title: 1509-3_S10_L002

tag: breed


title: U87-glial cells_0.095F_rep2

status: Public on Feb 08 2022

type: RNA

city: Belém

first: Bruna

last: Puty

state: Pará

address: Travessa Honório José dos Santos, 423, Jurunas

department: ICB

country: Brazil

institute: UFPA

description: Gene expression after 10 days

hyb_protocol: Hybridization was performed with 300ng of Cy3-labelled cRNA, 5µL of 10xgene expression blocking agent and 1µl OF 25X fragmentation buffer at 65°C for 17h  and 10rpm on  a SurePrint  G3 Human  Gene Expression 8x60K microarray chip (G4851A). After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: A microarray scanner (G4900DA, Agilent) was used  with the following set-up: scan area (61 x  21.6mm); 5µm of resolution; green Chanel.

data_processing: Microarray scan images were obtained by Feature extraction v10.10 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

molecule: total RNA

organism: Homo sapiens

source_name: U87-glial cells, 0.095, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using a Low Input Quick Labelling Kit (Agilent) according to manufacturer’s instruction. cRNA purification was performed using RNAeasy mini-spin kit. cRNA was quantified and analyzed (A260/280) with the NanoDrop Spectrophotometer.

growth_protocol: U87 glial-like cells were grown in T75 flasks containing 20mL of Dulbecco’s Modified Eagle’s Medium supplemented with 10% of fetal bovine serum, penicilin, streptomycin, gentamycin, and amphoterycin B,  at 37˚C in a controlled 5% CO2 atmosphere.

extract_protocol: RNA extraction was performed using the SV total RNA isolation system from Promega, according to manufacturer’s instruction. RNA was diluted on nuclease-free water  and quantification was performed using a Qubit 2.0. RNA integrity  was assessed by a Tapestation with a high sensitivity  RNA screentape. Only samples with RIN>7 were used for downstream analysis.

treatment_protocol: Cells were exposed to F(0.095µg/mL and 0.22µg/mL) or not for 10 days. Throughout the 10-days exposure period,  medium were replaced every two days.

tag: cell type

value: U87 glial cells

tag: origin

value: Brain tumor

tag: treatment

value: 0.095ug/mL fluoride


title: U87-glial cells_0_rep1

description: Gene expression after 10 days

source_name: U87-glial cells, 0, replicate 1


title: U87-glial cells_0_rep2

description: Gene expression after 10 days

source_name: U87-glial cells, 0, replicate 2


title: H4_DSSY695_Rep1

type: SRA

city: Berkeley

first: Daniel

middle: S

last: Saxton

state: CA

address: 100 University Ave

department: MCB

country: USA

institute: University of California Berkeley

library_source: genomic

data_processing:
Reads aligned to S288C reference genome (GenBank accession number GCA_000146045.2) using bowtie2
Coverage was computed with a custom Python script (Goodnight & Rine, 2021)
Coverage was normalized to the non-heterochromatin genome-wide median using a custom Python script (Goodnight & Rine, 2021)
Coverage was smoothed with a 300bp rolling mean in R
Genome_build: S288C (GenBank accession number GCA_000146045.2)
Supplementary_files_format_and_content: bedgraph

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: haploid cells

extract_protocol:
Bead beating > Sonication > Clarification of lysate > ChIP with indicated antibody
NEB Ultra II kit

tag: strain

tag: hm locus

tag: chip antibody


title: U87-glial cells_0_rep3

description: Gene expression after 10 days

source_name: U87-glial cells, 0, replicate 3


title: U87-glial cells_0.22F_rep3

description: Gene expression after 10 days

source_name: U87-glial cells, 0.22, replicate 3

value: 0.22ug/mL fluoride


title: 1509-3_S10_L001

city: Graz

first: Leila

last: Taher

address: Stremayrgasse 16/I

country: Austria

institute: Graz University of Technology

description:
passage 85; cell line's former name: DT15/09
1509-3_S10

library_source: transcriptomic

data_processing:
Bases were called with Illumina Casava bcl2fastq (version 2.15.0.4).
Sequencing reads were trimmed and filtered using trimmomatic (v0.36) with parameters "-phred33, HEADCROP:11 LEADING:20 TRAILING:20 AVGQUAL:20 MINLEN:25". Reads were mapped to the dog reference genome (Ensembl CanFam 3.1) and corresponding gene model annotation (v94) using STAR (v2.5.3) with parameters: "--sjdbOverhang 100 --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts". RSEM (v.1.3.0) was used to quantify gene expression with parameters "--bam --no-bam-output". Finally, for each library, read counts derived from multiple lanes were added together.
Genome_build: Ensembl CanFam 3.1
Supplementary_files_format_and_content: Tab-delimited text including raw gene counts for every gene Ensembl gene identifier

organism: Canis lupus familiaris

source_name: TCC1509 rep3

growth_protocol: Culturing conditions were Medium 199 (Life Technologies GmbH, Darmstadt, Germany) containing 10% fetal calf serum (FBS Superior, Biochrom GmbH, Berlin, Germany), 200 IU/ml penicillin and 200 mg/ml streptomycin (Biochrom GmbH) at 37°C in humidified air.

extract_protocol:
RNA from cell pellets was isolated using the RNeasy Mini Kit (Qiagen GmbH, Hilden, Germany), in accordance with the manufacturer’s protocols. For tissue samples, the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen GmbH) was utilized.
Samples with RNA integrity numbers ≥ 5.2 measured with RNA 6000 Nano LabChip on an Agilent Bioanalyzer 2100 (Agilent Technologies Inc., Santa Clara, CA, USA) were further processed for library preparation using the NEBNext Ultra RNA preparation kit (New England Biolabs Inc., Ipswich, MA, USA).

treatment_protocol: Each cell line was seeded in T25 flasks in triplicate beyond passage 60. At 70-80% confluency, cells were detached with TrypLE™Express (Life Technologies GmbH, Darmstadt, Germany), pelleted, fresh frozen in liquid nitrogen and stored at ‑80°C until further use.

tag: cell line

value: Bolonka Zwetna

tag: description

value: male neutered

tag: age

value: 9 years

tag: cell line short name

tag: histopathological classification

value: transitional cell carcinoma

tag: patient id

tag: original tumor tissue, from which the cell line was established


title: blood dryness syndrome (XZ1)

city: Guangzhou

first: Yue

last: Lu

address: 232 Huandong Road, University Town, Guangzhou

country: China

institute: Guangzhou University of Chinese Medicine

hyb_protocol: According to Affymetrix’s chip hybridization procedure, the biotin-labeled cRNA was added to the cartridge gene chip, the matching reagent kit was used, and the chip was subjected to hybridization for 16 h in the shaking hybridization oven at 45 °C. After hybridization was completed, the chip was washed in the washing workstation according to the standard operating procedure.

scan_protocol: The chip results were scanned using GeneChip® Scanner 3000DX2, the raw data were read by Command Console Software 3.1, and the data that passed quality control were normalized by Command Console Software 3.1 software.

data_processing:
The Gene level_SST_RMA algorithm was used to perform quality control on the data and issue the data report, and the Transcriptome Analysis Console software was used to perform preliminary analysis on gene differential expression.   The differentially expressed genes with p< 0.05 and fold change ≥ 2 were screened out and enriched using DAVID, and the pathways with p< 0.05 were selected for analysis.
The differentially expressed genes with p< 0.05 and fold change ≥ 2 were screened out and enriched using DAVID, and the pathways with p< 0.05 were selected for analysis.

label: biotin

source_name: blood Dryness syndrome group

label_protocol: At the same time, biotin was used to label cRNA.

growth_protocol: Affymetrix gene expression profiling kit geneChip WT PLUS Reagent Kit was used to carry out in vitro reverse transcription amplification of the mRNA from the samples according to the mhnufacturer's instructions. At the same time, biotin was used to label-cRNA

extract_protocol: The total RNA was extracted from the samples using the TRI Reagent according to the manufacturer’s instructions.  Then, miRNeasy Micro kit and RNase-Free DNase Set were used to purify total RNA.  After examining the quality, the purified total RNA was evaluated for RNA integrity using the Agilent Bioanalyzer 2100 electrophoresis apparatus.

treatment_protocol: Venous blood(10 mL) was collected from the median cubital vein into an anticoagulant-tube containing heparin. Peripheral blood monocytes (PBMC) were isolated by Eicoll-density gradient centrifugation method-(Mendez-David-et al.,2013) with lymphocyte-separation solution (absin. China, item No. abs930b). First, suck the lymphocyte layer-to-aclean-centrifuge tube-and add-6ml-PBS to it, gently-blow-to fully mix-the-lymphocyte layer with PBS, then centrifuge the centrifuge tube at 60-100g at-18-20℃for-10 minutes. Remove the upper separation solution, add 6-8ml PBS to the centrifuge-tube, gently blow with a Pasteur pipete to fully mix the lymphocytes, centrifuge for10-minutes at-18--20-Cand-100-×g, and remove the upper separation solution to obtain PBMC and stored in a refrigerator at-80C.

tag: disease state

value: Patient with psoriasis

tag: tcm syndrome

value: dryness syndrome

tag: tissue

value: Venous blood (10 mL)

value: monocytes


title: H929_Meayamicin.B_rep1_8h

city: Milan

first: Antonino

last: Neri

state: Milan

address: Via Francesco Sforza, 35

country: Italy

institute: Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico

description: H929 Human Myeloma Cell Line_Meayamicin B treated_rep1

hyb_protocol: The fragmented labeled single-stranded DNA target was hybridized for 16 hours and 30 minutes at 45°C on GeneChip ClariomD array, according to the standard protocol, using the GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning of the arrays was performed using the GeneChip Scanner 7G.

data_processing: Robust Multichip Average (RMA) processing was applied on raw data, that were annotated based on Clariom_D_Human.r1.na36.hg38.a1.transcript.csv file by means of Transcriptome Analysis Console (TAC 4.0) software. Following Alternative Splicing Analysis was performed using TAC 4.0 software. Alternative Splicing events were identified in Meayamycin B-treated versus untreated MM cells after filtering for transcripts expressed in both conditions, Exon expressed in at least one condition, Exon Splicing Index of at least 2 (< -2 or > 2), Exon p-value < 0.05. Intron Retention, Cassette Exon, Alternative 3’ Acceptor Site, Alternative 5’ Donor Site, Alternative Last Exon or Complex Event were assigned on the 15798 transcripts passing filtering criteria (11.72%) out of 134748 total analyzed transcripts.

source_name: Human Myeloma Cell Line

label_protocol: RNA samples were processed using WT PLUS Reagent Kit, according to manifacturer’s protocol (Thermo Fisher Scientific, Waltham, MA, USA).

growth_protocol: HMCLs were purchased from ATCC or DSMZ. Cell lines were Mycoplasma-free and routinely tested for it. Cells were cultured in RPMI-1640 medium containing 10% fetal bovine serum (FBS; GIBCO), 4mM glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin (GIBCO).

extract_protocol: Total RNA was extracted from cells using the RNeasy mini kit (Qiagen, #74134d) according to the manufacturer’s instructions.

treatment_protocol: H929 cells were treated with 3nM Meayamicin B for 8 hours.

value: Myeloma

value: Meayamicin B


title: 1509-2_S9_L004

description:
passage 85; cell line's former name: DT15/09
1509-2_S9

source_name: TCC1509 rep2

tag: breed


title: H3K79me3_DSSY696_exp_Rep2


title: H4_DSSY303_Rep1


title: 1509-2_S9_L003


title: H929_ctr_rep2_8h

description: H929 Human Myeloma Cell Line_untreated_rep2

tag: cell type

value: untreated


title: H3K79me3_DSSY696_mix_Rep2


title: H3K79me3_DSSY301_Rep2


title: 1509-2_S9_L001


title: MDA-MB-231 treated with control shRNA (nonsense shRNA)

city: Seoul

first: Jae

last: Song

address: Yonsei-ro 50-1

country: South Korea

institute: Yonsei University

description: Filtering differentially expressed gene probes between comparison samples -Fold change

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer.

