBP12_DMSO_6h


title: spleen, Cy3+HA+, Smart-seq, cell 67


title: Central forebrain, ZT08 undesturbed, rep1 [ZT08-1]


title: spleen, Cy3+HA+, Smart-seq, cell 66


title: Central forebrain, ZT06 undesturbed, rep5 [ZT06-5]

description:
WTTS-seq targets polyA-adjacent sequence
Raw_counts_WTTS_Gerstner_03202022
Raw_counts_no_mito_WTTS_Gerstner_03202022
meta2d_12h_no_mito_WTTS
meta2d_24h_no_mito_WTTS
ZT6vR0_25128_9-3-23_apeglm

value: ZT06 undesturbed


title: spleen, Cy3+HA+, Smart-seq, cell 75


title: Central forebrain, ZT06 undesturbed, rep4 [ZT06-4]


title: spleen, Cy3+HA+, Smart-seq, cell 63


title: P-12_1

city: Seoul

first: Seo

middle: Young

last: Lee

state: Goyang-si,Gyeonggi-do

address: Ilsan-ro, Ilsandong-gu

country: South Korea

institute: National Cancer Center

description: P-12_1 BCG

data_processing:
FASTQC (v0.11.8) was used to assess sequence data quliaty and fastp(vv0.19.5) used for removing adapter and low-quality bases.
Alignment to the Human reference genome(GRCH38) was carried out using STAR 2PASS (v2.7.10a)
Raw gene-level count data was quantification using RSEM (v1.1.17) and the processed data file was generated TPM expression.
The RSEM-TPM count matrix filtered for expressed protein-coding genes
Assembly: Human reference genome(GRCH38)
Supplementary files format and content: tab-delimited text file includes TPM count for each Sample

source_name: Bladder

extract_protocol:
Total RNA was extracted using QIAGEN Rneasy mini kit and TRIzol Reagent. 0.1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent SureSelect RNA Direct Kit following manufacturer's protocols.

value: Bladder

value: BCG


title: spleen, Cy3+HA+, Smart-seq, cell 65

value: spleen


title: spleen, Cy3+HA+, Smart-seq, cell 64

value: Cy3+HA+ gdT


title: spleen, Cy3+HA+, Smart-seq, cell 61

value: female


title: P-10_1

description: P-10_1 BCG


title: Central forebrain, ZT08 undesturbed, rep5 [ZT08-5]


title: spleen, Cy3+HA+, Smart-seq, cell 59

value: No (wild-type, naive)


title: P-4_1

description: P-4_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 60


title: Central forebrain, ZT06 undesturbed, rep3 [ZT06-3]


title: spleen, Cy3+HA+, Smart-seq, cell 58


title: Central forebrain, ZT06 undesturbed, rep2 [ZT06-2]


title: P-2_2

description: P-2_2 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 55


title: spleen, Cy3+HA+, Smart-seq, cell 56


title: spleen, Cy3+HA+, Smart-seq, cell 53


title: Central forebrain, ZT02 undesturbed, rep5 [ZT02-5]

value: ZT02 undesturbed


title: P-13_1

description: P-13_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 52


title: P-4_2

description: P-4_2 BCG


title: Central forebrain, ZT02 undesturbed, rep4 [ZT02-4]

value: central forebrain


title: spleen, Cy3+HA+, Smart-seq, cell 51


title: spleen, Cy3+HA+, Smart-seq, cell 50


title: P-11_2

description: P-11_2 BCG


title: P-9_1

description: P-9_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 47


title: Central forebrain, ZT02 undesturbed, rep3 [ZT02-3]

value: age 7-9 weeks


title: spleen, Cy3+HA+, Smart-seq, cell 48


title: Central forebrain, ZT02 undesturbed, rep2 [ZT02-2]

value: male


title: P-2_1

description: P-2_1 BCG


title: Central forebrain, ZT06 undesturbed, rep1 [ZT06-1]


title: P-11_1

description: P-11_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 45


title: spleen, Cy3+HA+, Smart-seq, cell 46


title: P-5_1

description: P-5_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 44


title: spleen, Cy3+HA+, Smart-seq, cell 54


title: spleen, Cy3+HA+, Smart-seq, cell 43


title: Y2-BY4742-rnh201-null

description: WGS with KAPA Hyper Prep library preparation kit

data_processing:
trimming with Cutadapt to trim adapter sequence "AGTTGCGACACGGATCTATCA" with filteration of reads with less than 62 bases and quality 15
deduplication and alignment to sacCer2 using Alignment module of Ribose-Map toolkit (bam files)
subtraction of rNMPs with restriction enzyme sites and filteration of mismatches with the reference genome (bedgraph files)
Assembly: sacCer2
Supplementary files format and content: bedgraph format
Library strategy: dna-seq


title: Central forebrain, ZT02 undesturbed, rep1 [ZT02-1]


title: P-1_2

description: P-1_2 BCG


title: Y5-BY4742-rnh201-G42S


title: spleen, Cy3+HA+, Smart-seq, cell 42


title: spleen, Cy3+HA+, Smart-seq, cell 41


title: P-1_1

description: P-1_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 40


title: Y6-BY4742-rnh203-K46W


title: P-7_2

description: P-7_2 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 39


title: Y1-BY4742-WT

value: wildtype


title: spleen, Cy3+HA+, Smart-seq, cell 38


title: spleen, Cy3+HA+, Smart-seq, cell 37


title: P-7_1

description: P-7_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 36


title: spleen, Cy3+HA+, Smart-seq, cell 35


title: P-3_1

description: P-3_1 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 34


title: FS328-BY4742-rnh201-G42S

description: ribose-seq


title: P-8_1

description: P-8_1 BCG


title: FS322-BY4742-rnh201-null

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 32


title: spleen, Cy3+HA+, Smart-seq, cell 29


title: FS336-BY4742-rnh203-K46W

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 30


title: FS337-BY4742-rnh203-K46W

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 31


title: P-6_4

description: P-6_4 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 27


title: P-6_3

description: P-6_3 BCG


title: FS334-BY4742-rnh203-K46W

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 26


title: P-6_2

description: P-6_2 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 25


title: spleen, Cy3+HA+, Smart-seq, cell 24


title: FS325-BY4742-rnh203-K46W

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 22


title: spleen, Cy3+HA+, Smart-seq, cell 49


title: P-6_1

description: P-6_1 BCG


title: P-8_2

description: P-8_2 BCG


title: spleen, Cy3+HA+, Smart-seq, cell 33


title: spleen, Cy3+HA+, Smart-seq, cell 20


title: spleen, Cy3+HA+, Smart-seq, cell 21


title: FS253-BY4742-WT

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 19


title: P-10

description: P-10 Primary tumor

value: Primary tumor


title: P-12

description: P-12 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 18


title: FS335-BY4742-rnh203-K46W

description: ribose-seq


title: spleen, Cy3+HA+, Smart-seq, cell 16


title: ATAC_T4hrs_Th2_Control_rep2

city: Beijing

first: Yu

last: Hou

state: Beijing

address: No.5 Yiheyuan Street

department: School of life sciences

institute: Peking University

data_processing:
For bulk RNA-seq and ATAC-seq, sequenced raw reads were trimmed for adaptor sequence, amplification primers, and masked for low-complexity or low-quality sequence with trimmomatic V0.30
For bulk RNA-seq and ATAC-seq, clean sequencing reads were mapped to mm10 using bowtie2 v2.3.4.3.
For bulk RNA-seq, reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks V2.0.2
For scRNA-seq (GEX library), reads were mapped to mm10 and UMI count matrices were computed by CellRanger v3.0.2.
For hashtags (ADT library), reads were mapped to hashtag oligo sequences and UMI count matrices were computed by CellRanger v3.0.2.
For ATAC-seq, peak calling was performed with MACS2, peaks were visualized using Integrative Genomics Viewer (IGV)
Assembly: mm10
Supplementary files format and content: FPKM files, tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: For scRNA-seq, barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files together define a matrix of raw UMI counts
Supplementary files format and content: For bulk RNA-seq bifurcation conditions, expression matrix contains the expression level of each single cell at each sampling time point
Supplementary files format and content: For ATAC-seq, bigwig file is included for each sample, bigwig format is as described at the UCSC Genome Bioinformatics web site

growth_protocol: For T cell in vitro activation, naïve CD4+ T cells were isolated from the spleen of C57BL/6 mice followed with Flow cytometry sorting for CD4+ CD25- CD44- CD62L+ cells. Sorted Naïve CD4+ T cells were activated with plate-bound anti-CD3 (1ug/ml, clone 145-2C11, Bio X Cell) and anti-CD28 (1ug/ml, clone PV-1, Bio X Cell).

