title: Control-3

city: Chongqing

first: Fanli

last: Chong

address: 183 Xinqiao Street, Shapingba District

institute: Xinqiao Hospital, Army Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Assembly: mm10
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Rattus norvegicus

source_name: Intervertebral disc

growth_protocol: Nucleus pulposus cells were cultured in a DMEM-F12 medium containing 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (Gibco) at 37°C humidified with 5% CO2NPCs were cultured in a DMEM-F12 medium containing 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from each cells sample using the Trizol method.
After incubation of RNA with a biotin-modified probe, the probe was captured by a streptavidin magnetic bead to eliminate rRNA. The obtained samples were purified by AMPure XP magnetic beads, and then buffer composed of elution, fragmented, and random primers was added and the samples were incubated at 94°C. Thermal fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit. al fracture led to fragments distributed between 100 and 300 bp. Using first-strand synthesis buffer and Invitrogen SuperScript IV reverse transcriptase, this fragmented RNA was used as a template to synthesize the first-strand cDNA. Actinomycin D was added to the first-strand synthesis buffer to prevent the reverse transcription of DNA templates and to ensure the reverse transcription specificity of RNA templates. After that, the double-stranded synthesis premix system was added to the synthesized first-strand cDNA, and the product was purified by Agencourt AMpure XP magnetic beads. From this reaction we obtained purified double-stranded cDNA and then added a 3' end plus "A" buffer reaction system to this system. Finally, ligation buffer and a double-stranded sequencing linker was added to the library; we used T4 DNA ligase to attach the Illumina sequencing linker to the DNA library. The library was purified using the Agencourt SPRI select Nucleic Acid Fragment Screening kit.

treatment_protocol: Nucleus pulposus cells were cultured in a medium without FBS (serum-starvation).

value: Intervertebral disc

value: Primary cell

tag: Sex

value: Male

value: no

tag: time

tag: passages


title: Daoy_ PELP1 shRNA_2

status: Public on May 01 2025

type: SRA

city: SAN ANTONIO

first: YI

last: ZOU

state: TX

address: 8403 Floyd Curl Drive

country: USA

institute: UTHSA-GCCRI

description: Daoy cells expressing PELP1 shRNA vector

library_source: transcriptomic

data_processing:
Illumina bcl2fastq software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: total RNA

organism: Homo sapiens

source_name: Daoy

growth_protocol: Daoy cells were cultured in DMEM media supplemented with 10% FBS

extract_protocol:
Daoy cells transduced with lentiviral particles expressing either control shRNA or PELP1 shRNA vector and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 1-2 micro grams were used for sequencing library preparation according to Illumina TruSeq Total RNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from Daoy cells stably expressing control shRNA or PELP1 shRNA and subjected to RNA-seq analysis

tag: cell type

value: Medulloblastoma cell line

tag: treatment

value: PELP1 shRNA

tag: cell line

value: Daoy


title: Gr6_5

type: RNA

city: Yangsan

first: Ju Young

last: Yoon

address: Geumo-ro 20

department: Pediatrics

country: South Korea

institute: Pusan National University Children's Hospital

description: not PWS,not obese

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human or Mouse 2.0 ST Array at 45°C for 16hour. Hybridized arrays were washed and stained on a GeneChip Fluidics Station

scan_protocol: GeneChips were scanned on a GCS3000 Scanner (Affymetrix).