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner.

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0).

source_name: MDA-MB-231 cells, control shRNA treated, 48h

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX).

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum at 37°C under 5% CO2.

extract_protocol: Total RNA was extracted and purified using the RNeasy Plus Mini Kit (Qiagen, 74134) according to the manufacturer’s instructions.

treatment_protocol: Cells were infected with adenovirus expressing HSP27 (Ad-shHSP27), TGF-β1 (Ad-shTGF-β1) or HSP27-TGF-β1 (Ad-shHSP27-shTGF-β1) shRNA at an MOI of 100. Adenovirus expressing nonsense shRNA (Ad-control) was used as negative control.

tag: source

value: Epithelial cell line isolated from the breast tissue of an adenocarcinoma patient

value: control shRNA treated, 48h


title: 1509-2_S9_L002


title: MDA-MB-231 treated with HSP27 and TGF-β1 targeting shRNAs

source_name: MDA-MB-231 cells, HSP27 and TGF-β1 shRNAs treated, 48h

tag: treatment

value: HSP27 and TGF-β1 shRNAs treated, 48h


title: H3K79me3_DSSY696_sil_Rep2

tag: strain


title: MDA-MB-231 treated with TGF-β1 targeting shRNA

source_name: MDA-MB-231 cells, TGF-β1 shRNA treated, 48h

value: TGF-β1 shRNA treated, 48h


title: MDA-MB-231 treated with HSP27 targeting shRNA

source_name: MDA-MB-231 cells, HSP27 shRNA treated, 48h

value: HSP27 shRNA treated, 48h


title: 1509-1_S2_L004

description:
passage 77; cell line's former name: DT15/09
1509-1_S2

source_name: TCC1509 rep1


title: MIA PaCa-2 treated with HSP27 and TGF-β1 targeting shRNAs

source_name: MIA PaCa-2 cells, HSP27 and TGF-β1 shRNAs treated, 48h

value: MIA PaCa-2

value: Epithelial cell line isolated from the pancreas tissue of an carcinoma patient


title: H3K79me3_DSSY694_Rep2

tag: hm locus


title: 1509-1_S2_L003

value: Bolonka Zwetna

value: male neutered


title: H3K79me3_DSSY696_exp_Rep1

tag: chip antibody


title: H3K79me3_DSSY696_sil_Rep1


title: MIA PaCa-2 treated with control shRNA (nonsense shRNA)

source_name: MIA PaCa-2 cells, control shRNA treated, 48h

tag: cell line


title: 1509-1_S2_L001

tag: description

value: 9 years

value: transitional cell carcinoma


title: H929_ctr_rep1_8h

description: H929 Human Myeloma Cell Line_untreated_rep1


title: H3K79me3_DSSY301_Rep1


title: noTraining_noNR_noPT_8

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
FASTQ generation was perfomed on BaseSpace
The STAR aligner (Dobin et al., 2013) v2.7.3a was used to align reads to the mm10 mouse genome with the GENCODE Comprehensive gene annotations (Frankish et al., 2019) vM22 gene model.
Reads were summarised onto the same gene model using featureCounts (Liao et al., 2014) v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: csv file with raw read counts for every sample and gene

molecule: polyA RNA

organism: Mus musculus

source_name: Quadriceps

extract_protocol:
1 ml TRIzol reagent (Life Technologies, USA) was added to each tissue and each sample was homogenised through the use of steel beads and a Tissuelyzer II (Qiagen, Germany). Beads were collected, and 200 μl chloroform was added and mixed thoroughly. After a 5 min incubation, the tubes were spun at 12,000 g for 15 min in a precooled centrifuge. The aqueous supernatant was mixed in two volumes of 99% ethanol in new tubes, and stored at -20℃ overnight. These samples were then added to RNA columns from an RNeasy kit (Qiagen, Germany) and isolated according to manufacturer’s instructions. We included the optional DNase digestion steps. RNA concentration was measured by Nanodrop (Thermo Fisher Scientific, USA), and RNA integrity was tested on a Bioanalyzer instrument (Agilent Technologies, USA) according to manufacturer’s instructions. All RIN values were above our preselected minimum of 8.
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina, USA). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesised using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific, USA). cDNA was adenylated to prime for adapter ligation and after a clean-up using AMPure beads (Beckman coulter, USA), DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality controlled once more using a Bioanalyzer instrument (Agilent Technologies, USA) and subjected to 52-bp paired-end sequencing on a NovaSeq 6000 (Illumina, USA). A total of 1.6 billion reads was generated.

value: noTraining

value: noNR

value: noPT

tag: cohort

tag: rin

tag: Sex

value: Male

value: Noon


title: noTraining_noNR_PT_8

value: PT


title: Training_noNR_PT_8

value: Training

value: Morning


title: Training_noNR_PT_7


title: H4K16ac_DSSY696_mix_Rep2


title: noTraining_NR_noPT_8

value: NR


title: 1509-1_S2_L002

tag: age

tag: cell line short name

tag: histopathological classification

tag: patient id


title: H4K16ac_DSSY696_sil_Rep2


title: noTraining_noNR_noPT_7


title: total_B_cells_1

city: Udine

first: Silvia

last: Tonon

state: IT

address: Piazzale Kolbe 4

department: Dep of Medical Area

institute: University of Udine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw data were obtained from scanned images using Illumina GenomeStudio v1.9.0. Data were log2 transformed and normalized using RSN normalization implemented in the Bioconductor package lumi.

label: Biotin

source_name: spleen B cells

label_protocol: Biotinylated cRNA were prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

growth_protocol: B cells were freshly isolated from murine spleen of C57BL/6 mice

extract_protocol: murine splenic IL-10+ and IL-10- B cells were isolated using Regulatory B Cell Isolation Kit (Miltenyi Biotec) cupled to FACS-sorting to increase the purity of the subsets

treatment_protocol: B cells were stimulated for 5h with 10 µg/ml LPS, 50 ng/ml PMA and 500 ng/ml  inomycin

value: total B cells

tag: tissue

value: spleen


title: B_cells_IL10_negative_rep5

value: splenic IL10neg B cells


title: total_B_cells_2


title: B_cells_IL10_positive_rep3

value: splenic IL10pos B cells


title: B_cells_IL10_positive_rep4


title: noTraining_noNR_noPT_6


title: MIA PaCa-2 treated with HSP27 targeting shRNA

source_name: MIA PaCa-2 cells, HSP27 shRNA treated, 48h

value: MIA PaCa-2

value: Epithelial cell line isolated from the pancreas tissue of an carcinoma patient

value: HSP27 shRNA treated, 48h


title: B_cells_IL10_positive_rep5


title: B_cells_IL10_negative_rep3


title: MIA PaCa-2 treated with TGF-β1 targeting shRNA

source_name: MIA PaCa-2 cells, TGF-β1 shRNA treated, 48h

value: TGF-β1 shRNA treated, 48h


title: blood dryness syndrome (XZ4)

tag: disease state

value: Patient with psoriasis

tag: tcm syndrome

value: dryness syndrome

value: Venous blood (10 mL)

value: monocytes


title: B_cells_IL10_negative_rep2

tag: cell type


title: H4K16ac_DSSY301_Rep2

source_name: haploid cells


title: H3K79me3_DSSY694_Rep1


title: H4K16ac_DSSY696_exp_Rep2


title: H4K16ac_DSSY694_Rep2


title: noTraining_noNR_PT_7

value: noTraining

value: noNR

value: Male


title: H4K16ac_DSSY696_exp_Rep1


title: Training_noNR_noPT_6

value: Training

value: noPT

value: Morning


title: Sir4myc_DSSY697_mix_Rep2

value: anti-myc


title: Sir4myc_DSSY697_exp_Rep2


title: H4K16ac_DSSY696_sil_Rep1


title: Training_NR_noPT_7

value: NR


title: noTraining_noNR_noPT_5


title: Sir4myc_DSSY697_sil_Rep2


title: Training_NR_PT_8

value: PT

value: Noon


title: Sir4myc_DSSY281_Rep2


title: H4K16ac_DSSY301_Rep1


title: B_cells_IL10_positive_rep2

value: splenic IL10pos B cells

value: spleen


title: H4K16ac_DSSY694_Rep1


title: Training_noNR_PT_6


title: noTraining_NR_PT_8


title: H4_DSSY696_exp_Rep2


title: H4_DSSY696_mix_Rep2


title: Sir4myc_DSSY695_Rep2


title: blood dryness syndrome (XZ2)


title: Sir4myc_DSSY697_mix_Rep1


title: H4K16ac_DSSY696_mix_Rep1


title: noTraining_NR_PT_7


title: noTraining_noNR_PT_6


title: Sir4myc_DSSY697_sil_Rep1


title: noTraining_NR_noPT_7


title: H4_DSSY696_sil_Rep2


title: H4_DSSY694_Rep2


title: B_cells_IL10_positive_rep1


title: Sir4myc_DSSY695_Rep1


title: Sir3myc_DSSY693_exp_Rep2


title: noTraining_noNR_PT_5


title: Sir4myc_DSSY281_Rep1


title: H4_DSSY696_exp_Rep1


title: H4_DSSY696_mix_Rep1


title: Sir3myc_DSSY693_mix_Rep2


title: Sir4myc_DSSY697_exp_Rep1


title: Sir3myc_DSSY693_sil_Rep2


title: Training_NR_PT_7


title: H4_DSSY696_sil_Rep1


title: Training_NR_PT_6


title: H4_DSSY301_Rep1


title: H4_DSSY301_Rep2


title: Sir3myc_DSSY281_Rep2


title: H4_DSSY694_Rep1


title: Training_noNR_noPT_5


title: Sir3myc_DSSY691_Rep2


title: Sir3myc_DSSY693_exp_Rep1


title: mig1_2

city: Tianjin

first: Qinhong

last: Wang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
ScY01a (mig1∆)
Differential gene expression_mig1 vs. ScY01a.xlsx
mig1_2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to reference genome using Bowtie2 with default parametres
Abundance measurements by RSEM
Differential gene expression by R package DESeq2, a p-value cutoff of 0.05 or less and an absolute fold-change threshold of 2.0 or greater.
Genome_build: R64
Supplementary_files_format_and_content: Differential gene expression_srb2 vs. ScY01a.xlsx: Windows Excel file include different expression gene list
Supplementary_files_format_and_content: Differential gene expression_sin3 vs. ScY01a.xlsx:  Windows Excel file include different expression gene list
Supplementary_files_format_and_content: Differential gene expression_mig1 vs. ScY01a.xlsx:  Windows Excel file include different expression gene list