extract_protocol:
For bulk RNA-seq, in vitro cultured T cells were collected at each time point into RLT-plus buffer, and RNA was extracted with RNeasy Plus Mini Kit (Qiagen). Extracted RNA was further used for cDNA amplification with SMARTA-Seq2 for 12 cycles.
For single cell RNA-seq, if no hashtag is added, 7500 cells were loaded for each 10x genomics channel. If using hashtag, we loaded 5000 cells for each hashtag labelled sample for each 10x genomics channel.
For bulk RNA-seq, sequencing libraries were prepared with fragmented cDNA amplification products using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with 2 x 150 paired-end reads.
ATAC-seq was performed following the Omni-ATAC protocol (Corces et al., 2017). 10,000 cells were sorted for each ATAC-seq sample preparation.

treatment_protocol:
For T cell in vitro polarization, naïve CD4+ T cells were treated with polarization cytokines under Th0 (without cytokine),  Th1 (IL-12, 20ng/mL, R&D Systems) or Th2 (IL-4, 20ng/mL, R&D Systems) conditions.
For LCMV infection, mice were perfused intracardially with cold PBS. Spleen was harvested and smashed through 40 um sterile strainers to get single cell suspension for staining and sorting. ACK lysis (Buffer from Lonza) was performed with the spleen for 5 min at RT to remove red blood cells.
For Th1-Th2 bifurcation culture condition, both IL-12 and IL-4 were added during 3 days in vitro cell polarization.

value: CD4 T cells


title: ATAC_T4hrs_Th2_Control_rep3


title: P-14

description: P-14 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 28


title: spleen, Cy3+HA+, Smart-seq, cell 17


title: ATAC_T4hrs_Th2_Control_rep1


title: spleen, Cy3+HA+, Smart-seq, cell 15


title: spleen, Cy3+HA+, Smart-seq, cell 14


title: spleen, Cy3+HA+, Smart-seq, cell 23


title: spleen, Cy3+HA+, Smart-seq, cell 13


title: ATAC_T4hrs_Th2_CGRP_rep3


title: P-2

description: P-2 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 12


title: ATAC_T4hrs_Th2_CGRP_rep2


title: spleen, Cy3+HA+, Smart-seq, cell 92


title: spleen, Cy3+HA+, Smart-seq, cell 11


title: P-13

description: P-13 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 10


title: ATAC_T4hrs_Th2_CGRP_rep1


title: spleen, Cy3+HA+, Smart-seq, cell 9


title: P-9

description: P-9 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 6


title: spleen, Cy3+HA+, Smart-seq, cell 7


title: spleen, Cy3+HA+, Smart-seq, cell 8


title: P-5

description: P-5 Primary tumor


title: ATAC_T4hrs_Th1_Control_rep3


title: spleen, Cy3+HA+, Smart-seq, cell 4


title: P-1

description: P-1 Primary tumor


title: ATAC_T4hrs_Th1_Control_rep1


title: ATAC_T4hrs_Th1_Control_rep2


title: spleen, Cy3+HA+, Smart-seq, cell 5


title: spleen, Cy3+HA+, Smart-seq, cell 3


title: P-4

description: P-4 Primary tumor


title: ATAC_T4hrs_Th1_CGRP_rep3


title: P-7

description: P-7 Primary tumor


title: spleen, Cy3+HA+, Smart-seq, cell 1


title: P-3

description: P-3 Primary tumor


title: ATAC_T4hrs_Th1_CGRP_rep2


title: P-8

description: P-8 Primary tumor


title: SS_8IN

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

country: United Kingdom

institute: Centre for Immunity, Infection and Evolution

data_processing:
The raw sequences were quality assessed using fastQC
Primer sequences were removed using cutadapt v1.9 and parameters -b "GTTCAGAGTTCTACAGTCCGACGATC" -b "TGGAATTCTCGGGTGCCAAGG" -b "GATCGTCGGACTGTAGAACTCTGAAC" -b "CCTTGGCACCCGAGAATTCCA" -O 6 -m 17 –format=fastq, followed by removal of the terminal 4 bases from each end.
Trimmed sequences were “collapsed” to generate a non-redundant set of sequences in a fasta format suitable for mirdeep2 analysis
Alignments to the reference miRNA transcript set from mirBase v22 were performed using the mirdeep2.pl software, with parameters -o 20 -l 17 -r 100 -c
Raw "tag counts" were processed for differential gene expression analysis using the DESeq2 Bioconductor package.
Pairwise comparisons of the two sample groups (e.g. cases relative to controls) were performed on the normalised tag counts using linear modeling (Bioconductor limma package).
Genome_build: GRCz11; mirBase v22
Supplementary_files_format_and_content: Fasta file of trimmed, collapsed small RNAs, which gives quantitaive information as to the sequence levels of each sequence in each sample

organism: Danio rerio

source_name: INH_5dpf larvae

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5 °C

extract_protocol:
Total RNA was extracted from pooled zebrafish larvae (30 larvae per sample) for qPCR and RNA-sequencing. Larvae were fixed in Qiazol after which they were disrupted using a tissue disruptor. Subsequently, total RNA was extracted using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) eluted in 30 µl RNAse free water.
Libraries were prepared from total-RNA samples using the NEXTFLEX small RNA-seq Kit  v3. Libraries were checked for size, purity and concentration with a high sensitivity DNA chip on the Agilent Technologies 2100 Bioanalyzer.

treatment_protocol:
Control: Zebrafish larvae were maintained in system water
INH: Zebrafish larvae were exposed to 10 mM isoniazid for 24 hours from 4-5 days post fertilisation, 30 larvae per sample;
PYR: Zebrafish larvae were exposed to 6 mM pyrazinamide for 24 hours from 4-5 days post fertilisation, 30 larvae per sample;

tag: developmental stage

value: 5dpf larvae

value: INH

tag: molecule subtype

value: small RNA


title: SS_8PY

source_name: PYR_5dpf larvae

value: PYR


title: spleen, Cy3+HA+, Smart-seq, cell 2


title: SS_7PY


title: SS_8Co

source_name: Control_5dpf larvae

value: Control


title: ATAC_T4hrs_Th1_CGRP_rep1


title: P-6

description: P-6 Primary tumor

value: Bladder


title: SS_7IN


title: RNA_T4hrs_Th2_Control_rep3

value: spleen


title: SS_7Co


title: SS_6PY


title: Penfluridol_3

city: Shanghai

first: Song

middle: Ling

last: yi

address: Xuhui

institute: Lingyi Song

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp software
Trimmed sequence reads were mapped to GRCh38.p13 human genome
Read count extraction and normalization were performed using RSEM software
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: endometrium tissue

growth_protocol: Ishikawa cells were cultured in DMEM/F12  supplemented with 10% FBS and 1% penicillin-streptomycin in humidified air with 5% CO2 at 37 °C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (VZ6). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Ishikawa cells were cultured in 10 cm dishes, and treated with DMSO or 5 μM Penfluridol

value: endometrium tissue

value: Ishikawa

value: Penfluridol 5 microM treatment


title: Penfluridol_2


title: SS_6IN


title: Penfluridol_1


title: RNA_T4hrs_Th2_Control_rep1


title: SS_6Co


title: SS_5Co


title: SS_5IN


title: SS_5PY


title: Control_3

value: DMSO treatment


title: SS_4PY


title: RNA_T4hrs_Th2_CGRP_rep2


title: Control_2


title: SS_4IN


title: Control_1


title: RNA_T4hrs_Th2_CGRP_rep1


title: SS_3PY


title: SS_3IN


title: Snu449 Eze

city: Guangzhou

first: yuting

last: Yin

state: China

address: Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, China 510060.