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software.

label: biotin

source_name: whole blood

label_protocol: biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

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

tag: ID

tag: bmi

tag: bmi-sds


title: BT549_MS177N1_2

city: Durham

first: Joshua

last: Corbin

state: NC

address: 3 Genome Ct

institute: Duke University

description: BT549_MS177N1_vs_DMSO_normalizedExpression.txt

data_processing:
RNA-seq reads were mapped using MapSplice and quantified using RSEM. Read counts were upper-quantile normalized and log2 transformed.
Raw read counts were used for differential gene expression analysis by DESeq.
Assembly: hg38
Supplementary files format and content: matrix of RNA-seq read counts

molecule: polyA RNA

growth_protocol: T47D, T47D-TR and BT-549 breast cancer cells were grown in RPMI1640 base medium plus 10% of FBS, 1,000 U/ml penicillin and streptomycin and 8 ug/ml insulin.

extract_protocol:
RNA was extracted by using Qiagen RNeasy Mini Kit. 1 ug of total RNA for the construction of the pooled sequencing libraries.
NEBNext Ultra II RNA library Prep kit (NEB, #E7770) was used

value: Human breast cancer cell


title: HCC1937-TM bio rep 2

city: Macau

first: Dongyang

last: Tang

address: Keyan Street

country: China

institute: University of Macau

description:
Library name: HCC1937-TM-L005
NovaSeq PE150

data_processing:
A quality check was conducted via MultiQC (v1.11). The RNA reads were aligned to the human or mouse reference genome and counted via featureCounts (2.0.1).
Assembly: GRCh38 for human cell line. GRCm38 for mouse tumor.
Supplementary files format and content: tab-delimited txt file includes raw count for each sample

source_name: Breast

extract_protocol:
Cells were tissues were kept in Trizol and RNA was isolated by Novogene.
mRNA library preparation (poly A enrichment) according to the standard protocol

tag: tissue

value: Breast

value: Breast cancer cell line


title: BT549_MS177_2

description: BT549_MS177_vs_DMSO_normalizedExpression.txt


title: Control-1


title: HCC1937-vehicle bio rep 3

description:
Library name: HCC1937-vehicle-L003
NovaSeq PE150


title: Control-2


title: HCC1937-TM bio rep 1

description:
Library name: HCC1937-TM-L004
NovaSeq PE150


title: BT549_MS177N2_2

description: BT549_MS177N2_vs_DMSO_normalizedExpression.txt


title: Gr6_4

description: not PWS,not obese


title: Serum starvation-2

value: Serum starvation


title: BT549_MS177N1_1


title: HCC1937-vehicle bio rep 2

description:
Library name: HCC1937-vehicle-L002
NovaSeq PE150


title: BT549_MS177_1


title: HCC1937-vehicle bio rep 1

description:
Library name: HCC1937-vehicle-L001
NovaSeq PE150


title: Serum starvation-1


title: BT549_DMSO_1

description:
BT549_C24_vs_DMSO_normalizedExpression.txt
BT549_MS177_vs_DMSO_normalizedExpression.txt
BT549_MS177N1_vs_DMSO_normalizedExpression.txt
BT549_MS177N2_vs_DMSO_normalizedExpression.txt

value: 0.125% DMSO vehicle control


title: Serum starvation-3


title: 22719X60 19 Post Old

city: Salt Lake City

first: Joel

middle: Douglas

last: Trinity

state: Utah

address: 500 Foothill Drive

institute: University of Utah

description: Library name: 22719X60

data_processing:
The human GRCh38 genome and gene annotation files were downloaded from Ensembl release 110 and a reference database was created using STAR version 2.7.9a
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6.3
Assembly: GRCh38
Supplementary files format and content: FeatureCount ouput files combined into a single tab-delimited matrix

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA extraction for PBMC samples was achieved using RNeasy Plus Mini Kit (Cat No: 74134; Qiagen), with DNase treatment.
Total RNA samples (5-500ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples. A total amount of 200ng RNA per sample was used as input material for the RNA-seq sample preparations. Stranded RNA sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).