source_name: Early-log phase cells grown on YP medium containing 200 g/l glucose at 30ºC

extract_protocol:
Sample were grown on YP medium containing 200 g/l glucose at 30ºC at 200 rpm for 10 h to the early-log phase, and harvested in Falcon tubes precooled in liquid N2 by centrifuging for 5 minutes at 4000 rpm (3220 × g). The supernatant was discarded, and the pellet was stored at −80°C until further use. Total RNA extraction, library construction and sequencing were conducted by Novogene Bioinformatics Technology Co., Ltd (Beijing, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ScY01a (mig1delta)

tag: genotype

value: MIG1 deletion strain


title: noTraining_NR_PT_6


title: Training_NR_noPT_6


title: mig1_1

description:
ScY01a (mig1∆)
Differential gene expression_mig1 vs. ScY01a.xlsx
mig1_1

tag: strain


title: Sir3myc_DSSY693_mix_Rep1

tag: hm locus


title: sin3_2

description:
ScY01a (sin3∆)
Differential gene expression_sin3 vs. ScY01a.xlsx
sin3_2

value: ScY01a (sin3delta)

value: SIN3 deletion strain


title: Sir3myc_DSSY693_sil_Rep1

tag: chip antibody


title: sin3_1

description:
ScY01a (sin3∆)
Differential gene expression_sin3 vs. ScY01a.xlsx
sin3_1


title: Training_noNR_PT_5


title: Training_NR_noPT_5


title: srb2-3

description:
ScY01a (srb2∆)
Differential gene expression_srb2 vs. ScY01a.xlsx
srb2-3

value: ScY01a (srb2delta)

value: SRB2 deletion strain


title: Sir3myc_DSSY281_Rep1


title: Sir3myc_DSSY691_Rep1


title: Training_noNR_noPT_4

value: noNR


title: 0846-3_S10_L002

description:
passage 448; cell line's former name: DT08/46
0846-3_S10

source_name: Adcarc0846 rep2

tag: cell line

tag: breed

value: German Rough-haired Pointer

value: male

value: 6 years

value: prostate adenocarcinoma

tag: original tumor tissue, from which the cell line was established


title: 0846-3_S10_L004

tag: description


title: srb2-2

description:
ScY01a (srb2∆)
Differential gene expression_srb2 vs. ScY01a.xlsx
srb2-2


title: noTraining_NR_PT_5

value: noTraining

tag: cohort

tag: rin

tag: Sex

value: Male

value: Morning


title: Training_NR_PT_5

value: Training

value: NR

value: PT


title: 0846-3_S10_L003

tag: age

tag: cell line short name

tag: histopathological classification


title: 0846-3_S10_L001

tag: patient id


title: Sir4myc_DSSY696_mix_Rep2

value: anti-myc


title: 0846-2_S9_L004

description:
passage 447; cell line's former name: DT08/49
0846-2_S12

source_name: Adcarc0846 rep4

value: 9 years


title: Sir4myc_DSSY696_exp_Rep2


title: ScY01a-3

description:
ScY01a
ScY01a-3

value: wild type strain


title: Sir4myc_DSSY696_sil_Rep2


title: 0846-2_S9_L002

description:
passage 447; cell line's former name: DT08/47
0846-2_S10

value: 7 years


title: 0846-2_S9_L003

description:
passage 447; cell line's former name: DT08/48
0846-2_S11

source_name: Adcarc0846 rep3

value: 8 years


title: 0846-2_S9_L001

description:
passage 447; cell line's former name: DT08/46
0846-2_S9

source_name: Adcarc0846 rep1


title: Sir4myc_DSSY279_Rep2


title: noTraining_noNR_noPT_4

value: noPT

value: Noon


title: Sir4myc_DSSY694_Rep2


title: noTraining_NR_PT_3


title: noTraining_NR_noPT_6


title: 0840-3_S8_L003

description:
passage 352; cell line's former name: DT08/40
0840-3_S8

source_name: TCC0840 rep2

value: Pitbull Terrier

value: male neutered

value: 10 years

value: transitional cell carcinoma


title: PS_female_amygdala_LM30

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

data_processing:
RNA-seq reads were aligned to mouse genome, mm10, using STAR aligner. Raw reads counts aligned to each genes were measured using FeatureCounts.
Differential gene expression analysis was done using EdgeR and RUVseq.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file containing EdgeR results, CPM-normalized values, and raw read count per gene. EdgeR results include log2FC, PValue, and FDR.

source_name: amygdala

extract_protocol:
PN28 mice were sacrificed via cervical dislocations and brains were harvested, immediately frozen on dry ice, and stored at -80⁰C. Frozen brains were then submerged in RNAlater-ICE (Cat# AM7030) and allowed to thaw overnight at -20⁰C per manufacturer’s protocol. Amygdalar dissections were performed under a dissecting microscope. RNA was purified using RNeasy Micro Kit (Qiagen, Cat# 74004) following manufacturer’s instructions. PolyA RNA was isolated using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs, Cat# E7490) with a total of 1 µg of good quality total RNA as input and enriched using the SMARTer Apollo NGS library prep system (Takara Bio USA). Sequencing libraries were prepared using the NEBNext Ultr II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat# E7760).
RNA libraries were prepared for sequencing using standard Illumina protocols, using the NEBNext Ultr II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat# E7760).

treatment_protocol: PS (prenatally stressed) mice were exposed to chronic psychosocial stress paradigm in-utero. Control mice were left undisturbed.

tag: tissue

value: amygdala

tag: Stage

value: female

tag: treatment

value: prenatally stressed


title: Sir4myc_DSSY696_exp_Rep1

tag: strain


title: PS_female_amygdala_LM29


title: noTraining_NR_PT_4

value: noTraining

value: Male


title: PS_female_amygdala_LM32


title: 0840-3_S8_L002


title: noTraining_NR_noPT_5

value: NR

value: Morning


title: PS_male_amygdala_LM28

value: male


title: ScY01a-2

description:
ScY01a
ScY01a-2

tag: genotype

value: wild type strain


title: Sir4myc_DSSY696_mix_Rep1

tag: hm locus

tag: chip antibody

value: anti-myc


title: 0840-3_S8_L004

tag: cell line

tag: breed


title: Training_NR_PT_4

value: Training

value: PT


title: Training_NR_PT_2

value: Noon


title: Training_NR_PT_3


title: Sir4myc_DSSY279_Rep1


title: PS_male_amygdala_LM27


title: 0840-3_S8_L001

value: Pitbull Terrier

tag: description


title: noTraining_NR_PT_2

tag: cohort


title: PS_female_amygdala_LM31


title: Sir4myc_DSSY694_Rep1


title: PS_male_amygdala_LM26


title: 0840-2_S7_L004

description:
passage 350; cell line's former name: DT08/40
0840-2_S7

source_name: TCC0840 rep1

value: male neutered


title: 0840-2_S7_L003

value: 10 years


title: Training_NR_noPT_4

value: noPT

tag: rin


title: PS_male_amygdala_LM25

value: amygdala

tag: Sex


title: Sir3myc_DSSY692_exp_Rep2


title: Sir4myc_DSSY696_sil_Rep1


title: 0840-2_S7_L001

tag: age

value: transitional cell carcinoma


title: Sir3myc_DSSY692_mix_Rep2


title: Ctrl_female_amygdala_LM24

value: female

value: control


title: Ctrl_female_amygdala_LM23


title: Sir3myc_DSSY692_sil_Rep2


title: Ctrl_female_amygdala_LM21


title: Sir3myc_DSSY279_Rep2


title: Sir3myc_DSSY690_Rep2


title: Sir3myc_DSSY692_exp_Rep1


title: Ctrl_female_amygdala_LM22


title: Ctrl_male_amygdala_LM20


title: noTraining_noNR_PT_3

value: noTraining

value: noNR

value: Male


title: Training_noNR_PT_4


title: noTraining_noNR_noPT_3


title: noTraining_NR_noPT_4

value: NR

value: Morning


title: Ctrl_male_amygdala_LM19

value: male


title: noTraining_noNR_PT_2


title: Sir3myc_DSSY692_mix_Rep1

value: anti-myc


title: 0840-2_S7_L002

tag: cell line short name


title: H3K79me3_DSSY696_mix_Rep1


title: Training_noNR_PT_3

value: Training

value: PT


title: noTraining_noNR_PT_4


title: Ctrl_male_amygdala_LM18


title: Sir3myc_DSSY692_sil_Rep1


title: Training_NR_PT_1

value: Noon


title: Sir3myc_DSSY279_Rep1


title: Liver_infected_biological_rep2

city: Harbin

first: Su

last: Han

address: 157 Health Care Road, Nangang District

institute: Department of Parasitology, Harbin Medical University, Harbin, P. R. China

description: Gene expression in the liver tissue of mice with C. sinensis infected.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 8.1 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Liver, infected, biological, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All the animals were housed in an air-conditioned room at 24°C under a 12-h dark/light cycle with free access to standard laboratory food and water.

extract_protocol: Total RNA was extracted from 100 mg of tissue using TRIzol Reagent (Life Technologies, Carlsbad, CA, USA) following the manufacturer’s instructions. RNA quantity was measured using a SmartSpec Plus spectrophotometer (Bio-Rad, Hercules, CA, USA). RNA purity was evaluated by the A260/A280 ratio. Total RNA was quantified using a NanoDrop ND-2000 (Thermo Scientific, Waltham, MA, USA), and RNA integrity was assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA)

value: liver

tag: gender

value: orally infected with 100 metacercariae


title: Liver_infected_biological_rep3

source_name: Liver, infected, biological, replicate 3


title: Liver_control_biological_rep3

description: Gene expression in the liver tissue of mice without C. sinensis infected.

source_name: Liver, control, biological, replicate 3


title: Liver_control_biological_rep2

source_name: Liver, control, biological, replicate 2


title: Sir3myc_DSSY690_Rep1


title: Lyz2-KLF2-KO_rep1 [CWRU006087_S4]

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then Mouse samples were mapped to NCBI reference GRCm38 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v2.0.0 as part of the SubRead package using the NCBI Mus musculus Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.28.0 in R
Genome_build: GRCm38
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
Supplementary_files_format_and_content: normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+3) CPM

source_name: Lyz2-KLF2-KO mouse treated with AngII for 7 days

growth_protocol: in vivo

extract_protocol:
Mouse hearts were harvested and digested by collagenase to single cell suspension. Neutrophils were sorted by flow cytometry. Dead cells were excluded by live-dead dye staining. RNA was extratced from neutrophils by a Qiagen RNeasy micro kit and subjected to RNA-seq using paired-end sequencing.
RNA libraries were prepared for sequencing using the SMART-Seq v4 for CDNA and the Nextera XT kit for library creation

treatment_protocol: AngII infusion with subcutaneous Alzet mini-pumps. AngII Dose 1.0 ug/kg/min. Duration: 7 days.

