title: TSB65_BJ_Young_Dox_TY1-JMJD6

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.  Tet-inducible overexpression experiments were done by transducing a combination of pRetroX and TetOn retrovirus into young (<PD30) BJ fibroblasts.  3 days after transduction, cells were maintained under combined selection by 0.6 ug/ml puromycin (Gibco A1113803) and 0.3mg/ml G418 (GeminiBio 400-113) and expanded for 2 weeks until they were frozen down.  Frozen stable lines were then thawed and grown in the absence of doxycycline.

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Samples prepared for ChIP were double cross-linked in combined 1mM EGS and 1mM DSG treatment for 45 minutes at room temperature followed by 10 minute fixation with 1% formaldehyde.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of transcription factors were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 300mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (20mM Tris/HCl pH7.4, 400mM NaCl, 1% Triton-X-100, 2mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using either the KAPA Hyper Prep Kit (KK8500), following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 50 cycles.

treatment_protocol: In both young and senescent cells, an acute treatment of 48 hours of 20nM doxycycline was given for short term induction of each transgene prior to harvesting for ChIP of the tagged transgene.

value: TY1:diagenode C15200054

value: Dox


title: Pmel-1 T cells, untreated, Day 7, mouse 3

status: Public on May 30 2025

type: SRA

city: Pittsburgh

first: Aaron

last: Yang

state: PA

address: 4401 Penn Ave

country: USA

institute: University of Pittsburgh

library_source: transcriptomic

data_processing:
trimmed high quality reads were aligned to genome  using bowtie2
Raw count values generated with Subread
Gene expression values were nromalized to transcripts per million
Differential peak analysis determined using DESeq2 with cutoffs of 2 fold and p value<0.05
Assembly: mm10
Supplementary files format and content: csv file contains transcripts per million (TPM)

molecule: total RNA

organism: Mus musculus

source_name: splenocytes

growth_protocol: To expand Pmel-1 mouse CD8+ T cells in vitro, bulk splenocytes were plated in the presence of the T cells’ cognate peptide (1uM gp100) at a concentration of 1e7 cells/mL in RPMI supplemented with 10% FBS (v/v) and 50ug/mL mouse rIL-2 at 37°C with 5% CO2 for 24 hours. After 24 hours, cells were washed with fresh RPMI and plated at a concentration of 1e6/mL with 50ug/mL IL-2. Cultures were fed daily and kept at this concentration for the duration of expansion.

extract_protocol:
SMART-seq v4 Ultra Low Input RNA Kit for Sequencing
Nextera XT DNA Library Preparation kit (Illumina)

treatment_protocol: 5mM DCA was added to DCA-conditioned cultures daily

tag: strain

tag: tissue

value: splenocytes

tag: cell type

value: CD8+ T cell

tag: genotype

value: B6.Cg-Thy1a/Cy Tg(TcraTcrb)8Rest/J

tag: treatment

value: untreated

tag: time

value: Day 7


title: TSB56_BJ_Senescent_Dox_HA-JMJD6

city: La Jolla

first: Tom

last: Suter

state: CA

address: 9500 Gilman Dr

department: Department of Medicine

institute: UCSD

library_source: genomic

data_processing:
Data was aligned to hg18 using STAR-aligner with parameters adjusted avoid spliced alignments.
Aligned reads were processed for downstream analysis using the HOMER (Heinz et al., 2010) “makeTagDirectory” program, filtering for tags that were uniquely mapped and only selecting at most one sequencing read per position per length of read.
bigWig files were generated using the makeBigWig.pl function in HOMER, using the -chipseq style parameter
Genome_build: hg18
Supplementary_files_format_and_content: .bigWig : display of ChIP-seq data on genome browser as a graph

molecule: genomic DNA

organism: Homo sapiens

source_name: Foreskin dermal fibroblast

tag: cell line

value: BJ Fibroblast

tag: antibody

value: HA:abcam ab9110

tag: Stage

value: Senescent


title: GRC355_AC6_S11

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

description: Library name: GRC355_AC6_S11

data_processing:
For Experiment 1, basecall files were converted to FASTQ by bcl2fastq2, demultiplexed, quality trimmed, and filter using ea-utils (https://expressionanalysis.github.io/ea-utils/ ; last accessed 01-21-2020). Reads with Phred quality scores <7 or >4 Ns at either end of the read were trimmed. Reads with any one base comprising > 95% frequency of the read or having an average Phred quality score <25 were removed.
For Experiment 2, Illumina basecall files were converted to FASTQ and demultiplexed by bcl2fastq2. Reads with 3’ Phred quality scores < 20 or lengths <25 nucleotides were trimmed or removed, respectively in Partek Flow (v.8.0.19.0428; St. Louis, MO).
Experiments 1 and 2. Trimmed FASTQ files from both sequencing experiments were aligned to Danio rerio GRCz11 using STAR (v.2.5.3a) with default settings in Partek Flow and strand specificity detection enabled for the paired-end reads from Experiment 1 but not for Experiment 2.
Gene counts from both experiments were quantified from aligned reads using Partek Expectation Maximization and Ensembl Danio rerio GRCz11.93 gene annotation.
Assembly: GRCz11/93 gene annotation
Supplementary files format and content: tab delimited file for experiment1 containing raw counts for all samples
Supplementary files format and content: tab delimited file for experiment2 containing raw counts for all samples

molecule: polyA RNA

organism: Danio rerio

source_name: pooled heads collected anterior to swim bladder of larval zebrafish

extract_protocol:
Samples from experiment 1 underwent RNA isolation by Q2 Solutions Expression Analysis, LLC (Morrisville, NC, USA). Samples from experiment 2 underwent RNA extraction at US EPA (Durham, NC, USA) using Direct-zol™ RNA MiniPrep Plus kit (Zymo Research) per manufacturer instructions. RNA sample quality and concentration from both experiments were checked by Bioanalyzer and Nanodrop or Qubit.
For Experiment 1, paired-end (50 base pair) total RNA-sequencing libraries were prepared using Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold Library Prep Kit for rRNA depletion (Illumina, San Diego, California, cat. No. RS-1222303) at Q2 solutions Expression Anaysis according to manufacturer directions. Briefly, rRNA was selectively filtered from total RNA samples through streptavidin bead binding and cleanup. Purified RNA then underwent heat fragmentation with divalent cations prior to stranded cDNA synthesis and barcoding of samples using the TruSeq stranded Total RNA kit. cDNA libraries were quantified and cDNA insert size assessed by Agilent Bioanalyzer (DNA 1000 kit #5067-1504) and qPCR (KAPA Library Quant Kit #KK4824, KAPA Biosystems, Wilmington, MA). Sample libraries were then normalized, randomly pooled, and sequenced at 8 samples per lane to a target read depth of >20 million reads on an Illumina HiSeq 2500. For Experiment 2, purified RNA from each sample (500 ng per sample) were randomized and processed on Apollo324 for polyA selection and then continued on library prep with PrepX mRNA 48 Protocol v19 at US EPA (Durham, NC, USA). PCR amplification with 32 index primers were run for 13 cycles. The resulting PCR products were cleaned up on Apollo324 with PCR Cleanup 48 Protocol. The volume of purified libraries was about 10 μl. The PCR product’s quality was checked on Bioanalyzer with High Sensitivity DNA chips and the average size (bp) was obtained according to the electropherogram. The collected libraries were quantified by Qubit DNA HS kit. The molar concentration of each library was estimated by using average molecular size from Bioanalyzer data and concentration from Qubit measurement. Then an equal amount from each library (μl x nM) was pooled from 16 randomized libraries to make the sequencing samples (total 2 pools of 16 libraries each) and the concentration of the pooled libraries was checked by Qubit. The library pools were denatured and diluted according to Illumina NextSeq protocols. The final concentration for sequencing was 2.5 pM + 2% Phix and it was run for 75 cycles SR (Single Read).

value: mixed wild type zebrafish line US EPA

tag: lifestage

value: larvae

tag: age

value: 10 days post fertilization

value: Conventionally re-colonized with microbes on day 1

tag: experiment


title: TSB55_BJ_Young_Dox_HA-JMJD6

value: Young - Quiescent


title: Pmel-1 T cells, untreated, Day 7, mouse 1


title: GRC355_AC5_S14

description: Library name: GRC355_AC5_S14

value: pooled heads collected anterior to swim bladder of larval zebrafish


title: C-G2_2_rep2

city: Shanghai

first: hexin

last: Yan

address: Pujian Road

country: China

institute: Shanghai Reji Hospital

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads.
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse (mm39) reference genome.
featureCounts software (v2.0) was used to get the raw gene level mRNA expression counts.
Assembly: mm39
Supplementary files format and content: txt format raw counts of each gene
Supplementary files format and content: Expression.txt

growth_protocol: HepG2 and Hep3B cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with 10% fetal bovine serum, glutamine, and penicillin/streptomycin (Gibco) at 37 °C 5% carbon dioxide (CO2).

extract_protocol:
mRNA high throughput sequencing was performed by Biotree (Shanghai, China). Briefly, total RNA was extracted using Trizol Reagent (ThermoFisher, 15596026). The mRNAs were purified using a NEBNext Poly(A) mRNA Magnetic Isolation Module Kit (NEB, E7490) according to the user manual.
mRNA libraries were constructed by using Illumina TrueSeq mRNA sample prepa_x0002_ration kit (Cat. No. RS-122-2101) according to the manufacturer’s instructions. Library sequencing was performed on an Illumina NovaSeq 6000 instrument.

treatment_protocol: HepG2 and Hep3B cells in logarithmic growth phase were seeded onto a 6-well plate. The following day, DAPT (10 μM) as Notch inhibitors, STAT3 inhibitors RUXO (10 μM), and their combination were administered for 72 hours. Samples were collected for transcriptome sequencing. HepLPC co-cultured HepG2 or Hep3B cells were used as positive controls.

value: liver cancer cells

value: co-culture with HepLPCs in normal DMEM medium


title: Pmel-1 T cells, untreated, Day 7, mouse 2


title: GRC355_AC4_S16

description: Library name: GRC355_AC4_S16


title: GRC355_AC3_S10

description: Library name: GRC355_AC3_S10


title: TSB26_BJ_Senescent_anti-p65

growth_protocol: BJ fibroblasts (ATCC® CRL-2522) were cultured at 37 °C in 20% O2 and 5% CO2 in 4.5 g/L DMEM (Gibco 10566-016) in 10% FBS.  Cell lines were initially plated at PD26, grown to confluence, and then split 1:8.  Population doubling was recorded and incremented by 3 upon each 1:8 split.  BJ fibroblasts were considered to be “young” when collected below population doubling (PD) 35, intermediate fibroblasts were harvested between PD 35-50, and fibroblasts were considered to be senescent when cells failed to divide after at least one week of passaging, which typically occurred after at least PD64 and was initially confirmed using beta galactosidase staining.  To mitigate the effects of cell cycle upon our results, non-senescent, still dividing fibroblasts were grown to confluence prior to harvesting for any experiments, in order to ensure contact inhibited quiescence and similar growth arrest among all populations of cells.