institute: Sun Yat-sen University Cancer Center (SYSUCC)

data_processing:
Raw Reads obtained from sequencing may contain Reads with low overall quality, contain sequencing primers, low end quality, etc. These unqualified Reads are likely to affect the quality of analysis, so they must be filtered to obtain clean Reads that can be used for data analysis, applying Seqtk  for filtering.Genome mapping of preprocessed reads was performed by applying the spliced mapping algorithm of Hisat2 (version:2.0.4), which allows splitting of reads that cannot be matched at full length for mapping, and is more suitable for eukaryotic (with inter-intron regions) transcriptome sequencing data; default parameters were used.In transcriptome sequencing, we can estimate the level of gene expression by the number of reads mapped to gene regions, but the number of reads is proportional to the gene expression level, but also related to the length of the gene itself and the amount of data sequenced. In order to make the gene expression levels comparable across genes and samples, the reads were converted into FPKM (Fragments Per Kilobase of exon model per Million mapped reads) for normalization of gene expression .
We first applied Stringtie (version:1.3.0)  to count the number of Fragments per gene after Hisat2 comparison, then normalized by the TMM (trimmed mean of M values)  method, and finally calculated the FPKM value for each gene using a perl script.The edgeRwas applied for the between-sample differential genetic analysis, and the p-value was derived and then corrected by multiple hypothesis testing, and the threshold of p-value was determined by controlling the FDR (False Discovery Rate) , and the corrected p-value was the q-value. at the same time, we calculated the differential expression multiplier based on the FPKM value , i.e., Fold-change.
The differential gene screening conditions are as follows.
1) q-value <= 0.05
2)Fold-change>=2

source_name: Liver

growth_protocol: The RPMI 1640 Medium (Invitrogen) was used to cultivate SNU-449 human HCC cells along with 10% FBS. At 37 °C, cells were incubated in a humid environment with 5% CO2.

extract_protocol: Following the manufacturer's instructions, total RNA was extracted using the RNeasy Micro Kit (Cat# 74004, Qiagen), and an Agilent 2100 Bioanalyzer was used to check for a RIN number to inspect RNA integrity (Agilent technologies, Santa Clara, CA, US). The RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc., Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany) were used to further purify the qualified total RNA.

treatment_protocol: Snu-449 cells were treated with Ezetimibe for 24h

value: Liver

value: treated with Ezetimibe for 24h


title: SS_4Co


title: RNA_T4hrs_Th2_Control_rep2


title: RNA_T4hrs_Th1_Control_rep2


title: SS_2Co


title: RNA_T4hrs_Th1_Control_rep1


title: RNA_T4hrs_Th2_CGRP_rep3


title: SS_2IN


title: SS_1IN


title: SS_1PY


title: RNA_T4hrs_Th1_CGRP_rep3


title: HeLa cells, shRPB9, 30min after release of a DRB block

city: San Diego

first: Yajing

last: Hao

address: George Palade Laboratories 9500 Gilman Drive, Room 217

department: Dept. of Cellular and Molecular Medicine

institute: University of California, San Diego

data_processing:
After obtaining raw RNA-seq data, Trimmomatic was first used to perform sliding window trimming, cutting the average quality once within the 2-bp window falling below 20 and trimming read if it had a length less than 38nt.
SortMeRNA was used to filter out ribosomal RNAs with default parameters. After filtering, reads from two biological replicates were combined for further analysis. Combined reads were mapped to the human genome (genome version: hg38) using STAR with default parameters. After obtaining the mapping files, duplicated reads were removed using Picard with parameters MarkDuplicates and REMOVE_DUPLICATES = true.
The bigwig files of each GRO-seq dataset from the sense and antisense strands were obtained using bamCoverage from DeepTools with a parameter --binSize 1, --ignoreDuplicates, –minMappingQuality 255 and –normalizeUsing CPM.
To avoid the contamination of mature RNAs, all GRO-seq library signals were normalized by deduction of the corresponding DRB-blocked GRO-seq library using bigwigCompare from DeepTools with a parameter --binSize 1, -of bigwig and --operation subtract. These normalized signals were used to track the transcriptional wave in an unbiased manner with a hidden Markov model (PMID: 24843027).
Assembly: hg38
Supplementary files format and content: bigWig files to show the signal distribution
Library strategy: GRO-seq

source_name: HeLa S3

growth_protocol: HeLa S3 cells were cultured in DMEM, high glucose with 10% fetal bovine serum and 1 x penicillin-streptomycin at 37 °C in a 5% of CO2 incubator.

extract_protocol:
RNA was harvested using Trizol. Total RNA was used for the construction of sequencing libraries.
Gro-seq RNA libraries were prepared  according to published methods (Core LJ, et al. Science. 2008. PMID: 19056941 ).

treatment_protocol: Grow cells to ~80-90% confluence in a 10-cm dish. Dilute 10 µl of 100 mM DRB in 10 ml culture medium to a final 100 µM concentration, and culture the cells for 3 hours. Aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 30, 20 and 10 min to get time-course samples at the same harvest time point. Also prepare DRB-untreated cells and DRB-treated cells without release as controls.

value: HeLa S3

value: A clonal derivative of the parent HeLa cell line

value: RPB9 knockdown

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 30 minutes.

value: 30 min


title: HeLa cells, shRPB9, 20min after release of a DRB block

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 20 minutes.

value: 20 min


title: α-RFP, HAC1:mCherry, -INA, MNase, rep2

first: Se-Hun

last: Yun

address: 1 Gwanak-ro, Gwanak-gu

institute: Seoul National Univ.

data_processing:
ChIP-seq reads were trimmed by using Trimmomatic v0.38 with options of “-phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Trimmed ChIP-seq reads were aligned to TAIR10 Arabidopsis genome by using Bowtie version 1.1.2 with options of “-S --best --strata -X 500 -m 1 --chunkmbs 500”.
BAM files were deduplicated by using Picard markDuplicate v.1.118.
Deduplicated BAM files were converted to bedgraph format by using bedtools genomecov v2.27.0.
Bedgraph files were converted to bigwig files by using bedGraphToBigWig v4.
Assembly: Arabidopsis thaliana (TAIR10)
Supplementary files format and content: Bigwig

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Plants were grown on Murashige and Skoog basal medium under 8-hour light / 16-hour dark photoperiod for 4 weeks.

extract_protocol:
Seedlings were fixed with formaldehyde and then qeunched with glycine. After isolating nuclei from crosslinked sample, chromatin was fragmentated by sonication or micrococcal nuclease (MNase) treatment. NPR1:GFP or HAC1:mCherry proteins within the chromatin were immunoprecipitated by using anti-GFP or anti-RFP antibody, respectively. Genomic DNAs co-immunoprecipitated with NPR1:GFP or HAC1:mCherry were purified and used for sequencing.
ChIP-seq libraries were prepared by using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (NEB, E7103) and NEBNext® Multiplex Oligos for Illumina® (NEB, E7335). 10 ng of DNA per sample was used for library-construction reaction. Prepared libraries were amplified by 9 cycles of PCR. For DNA samples collected from ChIP involving MNase digestion, sonication was additionally performed at mild condition before library preparartion.

treatment_protocol: 300 μM INA or distilled water was sprayed onto 4-week-old seedlings and then the seedlings were incubated for 12 hours.

value: Seedlings

value: HAC1:mCherry transgenic line

value: Distilled water

value: 12 hours

tag: chip antibody

value: RFP-trap agarose (ChromoTek, rta-20)


title: SS_1Co

value: 5dpf larvae

value: Control

value: small RNA


title: α-RFP, HAC1:mCherry, +INA, MNase, rep2

tag: tissue

value: 2,6-dichloroisonicotinic acid (INA)


title: HeLa cells, shRPB9,10min after release of a DRB block

tag: cell line

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 10 minutes.