tag: strain background

value: one week AngII infusion

tag: tissue/cell type

value: Neutrophils sorted from heart


title: Lyz2-KLF2-KO_rep2 [CWRU006088_S5]


title: Lyz2-KLF2-KO_rep3 [CWRU006089_S6]


title: Liver_control_biological_rep1

source_name: Liver, control, biological, replicate 1

tag: tissue


title: noTraining_noNR_noPT_2

source_name: Quadriceps

value: noPT


title: Lyz2-KLF2-KO_rep4 [Liao8_S8]

tag: treatment


title: Training_noNR_noPT_3


title: Training_NR_noPT_2


title: Lyz2-Cre_rep4 [Liao7_S7]

source_name: Lyz2-Cre mouse treated with AngII for 7 days

value: Cre control


title: alum-adjuvanted_S_vaccianted_inoculated_03

city: Bochum

last: Todt

address: Universitätsstr. 150

department: Molecular & Medical Virology

country: Germany

institute: Ruhr University Bochum

data_processing:
quality- and minimum length- read trimming with fastp algorithm
mapping to Mesocricetus_auratus.MesAur1.0.102 using CLC Genomics Workbench 21.0.3
Genome_build: MesAur1.0.102
Supplementary_files_format_and_content: csv files of raw and normalized read counts

organism: Mesocricetus auratus

source_name: lung tissue (right middle lobe)

extract_protocol:
The right middle lobe of the lungs of infected animals was homogenized in 1 ml TRIzol Reagent (Ambion, Thermo Fisher Scientific) in Lysing Matrix M tubes (MP Bioscience, Hilton, UK) using the Precellys24 tissue homogenizer (bertin TECHNOLOGIES) for 2x 15 sec at 6,000 rpm. Samples were kept on ice all the time.  Organ debris was removed by subsequent centrifugation (13 min, 6,800 rpm, 4°C). Clear supernatant was used for RNA purification with Direct-zol RNA MiniPrep kit (Zymo research, Freiburg (Breisgau), Germany) according to the manufactures introduction.
The isolated RNA samples were used for NNSR priming based RNA-Seq library preparation with the following modifications. Total RNA, was used for rRNA removal using the QIAseq FastSelect –rRNA HMR Kit (Qiagen) in combination with reverse transcription as follows. A 35 ul reaction mixture containing 1 ug RNA, 100 pmol NNSR_RT primer (gctcttccgatctctNNNNNN), 8 ul of 5x SuperScript IV buffer (Invitrogen) 20 pmol dNTPs and 1 ul of FastSelect-rRNA mix was subjected to the following hybridization protocol: 75°C 2 min, 70°C 2 min, 65°C 2 min, 60°C 2 min, 55°C 2 min, 37°C 5 min, 25°C 5 min, store at 4°C. For cDNA synthesis the reaction above was supplemented with dithiothreitol (10 mM), 20 units of RiboLock ribonuclease inhibitor (Thermo Fisher Scientific) and 200Us of SuperScript IV reverse transcriptase in a final reaction volume of 40 ul and incubated 45°C 5 min, 70°C 15 min.   The smears of 200-500 base pairs of the final barcoded libraries were purified from a 1.5% agarose gel and sequenced on a NextSeq 550 Illumina instrument using a single-end 86 bp setting. The RNS-Seq library preparation method used results in reads that start with the same two initial nucleotides. Hence, these were removed when performing quality- and minimum length- read trimming with the fastp algorithm with the default parameters.

tag: vaccine

value: alum-adjuvanted S protein

tag: infection

value: 4 x 10e3 TCID50 SARS-CoV-2 (isolate MUC-IMB1)

tag: volume

tag: time post vaccinatino

tag: time post infection


title: alum-adjuvanted_S_vaccianted_inoculated_04


title: alum-adjuvanted_S_vaccianted_inoculated_01


title: alum-adjuvanted_S_vaccianted_inoculated_02


title: Spleen_liposome_24h_exp2

city: Asahikawa

first: Hiroshi

last: Azuma

state: Hokkaido

address: Higashi 2-1-1-1, Midorigaoka

department: Pediatrics

country: Japan

institute: Asahikawa Medical University

description: Gene expression after 24h in splenocyte of liposome-loaded rat

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific-activity > 6.0 pmol Cy3/ug cRNA) was fragmented at 60°C. for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Rat Genome Microarray (G2519F) for 17 hours at 65°C. After hybridization, microarray was washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute at 37°C with Gene Expression Wash Buffer 2 (Agilent), then dried.

scan_protocol: Slide was scanned on the Agilent Microarray Scanner (G2505C) using one color scan setting for 4x44K array slide (Scan Area 61 x 21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%.)

data_processing: The scanned images were analyzed with Feature Extraction software (version 10.7.3.1, Agilent) as recommended in the manufacturer’s instructions. The 75th percentile shift normalization and subsequent data processing were performed using GeneSping GX software (version 11, Agilent).

organism: Rattus norvegicus

source_name: splenocytes

label_protocol: Cyaine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer’s instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop-1000 Spectrophotometer.

extract_protocol: RNA was prepared using RNeasy mini Kit (QIAGEN) following the manufactuer’s recommendations. RNA was quantified using a NanoDrop-1000 (Thermo Fisher Scientific) spectrophotometer and quality was monitored with the Bioanalyzer (Agilent).

treatment_protocol: Spleens were excised from liposome-loaded or control rats 24 hr after liposome or saline injection. Enrichment of MHC-class II-/CD11b/c+ cell was performed using magnetic beads(Miltenyi Biotech) according to the manufacturer’s protocol. Cells were applied to anti-MHC class II(OX-6) microbeads (Miltenyi Biotec) for negative selection of MHC-class II positive cells. Subsequently they were mixed with PE conjugated anti CD11b/c(OX-42), then stained with anti-PE microbeads and applied for the MACS column for positive selection of CD11b/c positive cells. Total RNA were extracted from MHC-class II negative and CD11b/c positive cell enriched fractions

tag: strain

value: WKAH

value: 8-12 weeks old

value: liposome-loaded

tag: cell type

value: splenocytes


title: Liver_infected_biological_rep1

source_name: Liver, infected, biological, replicate 1

value: Male


title: noTraining_NR_noPT_3

value: noTraining

value: NR

tag: cohort


title: Ctrl_male_amygdala_LM17

value: amygdala

tag: Stage

value: male

value: control


title: noTraining_noNR_PT_1

value: noNR

value: PT

tag: rin

tag: Sex

value: Morning


title: MeVvac2-SARS2-S_vaccinated_inoculated_04

value: MeVvac2-SARS2-S (H)


title: Lyz2-Cre_rep3 [CWRU006086_S3]

tag: genotype

value: Cre control

value: one week AngII infusion

value: Neutrophils sorted from heart


title: Training_NR_noPT_3

value: Training

value: noPT


title: Spleen_liposome_24h_exp1

value: WKAH

tag: gender

tag: age

value: 8-12 weeks old

value: liposome-loaded


title: SNU-398 treated with HSP27 and TGF-β1 targeting shRNAs

description: Data were summarized and normalized with RMA method implemented in Affymetrix® Power Tools (APT). The results were exported to gene level RMA analysis and differentially expressed gene (DEG) analysis was performed.

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16h

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin-labeled

source_name: SNU-398 cells, HSP27 and TGF-β1 shRNAs treated, 48h

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

tag: cell line

tag: source

value: Isolated from the liver tissue of a 42-year-old Mongoloid male with hepatocellular carcinoma

value: HSP27 and TGF-β1 shRNAs treated, 48h


title: Spleen_saline_24h_exp1

description: Gene expression after 24h in splenocyte of saline-loaded rat

tag: treatment

value: saline-loaded

value: splenocytes


title: Spleen_saline_24h_exp2

value: male


title: SNU-398 treated with TGF-β1 targeting shRNA

source_name: SNU-398 cells, TGF-β1 shRNA treated, 48h

value: TGF-β1 shRNA treated, 48h


title: Training_noNR_noPT_2

value: noNR

value: Male


title: Lyz2-Cre_rep1 [CWRU006084_S1]

tag: strain background

tag: tissue/cell type


title: SNU-398 treated with HSP27 targeting shRNA

source_name: SNU-398 cells, HSP27 shRNA treated, 48h

value: HSP27 shRNA treated, 48h


title: MeVvac2-SARS2-S_vaccinated_inoculated_02

tag: vaccine

value: MeVvac2-SARS2-S (H)

tag: infection

value: 4 x 10e3 TCID50 SARS-CoV-2 (isolate MUC-IMB1)

tag: volume


title: MeVvac2-SARS2-S_vaccinated_inoculated_03

tag: time post vaccinatino

tag: time post infection


title: MeVvac2-SARS2-S_vaccinated_inoculated_01


title: Training_noNR_noPT_1

tag: cohort

value: Noon


title: medium_vaccianted_inoculated_04

value: medium


title: EC_TAC_1Week_scDrop_seq_rep2

city: Mannheim

first: Joerg

last: Heineke

state: Baden Wuttemberg

address: Ludolf-Krehl-Str. 7-11

department: – Department of Cardiovascular Research (HKF)

institute: Medizinische Fakultät Mannheim

description: EC_DROP_seq_markers_per_CLUSTERS_WIllcoxin_test.xlsx

data_processing:
Analyses were performed via the snakemake pipeline dropSeqPipe version 0.4 (https://github.com/Hoohm/dropSeqPipe) and drop-seq-tools version 1.13. 800 cells per sample were defined as the number of input cells. Cell barcode was set to positions 1-12, while UMI was set to 13-20. UMI edit distance was set to 4. TruSeq adapters were trimmed using default parameters. Alignments were performed against the mouse mm10 reference genome, with quantification performed against the mm10.gtf annotation. UMAP and clusters analysis and plots were  performed by the help of Seurat (version 4.0.2)
Genome_build: mm10
Supplementary_files_format_and_content: text and excel

source_name: isolated cardiac endothelial cells

growth_protocol: Viable single cells were selected after staining with 4′,6-Diamidin-2-phenylindol (DAPI) by flow cytometry