extract_protocol:
Fixed chromatin immunoprecipitation assays were performed as previously described (Li et al., 2013), with the following modifications: Samples prepared for ChIP of histone modifications were fixed in 1% formaldehyde for 10 minutes at room temperature, while samples prepared for ChIP of transcription factors were double cross-linked in 2mM DSG alone for 45 minutes at room temperature followed by 10 minute fixation with 1% formaldehyde.  After neutralization with 0.125M glycine, samples underwent nuclear extraction, and were afterwards resuspended in nuclear lysis buffer (50mM Tris/HCl pH7.4, 1% SDS, 10mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail (Sigma 11836145001)), and samples were sonicated using the Bioruptor (Diagenode).  The concentration of chromatin in each sample was detected using the Qubit Fluorometer (Thermo Fisher), and samples were then diluted 1:10 in dilution buffer (20mM Tris/HCl pH7.4, 100mM NaCl, 0.5% Triton-X-100, 2mM EDTA, 1x dissolved cOmplete Protease Inhibitor Cocktail).  Between 20-50 ug of chromatin from each sample was then used for each histone or transcription factor ChIP assay, and the volume of each sample was raised to 0.5 mL using 1:10 sonication:dilution buffer mixture.  Antibodies were then incubated with each sample overnight.    Antibody:chromatin complexes were then immunoprecipitated as described using 20 uL Protein G Dynabeads (Thermo Fisher), which were then washed using the following washes:  ChIPs of histone modifications were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 0.1% SDS, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 500mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (10mM Tris/HCl pH7.4, 250mM LiCl, 1% NP-40, 1% Deoxycholate, 1mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  ChIPs of transcription factors were washed with the following buffers in order: 2xWB1 (20mM Tris/HCl pH7.4, 150mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB2 (20mM Tris/HCl pH7.4, 300mM NaCl, 1% Triton-X-100, 2mM EDTA), 1xWB3 (20mM Tris/HCl pH7.4, 400mM NaCl, 1% Triton-X-100, 2mM EDTA), 2xTE (10mM Tris/HCl pH 8.0, 1mM EDTA).  After washing, samples were eluted overnight at 65 °C as described, purified using the QIAquick PCR Purification Kit (QIAGEN), and were eluted in EB (1% SDS, 0.1M NaHCO3).  Samples were then further sonicated for 10 minutes to ensure the majority of purified chromatin fell between 100-300bp.
Purified chromatin was then prepared for deep sequencing with the Illumina HiSeq 2500 system using either the KAPA LTP Library Preparation Kit (KK8232) or KAPA Hyper Prep Kit (KK8500) for histone or transcription factor ChIPs, respectively, following manufacturer’s instructions.  Samples were run on the Illumina HiSeq 2500 as single-read reactions of 50 cycles.

value: p65:Santa Cruz sc-372 (C-20)


title: TSB24_BJ_Intermediate_Early_anti-p65

value: Intermediate Early - Quiescent


title: TSB66_BJ_Senescent_Dox_TY1-JMJD6

value: TY1:diagenode C15200054

value: Dox


title: G2_NC_1_rep1

value: normal control


title: GRC355_AC2_S1

description: Library name: GRC355_AC2_S1


title: G2_NC_2_rep2


title: 30dpi_S4_control

city: Guayaquil

first: Maria

middle: Gabriela

last: Maridueña

state: Guayas

address: Km 30.5 via perimetral

country: Ecuador

institute: Escuela Superior Politécnica del Litoral

data_processing:
Galaxy (version 2.1.0+ galaxy5)
Fast QC (Gordon, 2010) was used to assess the quality of the sequences
Trimmomatic tool (version 0.38) was applied to cut the bases off at the start (headcrop) and end (trailing) of the reads below the required threshold of 27
HiSAT2 tool
Feature counts
Assembly: GCA_000150535.2
Supplementary files format and content: RPKM values for each sample in txt format

organism: Carica papaya

source_name: Leaves

extract_protocol:
RNeasy® mini kit protocol (QIAGEN, Inc., Hilden, Germany)
Illumina’s Truseq RNA library prep kit
NovaSeq 6000 system to generate 40 million 150-pair-end (PE) reads

value: Leaves

value: EukaryoticCell

value: sun up

value: control


title: GRC355_AC1_S4

description: Library name: GRC355_AC1_S4

value: mixed wild type zebrafish line US EPA


title: C-Hep3B_2_rep2

data_processing:
Bioinformatics data analysis was provided by NewCore BioTech. (Shanghai, China). Briefly, fastp software (v0.20.0) was used to trim adaptor and remove low quality reads to get high quality clean reads.
STAR software (v2.7.9a) was used to align the high-quality clean reads to the mouse (mm39) reference genome.
featureCounts software (v2.0) was used to get the raw gene level mRNA expression counts.
Assembly: mm39
Supplementary files format and content: txt format raw counts of each gene

treatment_protocol: We established a co-culture experiment in a non-contact manner, which allowed adequate communication between these compartments in this setting. We optimized co-cultures of HepLPCs with liver cancer cell lines (HepG2 and Hep3B) to sustain the viability of both HepLPCs and HCC for 4 days, adequate time to capture the long-lasting effects of HepLPCs on a full cycle of HCC.


title: 30dpi_S3_control


title: G2_D_1_rep1

value: Adding Notch inhibitor (10 μM DAPT) to the culture medium to treat cells


title: C-Hep3B_2_rep1


title: 30dpi_S2_control


title: Whole_Body_Mut_R2

city: Kansas City

first: Hua

last: Li

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

data_processing:
Reads were de-multiplexed using Illumina’s bcl2fastq v2.20.
Reads were aligned to the zebrafish genome (GRCz11/danRer11) using kallisto v0.46.0.
DESeq2 (Galaxy Version 2.11.40+galaxy2) was used for differential expression analysis
Genes with a minimum two-fold upregulation in znf574-/- larvae and an adjusted p-value of less than 0.05 were selected for further analysis. Pathway analysis was performed using the Kyoto Encyclopedia of Genes and Genomes database (KEGG) (www.genome.jp/kegg).
Pathway enrichment analyses were performed by using the Database for Annotation, Visualization and Integrated Discovery (DAVID Bioinformatics, https://david.ncifcrf.gov/tools.jsp).
Assembly: GRCz11/danRer11
Supplementary files format and content: tab-separated value file that includes the raw count for each sample

source_name: whole larvae

growth_protocol: Adult zebrafish were maintained on a 14 h light–10 h dark cycle and fed once daily with ~3.5% body weight of Gemma Micro 500 (Skretting USA). All genotypes were bred into the wild-type AB background.  All procedures comply with all relevant ethical regulations and were approved by the Carnegie Institution Animal Care and Use Committee (Protocol #162) and the animal ethics committee (IACUC review board) at the Stowers Institute for MedicalResearch (Protocol #2024-171).

extract_protocol:
RNA from whole animals was extracted using phenol/chloroform-isoamyl alcohol extraction.
Libraries were cloned using Illumina TruSeq® Stranded mRNA Library Prep (20020595).

treatment_protocol: znf574+/- heterozygous animals were in-crossed, and fertilized eggs were collected and maintained in a zebrafish incubator for 8 days. Water was exchanged daily. Seven days post-fertilization, znf574 mutant animals can be easily distinguished from wild-type siblings.

value: whole larvae

value: all cell types


title: TS127_BJ_Intermediate_Late_anti_h3k79me2

value: BJ Fibroblast

value: H3K79me2:abcam ab3594

value: Intermediate Late - Quiescent


title: Whole_Body_Mut_R1


title: Hep3B_1_rep2

value: liver cancer cells


title: 30dpi_S1_control


title: C-G2_1_rep1

value: co-culture with HepLPCs in normal DMEM medium


title: TS126_BJ_Intermediate_Early_anti_h3k79me2

value: Intermediate Early - Quiescent


title: 30dpi_S4_virus

value: virus


title: Hep3B_1_rep1


title: Ibudilast_scRNAseq

city: guangzhou

first: Fan

last: Xing

address: Zhongshan Road

institute: Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

source_name: brain

growth_protocol: Dissociated 3 × 105 GL261 mouse glioma cells were injected 2 mm lateral and 0.5 mm anterior to the bregma and 2.5 mm below the skull of C57BL/6 mice to generate GL261 intracranial mouse glioma model. The mice were randomly divided into two groups: the control group and ibudilast group.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were intragastrically administrated with PBS or 20 mg/kg ibudilast (5 times a week) for two weeks.

value: brain

value: CD45+ tumor-infiltrating lymphocytes

value: treated with ibudilast for 2 weeks


title: Control_scRNAseq

description: 10x Genomics

value: untreated


title: TS125_BJ_Young_anti_h3k79me2

value: Young - Quiescent


title: Whole_Body_WT_R2


title: TSB25_BJ_Intermediate_Late_anti-p65

value: p65:Santa Cruz sc-372 (C-20)


title: C-HepG2_2_rep2


title: TS124_BJ_Senescent_anti_H2Bub

value: H2Bub:Millipore CS200595

value: Senescent


title: Whole_Body_WT_R1

value: whole larvae


title: C-HepG2_2_rep1


title: 30dpi_S2_virus

value: Leaves

value: EukaryoticCell

value: sun up


title: TSB23_BJ_Young_anti-p65

value: BJ Fibroblast


title: TS123_BJ_Intermediate_Late_anti_H2Bub

value: Intermediate Late - Quiescent


title: HepG2_1_rep2

value: liver cancer cells

value: normal control


title: AA(-)_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

department: Department of Surgery

institute: Union Hospital of Tongji Medical College

description:
Library name: Sample 6
Gene expression after asparagine/alanine deprivation

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: neuroblastoma

growth_protocol: Human neuroblastoma cell line SK-N-BE(2) was grown in MEM/F12 supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
A sucrose density gradient of 15-45% (w/v) was newly made in a SW41 ultracentrifuge tube from Beckman (Indianapolis, IN). Cells were broken down in a solution containing polysome lysis buffer (100 mmol·L-1 KCl, 100 mg·ml-1 cycloheximide, 2% Triton X-100, 5 mmol·L-1 MgCl2, 10 mmol·L-1 HEPES, pH 7.4), and then placed on sucrose gradients for centrifugation at 36,000 × g for 2 hours. A portion of each ribosome fraction was used to isolate total RNA using TRIzol™ reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg 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 asparagine/alanine (Asn/Ala) supplement or deprivation.