value: peripheral blood mononuclear cells

tag: group

value: Post exercise


title: Gr6_2

description: not PWS,not obese


title: 22719X59 19 Pre Old

description: Library name: 22719X59

value: Pre exercise


title: T47DTR_C24_2

description: T47DTR_C24_vs_DMSO_DGEcount_vsdDESeq.tsv


title: Mes_6

city: Fuzhou

first: Aling

last: Shen

state: Fujian

address: 1 Qiuyang road, Minhou Shangjie

institute: Fujian university of Traditional Chinese Medicine

description: Model + Mesalazine group with treated with Mesalazine and 2%DSS

data_processing:
Data were filtered using the following specifications fastq software. The filtering standards from raw data to clean reads are: check the sample for contamination and, if there is pollution, remove it if the reads contains a joint sequence, the joint sequence is cut off first a base having an average base mass of less than 15 on both ends of the readth window is cut with four base lengths as a sliding window, remove the number of threads with a high N content. If the N content in a read is more than 5%, the whole read is removed, and the read pair with high low-quality base content is removed. If the low-quality base in one read (the mass value is not higher than the base of 20) exceeds 30%, the whole pair of the reads is removed, if the truncated read length is less than 50 bp, the entire read is removedRemove unmatched reads  Q30，Q20 explanation：  Q30 indicates that the sequencing error rate of the base is 0.1%.  Q20 indicates that the sequencing error rate of the base is 1%.
Using String Tie for readcount and FPKM calculation.
Differential expression analyses were performed using the limma package.
Assembly: RGSC6.0/RN6 (UCSC)
Supplementary files format and content: tab_delimited text files include FPKM values for each sample

organism: Mus musculus

source_name: colon tissue

extract_protocol:
The abdominal aorta were dissected and  stored in RNA later.Total RNA was extracted with  TRIzol® Reagent (Invitrogen,Carlsbad, CA, USA). RNA integrity was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and RNA concentration was measured by Qubit RNA Assay Kit in a Qubit Fluorometer (Invitrogen, CA, USA).
A total amount of 1 μg RNA per sample was used. In brief, the NEBNext rRNA Depletion Kit was used to remove rRNA from the total RNA. The NEB Next Ultra RNA Library Prep Kit for Illumina (NEB, Beijing, China) was used to construct the libraries for sequencing following the manufacturer's instructions.

treatment_protocol: Mice in Control and Model groups were intragastrically with double distilled water, while mice in Model + QHCY group was intragastrically with 1.6 g/kg/day of QHCY and mice in Model + Mesalazine group was intragastrically with 0.2 g/kg/d of Mesalazine. Then the colon tissues were used to identify differentially expressed genes among different groups.

value: colon tissue

value: 2% DSS treatment (three cycles of 7-day), with two intervals of 14-day recovery with drinking water