extract_protocol:
Individual cells were then packaged in picoliter droplets together with the barcoded ‘Seq B’ microparticles (Chemgenes Corp; Wilmington, MA; referenced in the Macosko et al. (PMID 26000488)) following drop-seq laboratory protocol v. 3.1 from McCarrol Lab (http://mccarrolllab.org/dropseq/; accessed last time March 3rd, 2021). For packaging, the high-throughput single-cell RNA sequencing system from Dolomite Bio (Royston, UK) was used. In brief, the beads were resuspended in lysis buffer at a concentration of 600 beads/µl and then loaded into a sample loop. The cells were resuspended at a concentration of 300 cells/µl in PBS, including 0.01% bovine serum albumin (BSA), and then loaded into an agitated tube. Monodisperse droplets were generated in droplet generation oil (Bio-Rad) by pumping the suspensions through glass single cell RNA seq chips (Dolomite Bio) at a speed of 200 µl/min for the oil and 30 µl/min for beads and cells. The aqueous droplets containing single cells and/or beads in oil were collected in 50 ml falcon tubes. We immediately proceeded with droplet breakage and cDNA synthesis according to the drop-seq laboratory protocol v. 3.1 from McCarrol Lab. Briefly, droplet contents (mRNA bound on the beads’ oligos) were released and washed from oil using 6x SSC buffer and perfluorooctanol, and cDNA was generated by reverse transcription using Maxima H-RTase (Thermofisher Scientific). Subsequently, beads were subjected to exonuclease I treatment prior cDNA amplification by SMART PCR (4 + 14-18 cycles), purification, and tagmentation for sequencing exactly according to the drop-seq laboratory protocol v. 3.1.
BGI

treatment_protocol: TAC or sham surgery was performed by subjecting the aorta to a defined 26-gauge constriction in 8-9 week old mice as described previously (Appari M, et al and Grund A et al 2019)

tag: strain

value: mixed background

tag: tissue

value: heart

value: 8-9 week


title: EC_TAC_1Week_scDrop_seq_rep1

description: EC_DROP_seq_counts_expression_matrix.tsv


title: medium_vaccianted_inoculated_03


title: Training_NR_noPT_1

value: Training

value: NR

value: noPT

tag: rin

tag: Sex

value: Morning


title: Training_noNR_PT_2

value: PT


title: noTraining_NR_noPT_2

value: noTraining


title: noTraining_NR_PT_1


title: EC_Sham_scDrop_seq_rep1

value: ctrl


title: Lyz2-Cre_rep2 [CWRU006085_S2]

tag: genotype

value: Cre control

value: one week AngII infusion

value: Neutrophils sorted from heart


title: medium_vaccianted_inoculated_02


title: Training_noNR_noPT_7

value: noNR

value: Male


title: medium_vaccianted_inoculated_01

value: 4 x 10e3 TCID50 SARS-CoV-2 (isolate MUC-IMB1)


title: EC_Cdh5CreERT2_TAC_1Week_RiboTag_rep5

description: 01EC_RiboT_Matrix_DE_Expression_Deseq2.xlsx

data_processing:
Library strategy: RiboTag-seq
Translation prediction using Ribo-seq data was performed with Rp-Bp v2.0, based on Ensembl release 96. Adapters removal and quality filtering was done with flexbar v3.0. using standard filtering parameters implemented in Rp-Bp.
Reads aligning to a custom bowtie2 v2.3.0 ribosomal index were discarded. Remaining reads were then aligned in genomic coordinates to the mouse genome with STAR v2.5.3a.
Differential gene expression was peformed using DESeq2 based on the translation predictions. Briefly, in-frame counts from open reading frames (ORFs) were aggregated at the gene level, and the resulting matrix was used as input for differential expression. We used periodic fragment lengths that showed a distinctive triplet periodicity, as determined with the automatic Bayesian selection of read lengths and ribosome P-site offsets (BPPS) method (Maloet et al 2017). We required the ORFs to have evidence from uniquely mapping reads, at least 10 in-frame P-sites, and be detected as translated in at least 2 out of 9 biological replicates.
Genome_build: mm10
Supplementary_files_format_and_content: excel

growth_protocol: The Ribo-Taq mouse model and ribosome-protected fragments immunoprecipitation were described previously (Doroudgar S, et al 2019)

extract_protocol:
RNA extraction using TRIZOL for library construction. Ribo-Seq libraries were generated according the to the mammalian Ribo-seq kit (Illumina) after size selection using Urea gels.
Ribo-seq kit (Illumina).

treatment_protocol: The Ribo-tag mice were purchased from Jackson Laboratory (JAX ID 011029). Mice were housed in a temperature- and humidity-controlled facility with a 12-h light-dark cycle. For endothelial cell-specific tagging of ribosomes, Ribo-tag mice were crossed with Cdh5-CreERT2 mice expressing the Cre recombinase under the control of the Cadherin 5 (Cdh5) promoter (Cdh5-CreERT2:Ribo-tag). At 9 weeks of age, male mice underwent transverse aortic constriction or sham operation, as previously described. Ribosome footprints were generated after immunoprecipitation of endothelial cell-specific monosomes with anti-HA magnetic beads after treating the lysate with RNase I. Libraries were generated according to the mammalian Ribo-seq kit (Illumina). Barcodes were used to perform multiplex sequencing and create sequencing pools containing at least eight different samples. For heart homogenates, mice were sacrificed, and their hearts were quickly excised, washed in PBS containing 100 μg/ml cycloheximide (CHX), and snap frozen in liquid nitrogen. Left ventricular tissue was homogenized using a tissue homogenizer in 5 volumes of ice-cold polysome buffer (20 mM Tris pH 7.4, 10 mM MgCl, 200 mM KCl, 2 mM DTT, 1% Triton X-100, 1U DNAse/μl) containing 100 μg/ml CHX. The tissue was homogenized further by passing the lysate through a 23-gauge syringe needle ten times. For complete lysis, the samples were kept on ice for 10 min and subsequently centrifuged at 20,000×g to precipitate cell debris and the supernatant was immediately used in the further steps. From the lysate, 100 μL was used as input, from which RNA was extracted using Trizol. The remaining lysate was used for RPF generation after RNAse digestion for 45min at room temperature. RNAse digestion was stopped by adding SUPERase-In (Ambion). The lysate was used for anti-HA IP of monosomes. Anti-HA magnetic beads (Thermo Fisher, 88836; 25μl per heart) were washed with 1000 μL polysome lysis buffer three times. The lysate was then added to anti-HA magnetic beads and incubated with rotation at 4°C for 4h. Beads were then washed five times with 500 μL of high salt buffer (20 mM Tris pH 7.4, 10 mM MgCl, 300 mM KCl, 2 mM DTT, 1% Triton X-100).

tag: age

value: 9 weeks

value: TAC


title: EC_Cdh5CreERT2_TAC_1Week_RiboTag_rep4

value: mixed background

value: heart


title: SNU-398 treated with control shRNA (nonsense shRNA)

source_name: SNU-398 cells, control shRNA treated, 48h

tag: cell line

value: Isolated from the liver tissue of a 42-year-old Mongoloid male with hepatocellular carcinoma

value: control shRNA treated, 48h


title: A549 treated with HSP27 and TGF-β1 targeting shRNAs

data_processing:
The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
Data were summarized and normalized with RMA method implemented in Affymetrix® Power Tools (APT). The results were exported to gene level RMA analysis and differentially expressed gene (DEG) analysis was performed.

source_name: A549 cells, HSP27 and TGF-β1 shRNAs treated, 48h

tag: source

value: Isolated from the lung tissue of a 58-year-old Caucasian male with lung cancer

value: HSP27 and TGF-β1 shRNAs treated, 48h


title: Training_noNR_PT_1

value: Training

value: PT

value: Morning


title: A549 treated with control shRNA (nonsense shRNA)

source_name: A549 cells, control shRNA treated, 48h

tag: treatment


title: EC_Sham_scDrop_seq_rep2

value: 8-9 week

value: ctrl


title: A549 treated with TGF-β1 targeting shRNA

source_name: A549 cells, TGF-β1 shRNA treated, 48h

value: TGF-β1 shRNA treated, 48h


title: A549 treated with HSP27 targeting shRNA

source_name: A549 cells, HSP27 shRNA treated, 48h

value: HSP27 shRNA treated, 48h


title: non_vaccinated_non_inoculated_03


title: non_vaccinated_non_inoculated_04


title: non_vaccinated_non_inoculated_02


title: EC_Cdh5CreERT2_TAC_1Week_RiboTag_rep1


title: non_vaccinated_non_inoculated_01


title: EC_Cdh5CreERT2_TAC_1Week_RiboTag_rep2


title: noTraining_NR_noPT_1

value: noTraining

value: NR

value: noPT

value: Male

value: Noon


title: EC_Cdh5CreERT2_Sham_RiboTag_rep4

value: mixed background

value: heart

value: 9 weeks

value: sham


title: T_R2_P1

city: Montpellier

first: Virginie

last: Galeote

address: 2, place Pierre Viala

country: France

institute: UMR SPO, INRAE

description: Gene expression in sample from EC1118 strain, without nitrogen addition, sampling 30min after addition

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using R 4.0.2 software and the limma package. Normalization was done by the quantile method considering all arrays.

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: The cells were grown in a medium containing 180 g/l glucose, 140 mg/l of assimilable nitrogen (amino acids and ammonium) at 24°C.

extract_protocol: Total RNA extraction was perform with Trizol reagent, and purified with RNeasy kit (Qiagen).

treatment_protocol: 109 cells were harvested by filtration and frozen at -80°C.

tag: nitrogen (g/l)

tag: batch


title: A20_R3_P1

description: Gene expression in sample from EC1118 strain, after addition of nitrogen at 20g/L of CO2 released, sampling 30min after addition


title: T_R2_P4

description: Gene expression in sample from EC1118 strain, without nitrogen addition, sampling 2h after addition


title: Lung treated with IFN-lammda2 for 3 days sample.12

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description:
Lung treated with IFN-lammda2 for 3 days
RNA extracted from mouse at 3 days after IFN-lammda2 treatment

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly and SARS-CoV-2 NCBI NC_045512 Wuhan-Hu-1 genome with STAR version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: mouse Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: text file

source_name: lung

extract_protocol:
Total RNAs were extracted with the RNeasy Mini Kit (QIAGEN).
cDNA libraries were constructed from 10 ng of total RNA from lung tissues of mice. Library construction was performed using 100 ng of cDNA undergoing end repair, A tailing, ligation of universal TruSeq adapters and amplification of 8 cycles to incorporate unique dual index sequences. Libraries were sequenced on the NovaSeq 6000 (Illumina, San Diego, CA) targeting 40 million read pairs and extending 150 cycles with paired end reads.

treatment_protocol: Eight-week-old female K18-hACE2 mice were administered 2 ug of IFN-lammda2 via intranasal route for 1 (D+1) or 3 (D+3) days.