value: 10 min


title: RNA_T4hrs_Th1_CGRP_rep1

tag: cell type

value: CD4 T cells

value: spleen


title: WS_PreA [030]

data_processing:
The raw sequences were quality assessed using fastqc; five pairs of samples were removed from further analyses (and thus not included in this submission)
There were no primer sequences that needed removing: all had been removed by BGI Genomics Co., Ltd. (Shenzen, China)
Sequences were “collapsed” to generate a non-redundant set of sequences in a fasta format suitable for mirdeep2 analysis
Alignments to the reference miRNA transcript set from mirBase v21 were performed using the mirdeep2.pl software, with parameters -o 20 -l 17 -r 100 -c
Raw "tag counts" per sample were scale normalised to the sample with the lowest number of alignments, and counts converted to log2; "abundance normalised" data were not further quantile normalised for linear model fitting purposes.
Pairwise comparisons of the two sample groups (e.g. post-surgery relative to pre-surgery) were performed on the normalised tag counts using linear modeling (Bioconductor limma package).
Genome_build: hg19; mirBase v21
Supplementary_files_format_and_content: fasta formatted non-redundant sequences.  The frequency of each read is given in the read name eg. x8601610 means that there were 8601610 reads with that sequence.

source_name: serum_pre cardiac surgery

growth_protocol: Serum samples were taken from 15 human subjects: once before and once after cardiac surgery, yielding a total of 30 samples.

extract_protocol:
Total RNA was extracted using the miRNeasy mini kit (Qiagen, Venlo, The Netherlands) eluted in 30 µl RNAse free water.
RNA libraries were prepared for each sample with the Truseq Stranded Total RNA Sample Prep LT Kit. Libraries were checked for size, purity and concentration with a high sensitivity DNA chip on the Agilent Technologies 2100 Bioanalyzer.

treatment_protocol: Serum samples were paired from the same individual: pre- and post- cardiac surgery.

tag: time point

value: pre cardiac surgery

value: serum


title: WS_PostA [029]

source_name: serum_post cardiac surgery

value: post cardiac surgery


title: SS_3Co

tag: treatment


title: HeLa cells, shRPB9, DRB block transcription

value: HeLa S3

value: A clonal derivative of the parent HeLa cell line

tag: genotype

value: RPB9 knockdown

value: culture cells in normal medium with continual 100 uM DRB


title: RNA_T4hrs_Th1_Control_rep3


title: α-RFP, Col, -INA, MNase, rep2

value: Seedlings

value: Distilled water

value: 12 hours


title: SS_2PY

value: 5dpf larvae

value: PYR


title: LCMV_Day8_CD4


title: WR_PreA [028]

value: small RNA


title: Snu449

value: Liver

value: control


title: Bifur_channel_3_RNA

value: CD4 T cells


title: Input, HAC1:mCherry, +INA, MNase, rep2

value: HAC1:mCherry transgenic line

value: 2,6-dichloroisonicotinic acid (INA)

value: none (input)


title: WR_PostA [027]

value: post cardiac surgery

value: serum


title: α-RFP, HAC1:mCherry, +INA, MNase, rep1

value: RFP-trap agarose (ChromoTek, rta-20)


title: Bifur_channel_3_ADT

value: spleen


title: WH_PreA [026]

value: pre cardiac surgery


title: HeLa cells, shControl, 20min after release of a DRB block

value: HeLa S3

value: A clonal derivative of the parent HeLa cell line

value: shControl

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 20 minutes.

value: 20 min


title: HeLa cells, shControl, 30min after release of a DRB block

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 30 minutes.

value: 30 min


title: α-RFP, HAC1:mCherry, -INA, MNase, rep1

value: Seedlings

value: Distilled water

value: 12 hours


title: RNA_T4hrs_Th1_CGRP_rep2

value: CD4 T cells


title: WH_PostA [025]

value: small RNA


title: Bifur_channel_2_RNA


title: HeLa cells, shControl,10min after release of a DRB block

value: culture the cells with 100 uM DRB for 3 hours, then aspirate the old medium and rinse cells three times with 10 ml 1x PBS. Add culture medium and incubate the cells for 10 minutes.

value: 10 min


title: α-RFP, Col, -INA, MNase, rep1

value: RFP-trap agarose (ChromoTek, rta-20)


title: LS_PostA [019]

value: post cardiac surgery

value: serum


title: Input, HAC1:mCherry, +INA, MNase, rep1

value: HAC1:mCherry transgenic line

value: 2,6-dichloroisonicotinic acid (INA)

value: none (input)


title: HeLa cells, shControl, no DRB treatment

value: HeLa S3

value: A clonal derivative of the parent HeLa cell line

value: shControl

value: culture cells in normal medium without DRB treatment


title: LS_PreA [020]

value: pre cardiac surgery


title: KB_PostA [017]


title: HeLa cells, shRPB9, no DRB treatment

value: RPB9 knockdown


title: Bifur_channel_1_ADT

value: spleen


title: Bifur_channel_1_RNA

value: CD4 T cells


title: KB_PreA [018]

value: small RNA


title: α-GFP, NPR1:GFP, -INA, MNase, rep4

value: Seedlings

value: NPR1:GFP transgenic line

value: Distilled water

value: 12 hours

value: GFP-trap agarose (ChromoTek, gta-20)


title: OA2, Input

city: zhengzhou

first: Yang

last: Yu

address: jianshe road

department: Department of orthopedics

institute: the First Affiliated Hospital of Zhengzhou University

description: All.count.txt

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
data processing step：For MeRIP-seq: The 150 bp paired-end reads were mapped to the reference genome by using hisat2 (v2.1.0).
data processing step：For MeRIP-seq: The m6A peaks were identified using exomePeak R package (v2.13.2) under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”. Identified m6A peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 6 -rna”.
Assembly: GRCh38/hg38
Supplementary files format and content: peaks, counts

source_name: cartilage

extract_protocol:
Knee cartilage samples of medial condyle were collected from three patients who underwent knee arthroplasty and three patients who underwent thigh amputation due to trauma. Total RNA was extracted using TRIzol™ Reagent (Invitrogen, 15596018). The concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). 100μg total RNA was fragmented into 100-200 nt RNA fragments using 10X RNA Fragmentation Buffer (100 mM Tris-HCl, 100 mM ZnCl2 in nuclease-free H2O).
For MeRIP-seq: Briefly, the concentration of total RNA was measured by Qubit RNA HS assay kit (Invitrogen, Q32852). Total RNA was fragmented into 100-200 nt RNA fragments using ZnCl2. Subsequently, the purified RNA was incubated with anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572) for 3 h at 4℃ and then with protein A/G magnetic beads (Thermo Fisher Scientific, 88802) at 4 ℃ for an additional 2 h to obtain immunoprecipitated RNA fragments. The m6A-enriched RNA was eluted from the beads in RLT buffer supplied in RNeasy Mini Kit (QIAGEN, 74106). The RNA-seq library was prepared by NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7775).
MeRIP-seq

value: cartilage

value: female

tag: disease state

value: OA


title: OA3, Input

description: All.count.txt


title: α-GFP, Col, -INA, MNase, rep4

tag: time


title: Th2_72hr

data_processing:
Sequenced raw reads were trimmed for adaptor sequence, amplification primers, and masked for low-complexity or low-quality sequence with trimmomatic V0.30
Clean sequencing reads were mapped to mm10 using bowtie2 v2.3.4.3.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks V2.0.2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: CD4 T cells

growth_protocol: Naïve CD4+ T cells were isolated from the spleen of C57BL/6 mice followed with Flow cytometry sorting for CD4+ CD25- CD44- CD62L+ cells. Sorted Naïve CD4+ T cells were activated with plate-bound anti-CD3 (1ug/ml, clone 145-2C11, Bio X Cell) and anti-CD28 (1ug/ml, clone PV-1, Bio X Cell).