value: Mesalazine

value: Model + Mesalazine


title: Gr5_5

description: not PWS,obese


title: Gr6_1

description: not PWS,not obese


title: BT549_DMSO_2


title: Gr5_4

description: not PWS,obese


title: Gr5_3

description: not PWS,obese


title: Mes_5


title: 22719X58 18 Post Young

description: Library name: 22719X58


title: Mes_4


title: T47DTR_C24_1


title: T47DTR_MS177N2_2

description: T47DTR_MS177N2_vs_DMSO_DGEcount_vsdDESeq.tsv


title: Gr6_3

description: not PWS,not obese


title: Mes_2


title: 22719X56 14 Post Old

description: Library name: 22719X56


title: T47DTR_MS177N1_2

description: T47DTR_MS177N1_vs_DMSO_DGEcount_vsdDESeq.tsv


title: 22719X57 18 Pre Young

description: Library name: 22719X57


title: Mes_3


title: 22719X55 14 Pre Old

description: Library name: 22719X55


title: Mes_1


title: 22719X54 13 Post Old

description: Library name: 22719X54


title: 22719X53 13 Pre Old

description: Library name: 22719X53


title: T47DTR_MS177_2

description: T47DTR_MS177_vs_DMSO_DGEcount_vsdDESeq.tsv


title: Qhcy_6

description: Model + QHCY group with treated with QHCY and 2%DSS

value: QHCY

value: Model + QHCY


title: T47DTR_MS177N1_1


title: Gr4_4

description: not PWS,not obese


title: T47DTR_MS177N2_1


title: 22719X52 12 Post Old

description: Library name: 22719X52


title: Gr5_1

description: not PWS,obese


title: Gr5_2

description: not PWS,obese


title: T47DTR_MS177_1


title: Gr4_3

description: not PWS,not obese


title: Qhcy_4


title: Gr4_1

description: not PWS,not obese


title: 22719X51 12 Pre Old

description: Library name: 22719X51


title: T47DTR_DMSO_2

description:
T47DTR_C24_vs_DMSO_DGEcount_vsdDESeq.tsv
T47DTR_MS177_vs_DMSO_DGEcount_vsdDESeq.tsv
T47DTR_MS177N1_vs_DMSO_DGEcount_vsdDESeq.tsv
T47DTR_MS177N2_vs_DMSO_DGEcount_vsdDESeq.tsv


title: Gr4_2

description: not PWS,not obese


title: Qhcy_5


title: 22719X50 11 Post Old

description: Library name: 22719X50


title: T47DTR_DMSO_1


title: Gr3_9

description: PWS,obese


title: 22719X49 11 Pre Old

description: Library name: 22719X49


title: T47D_C24_2

description: T47D_C24_vs_DMSO_normalizedExpression.txt


title: Qhcy_2


title: Gr3_8

description: PWS,obese


title: T47D_C24_1


title: 22719X48 10 Post Old

description: Library name: 22719X48


title: Model_6

description: Model group with treated with  2%DSS

value: double distilled water

value: Model


title: T47D_MS177N2_2

description: T47D_MS177N2_vs_DMSO_normalizedExpression.txt


title: Gr3_7

description: PWS,obese


title: Model_5

description: Model group with treated with  2%DSS


title: 22719X47 10 Pre Old

description: Library name: 22719X47


title: T47D_MS177N2_1


title: Gr3_5

description: PWS,obese


title: Gr3_6

description: PWS,obese


title: T47D_MS177N1_2

description: T47D_MS177N1_vs_DMSO_normalizedExpression.txt


title: Qhcy_3


title: 22719X45 09 Pre Old

description: Library name: 22719X45


title: 22719X44 08 Post Old

description: Library name: 22719X44


title: Gr3_4

description: PWS,obese


title: Gr3_3

description: PWS,obese


title: Qhcy_1


title: Model_2

description: Model group with treated with  2%DSS


title: Gr3_2

description: PWS,obese


title: T47D_MS177_2

description: T47D_MS177_vs_DMSO_normalizedExpression.txt


title: 22719X43 08 Pre Old

description: Library name: 22719X43


title: T47D_MS177_1


title: 22719X42 06 Post Young

description: Library name: 22719X42


title: Gr2_7

description: PWS,not obese


title: 22719X46 09 Post Old

description: Library name: 22719X46


title: Model_4

description: Model group with treated with  2%DSS


title: Ctrl_6

description: Control group  treated with double distilled water

value: Control


title: Gr3_1

description: PWS,obese


title: T47D_DMSO_2

description:
T47D_C24_vs_DMSO_normalizedExpression.txt
T47D_MS177_vs_DMSO_normalizedExpression.txt
T47D_MS177N1_vs_DMSO_normalizedExpression.txt
T47D_MS177N2_vs_DMSO_normalizedExpression.txt

value: Human breast cancer cell


title: 22719X41 06 Pre Young

description: Library name: 22719X41


title: Ctrl_5


title: 22719X40 05 Post Young

description: Library name: 22719X40


title: T47D_DMSO_1


title: Model_3

description: Model group with treated with  2%DSS


title: Ctrl_4


title: Gr2_4

description: PWS,not obese


title: 22719X39 05 Pre Young

description: Library name: 22719X39


title: T47D_MS177N1_1


title: Ctrl_3


title: BT549_H3K27ac

library_source: genomic

data_processing:
Fastq files were mapped to the reference genome (hg38) using bowtie2.3.5.
The non-primary alignment, PCR duplicates, or blacklist regions were removed from aligned data by Samtools (v1.9), Picard ‘MarkDuplicates’ function (v2.20.4), and bedtools (v2.28.0), respectively
Peak calling was performed using MACS2 (macs2 callpeak -f BAMPE -g hs/mm –keep-dup 1).
Deeptools (v3.3.0) was used to generate bigwig files, heatmaps and averaged plotting of CUT&RUN signals.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