tag: days under treatment


title: A20_R2_P2

description: Gene expression in sample from EC1118 strain, after addition of nitrogen at 20g/L of CO2 released, sampling 2h after addition


title: Lung treated with IFN-lammda2 for 3 days sample.11

tag: infection


title: Lung treated with IFN-lammda2 for 3 days sample.14


title: noTraining_noNR_noPT_1

value: noNR


title: T_R1_P3


title: EC_Cdh5CreERT2_Sham_RiboTag_rep3


title: Lung treated with IFN-lammda2 for 3 days sample.13


title: Lung treated with IFN-lammda2 for 1 day sample.9

description:
Lung treated with IFN-lammda2 for 1 day
RNA extracted from mouse at 1 day after IFN-lammda2 treatment


title: EC_Cdh5CreERT2_TAC_1Week_RiboTag_rep3

value: TAC


title: EC_Cdh5CreERT2_Sham_RiboTag_rep2


title: Lung treated with IFN-lammda2 for 1 day sample.10


title: A50_R3_P2

description: Gene expression in sample from EC1118 strain, after addition of nitrogen at 50g/L of CO2 released, sampling 2h after addition


title: EC_Cdh5CreERT2_Sham_RiboTag_rep1


title: Lung treated with IFN-lammda2 for 1 day sample.6


title: Lung treated with IFN-lammda2 for 1 day sample.7


title: A50_R2_P1

description: Gene expression in sample from EC1118 strain, after addition of nitrogen at 50g/L of CO2 released, sampling 30min after addition


title: T_R3_P2


title: Lung from untreated mouse sample.5

description:
Lung from untreated mouse
RNA extracted from untreated mouse

value: CONTROL


title: A20_R2_P1


title: T_R1_P4


title: Lung from untreated mouse sample.3


title: Lung from untreated mouse sample.2


title: pulmonary recruited CD11b+Ly6g+ MDSCs - FR17

city: Hangzhou

first: Yi

last: Zhou

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling. 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 poly-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.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Prior to differential gene expression  analysis, for each sequenced library, the read counts were adjusted by edgeR program  package through one scaling normalized factor. Differential expression analysis of  two conditions was performed using the edgeR R package (3.18.1). The P values were  adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Genome_build: grcm38.p6
Supplementary_files_format_and_content: Excel files include count and FPKM values for each Sample and relevant comparison
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: pulmonary recruited CD11b+Ly6g+ MDSCs sorted from PMN mice treated with FR17

extract_protocol:
On Day 10 of PMN mice model, lung tissues were harvested from different treatment groups and digested into single cells. Briefly, lung tissues harvested from mice were mechanically minced into 1-2 mm pieces using scissors and then dissociated into single cell suspension at 37 °C on a shaker for 30 min by enzymes. The digesting solution contains 2 mg/mL collagenase I (Cat. BS163, BioSharp, Germany), 2 mg/mL collagenase II (Cat. BS164, BioSharp, Germany) and DNase I (Cat. KGF008, KeyGEN BioTech., China). Digestion was stopped by adding 2 volumes PBS and filtered through a 70 μM cell strainer (Cat. CSS013070, Jet BIOFIL®, China). The cell suspension was centrifuged at 400 g for 5 min to discard the supernatant. Cell precipitations were then resuspended in 5 mL RBC lysis buffer (Cat. R1010, Solarbio, China) and centrifuged again to discard the supernatant. The single-cell-suspensions after washing with PBS and re-suspension were incubated with APC-antimouse-CD11b (Cat. 101211, Biolegend, USA) and PE/Cy7-antimouse-Ly6g (Cat. 127617, Biolegend, USA) antibodies in 100 μL 1% BSA for 30 min at 4 °C in the dark. After centrifuged and washed with PBS, CD11b+Ly6g+ MDSCs were sorted from the PMN lungs of 10-12 individual mice from each group per sample by FACS (Beckman moflo Astrios EQ).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For mice PMN model, MCM (300 μL per mice) was intraperitoneally injected to the mice for 10 consecutive days. On Day 7, a tail vein injection of B16F10 cells (1 × 10^5 per mice) was given to the mice. Mice were randomly divided into 4 groups, namely control, TP5, sFD17 and FR17. Peptides, including TP5, sFD17 and FR17, were administrated separately to the mice subcutaneously from Day 3 at 40 μM/kg/day. On Day 10, the lung tissues were collected from the mice.

value: lung

tag: cell type

value: pulmonary recruited CD11b+Ly6g+ MDSCs

tag: disease state

value: PMN model

value: 6-8 week, post PMN inducement day 10

value: FR17 administration on PMN mice


title: Lung from untreated mouse sample.4


title: pulmonary recruited CD11b+Ly6g+ MDSCs - sFD17

source_name: pulmonary recruited CD11b+Ly6g+ MDSCs sorted from PMN mice treated with sFD17

value: sFD17 administration on PMN mice


title: pulmonary recruited CD11b+Ly6g+ MDSCs - TP5

source_name: pulmonary recruited CD11b+Ly6g+ MDSCs sorted from PMN mice treated with TP5

value: TP5 administration on PMN mice


title: pulmonary recruited CD11b+Ly6g+ MDSCs - Ctrl

source_name: pulmonary recruited CD11b+Ly6g+ MDSCs sorted from PMN model mice

value: untreated PMN model mice


title: T_R1_P2


title: T_R2_P3


title: VCD_E2_ICI

city: Duarte

first: wei

last: chen

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Raw sequencing data were processed using the 10x Genomics Cell Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using CellRanger's default settings
Gene expression level of Refseq coding genes were quantified using CellRanger (V3.1.0)'s default settings
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count

source_name: Mammary gland

extract_protocol:
dissociated mouse mammary gland sample cells were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3′ Reagent Kits v3 (1000075) according to manufacturer’s protocol (10x Genomics). The generated scRNA-seq libraries were sequenced on a HiSeq using a read structure of 28 bp for Read 1, 8 bp for Index 1, and 101 bp for Read 2.
Library was construted by using 10x Genomics Chromium Single Cell 3’ Solution v3 chemistry kit according to manufacturers protocol (10x Genomics, Chromium single-cell).

treatment_protocol: VCD (160 mg/kg/day) was administered via intraperitoneal injection for 15 days. For low-dose group, after 100 days of VCD treatment onset, special food with PBDEs mixture (PBDE-47; 0.05 mg/kg/day, PBDE-100; 0.0028 mg/kg/day and PBDE-153; 0.0063 mg/kg/day) was administered per oral for 20 weeks. For high-dose group, special food with PBDEs mixture (PBDE-47; 1 mg/kg/day, PBDE-100; 0.056 mg/kg/day, and PBDE-153; 0.126 mg/kg/day) was administered per oral for 1 week during the final week of the low-dose group treatment. Non-PBDE groups were fed with nutrient-matched special food with DMSO. E2 (1 µg/animal/day) and P4 (1 mg/animal/day) were administered via intraperitoneal injection for 1 week at the final week of PBDEs treatment. ICI (5 mg/animal) was administered once via intraperitoneal injection at the onset of E2 treatment. Sesame oil was used as vehicle for VCD and the hormonal treatments and was injected in the vehicle control groups.

value: Mammary gland

value: 43 weeks


title: VCD_High_PBDE_E2_P4


title: A20_R1_P2


title: T_R1_P1


title: VCD_High_PBDE_E2


title: Tumor infiltrating CART cells

city: Boston

first: Aedin

last: Culhane

state: MA

address: 450 Brookline Ave

institute: DANA-FARBER CANCER INST

data_processing:
10x Cell Ranger Pipeline outs/filtered_feature_bc_matrix
BRI-755 was sequenced on Novaseq S1 flowcell, which contains 2 lanes.
The single-cell RNA-seq data were processed by Cell Ranger workflow. The samples are first processed through GEM wells, and then libraries are generated and sequenced. The raw base call files (BCL) generated by Illumina sequencers are then de-multiplexed into FASTQ files using cellranger mkfastq. Running cellranger count takes FASTQ files and performs alignment,  filtering, barcode counting and UMI counting.
Data were processed by Cell Ranger version 3.1.0
Data were sequenced by the Brigham and Women’s Hospital Single Cell Genomics Core
Genome_build: GrH38
Supplementary_files_format_and_content: Cell Ranger output files 'matrix.mtx.gz', 'barcodes.tsv.gz' and 'features.tsv.gz'

source_name: Tumor infiltrating CART cells

growth_protocol: 5E4 skrc-59 CAIX+ luciferase+ cells were resuspended in 10 µL of RPMI-1640 medium and diluted 1:1 in Matrigel (Corning). This cell mixture was injected under the left kidney capsule of NSG-SGM3 mice (Jackson Laboratories). One week after, tumor engraftment was confirmed with bioluminescence (BLI) imaging and 3E6 cells of CAR-T cells or untransduced T cells (UNT) were injected through the tail vein of the mice (Day 0, N=5 mice per group). The tumor BLI was determined after 7, 14, 21, and 28 days post CAR-T cell injection. Magnetic Resonance Imaging (MRI) were performed on Day 14 and Day 28. The mice were sacrificed by CO2 inhalation, final blood was drawn and organs and tumors were harvested for downstream analysis. Renal tumor samples were dissociated into single cells by a semi-automated combined mechanical/enzymatic process. The tumor tissue was cut into pieces of (2-3mm) in size and transferred to C Tubes (Miltenyi Biotech) containing a mix of Enzymes H, R and A (Tumor Dissociation Kit, human; Miltenyi Biotech). Mechanical dissociation was accomplished by performing a program (37C_h_TDK_1) on the gentleMAC Octo Dissociator with Heaters (Miltenyi Biotech).

extract_protocol:
Single cell suspensions generated from ccRCC tumor samples were FACS sorted on a SONY MA900 sorter (SONY) for viable human CAR-T cells (Zombie- mCD45- hCD45+ CD3+, BioLegend).
7,500 cells from each condition were resuspended in 0.4% BSA in PBS at a concentration of 1,000 cells per μl, pooled together, then loaded onto a single lane (Chromium chip B, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 3′ kit V3, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol.

treatment_protocol: BBz, 28z, 28BBz, UNT CD8 and UNT CD4/8 cells were administered to RCC bearing NSG-SGM3 mice.