value: neuroblastoma

value: neuroblastoma cells

value: asparagine/alanine deprivation


title: TS128_BJ_Senescent_anti_h3k79me2

value: H3K79me2:abcam ab3594


title: HepG2_1_rep1


title: TS122_BJ_Intermediate_Early_anti_H2Bub

value: Intermediate Early - Quiescent


title: AA(-)_1

description:
Library name: Sample 4
Gene expression after asparagine/alanine deprivation


title: 15dpi_S4_control

value: control


title: TS121_BJ_Young_anti_H2Bub

value: Young - Quiescent


title: For_PU.1_OCIAML5_shPU1_2

city: San Antonio

first: Pinpin

last: Sui

state: TX

address: 8403 Floyd Curl Dr., STRF

department: Molecular Medicine

institute: UT health San Antonio

data_processing:
The raw data was trimmed by trim_galore(v 0.6.7) with the parameter of –paired -q 25 –phred33 –length 35 -e 0.1 –stringency 2.
The clean reads were aligned to the human genome(GRCh38) using STAR(v 2.7.10a) and then HTSeq(v 2.0.2) was used to calculate the raw read counts for each gene within GTF file and each sample.
The count matrix was used to identify differentially expressed genes(DEGs) by DESeq2(v 1.36.0) with the cutoff of FDR < 0.05 and |Fold change| >1.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: MOLM13 was cultured in RPMI 1640 medium (Sigma-Aldrich) containing 10% FBS (Gibco) and 1% Penicillin-Streptomycin (P/S) (Gibco). OCI-AML5 cells were cultured in α-MEM medium (Corning) with 20% FBS, 1% P/S, and 10 ng/mL hGM-CSF was added for OCI-AML5 cells

extract_protocol:
Total RNA was extracted using TRIzol Reagent.
Total RNAs were consumed to construct the mRNA-seq libraries using KAPA stranded mRNA Seq kit. Each library was quantified using a Qubit fluorometer (Thermo Fisher Scientific) and the size distribution was assessed by Bioanalyzer (Agilent Technologies).

treatment_protocol: Lentiviral particles for overexpression or knockdown plasmids were produced in HEK293T cells transfected with packaging (psPAX2) and envelope (VSV-G) plasmids using Lipofectamine 3000 (Invitrogen). The lentiviral supernatants were harvested twice at 24- and 48-hour time point after transfection, passed through a membrane filter with 0.45 μm pore size and concentrated with Lenti-X concentrator (Takara, #631232). Host cells were infected with the lentiviral particles in the presence of 8 μg/mL polybrene (Sigma-Aldrich, #TR-1003-G), then selected using 1 μg/mL puromycin (Gibco, #A1113803) or sorted for GFP+ cells.

value: PU.1 KD


title: AA(+)_3

description:
Library name: Sample 3
Gene expression after asparagine/alanine supplement

value: asparagine/alanine supplement


title: 15dpi_S3_control


title: TS188_BJ_Senescent_anti-H3K4me2

value: H3K4me2:abcam ab7766

value: Senescent


title: For_PU.1_OCIAML5_shPU1_1


title: TS187_BJ_Intermediate_Late_anti-H3K4me2


title: 30dpi_S3_virus

value: Leaves

value: EukaryoticCell

value: virus


title: 15dpi_S1_control

value: sun up


title: For_PU.1_OCIAML5_shCTL_2

value: Control


title: AA(+)_1

description:
Library name: Sample 1
Gene expression after asparagine/alanine supplement


title: TS186_BJ_Intermediate_Early_anti-H3K4me2

value: BJ Fibroblast


title: AA(-)_2

description:
Library name: Sample 5
Gene expression after asparagine/alanine deprivation

value: neuroblastoma


title: EBSS_3

description:
Library name: Sample 6
Gene expression after EBSS treatment

growth_protocol: Human neuroblastoma cell line SH-SY5Y was grown in DMEM/F12 medium supplemented with 10% fetal bovine serum, penicillin (100 U/ml) and streptomycin (100 μg/ml), and maintained at 37°C in a humidified atmosphere of 5% CO2.

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg 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 complete medium or Earle's balanced salt solution (EBSS) for 6 hours.

value: neuroblastoma cells

value: EBSS treatment


title: For_PU.1_OCIAML5_shCTL_1


title: 15dpi_S4_virus


title: TS185_BJ_Young_anti-H3K4me2


title: EBSS_2

description:
Library name: Sample 5
Gene expression after EBSS treatment


title: For_PSPC1_OCIAML5_shPSPC1_1

value: PSPC1 KD


title: Tom168_BJ_Senescent_anti-H3K79me3

value: H3K79me3:abcam ab2621


title: 30dpi_S1_virus


title: 15dpi_S2_virus


title: 15dpi_S1_virus


title: 15dpi_S2_control

value: control


title: AA(+)_2

description:
Library name: Sample 2
Gene expression after asparagine/alanine supplement


title: For_PSPC1_OCIAML5_shCTL_1


title: CTL_2

description:
Library name: Sample 2
Gene expression after complete medium treatment

value: control complete medium treatment


title: Tom166_BJ_Intermediate_Early_anti-H3K79me3

value: Intermediate Early - Quiescent


title: EBSS_1

description:
Library name: Sample 4
Gene expression after EBSS treatment


title: Tom167_BJ_Intermediate_Late_anti-H3K79me3

value: Intermediate Late - Quiescent


title: 10dpi_S4_control


title: For_PSPC1_OCIAML5_shCTL_2


title: CTL_1

description:
Library name: Sample 1
Gene expression after complete medium treatment


title: Tom165_BJ_Young_anti-H3K79me3

value: Young - Quiescent


title: For_PSPC1_MOLM13_shPSPC1_2


title: 10dpi_S3_control


title: For_PSPC1_OCIAML5_shPSPC1_2


title: 15dpi_S3_virus


title: Tom164_BJ_Senescent_anti-H3K27ac

value: H3K27ac:abcam ab4729

value: Senescent


title: For_PSPC1_MOLM13_shPSPC1_1


title: For_PSPC1_MOLM13_shCTL_2


title: RIP_AKTwt, IP

city: Guangzhou

first: Jingyi

last: Wang

state: Guangdong

address: Yingfeng

institute: Sun Yat-sen Memorial Hospital

data_processing:
Sequencing were performed using Illumina HiSeq X Ten
RIP-seq reads were aligned to the Ensembl_release100 genome using Bowtie version 2.2.8. Only uniquely mapping reads with at most two mismatches were retained.
The reconstruction of transcripts was carried out with software StringTie3, which allows to identify splice variants.
Peaks were called using RIPSeeker with the significance cut-off eFDR < 0.05
Processed data files were based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold
Assembly: hg18
Supplementary files format and content: tab-delimited text files include fold change values for each RNA precipitation Sample normalised to input respectively.
Supplementary files format and content: Peak related genes were used to analyse differences between two samples, different genes analysis was based on the fold enrichment (the odds ratio between IP fpkm and Input fpkm in a experiment) of different experiments. The odds ratio of fold enrichment between two experiment> 2 was used to selected different genes. Using the same method, different genes associated with peaks were identified, and also do GO and KEGG enrichment analysis.

growth_protocol: MDA-MB-231 cell lines were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (Gibco, USA).

extract_protocol:
Cell lysates were collected with IP lysis buffer supplementary with protease inhibitors, phosphatase inhibitors, RNAase inhibitors and EDTA. The cells were lysed at 4°C for 20 minutes and centrifuged at 4°C at 12000 g for 20 minutes. The supernatant was transferred to a new EP tube. 30ul were reserved for transfection efficiency testing, and 5% of the volume was taken as input storing at -80°C. The remaining supernatant was divided equally and incubated separately with magnetic beads coupled with specific protein antibodies or control IgG. The incubation was carried out overnight at 4°C with rotation. The magnetic rack was used for collecting magnetic beads. The beads were washed by 500ul of TBST for 3-5 times. RNA was extract by TRIzol reagent and were used for sequencing
RNA libraries for RNA-seq were prepared using illumina Ribo-Zero Gold（Human/Mouse/Rat）kit following manufacturer's protocols

treatment_protocol: To identify lncRNAs binding to the AKT1 E17K mutant protein, we transfected Flag-tagged AKT1 wild-type (AKT1WT) or E17K mutant (AKT1E17K) plasmids into breast cancer cell line MDA-MB-231. RNA immunoprecipitation (RIP) and deep sequencing showed that several lncRNAs preferentially bound to the AKT1 E17 mutant protein.

value: Breast cancer

value: AKT wild-type

value: Flag antibody immunoprecipitation


title: Tom163_BJ_Intermediate_Late_anti-H3K27ac


title: RIP_AKTwt, Input

value: input


title: 10dpi_S2_control

value: Leaves

value: EukaryoticCell

value: sun up


title: For_PSPC1_MOLM13_shCTL_1

value: Control


title: RIP_AKTmt, IP

value: AKT E17K mutant


title: Tom162_BJ_Intermediate_Early_anti-H3K27ac

value: BJ Fibroblast


title: 10dpi_S1_control

value: control


title: 10dpi_S4_virus

value: virus


title: RIP_AKTmt, Input


title: 10dpi_S3_virus


title: 9: Set 3 - 14 days post infection

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

data_processing:
Reads were trimmed and filtered with Trimmomatic; quality was evaluated with FASTQC before and after trimming.
Alignment of reads was performed with STAR to mixed genome assembly of GRCh38 and JC polyomavirus, with annotation from Ensembl 95 and JC polyomavirus
Read counts for reads overlapping genomic regions were counted with FeatureCounts from the Subread package.
Genome_build: Mixed genome assembly of GRCh38 and JC polyomavirus, Ensembl release 95 and JC polyomavirus annotation
Supplementary_files_format_and_content: Gene read counts from FeatureCounts

source_name: mRNA expression of dissociated CD44-sorted astrocytes from normal fetal brain tissue

growth_protocol: All dissociates were maintained overnight in DMEM/F12/N1-based medium (Life Technologies) supplemented with 10 ng/ml FGF2

extract_protocol:
mRNA was extracted and purified with the Qiagen RNeasy kit, according to the manufacturer's instructions.
Libraries were prepared with the TruSeq Stranded mRNA Prep Kit (Illumina)

treatment_protocol: Cortical tissues were minced and dissociated using papain (Worthington) and DNase (Sigma-Aldrich)

value: 14 days post infection

value: primary fetal astrocytes

tag: cell sort marker

tag: developmental stage

value: fetal


title: OCIAML6_RNAPOII_Ser5

data_processing:
The raw data was trimmed by trim_galore(v 0.6.7) and then the clean reads were aligned to the human genome(GRCh38) using bowtie2(v 2.4.5).
The raw SAM files generated by bowtie2 were sorted using SAMtools (v1.15.1) and then PCR duplications were removed by Sambamba (v 0.8.2).
Peak calling was performed with MACS2 (v 2.2.7.1) with the parameter of -f BAMPE -g hs  -B -q 0.05. DeepTools (v 3.5.1) was used for signal normalization and outputting BigWig file for visualization with options: --normalizeUsing CPM --binSize 50.
ChIPseeker(v 1.32.1) were used to annotate peaks and find peak-related genes. Motif prediction was performed using homer(v 4.11) findMotifsGenome.pl.
Assembly: hg38
Supplementary files format and content: bigwig file for each library
Supplementary files format and content: narrowpeak file for each ChIP sample