molecule: genomic DNA

extract_protocol:
CUT&RUN: T47D and BT-549 cell lines were fixed in 0.1% formaldehyde for 1 minute. 5e5 cells were then washed and bound to activated ConA beads. The cell:bead complexes were then incubated with EZH2, H3K27me3 or H3K27ac antibodies overnight. Samples were then incubated with activated pAG-MNase and chromatin was subsequently released. 5 ng of purified DNA was used for multiplex library construction using the NEBNext Ultra II DNA Library Prep Kit. CUT&Tag: Nuclei were extracted from T47D cell line and were bound to activated ConA beads. The nuclei:bead complexes were then incubated with H3K27ac antibody overnight. Sample was then incubated with secondary antibody followed by activated pAG-Tn5. Tagmented chromatin was released and PCR amplified using barcoded Illumina primers for multiplex library creation.
DNA purification was carried out with the PCR cleanup kit (NEB, Monarch PCR & DNA Cleanup Kit, #T1030).
Libraries were prepared by NEBNext Ultra II kit (NEB, #E7645L) with 5ng CUT&RUN DNA as input.

value: breast cancer cell

tag: cut&run antibody

value: H3K27ac, Cell Signaling Technology #8173


title: BT549_H3K27me3

value: H3K27me3, Cell Signaling Technology #9733


title: Model_1

description: Model group with treated with  2%DSS


title: 22719X38 04 Post Young

description: Library name: 22719X38


title: 22719X37 04 Pre Young

description: Library name: 22719X37


title: Ctrl_2


title: BT549_EZH2

value: EZH2, Cell Signaling Technology #5246


title: Ctrl_1


title: 22719X36 03 Post Young

description: Library name: 22719X36

value: peripheral blood mononuclear cells


title: T47D_H3K27ac


title: T47D_H3K27me3


title: Gr2_5

description: PWS,not obese


title: paraquat_rep2

city: San Diego

first: Yuan

last: Yuan

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

description: Library name: Sample 16

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts are generated using featureCounts
Assembly: U00096.3
Supplementary files format and content: Comma-separated text file including raw counts for each gene and sample

organism: Escherichia coli

source_name: K-12 substr. MG1655

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with sample-specific carbon source, supplemented with trace element solution. The culture was incubated at 37C overnight with agitation, and then was used to inoculate the fresh media. The fresh culture was incubated at 37C with agitation to the mid-log phase (OD600 ≈ 0.5). For stationary phase cultures,  the fresh culture was incubated at 37C with agitation to the later-log phase (OD600 ≈ 2.0).

extract_protocol:
Total RNA was prepared using a PuroMAG™ Total RNA Purification Kit (Luna Nanotech Inc.), following the vendor's manual, including a 15 minute DNase-treatment at room temperature. RNA quality and concentration were assessed using an Agilent TapeStation and a Nanodrop, respectively.
One microgram of total RNA underwent ribosomal RNA removal using RiboRid, and the resulting rRNA-depleted RNA was used to make RNA-Seq libraries with a Kapa Biosystems (Roche) RNA HyperPrep Kit, following the manufacturer’s protocol.

treatment_protocol: For paraquat samples,when fresh culture reached the mid-log phase (OD600 ≈ 0.5),  paraquat was added and the culture was continually incubated at 37C with agitation for 30 min.