tag: hashtag

value: BBz (hashtag 1), 28z (hashtag 2), 28BBz (hashtag 6), UNT CD8 (hashtag 7), UNT CD4/8 (hashtag 8)

tag: host strain

value: ccRCC NSG-SGM3 mouse

value: Tumor infiltrating CART cells


title: D56_2

city: La Jolla

first: Yan

last: Liang

address: 9500 Gilman Drive, BRFII Room 1220 Bay B

institute: UC San Diego

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -10)

data_processing:
Sequenced reads were processed using CellRanger package (v3.0.2) with default parameters.
Genome_build: GRCm38
Supplementary_files_format_and_content: h5 files with raw counts for every gene and every cell

source_name: Liver

extract_protocol:
For neonatal samples (D1, D3 and D7), decapitation was used for neonates sacrifice because they were resistance to hypoxia at this age. First, fetal livers were removed from body, cut up into small pieces and rinsed using Ca2+-free HBSS buffer (gibco) in order to reduce blood. Next, liver pellets were transferred into HBSS buffer with collagenase H (Roche) and DNase I (Roche), further dissociated with gentleMACS (Miltenyi) program m_liver_03 and then incubated at 37C for 30 minutes. After incubation, the additional gentleMACS program m_liver_04 was used for better dissociation result. Liver was passed through a 100um cell strainer. Cells were then centrifuged at 50g for 3 minutes, in order to separate hepatocytes (in pellets) from non-parenchymal cells (in suspension). In non-parenchymal cell suspension, ACK buffer (gibco) was added to lyse red blood cells. Hepatocytes and non-parenchymal cells were further washed with PBS separately, resuspended in DMEM with 10% FBS, counted with hemocytometer and mixed by ratio of cell numbers.  For D21 and D56 samples, 2 male mice were included in each time point. Mice were first sacrificed using CO2. Liver was perfused using two-step method with Ca2+-free HBSS buffer and then with collagenase H in HBSS buffer containing Ca2+, gently minced and passed through a 100um cell strainer. Cells were centrifuged at 50g for 3 min, in order to separate hepatocytes (in pallets) from non-parenchymal cells (in suspension). To remove dead cells and debris, the pelleted hepatocytes were resuspended in 45% Percoll (Cytiva) and centrifuged at 50g for 10 min, without brake. Meanwhile, the ACK buffer and Dead Cell Removal Kit were used to lyse red blood cells and eliminate dead cells in non-parenchymal cells. Hepatocytes and non-parenchymal cells were further washed with PBS separately, resuspended in DMEM with 10% FBS and counted with hemocytometer.  The isolated single cells were loaded onto 10x Chromium Controller.
Chromium Single Cell 3’ Reagent Kits (V2 chemistry, 10x Genomics)

tag: strain

value: WT

value: All liver cell types


title: T_R3_P4


title: Patient3_Normal [p044n]

city: Berlin

first: Philip

last: Bischoff

address: Charitéplatz 1

department: Institute of Pathology

institute: Charité - Universitätsmedizin Berlin

description: single-cell RNA sequencing

data_processing:
raw reads were assigned and count matrices produced by cellranger, version 3.0.2, reference GRCh38
raw data was loaded, merged and filtered in R using Seurat v4
Genome_build: GRCh38
Supplementary_files_format_and_content: meta data (epithelial_metadata.tsv.gz, immune_metadata.tsv.gz, stromal_metadata.tsv.gz): Meta data of the cells, one row per cell, contains information about cell type clusters, signature scores, etc. Tab delimited files.
Supplementary_files_format_and_content: cellranger files (p0XXt/n.h5): contain filtered cellranger output files.
Supplementary_files_format_and_content: count matrices (p0XXt/n.tsv.gz): contain the raw expression counts for all cells of a sample. Each row is a gene, each column is a cell. Cell ids correspond to the cell ids in the meta data table.

source_name: C34.3 (Lung, lower lobe)

extract_protocol:
drop seq
10x genomics 3' v3

treatment_protocol: surgical resection

tag: tissue type

value: Normal Lung

tag: tnm stage

tag: histological subtype


title: Patient3_Tumor [p044t]

description: single-cell RNA sequencing

value: Lung Carcinoid Tumor

value: pT1b pN1b (5/20) G2 R0 L0 V0 Pn0 PL0

value: Atypical carcinoid


title: Pcyt2+/- Female - 8 mon, biological rep2

city: guelph

first: Chelsea

last: Furtado

state: Ontario

address: 50 stone road E

department: Human Health and Nutritional Sciences

country: Canada

institute: University of Guelph

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Gene 2.1 ST array strips, according to manufacturer's instructions. GeneChips were washed and stained on the GeneAltas platform.

scan_protocol: GeneChips were scanned on the GeneAltas platform.

data_processing: The data were analyzed with GeneSpring GX Software v. 14.8 using default Affymetrix settings.

source_name: Pcyt2+/- Female - 8 mon

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA

extract_protocol: Total RNA was extracted using the Purelink RNA extraction kit according to the manufacturer's instructions.

treatment_protocol:
The mice were collected at 8 months of age, 3-4 hours after lights on.
The hearts were collected and snap frozen in liquid nitrogen and stored at -80°C.

tag: tissue

value: myocardium


title: Pcyt2+/- Female - 8 mon, biological rep3


title: VCD_Vehicle_NormEnv

tag: age


title: VCD_High_PBDE


title: A50_R3_P1


title: Pcyt2+/- Female - 8 mon, biological rep1


title: T_R3_P1


title: A50_R1_P1


title: Pcyt2+/- Male - 8 mon, biological rep4

source_name: Pcyt2+/- Male - 8 mon


title: Pcyt2+/- Male - 8 mon, biological rep2


title: Pcyt2+/- Male - 8 mon, biological rep1


title: D21_2

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -8)

tag: genotype


title: Patient1_Tumor [p039t]

description: single-cell RNA sequencing

value: Typical carcinoid


title: A50_R1_P2


title: Pcyt2+/- Male - 8 mon, biological rep3


title: Pcyt2+/- Female - 8 mon, biological rep4


title: Patient1_Normal [p039n]

description: single-cell RNA sequencing


title: VCD_Low_E2


title: D7_2

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -6)


title: Patient10_Normal [p033n]

description: single-cell RNA sequencing


title: D21_1

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -7)


title: VCD_Low_PBDE


title: D56_1

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -9)


title: A20_R1_P1


title: D7_1

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -5)


title: T_R2_P2


title: VCD_E2_P4


title: T_R3_P3


title: D3_2

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -4)


title: Patient8_Normal [p030n]

description: single-cell RNA sequencing


title: VCD_E2


title: Patient7_Normal [p029n]

description: single-cell RNA sequencing

source_name: C34.2 (Lung, middle lobe)


title: D3_1

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -3)


title: VCD_Low_E2_P4


title: VCD_Vehicle


title: D1_2

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -2)


title: Patient2_Tumor [p028t]

description: single-cell RNA sequencing

source_name: C34.1 (Lung, upper lobe)


title: M595

first: Debbie

last: Thurmond

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

institute: City of Hope

description: RNA-Seq data, Pak1Loxp-Dox, replicate 2

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq v2.18 was used to generate FASTQ files
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search --library-type fr-firststrand
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Mmusculus.UCSC.mm10.knownGene (Bioconductor annotations, downloaded 12/22/2016).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM normalized expression (using aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

source_name: mouse skeletal muscle

growth_protocol: Inducible skeletal muscle specific PAK1 knock out and over expression mouse were driven by doxycyclin

extract_protocol:
RNAs were isolated by TRIZol method
KAPA Stranded RNA-Seq Kit
stranded polyA RNA-Seq

treatment_protocol: 2 mg/mL of doxycyclin conferring skeletal muscle specific over expression or knocking out of PAK1

tag: group

tag: dox

value: -Dox

tag: pak1 status


title: Intact

description: Intact

tag: treatment

value: Intact


title: M14

description: RNA-Seq data, dTg-Dox, replicate 3

value: dTg-Dox

value: dTg


title: Patient2_Normal [p028n]

description: single-cell RNA sequencing


title: D1_1

description: filtered_feature_bc_matrix.h5 (cell barcode ended with -1)


title: Patient6_Normal [p027n]

description: single-cell RNA sequencing


title: IP3

city: Beijing

first: Zhao-wei'

last: Sun

address: 38 Xue Yuan Road

institute: Peking University Health Science Center

data_processing:
Quality control of raw data and filitering of low-quality reads was conducted based on FastQC
Clean reads were aligned by Bowtie v2.0
Peaks were called by MACS v2.0
Peaks were annoted by KOBAS v3.0 and TopGO v2.46
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: wig files
Supplementary_files_format_and_content: peak txt files

source_name: DRG

extract_protocol:
Tissues were disaggregated into a single-cell suspension and the chromatin was fragmented by micrococcal nuclease to obtain chromatin fragments. Then the chromatin samples were incubated with ChIP-Grade Protein G magnetic beads and antibodies against CDYL.
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DRG were isolated from adult wild-type C57BL/6 male mice

value: DRG

value: wild type


title: M183

description: RNA-Seq data, dTg+Dox, replicate 3

value: +Dox


title: A20_R3_P2

tag: nitrogen (g/l)

tag: batch


title: Patient5_Normal [p019n]

description: single-cell RNA sequencing


title: IP2


title: Patient4_Normal [p018n]

description: single-cell RNA sequencing


title: Input3


title: GM12282_REF_CaptureC_rep3

city: Lausanne

first: Bart

last: Deplancke

address: EPFL SV IBI-SV UPDEPLA

country: Switzerland

institute: ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE

data_processing:
Library strategy: NGS Capture-C
Base call files were converted to fastq and adaptor sequences trimmed with bcl2fastq v2.20.0.
Fastq files were processed as follows: adapters were trimmed with Trim Galore v0.6.7 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), paired-end reads were reconstructed using FLASH v1.2.11 with the interleaved-output setting and reads were digested with a modified version of the DpnII2E.pl script to cut NlaIII sites (the genome was also digested with the NlaIII version of dpngenome3_1.pl script) (https://github.com/Hughes-Genome-Group/captureC/releases). Digested fastq files were aligned to the hg19 using BWA-MEM v.0.7.17-r1188 using one thread. Finally, SAM files were processed using the CCanalyser3.pl script (https://github.com/Hughes-Genome-Group/captureC/releases).
Genome_build: hg19
Supplementary_files_format_and_content: GFF file obtained from the CCanalyser3.pl script for each replicate.

growth_protocol: Cells were grown in RPMI 1640 GlutaMAX HEPES (Gibco) media supplemented with 15% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
20M GM12282 (homozygous REF) or GM11931 (homozygous ALT) cells were fixed with 2% PFA in PBS at RT for 10min. Fixation was stopped by adding glycine at a final concentration of 125 mM and incubated for 5 min at RT under rotation. Cells were then washed twice with ice cold PBS, resuspended in lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% NP40 and supplemented 1x cOmplete protease inhibitor (Roche)), incubated 20 min on ice and snapped frozen with the buffer. The Capture-C was performed as described in Davies J. et al., 2015 with the following modifications: NlaIII restriction enzyme (New England Biolabs) was used and incubated for 24 h. Ligation was performed for 22 h. 5 μg of DNA (3C library) in 120 μl TE were sonicated using a Covaris E220 with the following settings: 180 s, 10% duty factor, 175 W of intensity, 200 bursts/cycle with the #500141 intensifier (Covaris). 1 μg of sonicated DNA was used to prepare the library using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) as described by the manufacturer. After adapter ligation, DNA was clean-up using 1.8X AMPure X beads (Beckman) and amplified with Herculase II (Agilent) for 6 cycles. Each biological replicate (3 biological replicate per cell line) was labelled with a different barcode and all samples (a total of 6) were pooled together (2 μg of each). For the first capture, 2.9 nM of each biotinylated probes (Supplementary Table 5) was used and incubated for a total of 72 h. The pooled captured library was amplified for 14 cycles and a second capture was performed with all resulting DNA (130 ng) and 2.9 nM of each biotinylated probes for 24 h. The pooled library was further amplified for 14 additional cycles.
NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs).