growth_protocol: OCI-AML5 cells were cultured in α-MEM medium (Corning) with 20% FBS, 1% P/S, and 10 ng/mL hGM-CSF was added for OCI-AML5 cells

extract_protocol:
ChIP was performed with a dual cross-linking protocol that starts with 2 mM disuccinimidyl glutarate (DSG) (CovaChem, #13301) for 30 minutes followed by 1% formaldehyde (Sigma-Aldrich) for 10 minutes at RT.
Cross-linking was quenched with 0.125 M Glycine for 5 minutes at RT. Nuclei were isolated sequentially using buffers LB1 [50 mM HEPES-KOH (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× protease inhibitor], LB2 [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0) and 1× protease inhibitor] and LB3 [10 mM Tris-HCl (pH 8.0), 100 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine and 1× protease inhibitor]. Isolated chromatin was fragmented in Q800R sonicator (QSONICA) and incubated with appropriate amounts of antibodies [5 g anti-PSPC1 (Bethyl Laboratories, #A303-206A) or 2.5 g anti-PU.1 (Abcam, #ab302623)] that have been conjugated to Protein G magnetic beads (Invitrogen) overnight at 4C. The immunoprecipitates were washed 5 times in RIPA wash buffer [50 mM HEPES-KOH (pH 7.5), 500 mM LiCl, 1 mM EDTA, 1% NP40, 0.7% sodium deoxycholate], twice in 1×TE buffer [10 mM Tris-HCl (pH 8.0) and 1 mM EDTA (pH 8.0)], and finally eluted in the elution buffer [1% SDS, 10 mM Tris-HCl (pH 8.0) and 10 mM EDTA (pH 8.0)]. ChIP’d DNA was reverse cross-linked at 65ºC overnight, purified by the treatment with RNase A and proteinase K, and finally subject to either qPCR reactions or ChIP-seq library construction. ChIP-seq libraries were prepared using MicroPlex Library Preparation Kit (Diagenode)

tag: chip antibody

value: anti-RNAPII pSer5 (cell signaling #13523)


title: 8: Set 3 - 4 days post infection

value: 4 days post infection


title: 10dpi_S2_virus


title: OCIAML5_IgG

value: anti-IgG (Bethyl Laboratories, #P120-101)


title: OCIAML5_PU1_ChIP_shPSPC1

value: PU.1 KD

value: anti-PU.1 (Abcam, #ab302623)


title: 10dpi_S1_virus


title: 7: Set 3 - 0 days post infection

value: 0 days post infection


title: MDA-MB-231, VecRPPH1, 2

city: Nanjing

first: Yi

last: Pan

address: 24 Tongjiaxiang Avenue

institute: China Pharmaceutical University

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks
Assembly: GRCh38
Supplementary files format and content: xls files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN)≥7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: overexpress RPPH1


title: MDA-MB-231, VecRPPH1, 1


title: 2dpi_S4_control

value: Leaves

value: EukaryoticCell


title: 6: Set 2 - 14 days post infection


title: OCIAML5_PU1_ChIP_shCTL

value: Control


title: MDA-MB-231, VecNC, 3

value: NC


title: OCIAML5_PSPC1_ChIP

value: anti-PSPC1 (Bethyl Laboratories, #A303-206A)


title: 2dpi_S3_control

value: sun up

value: control


title: MDA-MB-231, VecNC, 2


title: 2dpi_S2_control


title: 1491_spatial

city: Aurora

first: Andrew

middle: M

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

description:
gg_spatial_features.tsv.gz
gg_spatial_barcodes.tsv.gz
gg_spatial_matrix.mtx.gz
gg_spatial_metadata.csv.gz

data_processing:
Sequencing data were processed with Space Ranger (10x genomics, v1.2.1), followed by further analysis in R using the Seurat tool suite. Spots were filtered to ensure the number of genes detected between 50 and 15000, and less than 50% of UMIs mapped to mitochondrial genes. After initial SCTransform normalization on each sample and principal component analysis on merged data, sample integration was performed with Harmony (v0.1.0) using 30 principal components. UMAP dimension reduction and shared nearest neighbor clustering were carried out on 30 principal components, and clustering results at different resolution settings were explored through Clustree (v0.4.3) visualizations.
supplementary_files_format_and_content: UMI counts, barcodes, and genes in sparseMatrix format, spot metadata in CSV format, and image file in TIFF format.
Assembly: GRCh38
Library strategy: Spatial Transcriptomics

source_name: ganglioma

extract_protocol:
Samples utilized for spatial transcriptomics were snap frozen at surgery.Frozen samples  were OCT embedded and sectioned at 10μm on a Cryostar NX70 cryostat (Thermo Fisher Scientific). Capture sections were fixed with methanol, stained with H&E, and imaged on an Evos M7000 (ThermoFisher) with brightfield settings
10x Genomics Visium protocol

value: ganglioma


title: 5: Set 2 - 4 days post infection

value: primary fetal astrocytes


title: 1492_spatial


title: Tom161_BJ_Young_anti-H3K27ac

value: BJ Fibroblast

value: H3K27ac:abcam ab4729

value: Young - Quiescent


title: MDA-MB-231, VecNC, 1


title: 4: Set 2 - 0 days post infection

value: fetal


title: 3: Set 1 - 14 days post infection

value: 14 days post infection


title: 2dpi_S1_control


title: MDA-MB-231, VecRPPH1, 3


title: 1453_spatial

description:
pa_spatial_features.tsv.gz
pa_spatial_barcodes.tsv.gz
pa_spatial_matrix.mtx.gz
pa_spatial_metadata.csv.gz

source_name: pilocytic astrocytoma

value: pilocytic astrocytoma


title: 2: Set 1 - 4 days post infection

value: 4 days post infection


title: 2dpi_S4_virus

value: virus


title: 1330_spatial


title: BVDV Persistent Infection: 4 Months Postnatal PBMC DNA 7138

city: Fort Collins

first: Thomas

middle: R.

last: Hansen

state: Colorado

address: 3107 Rampart Road

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Quality of reads were checked with fastqc 0.11.9, reads were trimmed with trimgalore 0.6.4_dev
Reads were mapped to the bosTau9 genome using bismark 0.22.3
Obtained bam files were analyzed with methylKit 1.24.0
Assembly: bosTau9
Supplementary files format and content: bedGraph files generated from bismark for each sample
Supplementary files format and content: comma-delimited files for diffrenetially methylated cytosines and regions

organism: Bos taurus

source_name: PBMC

extract_protocol:
DNA was extracted from WBCs processed from whole blood using Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).
DNA samples were digested with 30 units of MspI, fragments purified with DNA Clean & Concentrator-5  and ligated to adapters with replacement of cytosine with 50-methyl-cytosine according to Illumina’s guidelines. Fragments greater than 50 base pairs were recovered and bisulfite treated using the EZ DNA Methylation-Lightning Kit . Samples were subjected to PCR with Illumina indices. Size and concentrations of purified products were confirmed with the Agilent 2200 TapeStation prior to sequencing on an Illumina platform

value: PBMC

value: White Blood Cells

value: BVDV Persistent Infection


title: BVDV Persistent Infection: 4 Months Postnatal PBMC DNA 6186


title: 2dpi_S3_virus

value: Leaves

value: EukaryoticCell


title: 1272_spatial


title: 1: Set 1 - 0 days post infection

value: 0 days post infection


title: BVDV Persistent Infection: 4 Months Postnatal PBMC DNA 6146


title: 2dpi_S2_virus

value: sun up


title: 2dpi_S1_virus


title: BVDV Persistent Infection: 4 Months Postnatal PBMC DNA 198


title: 1181_spatial

value: ganglioma


title: Sprague-Dawley rat chondrocytes, RA treatment (24h)-3

city: Datong

first: Tao

last: LU

state: Shanxi

address: 405 Xingyun Street, Pingcheng District, Datong Shanxi, China

institute: Shanxi Datong University - Yudong Campus: Shanxi Datong University

description: Library name: sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to mouse genome assembly Rnor6 (https://ftp.ensembl.org/pub/release-104/fasta/rattus_norvegicus/dna/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.104.gtf.gz.
Assembly: Rnor6
Supplementary files format and content: File include Count and  FPKM values for each sample

organism: Rattus norvegicus

source_name: Primary chondrocytes

extract_protocol:
Chondrocytes were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Hyclone, UT) containing 10% fetal bovine serum (FB-1058, Biosera) and 1% penicillin-streptomycin(ST488S, Beyotime).control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.

value: Primary chondrocytes

value: WT

value: Highglucose DMEM + 10% FBS + 1% penicillinstreptomycin + 1 μM alltrans retinoic acid (ATRA, S1653)  24 h


title: BVDV Persistent Infection: 4 Months Postnatal PBMC DNA 144

description: CpGp: Promoters hypomethylated


title: 1056_spatial


title: Sprague-Dawley rat chondrocytes, RA treatment (24h)-1

description: Library name: sample 4

growth_protocol: Chondrocytes were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Hyclone, UT) containing 10% fetal bovine serum (FB-1058, Biosera) and 1% penicillin-streptomycin(ST488S, Beyotime).control cells were cultured in a high-glucose DMEM medium containing 10% FBS for 24 h, while cells in the RA group were cultured in the same medium with 1 μM retinoic acid(S1653, Bimake) for 24 h.


title: Control: 4 Months Postnatal PMBC DNA 2163

description: CpGp: Promoters hypermethylated

value: control


title: 946_spatial


title: Sprague-Dawley rat chondrocytes, Control (24h)-3

description: Library name: sample 3

value: Highglucose DMEM (Hyclone) + 10% FBS (FB1058, Biosera) + 1% penicillinstreptomycin (ST488S)  24 h


title: Control: 4 Months Postnatal PMBC DNA 2156

description: CpGi: Islands hypomethylated


title: Lung cells, APC, biol rep 3

city: Hangzhou

first: Wanying

last: Zhang

state: Select...