extract_protocol:
In vitro cultured T cells were collected at each time point into RLT-plus buffer, and RNA was extracted with RNeasy Plus Mini Kit (Qiagen). Extracted RNA was further used for cDNA amplification with SMARTA-Seq2 for 12 cycles.
Sequencing libraries were prepared with fragmented cDNA amplification products using a NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) and sequenced with 2 x 150 paired-end reads.

treatment_protocol: Naïve CD4+ T cells were treated with polarization cytokines under Th0 (without cytokine),  Th1 (IL-12, 20ng/mL, R&D Systems) or Th2 (IL-4, 20ng/mL, R&D Systems) conditions.

tag: stain

value: Th2 condition


title: OA1, Input

description: All.count.txt


title: Th2_60hr


title: JM_PostA [013]

value: post cardiac surgery

value: serum


title: N3, Input

description: All.count.txt

value: control


title: JM_PreA [014]

value: pre cardiac surgery


title: Th2_66hr


title: Input, NPR1:GFP, +INA, MNase, rep4

value: 2,6-dichloroisonicotinic acid (INA)

value: none (input)


title: α-GFP, NPR1:GFP, +INA, MNase, rep3


title: Bifur_channel_2_ADT

value: CD4 T cells

value: spleen


title: α-GFP, NPR1:GFP, +INA, MNase, rep4

value: Seedlings


title: Th2_54hr


title: N2, Input

description: All.count.txt


title: N1, Input

description: All.count.txt


title: GM_PostA [011]

value: small RNA


title: Th2_48hr


title: HeLa cells, shControl, DRB block transcription

value: HeLa S3

value: A clonal derivative of the parent HeLa cell line

value: shControl

value: culture cells in normal medium with continual 100 uM DRB


title: α-GFP, NPR1:GFP, -INA, MNase, rep3

value: NPR1:GFP transgenic line

value: Distilled water

value: 12 hours

value: GFP-trap agarose (ChromoTek, gta-20)


title: Th2_32hr

value: Th2 condition


title: GJ_PreA [010]

value: serum


title: Th2_23hr


title: GJ_PostA [009]

value: post cardiac surgery


title: α-GFP, Col, -INA, MNase, rep3


title: OA2, IP

value: cartilage

value: female

value: anti-m6A polyclonal antibody (Sigma-Aldrich, ABE572)

value: OA


title: Input, NPR1:GFP, +INA, MNase, rep3

value: Seedlings

value: 2,6-dichloroisonicotinic acid (INA)

value: none (input)


title: OA1, IP


title: α-GFP, NPR1:GFP, -INA, Sonication, rep2


title: N3, IP

value: control


title: α-GFP, NPR1:GFP, +INA, Sonication, rep2


title: α-GFP, Col, -INA, Sonication, rep2


title: GM_PreA [012]

value: pre cardiac surgery

value: small RNA


title: DK_PostA [007]


title: BL_PreA [006]


title: N2, IP


title: Th2_13hr

value: spleen


title: Input, NPR1:GFP, +INA, Sonication, rep2

value: NPR1:GFP transgenic line


title: Th2_08hr


title: BL_PostA [005]


title: N1, IP


title: α-GFP, NPR1:GFP, +INA, Sonication, rep1

value: 12 hours


title: OA3, IP


title: RHW1-OE#1-rep2

first: Aiai

last: Xia

address: NO2 Yuanmingyuan West Road, Haidian, Beijing

department: Plant Genetics and Breeding

institute: China Agricultural University

data_processing:
Sequencing reads were processed with trimmomatic-0.35 to remove adaptor sequence and low-quality sequence, and then mapped to B73.v4 reference genome using HISAT2 (version: 2.1.0).
Uniquely mapped reads were kept for subsequent gene expression quantification using HTSeq-count.
DEGs analysis was performed using the edgeR package (version: 3.32.1)in R-project.
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using stringtie.
Assembly: B73.v4
Supplementary files format and content: tab-delimited text files include read counts for each sample

organism: Zea mays

source_name: Ear

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Plus kit,treated with RNase-free DNaseI and purified using the RNAclean Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep kit following manufacturer's protocols.

value: Ear

value: RHW1 overexpression


title: Th2_20hr

value: Th2 condition


title: DK_PreA [008]

value: serum


title: α-GFP, NPR1:GFP, -INA, Sonication,rep1

value: Distilled water

value: GFP-trap agarose (ChromoTek, gta-20)


title: Th2_02hr


title: Th2_05hr


title: Th2_01hr


title: Th2_18hr


title: Th1_72hr

value: Th1 condition


title: RHW1-crispr-rep2

value: RHW1 knockout


title: FP_F28_103V1

city: Baltimore

first: Josephine

middle: M.

last: Egan

state: MD

address: BRC Suite 100, 251 Bayview Boulevard

department: Laboratory of Clinical Investigation

institute: National Institute on Aging - NIH

data_processing:
Original image data file from the high-throughput sequencing platform was transformed to sequenced reads by CASAVA base recognition Software. Performed at Novogene Corporation Inc. (Sacramento, CA).
Remove reads with adaptor contamination, remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%) and remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read. Performed at Novogene Corporation Inc. (Sacramento, CA).
The STAR software was used to align filtered reads to human reference genome. Performed at Novogene Corporation Inc. (Sacramento, CA).
Per sample FPKM (Fragments Per Kilobase of transcript sequence per Million base pairs sequenced) values were calculated for each gene id. Performed at Novogene Corporation Inc. (Sacramento, CA).
DESeq2 R package was used to generate log2 fold changes and p-values for identification of DEGs. Performed at Novogene Corporation Inc. (Sacramento, CA).
Assembly: Genome Reference Consortium Human Build 38 patch release 13 (GRCh38.p13)
Supplementary files format and content: Male_Vs_Female_DEG_Novogene - Contains the results of the differential gene expression analysis (Male Vs Female), compiled into a tab delimited file.

source_name: Fungiform pappillae

growth_protocol: Human fungiform taste papillae biopsies were done with prior IRB approval (IRB/NIH approval # 2018-AG-N010) and participants gave informed written consent. All biopsies were carried out at the NIA Clinical Unit, Baltimore, MD. The study involved two visits: a screening visit coupled to information sharing, verbal and written, related to the study, followed by a study visit. Participants were excluded if they had less than 40 fungiform papillae on the anterior third portion of the tongue, if they were taking steroids, if they had diabetes based on a fasting plasma glucose of less than 126mg/dl, if there was any evidence of gum or mouth disease and if they were known to be allergic to lidocaine. Participants were asked to refrain from taking non-steroidal anti-inflammatory medications for 4 days prior to the biopsy. Biopsies were performed in the fasting state between 07:30-09:30hrs, blood was drawn for serum and plasma collection and the anterior portion of the tongue was photographed and anesthetized using topical 1% lidocaine. Fungiform papillae were obtained using sterile curved spring micro-scissors (McPherson-Vannas) Type # SR5603 (Roboz Surgical Instrument Co, Gaithersburg, MD). Individual papilla for RNA isolation were immediately placed in sterile 1.6 mL tubes and flash frozen in liquid nitrogen.