tag: cell line

tag: cell type

value: Lymphoblastoid Cell Line

value: REF


title: M500

description: RNA-Seq data, Pak1Loxp+Dox, replicate 3


title: IP1


title: ZNF117

city: Newhaven

first: Jiangbing

last: zhou

address: 310 Cedar Street, Ste LH 412A

institute: Yale university

data_processing:
Sequenced reads were tested by FASTQC, then mapped to hg19 whole genome using bwa mem
Peaks were called using MACS2.2.1.0 with the following setting“-P 2.25 -m 5 50”
Genome_build: human hg19
Supplementary_files_format_and_content: reads file Fastq, aligned reads file bam, peak file text

source_name: GBM

growth_protocol: Cells  were grown in Neurobasal-A media (Invitrogen) supplemented with B27 nutritional supplement (Gibco), basic fibroblast growth factor (bFGF), and epidermal growth factor (EGF), and were maintained at 37°C and 5% CO2.

extract_protocol: Lysates were clarified from sonicated nuclei and ZNF117-DNA complexes were isolated with antibody.

treatment_protocol: One biological replicates had three technical replicates which were pooled before library preparation and sequencing.

value: GS5 (human glioblastoma stem cells)

tag: antibody


title: Input


title: M592

description: RNA-Seq data, Pak1Loxp+Dox, replicate 2


title: M604

description: RNA-Seq data, Pak1Loxp-Dox, replicate 1


title: Input2


title: Input1


title: GM12282_REF_CaptureC_rep1


title: BoM1

city: Pittsburgh

first: Kai

last: Ding

state: PA

address: 204 Craft Ave

institute: University of Pittsburgh

description: cell type was annotated in BoM_MetaData.txt file

data_processing:
CellRanger for reads mapping
Seurat for cell filteration and data normalization
Genome_build: GRCh38
Supplementary_files_format_and_content: text file of normalized counts, with row as gene colume as cell

source_name: human breast cancer bone metastases

extract_protocol:
10X genomic cell isolation protocol
10X genomic single cell RNA protocol V3 3' end
single cell RNA

value: human breast cancer bone metastases


title: M593

description: RNA-Seq data, Pak1Loxp+Dox, replicate 1


title: GM11931_ALT_CaptureC_rep3

value: ALT


title: Hi-C-Seq pre-pro-B cells KO rep

city: Shenzhen

first: Guixin

last: Ruan

state: Guangdong

address: 1088 Xueyuan Avenue

department: Biology

institute: Southern University of Science and Technology

description: Hi-C-Seq pre-pro-B cells KO

data_processing:
Hi-C-Seq: Analysis of the sequencing data was truncated, aligned and filtered using HiCUP (version 0.7.4) pipeline by applying Bowtie2 and Samtools (version 1.9). Juicer tools (version 1.22.01) were used to generate normalized contact matrices. The resolution of the Hi-C data was calculated according to reference(Rao et al., 2014) using the calculate_map_resolution script in Juicer. Chromatin interactions were called using HiCCUPS and were visualized at the resolution of 5-kb using Juicebox (version 1.11.08).
Genome_build: GRCm38

source_name: pre-pro-B

extract_protocol:
Pre-pro-B cells were sorted using flow cytometry.
Hi-C libraries were prepared from the merge of three to four biological replicates as described previously(Niu et al., 2019; Rao et al., 2014).

value: Usp39 fl/fl mb1-cre

tag: cell preparation

value: FACS sorted from bone marrow

value: pre-pro-B


title: M109

description: RNA-Seq data, dTg+Dox, replicate 2

tag: strain


title: M182

description: RNA-Seq data, dTg-Dox, replicate 2


title: scATAC-Seq StageII-0618

first: Yulin

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The single-cell ATAC-seq reads were mapped to human reference genome hg19 using Cell Ranger ATAC v1.2.0.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped .tsv files of cellrangerATAC output containing fragment data of each cell and their .tbi index file.

source_name: human somatic cells during chemical reprogramming stage II without 5azac

growth_protocol: Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃. Adult human adipose derived mesenchymal stromal cells (hADSCs) were cultured in Mesenchymal Stem Cell Growth Medium 2 under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
The nuclei were isolated and washed according to the method supplied by 10X Gemomis: Nuclei Isolation for Single Cell ATAC Sequencing (CG000169). Then the nucleus were resuspend by chilled Diluted Nuclei Buffer (10xGenomics; 2000153). The volume of Diluted Nuclei Buffer used to resuspend nuclei was based on the number of starting cells and the final target nuclei concentration. Countstar (Rigel S2) was used to count the nuclei. The nuclei were then immediately proceed to single cell ATAC-seq libraries.
Following the 10x Genomics single cell ATAC solution, by using Chromium Chip E Single Cell Kit(Product Code 1000156 ) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nucleus in bulk sample are partitioned into nanoliter-scale Gel Beads-inemulsion (GEMs), a pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus, and libraries are generated (performed by CapitalBio Technology, Beijing). The libraries was sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nucleus with pair-end 50 bp (PE50) reading strategy (performed by CapitalBio Technology, Beijing).

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.


title: GM11931_ALT_CaptureC_rep2


title: GM11931_ALT_CaptureC_rep1


title: Hi-C-Seq pre-pro-B cells WT rep

description: Hi-C-Seq pre-pro-B cells WT

value: Usp39 fl/fl


title: scATAC-Seq StageI-0618

source_name: human somatic cells during chemical reprogramming stage II


title: GM12282_REF_CaptureC_rep2


title: scATAC-Seq hADSCs-0618

source_name: adult human adipose derived mesenchymal stromal cells


title: MEC1_crispred_REF_ATACseq_rep3

data_processing:
Base call files were converted to fastq and adaptor sequences trimmed with bcl2fastq v2.20.0.
Fastq files were aligned to hg19 with BWA-MEM67 v.0.7.17-r1188.
Duplicates were removed with Picard v22.2.9 (http://broadinstitute.github.io/picard/).
BigWig files were generated with bamCoverage62 v3.5.0 (10-bp bin size and RPKM normalized).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig of merged BAM files from the three MEC1 cirspred ALT replicates
Supplementary_files_format_and_content: BigWig of merged BAM files from the three MEC1 cirspred REF replicates

growth_protocol: Cells were grown in IMDM GlutaMAX HEPES (Gibco) media supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
50,000 cells were washed with PBS, resuspended in 50 μl RSB buffer (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20) and incubated on ice for 3 min. Cells were spun down, supernatant was discarded, cells were resuspended in 1 ml RBS buffer without NP40, inverted three times and spun down. Supernatant was discarded, cells were resuspended in 25 μl 2X Tagmentation buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 0.5 μl 10% Tween20, 16.5 μl PBS, 1 μl of homemade 24.5 μM Tn5 and 7 μl H2O and incubated 30 min at 37ºC rotating at 1000 rpm. DNA was then purified with a DNA Clean & Concentrator-5 (Zymo Research).
Tagmented and amplified 11 cycles.

value: Chronic lymphocytic leukemia cell line


title: M22

description: RNA-Seq data, WT+Dox, replicate 3

value: WT+Dox

value: WT


title: BoM2


title: M13

description: RNA-Seq data, dTg+Dox, replicate 1


title: Lyz2-Cre

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

description: cells from AngII-treated hearts

data_processing:
illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.3a) used for mouse reference genome (mm10) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: mm10
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes

source_name: non-myocyte cells from mouse heart

extract_protocol:
Hearts were excised, digested into single suspension and sorted by flow cytometry to enrich CD45+ and CD31+ cells. Dead cells were excluded by live-dead dye staining. Sorted live cells (7500 CD45+ cells and 7500 CD31+ cells) were subjected to droplet-based partitioning and reverse transcription using a 10Xgenomics device
Single cells were encapsulated into emulsion droplets using Chromium controller (10X genomics). The scRNA seq libraries were prepared using the chromium single cells 3’ regent kit (V3) (10X genomics) according to the manufacturer’s protocol. scRNA-seq libraries were evaluated and quantified by Agilent Bioanalyzer using High sensitivity DNA kit and Qubit. Individual libraries were diluted and pooled for sequencing. Pooled libraries were sequenced with Illumina NovaSeq platform.
single cell RNA-seq

treatment_protocol: AngII infusion at the dose of 1.0 ug/kg/min for one week

value: heart

value: Cre control


title: M92

description: RNA-Seq data, WT+Dox, replicate 2


title: Lyz2-KLF2-KO

description: cells from AngII-treated hearts


title: MEC1_crispred_REF_ATACseq_rep1


title: MEC1_crispred_REF_ATACseq_rep2


title: nucleus pulposus cells_input

last: Huang

address: 628 Zhenyuan Road, Xinhu Street, Guangming District

department: Department of Orthopedics Surgery

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
Basecalls performed using Off-Line Basecaller software (OLB V1.8)
ChIP-seq reads were aligned to the HG19 genome assembly using BOWTIE software (V2.2.7) .
Sequence reads were generated from Illumina NovaSeq 6000, image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8.0). After passing Solexa CHASTITY quality filter, the clean reads were aligned to Human genome (UCSC HG19) using BOWTIE software (V2.1.0).
Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4.The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database.
Genome_build: HG19
Supplementary_files_format_and_content: peaks files and wig

source_name: nucleus pulposus cells

growth_protocol: The NP tissues were digested in 0.2% type II collagenase (9001-12-1, BioFroxx) for 4h at 37°C. After washing with PBS, the digested tissues were transferred to DMEM/F12 (C11330500BT, Gibco, Life technologies) containing 10% fetal bovine serum (P30-3306, PAN Biotech) and 1% penicillin / streptomycin (15140-122, Gibco, Life technologies) in the incubator at 5% CO2 and 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA.    Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended; An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments; Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments. The enriched product of ~200-1500 bp was size selected using AMPure XP beads.    Sequencing: The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using Cluster Kit. Sequencing was carried out by running 2×150 cycles on Illumina NovaSeq 6000 according to the manufacturer’s instructions.    Data Analysis: After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). Sequence quality was examined using the FastQC software. After passing Solexa CHASTITY quality filter, the clean reads were aligned to human reference genome UCSC HG19 using BOWTIE (V2.2.7). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4. Then the peaks were annotated by the nearest gene using the newest UCSC RefSeq database.

value: nucleus pulposus cells

tag: chip antibody

value: untreated


title: M82

description: RNA-Seq data, WT+Dox, replicate 1

value: +Dox


title: nucleus pulposus cells_H3K27ac

value: H3K27ac (Cell Signaling Technology, lot:8173S)


title: M107

description: RNA-Seq data, dTg-Dox, replicate 1

value: dTg-Dox

value: dTg

value: -Dox


title: MEC1_crispred_ALT_ATACseq_rep3

value: ALT


title: N82-S1

data_processing:
Illumina NovaSeq 6000 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNAs were extract with Trizol reagent,according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The transfection using riboFECT™ CP (C10502-05, Robobio) was performed as the manufacturer’s instruction. The si-02569 and si-NC was purchased from RiboBio Company. NPCs were seeded in 6-well plates and incubated in 2 mL of medium for 24 h. Subsequently, the medium was replaced by fresh medium and then the siRNA- riboFECT complexes were added in the plates. After incubation for 6 h, the cells were washed with PBS solution and further incubated in fresh medium for another 48 h.

value: nucleus pulposus


title: N82-NC

value: si-NC


title: MEC1_crispred_ALT_ATACseq_rep2