address: 88 Jiefang Road, Hangzhou 310009, China;

institute: Zhejiang university

description:
Library name: Sample 6
10x Genomics

data_processing:
Quantification, quality control, and clustering analysis of single-cell expression: The CellRanger suite (10X Genomics, version 7.1.0) was used for mapping and quantification of the raw sequencing data.
Assembly: Mouse GRCm38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
Lung tissues were transported in In sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBSThermo Fisher, Cat.  no.  14190144) on ice to remove the residual tissue storage solution, then minced on ice.  Weused dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat.  no.25200-072) and 10 ug/mL 1DNase I (Sigma, Catno. 11284932001) dissolyed in PBS with 5% Fetal Bovine Serum (FBS: Thermo Fisher, Cat.  no.  SV30087.02) todigest the tissues.  Lung tissues were dissociated at 37℃ with a shaking speed of 50 r.p.m for about 40 min. Werepeatedly collected the dissociated cells at interval of 20 min to increase cell vield and viability, Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell LysisSolution (Thermo Fisher, Cat.  no.  00-4333-57).  Dissociated cells were washed with 1x DPBS containing 2% FBSCells were stained with 0.4% Trypan blue (Thermo Fisher, Cat.  no.  14190144) to check the viability on CountessRI Automated Cell Counter (Thermo Fisher).
Library was performed according to the manufacter's instructions (single cell 3' v2protocol, 10x Genomics). Beads with unique molecular identifier (UMI) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a Gel Beads-in-emulsion(GEM).  After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads.  Beads were retrieved into a single tube for reverse transcription.  On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin.  Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI.  All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (Chromium Single Cell 3ʹ v3.1).  Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific).  The sequencing were sequenced on Novaseq Xplus using PE150 mode

treatment_protocol: Intravenous injection of PBS or APC

value: lung

value: Lung cells

value: APC


title: Lung cells, APC, biol rep 1

description:
Library name: Sample 4
10x Genomics


title: Sprague-Dawley rat chondrocytes, Control (24h)-2

description: Library name: sample 2


title: Lung cells, APC, biol rep 2

description:
Library name: Sample 5
10x Genomics


title: 1492_sc

description:
single_cell_features.tsv.gz
single_cell_barcodes.tsv.gz
single_cell_matrix.mtx.gz
single_cell_metadata.csv.gz

data_processing:
Raw sequencing reads were processed into gene-expression matrices using Alevin (salmon version 1.3.0) with the hg38 human reference genome. The resulting count matrices were further filtered in Seurat (v.4.0.3-4.1.1) (https://satijalab.org/seurat/) to remove cell barcodes with less than 200 genes, more than 20% of UMIs derived frommitochondrial genes, or less than 500 UMIs and more than 50,000UMIs. UMI counts were log-normalized. PCA was performed on scaled normalized counts using highly variable genes (2,000). Harmony (v0.1.0) was applied to integrate samples (theta = 1). 25 harmony components were used for generating a UMAP projection and a shared nearest neighbor graph, which was clustered using graph based clustering implemented in Seurat. Doublet cells were identified using scDblFinder, and cells with doublet scores greater than 5 were excluded (v. 1.6.0)
supplementary_files_format_and_content: UMI counts, barcodes, and genes in sparseMatrix format, and cell metadata in CSV format.
Assembly: GRCh38

extract_protocol:
Surgical tissue was collected in serum-free media, brought to the laboratory for mechanical dissociation, and viably frozen in single cell suspension as previously described (Gillen, A.E., et al., Single-Cell RNA Sequencing of Childhood Ependymoma Reveals Neoplastic Cell Subpopulations That Impact Molecular Classification and Etiology. Cell Rep, 2020. 32(6): p. 108023).
Chromium Single Cell V3 Chemistry Library Kits, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics)


title: 1491_sc


title: Lung cells, PBS, biol rep 3

description:
Library name: Sample 3
10x Genomics

value: PBS


title: Sprague-Dawley rat chondrocytes, Control (24h)-1

description: Library name: sample 1


title: Saline, 90 days abstinent _ BIO REPLICATE 5

city: Philadelphia

first: Mathieu

last: Wimmer

address: 1701 N 13th Street

institute: Temple University

data_processing:
Pre_processing and annotation to the miRbase and Ensembl ncRNA rat databases were performed using the sRNAbench web platform.
Annotated miRNA and ncRNA reads were transferred to RStudio for assembly of count matrices.
Count matrices were used as input for the DESeq2 differential gene expression analysis pipeline
Assembly: rn6
Supplementary files format and content: tab_delimited text file includes raw miRNA counts for each sample ("miRNA_expression_matrix.txt")
Supplementary files format and content: tab_delimited text file includes raw Ensembl ncRNA counts for each sample ("ens_ncRNA_expression_matrix.txt")

source_name: Mature sperm cells

extract_protocol:
Sperm cells extracted from cauda epididymus and purified using a double swim_up assay. For sperm RNA extraction: Sperm cells were resuspended in nucleus isolation buffer (15mM Tris_HCL, pH 7.5, 60mM KCl,15mM NaCl, 5mM MgCl2, 1mM CaCl2, 250mM sucrose, 1mM dithiothreitol). Trizol_LS solution was added, and samples were homogenized using a Dounce homogenizer, then run through a 27g needle. Lysate was spun down to pellet salts and debris. Supernatant then combined with chloroform and spun down. Aqueous phase was combined with isopropyl alcohol & glycogen and incubated overnight at _20C to precipitate RNA. RNA pellets were washed twice with cold 75% EtOH. The final RNA pellet was resuspended in RNAse_free water.
Small RNA libraries were prepared from sperm RNA using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina. Libraries were purified using the Qiaquick PCR purification kit, then size selected using AMPure XP beads.

value: Mature sperm cells

tag: drug treatment

value: Saline

tag: collection timepoint

value: 90 days abstinent


title: Control: 4 Months Postnatal PMBC DNA 2147

description: CpG sites hypomethylated

value: PBMC

value: White Blood Cells


title: 1459_sc

source_name: pilocyticastrocytoma

value: pilocyticastrocytoma


title: Control: 4 Months Postnatal PMBC DNA 2149

description: CpGi: Islands hypermethylated


title: Lung cells, PBS, biol rep 2

description:
Library name: Sample 2
10x Genomics


title: Sprague-Dawley rat chondrocytes, RA treatment (24h)-2

description: Library name: sample 5


title: 1455_sc


title: Control: 4 Months Postnatal PMBC DNA 2132

description: CpG sites hypermethylated


title: Lung cells, PBS, biol rep 1

description:
Library name: Sample 1
10x Genomics


title: 1453_sc


title: OK107_60h

city: Ann Arbor

last: Ahmed

address: 1105 North University

institute: University of Michigan

description:
Library name: sample 6
10x Genomics

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10x Genomics) was used to align reads and generate count matrices.
Seurat (v4.3.0 and above) was used for normalization, integration, dimensional reduction and clustering steps. Details are specified in Methods. Final Seurat object used in figures and analyses is provided in files.
Assembly: dm6
Supplementary files format and content: 1. readme file with description of files and metadata; 2. Filtered counts data in 10X format (separately given for each developmental stage); 3. Metadata for integrated, clustered Seurat object of all stages Kenyon cells and non-Kenyon cells containing cell identities, developmental time points, and driver used; 4. Metadata for integrated, subsetted Kenyon cells of all stages containing cell identities, developmental time points, and driver used; 5. UMAP embeddings (separately given for a) Kenyon cell and non-Kenyon cell data, and b) subsetted Kenyon cells)

organism: Drosophila melanogaster

growth_protocol: Flies were raised on standard cornmeal-agarose with molasses at 25C on a 12 hour light/dark cycle.

extract_protocol:
Cells were FACS-sorted into PBS+1% BSA.
Single cell suspensions were subjected to counting and viability checks on the LUNA Fx7 Automated Cell Counter (Logos Biosystems) and diluted to a concentration of 700-1000 cells/ul. Single cell libraries were generated using the 10x Genomics Chromium Controller with 3' Gene Expression reagents following the manufacturer’s protocol (10x Genomics). Final library quality was assessed using the LabChip GX (PerkinElmer). Libraries were subjected to paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000).

treatment_protocol: 40-80 pupal brains were dissected per sample, optic lobes removed, and subjected to tissue dissociation and flow cytometry.

value: brain

value: 60h APF

value: UAS-CD8GFP/CyO; GH146QF, QUASTomato/TM6B; OK107-Gal4/OK107-Gal4

tag: Sex

value: pooled male and female


title: Morphine, 90 days abstinent _ BIO REPLICATE 6

value: Morphine


title: 1417_sc

tag: tissue

value: ganglioma


title: MB247_60h

description:
Library name: sample 5
10x Genomics

value: GH146 Gal4, UASmtdTomato/CyO; MB247-LexA, LexAop CD2-GFP/TM2


title: PC-2

city: nanjing

first: zichen

last: liang

state: jiangsu

address: Xianlin campus, Nanjing University, Qixia District

institute: nanjing university

description: Library name: Sample4

data_processing:
Illumina Casava2.19 software used for basecalling.
Raw data (raw reads) of fastq format were firstly processed through fastp software.
featureCounts (1.5.0-p3) were used to calculate the reads mapped to each gene. FPKM was then calculated for each gene based on its length and the readings mapped to that gene were calculated.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bone marrow

extract_protocol:
bone marrow-derived macrophages were generated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1002）
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone marrow

value: Primary cells

tag: cell type

value: Bone marrow-derived macrophages

value: WT

value: Bone marrow-derived macrophages were transfected with PC plasmid


title: PC-1

description: Library name: Sample3

tag: genotype


title: PCI-2

description: Library name: Sample2

tag: treatment

value: Bone marrow-derived macrophages were transfected with PCI plasmid


title: 1330_sc


title: OK107_48h

description:
Library name: sample 4
10x Genomics

value: 48h APF


title: 1272_sc


title: Saline, non_abstinent _ BIO REPLICATE 6

value: Mature sperm cells

value: Saline


title: PCI-1

description: Library name: Sample1


title: MB247_48h

description:
Library name: sample 3
10x Genomics


title: Morphine, non_abstinent _ BIO REPLICATE 6


title: OK107_36h

description:
Library name: sample 2
10x Genomics

value: 36h APF


title: heart from the DOX_AKK group, AKK4

city: ningbo

first: Hui

last: Lin

state: zhejiang

address: The Affiliated Lihuili Hospital of Ningbo University, Healthy Science Center, Ni

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis.
Assembly: mmu10
Supplementary files format and content: tab-delimited text files include FRKM and count values for each sample

source_name: heart

extract_protocol:
Total RNA was extracted from heart tissue using Trizol reagent (Invitrogen, Carlsbad, CA, USA). The RNA's quantity, purity, and integrity were assessed to ensure quality.
After total RNA was extracted, mRNA was purified from total RNA and fragmented into short fragments using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA.