extract_protocol:
Individual frozen taste papillae were homogenized in RLT-DTT buffer (Qiagen) using a single 30 second, 6000 rpm cycle on a Precellys24 homogenizer (Bertin Corp., Rockville, MD). RNA extraction followed the recommended RNeasy Mini fibrous kit protocol (Qiagen, Germantown, MD). RNA quality and quantity were determined using the Agilent Bioanalyzer RNA6000 Chip (Agilent, Santa Clara, CA).
Library construction and RNA sequencing was performed by Novogene Corporation Inc. (Sacramento, CA) using standard illumin protocols

value: Fungiform pappillae

value: WT

tag: gender

value: Female


title: RHW1-OE#1-rep1


title: RHW1-WT-rep2


title: Th1_66hr


title: Input, NPR1:GFP, +INA, Sonication, rep1

value: Seedlings

value: 2,6-dichloroisonicotinic acid (INA)

value: none (input)


title: FP_F29_022V3


title: FP_M32_077V3

value: Male


title: α-GFP, Col, -INA, Sonication, rep1


title: RHW1-WT-rep1


title: RHW1-crispr-rep1


title: PD-1 KO bone marrow derived dendritic cells, Mtb infected, 2

city: Wuhan

first: Bing

last: Yang

state: Hubei

address: No.1 Shizishan Street, Hongshan District

department: College of Vetirinary Medicine

institute: Huazhong Agricultural University

data_processing:
Raw reads were adaptor trimmed and quality controled with trimiomatic
Clean reads were aligned and processed with Hisat2 and Samtools
Alignment result were counted with StrignTie and FeatureCount
Differential analysis were conducted with DeSeq2
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include normalized counts of each sample

source_name: myeloid cells

growth_protocol: Bone marrow cells isolated from wild-type or PD-1 deficient mice were cultured in 2mL BMDCs culture medium (RPMI 1640 medium supplemented with 15% FBS, penicillin/streptomycin, 20ng/mL GM-CSF, and 10ng/mL IL-4) at 37℃ for 9 days.

extract_protocol:
RNA was harvested using RNAiso plus reagent (Takara). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Loosely adherent cells were harvested on day 10 and 2×106 cells were re-seeded in a cell-culture plate and stimulated with 1μg/mL LPS for 24 hours.
2.5×106 BMDCs were seeded at 6-well plates and treated with M.tb H37Ra at a multiplicity of infection of 10.

value: myeloid cells

value: bone marrow derived dendritic cells

value: PD-1 knockout

value: infect with Mtb-H37Ra

value: 24 hours


title: FP_F31_097V1


title: FP_M35_005V2


title: PD-1 KO bone marrow derived dendritic cells, Mtb infected, 3


title: Th1_60hr

value: spleen


title: PD-1 KO bone marrow derived dendritic cells, Mtb infected, 1


title: Th1_54hr


title: C3_HCT8 with hypoxia treatment

first: Zhenxing

last: Liang

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The Sixth Affiliated Hospital, Sun Yat-sen University

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HCT8 with hypoxia treatment

growth_protocol: All of the cells were cultured at 37°C in Dulbecco’s Modified Eagle Medium (DMEM; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) supplemented with 10% fetal bovine serum (FBS; Gibco, Thermo Fisher Scientific, St Peters, MO, USA) in a 5% CO2 atmosphere.

extract_protocol:
prefrontal cortex were rharvested , flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: CRC cell lines

tag: passages

value: hypoxia


title: FP_M22_085V1


title: PD-1 KO bone marrow derived dendritic cells, uninfection, 3

value: uninfection


title: PD-1 KO bone marrow derived dendritic cells, uninfection, 2


title: C2_HCT116 with hypoxia treatment

description:
R20021475-NBC20200608-A-HCT116-hypoxia
R20025170-NBC20200629-A-HCT116-hypoxia

source_name: HCT116 with hypoxia treatment


title: FP_M32_070V2


title: FP_F31_073V2


title: Th1_48hr

value: Th1 condition


title: Th1_32hr


title: PD-1 KO bone marrow derived dendritic cells, uninfection, 1


title: C1_DLD1 with hypoxia treatment

description:
R20021475-NBC20200608-A-DLD1-hypoxia
R20025170-NBC20200629-A-DLD1-hypoxia

source_name: DLD1 with hypoxia treatment


title: Th1_23hr


title: rne∆IDR 9 min rep 2

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

data_processing:
Single end reads were first stripped of 3' ligated adapter using a custom python script.
Adapter stripped reads were then aligned to rRNA using bowtie 0.12.8 to remove remaining rRNA reads.  Reads that did not align to rRNA were then aligned to the full Sinorhizobium meliloti Rm1021 genome (Accession PRJNA19) using bowtie 0.12.8.
mRNA levels were then calcualted by normalizing using the reads per kilobase per million mapped reads (RPKM).  The relative mRNA levels over time were then calculated using the rifcorrect software [Aretakis et al. BioRxiv 2022].
Assembly: Sinorhizobium meliloti Rm1021 (PRJNA19)
Supplementary files format and content: tab delimited text

organism: Sinorhizobium meliloti

source_name: Sinorhizobium meliloti cells

growth_protocol: WT(Sinorhizobium meliloti Rm1021) cells and rne delta IDR(rne∆IDR) cells were grown in TY media overnight at 28 C. The next day, the cells were diluted and grown until midlog-phase  (0.3 to 0.5 OD600) which were used for mRNA half-life profiling.

extract_protocol:
The cells were pelleted at 20,000 x g for 1 min in 1.5 mL eppendorf tubes to prepare for RNA extraction.Pelleted cells were resuspended in 1mL of pre-warmed (to 65 0C) TRizol Reagent (Ambion) and incubated for 10 min at 65 0C in a heat block. 200 mL of chloroform were added to the samples and tubes were gently inverted a few times. Then samples were incubated at room temperature for 5 min and spun at 20,000 x g for 10 min. The supernatant was moved to siliconized tubes and 500 mL of chloroform was added, vortexed, and spun at 20,000 x g for 10 minutes. RNA samples were precipitated using isopropanol (1x volume isopropanol, 0.1X volume 5M NaOAc pH 5.2) overnight at – 80 0C. The RNA samples were spun at 20,000 x g at 4 0C for 1 hour. Pellets were washed with cold 80% ethanol and spun for 10 min at 20,000 x g, air-dried, and resuspended in 10 mM Tris-HCl (pH 7.0). The RNA-Seq libraries were made using 5µg of total RNA of each sample. Library construction was performed according to the protocol in (Aretakis et al., 2018).
mRNA fragments were ligated to 5' adenylated DNA oligos. After reverse transcription, the single stranded DNA was circularized, and PCR amplified [Oh et al,. Cell 147, 1295 (2011)].  Updated adapter oligos that are compatible with the novaseq were used from [Aretakis et al. Methods in Enzymology (2019)].

treatment_protocol: The cells were treated with 200µg/mL rifampicin and placed immediately in RNAprotect bacterial reagent (QIAGEN) at the indicated timepoint (0,1,3,9 min).  0 minute time-points were collected just prior to rifampicin addition.

value: Sinorhizobium meliloti cells

value: rne IDR deletion


title: Th1_20hr


title: rne∆IDR 1 min rep 2


title: rne∆IDR 3 min rep 2


title: B2_HCT116


title: bone marrow derived dendritic cells, Mtb infected, 2

value: WT


title: Th1_18hr


title: B1_DLD1


title: rne∆IDR 0 min rep 2


title: Th1_13hr


title: bone marrow derived dendritic cells, Mtb infected, 1


title: rne∆IDR 9 min rep 1


title: bone marrow derived dendritic cells, uninfection, 3


title: A1_NCM460

description:
R20021317-NBC20200605-A-NCM460
R20025170-NBC20200629-A-NCM460

value: normal human intestinal epithelial cell lines


title: rne∆IDR 3 min rep 1


title: Th1_08hr


title: A2_HIEC6


title: bone marrow derived dendritic cells, uninfection, 2


title: bone marrow derived dendritic cells, uninfection, 1


title: RA_3

city: London

first: Naila

last: Haq

state: London

address: Room HB4.2E, 2nd Floor, Hodgkin Building, Guy's Campus, London Bridge,

institute: King's College London

data_processing:
STARsolo (2.7.10a).
Read quality checks were carried out using FastQC, after which BBDuk from the BBMap (version 38.87) software was used to trim Illumina adapters and polyA tails
Trimmed reads were mapped to the hg38 reference human genome using Star Aligner.
The R package DESeq2 v1.36.0 was used to determine differential gene expression, and DEGs with padj <0.1 were selected. Variance-stabilising transformations of raw count data were used to visualise the sample clustering. All data were subjected to global-scale normalisation and log-transformation.
Assembly: Hg38
Supplementary files format and content: tab-delimited text files includes raw conts for each samples
Supplementary files format and content: tab-delimited text files include RPKM for each samples

source_name: pancreatic islets

growth_protocol: Native islets from both human and mouse were maintained in culture overnight at 37°C, 95%air/5%CO2 in RPMI supplemented with 10% (v/v) foetal bovine serum (FBS), 100U/ml penicillin and 100μg/ml streptomycin, and 2mM L-glutamine. Reformed islets were maintained in media consisting of MEM supplemented with 5% (v/v) FBS, 1x B-27, 1%(v/v) penicillin and streptomycin, HEPES 10 mM, Glutamax 1x, Na-pyruvate 1mM, and 11 mM glucose.

extract_protocol:
Total RNA was extracted from three replicates of native human islets and reformed islets from one donor, using the TRIzol method. 1.2 ug of total RNA was used for the construction of the sequencing libraries.
Library preparation and RNA sequencing were performed by Single-Cell Discoveries using the QuantSeq 3 kit (Lexogen) and sequenced on an Illumina NextSeq 500 with a sequencing depth of 10 million reads per sample.

treatment_protocol: No treatment

value: pancreatic islets

value: islets

value: reformed islets

value: no treatment


title: Th1_02hr


title: rne∆IDR 1 min rep 1


title: B3_HCT8


title: RA_2


title: bone marrow derived dendritic cells, Mtb infected, 3

value: myeloid cells

value: bone marrow derived dendritic cells


title: rne∆IDR 0 min rep 1


title: rgl2_13_DOF6ioex_estra3

city: Singapore

first: Prakash

middle: P

last: Kumar

state: Singapore

address: 14 Science Drive 4

department: DBS

country: Singapore

institute: NUS

data_processing:
The original image data is transferred into sequence data via base calling (using Phred)
we filtered the low quality reads using software SOAPnuke (more than 20% of the bases qualities are lower than 10),
reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads.
Then we mapped those clean reads onto Arabidopsis reference genome (using HISAT), followed with novel gene prediction, SNP
& INDEL calling and gene splicing detection
Assembly: Arabidopsis reference genome

source_name: seeds

growth_protocol: Seeds were freshly harvested from DOF6ioex and rgl2-13 DOF6ioex Arabidopsis plants

extract_protocol:
RNA from seeds were extracted as described in Ravindran, Pratibha, et al. "A novel RGL2–DOF6 complex contributes to primary seed dormancy in Arabidopsis thaliana by regulating a GATA transcription factor." Molecular plant 10.10 (2017): 1307-1320.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Seeds were imbibed in mock or 50µM β-estradiol for 8h

value: freshly harvested seeds

value: imbibed for 8h in 50µM β-estradiol

value: estradiol inducible DOF6 overexpression in rgl2-13 background


title: Th1_01hr

value: spleen


title: rgl2_13_DOF6ioex_estra2


title: WT 3 min rep 2


title: Th0_72hr

value: Th0 condition


title: WT_3

value: Wild-type


title: WT_2


title: WT 1 min rep 2


title: Th0_66hr


title: DOF6ioex_estra3

value: estradiol inducible DOF6 overexpression


title: WT_1


title: Th0_60hr


title: Th1_05hr

value: Th1 condition


title: WT 0 min rep 2

value: Sinorhizobium meliloti cells


title: Th0_54hr


title: WT 9 min rep 1

value: WT


title: DOF6ioex_estra2


title: DOF6ioex_estra1


title: RH5_A485_072221_CWRU

description: RNA-seq

data_processing:
RNA-seq reads were aligned to the hg19 reference genome using STAR
Gene expression values were calculated as Transcripts per million (TPM) using RSEM and the UCSC reference at the gene level.
Differential gene expression was determined using custom R scripts (https://github.com/GryderArt/VisualizeRNAseq)
HiChIP data was processed by first trimming the bridge sequence (AGGTTCGTCCATCGATCGATGGACGAACCT), followed by use of the HiC-Pro pipeline (https://github.com/nservant/HiC-Pro) where the enzymatic digestion enzyme parameter was left blank, to account for MNase digestion methodology.
Processed file for Juicebox visualization was generated by hicpro2juicebox.sh (HiC-Pro tools) and Juicer tools (https://github.com/aidenlab/juicer).
Assembly: Hg38
Supplementary files format and content: TPM files are provided in txt format at the gene-level

source_name: alveolar rhabdomyosarcoma

extract_protocol:
For RNA-seq experiments, RH4 and RH5 cells were washed with PBS, then lysed on ice with RLT using the RNeasy mini kit (Qiagen). For HiChIP, the Dovetail MNase HiChIP kit (Catalogue #21007) was used. Briefly, cells were fixed with DSG and 37% formaldehyde, treated with MNase, and immunoprecipitated with anti-RNA Pol2 antibody (Santa Cruz Biotechnology, Mouse mAb #sc-47701 X). On-bead bridge incorporation and religation was performed, followed by reversal of crosslinks, proteinase K treatment, and DNA purification.
Standard Illumina barcodes were introduced during library preparation.

treatment_protocol: For RNA-seq and HiChIP experiments, RH4 and RH5 cells were treated with DMSO, dCBP1, or A485 for six hours.


title: RH5_dCBP1_072221_CWRU

description: RNA-seq


title: DOF6ioex_Mock3

value: imbibed for 8h in water


title: RH5_DMSO_072221_CWRU

description: RNA-seq

value: DMSO


title: Th0_32hr


title: WT 1 min rep 1


title: Th0_48hr


title: WT 3 min rep 1


title: WT 9 min rep 2


title: DOF6ioex_Mock2


title: rgl2_13_DOF6ioex_estra1


title: Th0_23hr


title: RH5_NT_072221_CWRU

description: RNA-seq

value: NT


title: WT 0 min rep 1


title: DOF6ioex_Mock1


title: Th0_20hr


title: RA_1

value: pancreatic islets

value: islets

value: reformed islets


title: BEAS 2B cell line, total RNA, miRNA-seq [BEAS_2B_B]

city: Austin

first: Eleftherios

last: Bochalis

state: Texas

address: 2515 Speedway

department: College of Pharmacy

institute: The University of Texas at Austin

data_processing:
In house miRNA-seq analysis pipeline was employed. Firstly, adapters and UMIs were extracted for each sample and reads were length filtered so that all reads were above 18nt. Mature and hairpin miRNA reads were aligned to both the miRBase mature and hairpin sequences and the hg38 genome. Differentially expressed miRNAs were obtained with the use of DESeq2 using an adjusted p-value < 0.05 and a log2fold change cutoff of plus-minus 1.
Assembly: hg38
Assembly: miRBase release 22.1
Assembly: mm10
Supplementary files format and content: Comma-separated values files and matrix files

extract_protocol:
Total RNA was extracted using QIAGEN miRNA minikit (REF 1038703) and RNA samples were forwarded to library construction.
Libraries were constructed from RNA samples with the QIAseq miRNA sequencing kit (REF 1103677) combined with the QIAseq miRNA NGS 12 Index IL (REF 331592). As an initial step, adapters were ligated to the 3’ and 5’ ends of miRNAs and subsequently, universal cDNA synthesis with Unique Molecular Indices (UMI) assignment, cDNA cleanup, library amplification and library cleanup were performed.

value: Epithelial


title: Th0_18hr


title: RH4_A485_072221_CWRU

first: Hyunmin

last: Kim

address: 10900 Euclid Ave.

institute: Case Western Reserve University

description: RNA-seq


title: BEAS 2B cell line, total RNA, miRNA-seq [BEAS_2B_A]


title: RH4_dCBP1_072221_CWRU

description: RNA-seq


title: Th0_13hr


title: H460 cell line, total RNA, miRNA-seq [H460_B]


title: EGFP+/sp7+, OMP, rep2

city: Nagatsuta

first: Hiroaki

last: Komiya

state: Yokohama

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

description:
Ob-G2
Mesenchymal cells

data_processing:
High-quality reads were mapped using hisat2 (ver. 2.2.1).
Trimmed sequence reads were mapped to GRCz11 using hisat2.
Read count extraction and normalization were performed using featureCounts (ver. 2.0.3).
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file includes basic gene information (gene id, length, Genbank id, RNA type, gene name, product), raw count, RPKM and TPM values.