value: heart


title: 1268_sc

source_name: low grade glioma

value: low grade glioma


title: heart from the DOX_AKK group, AKK3

institute: The Affiliated Lihuili Hospital of Ningbo University, Healthy Science Center, Ni


title: 1266_sc

value: pilocyticastrocytoma


title: Morphine, non_abstinent _ BIO REPLICATE 7


title: Morphine, 90 days abstinent _ BIO REPLICATE 5

value: 90 days abstinent


title: Saline, 90 days abstinent _ BIO REPLICATE 4


title: heart from the DOX_AKK group, AKK2


title: OTI WT E3

city: SANTIAGO

first: Daniela

last: Sauma

state: Región Metropolitana

address: Las Palmeras 3425

department: Facultad de Ciencias

country: Chile

institute: Universidad de Chile

description:
Library name: DS06
Column name in raw_counts_allsamples.csv: DS06

data_processing:
Reads were trimmed for adapters and low-quality bases using fastp, then aligned to the mm10 genome with HISAT2. Gene-level counts were quantified using featureCounts.
Assembly: mm10
Supplementary files format and content: Comma-separated file includes raw counts for all samples

source_name: OTI

growth_protocol: Total CD8+ T lymphocytes isolated from the spleen OT-I mice were cultured in 24-well plates at a concentration of 5 x 105 cells/mL in an medium which consisted of RPMI + 10% FBS, 10 mM Hepes (cat: 15630-080, Gibco), 1 mM sodium pyruvate (cat: 11360-070, Gibco), 1% v/v non-essential amino acids (cat: 11140-050, Gibco), 55 µM β-mercaptoethanol, recombinant mouse IL-7 at 5 ng/mL (cat: 577804, Biolegend) and recombinant mouse IL-15 at 5 ng/mL (cat: 566302, Biolegend). Every day for 5 days, 10 ng of SIINFEKL peptide (OT-I peptide, GenScript) was added, simulating chronic TCR activation. After 48 hours of incubation, CD8+ T lymphocytes were transferred to a Falcon tube and counted by flow cytometry. Subsequently, the cells were washed and resuspended in exhaustion medium at 5 x 105 cells/mL of medium and transferred to a 24-well plate. When a high confluence of cells was observed in a well, 1 mL of medium with peptide was added and divided into 2 wells (usually on day 4 after the start of the experiment).

extract_protocol:
RNA extraction was performed using the E.Z.N.A Total RNA Kit (cat: R6834-02CH, Omega Bio-tek), following the manufacturer's instructions. The resulting RNA was quantified using Qubit (Invitrogen) or Nanodrop. RNA integrity was determined by 1% agarose gel electrophoresis. 1 µg of total RNA was used for the construction of sequencing libraries.
RNAseq libraries for RNA-seq were prepared using QIAseq Stranded RNA Library Kit following manufacturer's protocol.

treatment_protocol: Exhaustion was induced in vitro by adding 10 ng of SIINFEKL peptide per mL of medium daily for 5 days in the presence of IL-7 (5 ng/mL) and IL-15 (5 ng/mL).

value: OTI

value: CD8 T cell

value: Exhaustion


title: Saline, non_abstinent _ BIO REPLICATE 7


title: OTI WT E2

description:
Library name: DS05
Column name in raw_counts_allsamples.csv: DS05


title: 1226_sc


title: Morphine, 90 days abstinent _ BIO REPLICATE 4

value: Morphine


title: MB247_36h

description:
Library name: sample 1
10x Genomics

value: brain

value: GH146 Gal4, UASmtdTomato/CyO; MB247-LexA, LexAop CD2-GFP/TM2

value: pooled male and female


title: Saline, non_abstinent _ BIO REPLICATE 5


title: 1181_sc

value: ganglioma


title: 1216_sc


title: heart from the DIC group, DOX6

value: DOX


title: OTI WT E1

description:
Library name: DS04
Column name in raw_counts_allsamples.csv: DS04

value: WT


title: heart from the DIC group, DOX4


title: Saline, non_abstinent _ BIO REPLICATE 4

value: Mature sperm cells


title: OTI CD73 KO E3

description:
Library name: DS03
Column name in raw_counts_allsamples.csv: DS03

value: CD73 KO


title: heart from the DIC group, DOX2


title: 1171_sc


title: Morphine, non_abstinent _ BIO REPLICATE 5


title: 1116_sc


title: heart from the control group, Control8


title: OTI CD73 KO E2

description:
Library name: DS02
Column name in raw_counts_allsamples.csv: DS02


title: 1057_sc


title: OTI CD73 KO E1

description:
Library name: DS01
Column name in raw_counts_allsamples.csv: DS01


title: heart from the control group, Control7


title: Saline, 90 days abstinent _ BIO REPLICATE 3

value: Saline


title: heart from the control group, Control3

value: heart


title: 1056_sc


title: Saline, 90 days abstinent _ BIO REPLICATE 2


title: 1033_sc


title: Morphine, 90 days abstinent _ BIO REPLICATE 3


title: RNA-seq of mouse uterus tissue (OT2)

city: Seoul

first: Kihae

last: Ra

address: Gwan-ak ro 1

department: Research Institute for Veterinary Science

country: South Korea

institute: Seoul National University

description: Library name: OT2-uterus

data_processing:
Potentially existing sequencing adapters and raw quality bases in the raw reads were trimmed by Skewer ver 0.2.2. The cleaned high quality reads after trimming the low quality bases and sequencing adapters were mapped to the reference genome by STAR ver 2.5 software. Since the sequencing libraries were prepared strand-speciﬁcally by using Illumina’s strand-speciﬁc library preparation kit, the strand-speciﬁc library option, --library-type=fr-ﬁrststrand was applied in the mapping process.
To quantify the mapped reads on the reference genome in to the gene expression values, Cufflinks ver 2.2.1 with the strandspecific library option, --library-type=fr-firststrand and other default options was used. The gene annotation of the reference genome mm10 from UCSC genome (https://genome.ucsc.edu) in GTF format was used as gene models and the expression values were calculated in Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) unit. The differentially expressed genes between the two selected biological conditions were analyzed by Cuffdiff software in Cufflinks package with the strandspecific library option, --library-type=fr-firststrand and other default options was used. To compare the expression profiles among the samples, the normalized expression values of the selected a few hundred of the differentially expressed genes were unsupervised clustered by in-house R scripts. The scatter plots for the gene expression values for the expression-fold changes and p-values between the two selected samples also were drawn by in-house R scripts.
Assembly: mm10
Supplementary files format and content: genes.fpkm_table.txt

source_name: uterus

extract_protocol:
RNA library was prepared using an Illumina TruSeq Stranded Total RNA Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions. Briefly, after removing rRNA from the total RNA (700 ng) using an rRNA removal kit, RNA was purified using beads. After rRNA depletion, a fragment mix (EPH) was used for the remaining RNA at 94°C for 6 min. Fragmented RNA primed with random hexamers was transcribed to first strand cDNA using reverse transcriptase and random primers at: 25°C for 10 min, 42°C for 15 min, and 70°C for 15 min.
to produce double stranded cDNA, the replacement strand was synthesized by incorporating dUTP in place of dTTP using polymerase at 16°C for 1 h. After cDNA was cleaned using sample purification beads, a single “A” nucleotide was attached to the 3' ends of the blunt fragments using A-Tailing mix reagent by incubation at 37°C for 30 min, and then at 70°C for 5 min. Indexing adapters were ligated to the ends of the DNA fragments using a ligation mix 2 reagents at 30 °C for 10 min. PCR was conducted to enrich the DNA fragments with adapter molecules on both ends after washing twice with sample purification beads under the thermocycler conditions as follows: 95°C for 3 min, followed by eight cycles of 98°C for 20 s, 60°C for 15 s, and 72°C for 30 min, with a final extension at 72°C for 5 min.

value: uterus

value: intravenous administration of human amniotic membrane-derived mesenchymal stem cell conditioned medium (AMSC-CM)

tag: sample group

value: old treatment


title: RNA-seq of mouse uterus tissue (OT3)

description: Library name: OT3-uterus


title: SA187W-18h-3

city: Jeddah

first: Sabiha

last: Parween

address: Thuwal

department: Hirt lab

country: Saudi Arabia

institute: KAUST

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
paired-end clean reads were aligned to the reference genome using Tophat v2.0.13
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups  was performed using the DESeq2Rpackage (1.20.0). Genes with an adjusted P-value <=0.05found by DESeq2 were assigned as differentially expressed.
The annotation was generated using an inhouse pipeline and is available on the series record.
Assembly: Enterobacter sp. SA187 (CP019113)
Supplementary files format and content: Excel,log2 transform count based normalization

organism: Enterobacter sp. SA187

source_name: 18hr bacterial culture

growth_protocol: Bacterial cultures were grown in LB  for 6hr and 18hr at 28C and 220 rpm

extract_protocol:
Total RNA of SA187Y and SA187W cultured in liquid medium for the selected two time points of bacterial growth (6 h and 18 h) was extracted by using RiboPure Bacteria kit (Ambion) following the manufacturer’s instructions with the modifications as described in (Andrés-Barrao et al., 2021).
RNA samples were shipped to Novogene for further analysis

treatment_protocol: two time points selected for the test at the logarithmic phase of 6hr and the stationary phase at 18hr

value: bacteral culture

tag: strain

tag: phenotype

value: white

value: RpoS Sigma factor gene mutant (SA187PBcda_000000191)

tag: time

value: 18 hours of growth


title: Morphine, 90 days abstinent _ BIO REPLICATE 2

value: Morphine

value: 90 days abstinent


title: SA187W-18h-2


title: 946_sc

value: pilocyticastrocytoma


title: RNA-seq of mouse uterus tissue (OT1)

description: Library name: OT1-uterus


title: 879_sc


title: SA187W-18h-1


title: RNA-seq of mouse uterus tissue (OC3)

description: Library name: OC3-uterus

value: old control


title: SA187W-6h-3

source_name: 6hr bacterial culture

value: 6 hours of growth


title: 855_sc


title: SA187W-6h-2


title: Morphine, non_abstinent _ BIO REPLICATE 3


title: RNA-seq of mouse uterus tissue (OC2)

description: Library name: OC2-uterus


title: Morphine, non_abstinent _ BIO REPLICATE 4


title: RNA-seq of mouse uterus tissue (OT4)

description: Library name: OT4-uterus


title: Saline, non_abstinent _ BIO REPLICATE 3


title: t-NMO DMD, replicate 6

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

country: Italy

institute: University of Bologna

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

source_name: hiPSCs derived from primary myogenic cells from Telethon biobank

extract_protocol:
Total cell RNA was isolated and purified using RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s instructions. Libraries were prepared from 125 ng of total RNA.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

value: neuromuscular differentiation from hiPSCs

tag: disease state

value: Duchenne muscular dystrophy

value: 3D organoid culture on decellularized murine diaphragm


title: RNA-seq of mouse uterus tissue (OC1)

description: Library name: OC1-uterus


title: Saline, 90 days abstinent _ BIO REPLICATE 1

value: Mature sperm cells

value: Saline


title: SA187W-6h-1


title: SA187Y-18h-3

value: yellow

value: wildtype


title: t-NMO DMD, replicate 5


title: Morphine, 90 days abstinent _ BIO REPLICATE 1


title: 957_sc


title: RNA-seq of mouse ovary tissue (OT3)

description: Library name: OT3-ovary

source_name: ovary

value: ovary

value: intravenous administration of human amniotic membrane-derived mesenchymal stem cell conditioned medium (AMSC-CM)

value: old treatment


title: SA187Y-18h-2

value: bacteral culture


title: t-NMO DMD, replicate 4


title: SA187Y-18h-1

value: 18 hours of growth


title: Saline, non_abstinent _ BIO REPLICATE 1


title: t-NMO DMD, replicate 3


title: RNA-seq of mouse ovary tissue (OT2)

description: Library name: OT2-ovary


title: Saline, non_abstinent _ BIO REPLICATE 2


title: RNA-seq of mouse ovary tissue (OT1)

description: Library name: OT1-ovary


title: SA187Y-6h-3


title: t-NMO DMD, replicate 2


title: Morphine, non_abstinent _ BIO REPLICATE 1

value: Morphine


title: RNA-seq of mouse ovary tissue (OC3)

description: Library name: OC3-ovary


title: SA187Y-6h-2


title: RNA-seq of mouse ovary tissue (OT4)

description: Library name: OT4-ovary


title: IEC4.1 PRDM1 KO +IFNγ 3

city: Chicago

first: Aiyu

last: Gong

state: IL

address: 1735 W. Harrison St

department: MPI

institute: Rush University

description: Gene expression

data_processing:
Base-calling sofeware, version, parameters;
BGI SOAPnuke v1.5.2 software used for basecalling.
Sequencing data filtering:this project uses the filtering software SOAPnuke developed by BGI independently for filtering. Software Information:  SOAPnuke:Version v1.5.2; Parameters -l 15 -q 0.2 -n 0.05
Data filtering steps; 1) Remove the reads containing the adaptor (adaptor pollution); 2) Remove reads whose N content is greater than 5%; 3) Remove low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" are saved in FASTQ format.
Read alignment: Align to the reference genome: After getting clean reads, used HISAT to align the clean reads to the reference genome. Software Information: HISAT2;  Version：v2.0.4; Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: mm10; Reference species: Species：Mus_musculus; Source：NCBI;  Reference Genome Version：GCF_000001635.26_GRCm38.p6
Supplementary files format and content: tab-delimited text files include gene expression RPKM values level for each Sample

extract_protocol:
IEC 4.1 cells were harvested, and RNA were extract using Rneasy Mini Kit (QIAGEN Cat. No. 74104).  Agilent 2100 or Fragment Analyzer was used to detect thequality of RNA. 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using DNBSEQ platform

tag: cell line

value: IEC4.1 CRISPR/Cas9 PRDM1KO

value: IFNgamma


title: t-NMO DMD, replicate 1


title: RNA-seq of mouse ovary tissue (OC2)

description: Library name: OC2-ovary

value: old control


title: t-NMO, replicate 3

source_name: hiPSCs reprogrammed from BJ cells

value: Healthy


title: SA187Y-6h-1

value: 6 hours of growth


title: aCSF1R_D42

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

institute: Seoul National University Hospital

description:
Library name: aCSF1R_D42
10X Genomics

data_processing:
The purified libraries were quantified using quantitative PCR (qPCR) according to the manufacturer’s protocol (Sigma-Aldrich) and were qualified using the Agilent 4200 TapeStation (Agilent Technologies) and sequenced using HiSeqX (Illumina) with a read length of 28 bp for read 1 (cell barcode and UMI), an 10 bp index read (sample barcode), and a read length of 90 bp for read 2 (RNA read). The Cell Ranger pipeline (version 3.1.0; 10× Genomics) was used to process the raw data set.
Assembly: m10
Supplementary files format and content: h5 format

source_name: Kidney

extract_protocol:
After digesting kidneys with 0.2 mg/ml liberase (Roche) at 37°C for 25 minutes in a shaking incubator, cells were filtered through a 70-μm and 40-μm strainer. The isolated cells were re-suspended in DMEM consist of 10% FBS.
Libraries were prepared using the chromium controller according to the 10× Chromium Next GEM Single Cell 3′ protocol (version 3.1; 10× Genomics).

treatment_protocol: Single-cell RNA sequencing (scRNA-seq) was performed on kidney cells isolated from eight C57BL/6 mice, randomly assigned to receive either an αCSF1R antibody (Ab) or an isotype control antibody (n = 2 per group). All mice received a single intraperitoneal injection at eight weeks of age. Kidneys were harvested on day 42 post-injection, two mice per group were sacrificed to generate the control_D42 and aCSF1R_D42 datasets. All animals were housed under standard laboratory conditions with controlled temperature and light cycles, and provided food and water.

value: Kidney

value: total cell

value: Wild type

value: αCSF1R Ab

tag: time point

value: harvested at 42 days post-injection


title: Morphine, non_abstinent _ BIO REPLICATE 2

state: PA

value: Mature sperm cells


title: WT_5

city: Helsinki

first: Jouni

middle: Antero

last: Kvist

state: Uusimaa

address: Haartmaninkatu 8

department: Research Program for Molecular Neurology

country: Finland

institute: University of Helsinki

data_processing:
Raw data (bcl-files) was demultiplexed with bcl2fastq2 (Illumina).
The fastq-files were filtered with cutadapt (Martin, 2011) to remove adapter sequences (AGATCGGAAGAGCACACGTCTGAACTCCAGTCA), ambiquous (N) and low quality bases (Phred score < 25). Reads that were too short (<25bp) after trimming were excluded.
The filtered fastq-files were mapped to the mouse reference genome (GENCODE-GRCm39) with STAR (Dobin et al., 2013). The mapped reads were analyzed with R (R Core Team, 2021).
Read counts for genes were extracted with Rsubreads (Liao et al., 2019) excluding duplicates, multimapping reads, chimeric fragments, and reads with mapping quality below 10.
Differential gene expression was analysed with DESeq2 (Love et al., 2014), comparing the genotypes to each other.
Genes with low reads depth (<50 reads in total) were excluded. Genes with FDR corrected p-value < 0.01 were considered differentially expressed.
Assembly: GRCm39
Supplementary files format and content: csv (DESeq2 results and read counts)

source_name: muscle

extract_protocol:
Total RNA was extracted from 20 mg mouse skeletal muscle using TRIsure-chloroform-ethanol (Bioline) method followed by in-column DNA digestion (Qiagen). RNA concentrations were measured with Agilent TapeStation and Nanodrop, RNA integrity was checked on a gel with Agilent TapeStation.
The RNA-seq libraries were made with NEBNext Ultra II Directional (PolyA) kit and sequenced with NextSeq High Output 1x75bp (Illumina) at Biomedicum Functional Genomics Unit (FuGU).

value: muscle

value: wt


title: Control_D42

description:
Library name: Control_D42
10X Genomics

value: Isotype control Ab


title: NMO, replicate 2

value: neuromuscular differentiation from hiPSCs

value: 3D organoid culture in Matrigel


title: t-NMO, replicate 2

value: 3D organoid culture on decellularized murine diaphragm


title: IEC4.1 PRDM1 KO ctrl 3

description: Gene expression

value: IEC4.1 CRISPR/Cas9 PRDM1KO

value: Control


title: RNA-seq of mouse ovary tissue (OC1)

description: Library name: OC1-ovary

value: ovary

value: old control


title: WT_4


title: aCSF1R_D7

description:
Library name: aCSF1R_D7
10X Genomics

treatment_protocol: Single-cell RNA sequencing (scRNA-seq) was performed on kidney cells isolated from eight C57BL/6 mice, randomly assigned to receive either an αCSF1R antibody (Ab) or an isotype control antibody (n = 2 per group). All mice received a single intraperitoneal injection at eight weeks of age. Kidneys were harvested on day 7 post-injection, two mice per group were sacrificed to generate the control_D7 and aCSF1R_D7 datasets. All animals were housed under standard laboratory conditions with controlled temperature and light cycles, and provided food and water.

value: harvested at 7 days post-injection


title: Control_D7

description:
Library name: Control_D7
10X Genomics

value: Kidney


title: IEC4.1 PRDM1 KO ctrl 1

description: Gene expression


title: IEC4.1 PRDM1 KO ctrl 2

description: Gene expression


title: IEC4.1 PRDM1 KO +IFNγ 1

description: Gene expression

value: IFNgamma


title: NMO, replicate 1

value: Healthy


title: t-NMO, replicate 1


title: IEC4.1 WT + IFNγ 3

description: Gene expression

value: IEC4.1 WT


title: aCSF1RAb_CD11b_6W

description: 10X Genomics

treatment_protocol: Single-cell RNA sequencing (scRNA-seq) datasets of mouse kidney cells were generated from six C57BL/6 mice, divided into two groups: three mice treated with an αCSF1R antibody (Ab) and three mice treated with a control antibody (Ab). At eight weeks of age, the mice received their respective treatments. Six weeks post-injection, the kidneys were harvested and prepared for scRNA-seq analysis using sorted DAPI-negative cells. For the αCSF1R_CD11b_6W group, three mice treated with the αCSF1R Ab were further sorted by CD11b+. All animals were maintained under standard laboratory conditions, which included controlled temperature, light cycles, and unrestricted access to food and water.

value: CD11b+ sorted cell

value: Wile type

value: αCSF1R Ab


title: NMO, replicate 3


title: IEC4.1 PRDM1 KO +IFNγ 2

description: Gene expression


title: WT_1

value: muscle

value: wt


title: Control_6W

description: 10X Genomics

value: immune cell

value: Isotype control Ab


title: 2D, replicate 2

value: neuromuscular differentiation from hiPSCs

value: 2D culture on 0.5% MRF coated wells


title: IEC4.1 WT + IFNγ 2

description: Gene expression


title: Hom_5

value: homozygote


title: aCSF1RAb_6W

description: 10X Genomics


title: WT_3


title: IEC4.1 WT + IFNγ 1

description: Gene expression


title: Hom_4


title: WT_2


title: 2D, replicate 1


title: Hom_3


title: IEC4.1 WT Ctrl 2

description: Gene expression

value: Control


title: 2D, replicate 3


title: PHH rep3

city: Beijing

first: Rui

last: Yao

address: Haidian District

institute: Tsinghua University

data_processing:
Sequencing was performed with an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Reads were filtered and mapped to the reference genome sequence with Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: Homo_sapiens_Ensemble_94
Supplementary files format and content: The fragments per kilobase of exon per million fragments mapped (FPKM) method was used to calculated gene expression levels.

source_name: liver

extract_protocol:
The samples for RNA-seq were collected in TriZol. 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: liver

value: primary human hepatocyte

value: hepatocyte

value: WT

value: planar cell culture


title: PHH rep1


title: IEC4.1 WT Ctrl 3

description: Gene expression

value: IEC4.1 WT


title: IEC4.1 WT Ctrl 1

description: Gene expression


title: AXL_het KO

description: 10X Genomics

treatment_protocol: No pharmacological treatments or chemical interventions were administered. The treatment protocol consisted solely of genetic manipulation, with two groups being analyzed: wild type (WT) mice, which possessed the intact Axl gene, and heterozygous (het) KO mice, carrying two different alleles of the Axl gene, one being wild type and the other being a knockout. All animals were housed under the same standard laboratory conditions, including controlled temperature, light cycles, and free access to food and water.