source_name: 14 dpa adult caudal fin

growth_protocol: Fish were maintained in a recirculating water system in a 14 h day/10 h night photoperiod at 28.5 °C. The wild-type zebrafish (Danio rerio) strain used in this study was originally derived from the Tubingen strain and has been maintained in our facility for more than 10 years by inbreeding.

extract_protocol:
The sorted cells were directly collected in a lysis buffer and used for RNA extraction using the RNeasy Plus Micro Kit (Qiagen).
RNA libraries were prepared by MGIEasy™ WES rapid library preparation kit according to the manufacturer’s protocol.

treatment_protocol: Different types of cells were sorted by the fluorescence-activated cell sorter SH800S (SONY).

value: 14 dpa adult caudal fin

value: Osteogenic mesenchymal progenitors

value: Tg(cryaa:EGFP, sox9a:Cre-ERt2; Ola.Actb:loxp-TagBFP-loxp-EGFP; Ola.Sp7:mCherry)


title: EGFP-/sp7+, Osteoblast, rep2

value: Osteoblasts


title: EGFP-/sp7+, Osteoblast, rep1

description: Ob-GR


title: RH4_DMSO_072221_CWRU

description: RNA-seq


title: Th0_08hr

first: Yu

last: Hou

institute: Peking University

value: spleen

value: Th0 condition


title: EGFP+/sp7+, OMP, rep1

description:
Ob-G
Mesenchymal cells


title: H460 cell line, total RNA, miRNA-seq [H460_A]


title: RH4_NT_072221_CWRU

description: RNA-seq


title: Th0_05hr


title: A549 cell line, total RNA, miRNA-seq [A549_B]


title: EGFP+/sp7-, CMP, rep2

description:
Mes-G2
Mesenchymal cells

value: Chondrogenic mesenchymal progenitors


title: Th0_02hr


title: RH4_dCBP1_6h

description: HiChIP


title: RH4_A485_6h

description: HiChIP


title: EGFP+/sp7-, CMP, rep1

description:
Mes-G
Mesenchymal cells


title: A549 cell line, total RNA, miRNA-seq [A549_A]


title: Th0_01hr


title: RH4_DMSO_6h

description: HiChIP


status: Public on Dec 24 2023

type: genomic

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

description: genomic DNA from fibroblasts from donor CS177VI, CS type II, csb

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Infinium BeadChip using standard Illumina protocol

scan_protocol: HiScan scanner (Illumina)

data_processing: Signal intensities files were extracted using the minfi Bioconductor package. The preprocessNoob function implemented in minfi was applied to normalize raw data.

label: Cy3 and Cy5

source_name: donor CS177VI

label_protocol: Standard Illumina Protocol

growth_protocol: Patient fibroblasts were derived from skin biopsies excised from unexposed body sites by dermatologists. Healthy, UVSS and CS cells initially thawed at passage number (PN) 12 were cultured in Dulbecco's modified eagle medium (DMEM; Gibco) supplemented with 2mM L-glutamine (GlutaMAX™; Gibco), 10% foetal bovine serum (FBS; Gibco), 1% Penicillin-streptomycin (Gibco) in 20% O2/5% CO2 at 37 °C. Cells were harvested at PN14 for further experiments.

extract_protocol: Total genomic DNA (gDNA) from WT, UVSS and CS primary skin fibroblasts was isolated using the QIamp® DNA mini kit (Qiagen) and used for microarray-based analysis of genome wide DNA methylation levels in two different sets. For the first set, extracted gDNA was quantified by NanoDrop (ND-1000; Thermo Fisher Scientific) and 1µg was bisulfite-treated using the EZ DNA Methylation™ kit (Zymo Research), according to manufacturer instructions. Genone-wide DNA methylation analysis was performed on this material by Aros Applied Biotechnology A/S (Eurofins Genomics; Denmark) using the Infinium HumanMethylation450 BeadChip (Illumina). For the second set, extracted gDNA was directly send to Aros Applied Biotechnology A/S for bisulfite conversion and genome-wide DNA methylation using the Infinium MethylationEPIC BeadChip (Illumina) following manufacturer's instructions.

tag: donor

tag: disease

value: Cockayne syndrome (CS)

tag: diagnosis

value: CS type II

tag: mutation

value: csb

tag: group

value: CS

tag: csa/csb

value: abscence of CSB

value: Female

tag: age at skin biopsy (yrs)

tag: age at death or latest report (yrs)


description: genomic DNA from fibroblasts from donor CS548VI, CS type I, csb

source_name: donor CS548VI

value: CS type I

tag: Sex


description: genomic DNA from fibroblasts from donor UVSS1VI, UVSS, csa

source_name: donor UVSS1VI

value: UV-sensitivity syndrome (UVSS)

value: UVSS

value: csa

value: NonAGED


description: genomic DNA from fibroblasts from donor 198VI, Healthy, Wild type (WT)

source_name: donor 198VI

value: Healthy

value: Wild type (WT)

value: Male


description: genomic DNA from fibroblasts from donor UVSTA24VI, UVSS, uvssa

source_name: donor UVSTA24VI

value: uvssa


description: genomic DNA from fibroblasts from donor 911VI, Healthy, Wild type (WT)

source_name: donor 911VI


description: genomic DNA from fibroblasts from donor CS816VI, CS type II, csb

source_name: donor CS816VI

value: truncated forms


title: seedling roots of nac103-11 rab8d-2 bio rep 2, 4 DAG

city: Jinan

first: Pengcheng

last: Li

address: 202 Gongye North Road

institute: Shandong Academy of Agricultural Sciences

data_processing:
To get clean sequencing reads, the sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapter, with a low-quality base ratio higher than 20%, and with an unknown base ('N' base) ratio higher than 5%.
The expression level of genes was calculated by RSEM (v1.3.1)
Assembly: TAIR10
Supplementary files format and content: TPM values and read counts for each gene in all samples

source_name: root

growth_protocol: For seed germination, seeds were sterilized with a mixture containing 75% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 10 minutes and then plated onto solid 1/2 Murashige and Skoog (MS) medium containing 1% (w/v) sucrose. The plates were kept in the dark in a refrigerator (4~5°C) for about 3 days and then transferred into a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
Total RNA was extracted from the root tips of 4-day-old seedlings using a PureLink RNA Micro Kit (Invitrogen)
Library construction was performed with a BGI Optimal Dual-mode mRNA Library Prep Kit (LR00R96, BGI) and an MGIEasy circularization kit

tag: tissue

value: root


title: seedling roots of nac103-11 rab8d-2 bio rep 1, 4 DAG

tag: treatment


title: seedling roots of gun1-101 rab8d-2 bio rep 3, 4 DAG

tag: genotype


title: seedling roots of gun1-101 rab8d-2 bio rep 1, 4 DAG


title: seedling roots of rab8d-2 bio rep 2, 4 DAG


title: seedling roots of rab8d-2 bio rep 1, 4 DAG


title: seedling roots of nac103-11 bio rep 2, 4 DAG


title: seedling roots of nac103-11 bio rep 3, 4 DAG


title: seedling roots of nac103-11 bio rep 1, 4 DAG


title: seedling roots of gun1-101 bio rep 1, 4 DAG


title: seedling roots of gun1-101 bio rep 2, 4 DAG


title: seedling roots of WT bio rep 2, 4 DAG


description: genomic DNA from fibroblasts from donor CS466VI, CS type I, csa

source_name: donor CS466VI

value: Cockayne syndrome (CS)

value: abscence of CSA


title: seedling roots of WT bio rep 3, 4 DAG


title: seedling roots of gun1-101 bio rep 3, 4 DAG