value: Kidney

value: Axl heterozygous KO

value: No


title: Hom_1

value: muscle


title: PHH rep2


title: Hom_2


title: AXL_WT

description: 10X Genomics

value: Axl WT (Wild Type)


title: Het_4

value: heterozygote


title: Sham

city: Tampa

first: Ashutosh

last: Dharap

state: FL

address: 4001 E Fletcher Ave

institute: University of South Florida

description: Library name: Sample 1

library_source: other

data_processing:
Processing of raw Hi-C data was performed using HiCPro. Hi-C sequencing reads were aligned to the reference genome using Bowtie2 in end-to-end manner or via 3’ end trimming and realignment for reads spanning ligation junctions. Aligned reads from chimeric reads were combined into single paired-end bam files. Singleton reads or those with low mapping quality were filtered out. Valid chimeric reads were detected, and duplicate reads were removed for generation of normalized Hi-C contact maps using an ICE normalization strategy.
Chromatin loops were called and annotated using the cLoops2 package.
Assembly: mm10
Supplementary files format and content: .txt files containing the output of cLoops2 looping calling for each group.

molecule: other

source_name: cerebral cortex

extract_protocol:
Three cortices representing three biological replicates from the sham and stroke groups were submerged in liquid nitrogen and pulverized into a fine powder using a cold pestle. Frozen pulverized tissue was resuspended in 1X PBS and formaldehyde-containing TC buffer and incubated at room temperature (RT) for 20 min. Following fixation, Stop Solution 1 was added and the reaction was kept at RT for 5 min. The sample was centrifuged at 2000 X G for 15 min., and the pellet was resuspended in 1X PBS and a 10% aliquot was used for the input DNA estimation workflow. Pulverized tissue comprising 3 ug of DNA was incubated in lysis buffer at 4° C for 30 min. Conditioning solution was added to the reaction and incubated at 62 °C for 10 min, followed by addition of Stop Solution 2 and incubation at 37°C for 15 min. Mastermix A (Buffer A, Enzyme A1, Enzyme A2) was added and the reaction was sequentially incubated at 37°C for 60 min., then 65°C for 20 min., then 25°C for 10 min. Mastermix B (Buffer B + Enzyme B) was added and the reaction was incubated at RT for 45 min., followed by addition of Mastermix C (Buffer C + Enzyme C) and incubation at RT for 15 min. Mastermix D (Buffer D + Enzyme D) and Buffer E were then added simultaneously, and the reaction was sequentially incubated at 55°C for 30 min., then 68°C for 90 min, and then 25°C for 10 min. 100 uL of AMPure XP DNA purification beads were resuspended in the reaction and incubated at RT for 5 min. The magnetic beads were isolated and washed twice for 1 min. with 80% ethanol and then air-dried at RT for 3-5 min, followed by resuspension in elution buffer and incubated at RT for 5 min. The elution buffer containing proximity-ligated fragments was isolated and quantified using a Qubit. 75 ng of purified DNA was used for the Arima-QC1 quality control workflow, which confirmed adequate isolation of biotin-labeled proximity-ligated DNA. The remaining isolated DNA was fragmented to an average size of 400 bp, incubated with AMPure XP DNA purification beads at RT for 5 min, after which the supernatant was isolated and re-incubated with fresh beads at RT for 5 min. Beads were washed with 80% ethanol twice and air-dried at RT for 1 min. before incubation with elution buffer for 5 min. at RT to isolate size-selected DNA. T1 beads were washed thrice with binding buffer and subsequently incubated with size-selected DNA. Beads were washed twice with wash buffer at 55°C for 2 min.
Bead-bound Hi-C libraries were processed for library preparation per the Arima protocol. Briefly, libraries were end repaired and A-tailed, followed by adaptor ligation. Adaptor-ligated Hi-C libraries were PCR-amplified, purified using AMPure XP beads and several 80% ethanol washes, and finally eluted via incubation with nuclease-free water at RT for 5 min.

treatment_protocol: For animals in the stroke group, transient focal ischemia was induced using the intraluminal filament model of middle cerebral artery occlusion (MCAO). Briefly, general anesthesia was induced under 2% isoflurane and maintained at 1% isoflurane intra-operatively with simultaneous and continuous temperature monitoring. A longitudinal midline incision was made, followed by careful separation of perivascular structures to expose the common carotid artery (CCA) and carotid artery bifurcation. An arteriotomy was performed on the CCA, and a 6-0 silicon-coated monofilament (Doccol Corporation, USA) was advanced into the internal carotid artery (ICA) until it reached the middle cerebral artery (MCA), thus occluding blood flow into the MCA. Cessation of cerebral blood flow was verified using laser speckle contrast imaging (LSCI) and the occlusion was maintained for 1 h, after which the filament was removed, and the animals were allowed to recover in pre-warmed cages with ad libitum access to food and water.  Sham animals were subjected to the full surgical procedure except advancement of the filament and occlusion of the MCA. Following 6 h of recovery/reperfusion, animals anesthetized using isoflurane and sacrificed via decapitation. Ipsilateral cortical tissue from the ischemic territory was isolated, flash-frozen in liquid-nitrogen, and stored at -80°C.

value: cerebral cortex


title: MCAO_6h

description: Library name: Sample 2


title: Het_5


title: 2DD rep1

value: hepaRG

value: liver stem cells

value: planar cell differentiation


title: 2DD rep3


title: mbdIL7-Len-3

type: RNA

city: Charlestown

first: Michael

middle: C

last: Kann

state: MA

address: 149 13th Street

department: CCR

institute: MGH

hyb_protocol: Nanostring nCounter protocol

scan_protocol: Nanostring nCounter protocol

data_processing: Nanostring nSolver

label: mCherry+ CAR

source_name: Human CAR-T, antigen exposed 4 weeks.

label_protocol: Nanostring nCounter protocol

growth_protocol: CAR19+ cells exposed and replated at 1:1 ratio to CD19+ irradiated K562 every week for 4 weeks. CAR+ cells FACs sorted and total RNA extracted and run on Nanostring nCounter

extract_protocol: QIAGEN Rneasy, all samples run with same total mass of RNA

treatment_protocol: Treated every 48-72hr with 1uM lenalidomide or eq. DMSO control

tag: car

value: CAR19 mbdIL7

tag: agent

value: 1uM Len


title: Brain_KO_NBH_2

city: Edinburgh

first: Barry

middle: W

last: McColl

address: 49 Little France Crescent

department: Centre for Discovery Brain Sciences

country: United Kingdom

institute: University of Edinburgh

description: Trem2-/- animal treated with NBH

hyb_protocol: The miRNeasy mini kit was carried out according to manufacturer’s instructions with the final RNA elution repeated twice in 50µl RNase-free water. RNA concentration was quantified using the Thermo Scientific ND 1000 Nanodrop.

scan_protocol: Scanned images (DAT files) were transformed into intensities (CEL files) using the AGCC software (Affymetrix).

data_processing: Initial quality control was performed using arrayQualityMetrics package from Bioconductor. Intensities for 45141 probes were normalized using the RMA algorithm implemented in the affy package from Bioconductor. We filtered out probes without RMA normalized intensities greater than 4 in at least 2 samples. Probe to gene annotations were retrieved from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=ht_mg-430_pm_ap). RMA normalized intensities were aggregated to gene level using the mean, obtaining relative gene expression values for 12758 genes across 14 samples.

label: biotin

source_name: brain

label_protocol: biotin

growth_protocol: Animals were maintained in standard 12-hour light- 12-hour dark cycles and given access to food and water ad libitum.

extract_protocol: RNA was extracted using the miRNeasy mini kit (Qiagen).

treatment_protocol: Animals of 7-13 weeks of age were inoculated intracerebrally with 20µl of a 1% (w/v) brain homogenate obtained from mice terminally infected with mouse-passaged ME7 scrapie prion strain.  Control mice were instead injected with normal brain homogenate (NBH). Female animals only at 90 days post-inoculation were used for microarray analysis.

tag: group

value: KO

value: NBH

tag: replicate

value: female

tag: extraction


title: Het_2


title: Brain_KO_NBH_4

description: Trem2-/- animal treated with NBH

tag: Sex


title: Brain_WT_NBH_2

description: WT animal treated with NBH

value: WT


title: Het_1

tag: tissue


title: 2DD rep2

value: liver

tag: cell type


title: Het_3

tag: genotype


title: Model B rep2

tag: treatment

value: 3D bio-printed and differentiation


title: Brain_KO_NBH_3

description: Trem2-/- animal treated with NBH


title: Model B rep3


title: Model A rep 3


title: mbdIL7-Len-1


title: mbdIL7-Len-2


title: Model B rep1


title: CAR19-Len-1


title: mbdIL7-DMSO-3

value: DMSO


title: CTL_3

city: Wuhan

first: Qiangsong

last: Tong

state: Hubei

address: 1277 Jiefang Avenue

institute: Union Hospital of Tongji Medical College

description:
Library name: Sample 3
Gene expression after complete medium treatment

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene, considering the effect of sequencing depth and gene length for the reads count at the same time (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample.

source_name: neuroblastoma

extract_protocol:
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 μg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: neuroblastoma

value: neuroblastoma cells

value: control complete medium treatment


title: X6987

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
Raw read trimming with fastp
Transcript quantification with salmon
Normalization of expression levels with Salmon
Assembly: GRCm38
Supplementary files format and content: Tab-delimited tables containing abundance estimates, summarised at the gene level. Ensembl IDs

source_name: Hippocampus

extract_protocol:
Total hippocampal RNA was extracted using TRI reagent kit (T9242, Sigma-Aldrich, MO,USA), followed by mRNA isolation
mRNA libraries were constructed with Illumina TruSeq™ RNA Sample Prep Kit v2 protocol. Standard quality checks for material degradation (Bioanalyzer, Agilent Technologies) and concentration (Qubit, Life Technologies) were done after library construction.

value: Hippocampus

value: TYR

value: NAP


title: X6765


title: Model A rep 1

value: hepaRG

value: liver stem cells


title: X6799

value: Saline


title: Brain_WT_NBH_1

description: WT animal treated with NBH


title: X6956


title: CAR19-Len-3

value: 1uM Len


title: Model A rep 2


title: CAR19-Len-2


title: Brain_WT_ME7_3

description: WT animal treated with ME7


title: mbdIL7-DMSO-2

value: CAR19 mbdIL7


title: X6719


title: Cd200 rep3

city: Nanjing

first: Ling

last: Li

address: Zhongshanmenwai, Qianhuahoucun No.1

institute: nstitute of Botany, Jiangsu Province and Chinese Academy of Sciences

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality linit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm 10 using CLC geomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost:3 length fraction: 0.8 similarity: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
the clean reads were aligned to the centipedegrass genome using HISAT2
Assembly: GCF_000003195.3
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM for each Sample

organism: Eremochloa ophiuroides

source_name: root

growth_protocol: All plants were  relocated to polyethylene plastic pots containg red soil.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 μg of total RNA wsa used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturerʼs protocols

treatment_protocol: Plants were treated with Cd at 0, 50, 100, 200 mg/kg

value: root

value: Yuxi cultivar


title: X6732

value: WT


title: Cd200 rep2


title: Brain_WT_ME7_5

description: WT animal treated with ME7

value: female