value: K-12 substr. MG1655

tag: genotype

value: WT

value: 160uM paraquat was added during mid-log phase


title: 22719X35 03 Pre Young

description: Library name: 22719X35

value: Pre exercise


title: Gr2_6

description: PWS,not obese


title: paraquat_rep1

description: Library name: Sample 15


title: 22719X34 02 Post Young

description: Library name: 22719X34

value: Post exercise


title: Gr1_5

description: PWS,obese


title: T47D_EZH2


title: LiAcet_rep2

description: Library name: Sample 14

value: Carbon source:4g/L glucose, supplemented with 10mM Lithium Acetate


title: GSC923 cells, Biological replicate 2

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases. Alignment with the reference genome (hg19) and the annotated transcripts was completed using STAR.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

extract_protocol:
RNA from cell models was extracted using PureLink RNA Mini Kit (#12183018A, Thermo Fisher Scientific) following manufacturer’s instructions, including on-column DNase treatment to remove contaminating DNA (#12185010, PureLink DNase Set, Invitrogen).
Next generation sequencing of the patient’s tumor samples was performed using commercial NGS panels TruSight Oncology 500 (TSO 500; Illumina, San Diego, USA) and TruSeq RNA Exom. Libraries were prepared according to the manufacturer’s instructions

value: IDH WT


title: 22719X33 02 Pre Young

description: Library name: 22719X33


title: 22719X32 01 Post Young

description: Library name: 22719X32


title: 22719X31 01 Pre Young

description: Library name: 22719X31


title: Gr1_4

description: PWS,obese


title: Gr1_3

description: PWS,obese


title: 403L cells, Biological replicate 2

value: Astrocytoma, WHO grade 2, patient derived cell line


title: Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp3

city: Chicago

first: Chuan

last: He

state: IL

address: 929 E 57th St

department: Chemistry Department

institute: University of Chicago

data_processing:
RNA-seq data was analyzed by following pipeline discribed: The adaptor sequences were trimmed with Cutadapt (v4.2) using the parameter "cutadapt -j 15 -m 26 --nextseq-trim=20 -O 6 -n 3 --pair-filter=any  -a AGATCGGAAGAGCACACGTCTG -A AGATCGGAAGAGCGTCGTG". The trimmed reads were deduplicated by BBMap tools. The deduplicated reads were mapped to both HIV genome (AF033819.3) and hg38 genome using STAR(v2.7.9a) with parameters "--alignEndsType Local --outFilterMatchNminOverLread 0.66 --outFilterMatchNmin 15 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.2 --outFilterMultimapNmax 10".
SAC-seq data was analyzed according to the reported protocol (Nat Protoc 18, 626–657 (2023)).
Assembly: hg38, HIV-1 (AF033819.3)
Supplementary files format and content: "Mock_vs_HIV.RNA-seq.DEresults.txt" shows the differentially expression levels of cellular genes with or without HIV-1 treatment; "SAC_seq_D28-30_Mock_vs_HIV-mRNA-sites.xlsx" shows the differential fraction of each m6A site with or without HIV-1 treatment; "SAC-seq-m6a_site-D28-D30-HIV-sites.xlsx" shows the HIV-1 m6A methylome by SAC-seq.

source_name: Peripheral blood

growth_protocol: Cell were grown in RPMI-1640, with 10% FBS and 1% penicillin-streptomycin. Cells were maintained at 37°C with 5% CO2.

extract_protocol:
RNA was isolated using Trizol method and precipitated using ethanol.
m6A SAC-seq libraries were prepared according to the reported protocol (Nat Protoc 18, 626–657 (2023)).

treatment_protocol: Primary activated CD4 T cells were infected with either Mock or HIV-1NL4-3 for 96 hours.

value: Peripheral blood

value: T-lymphoblast

value: pseudodiploid


title: 403L cells, Biological replicate 3


title: anaerobic_rep2

description: Library name: Sample 12

value: Anaerobic culture


title: GSC923 cells, Biological replicate 1


title: Gr2_2

description: PWS,not obese


title: Gr1_2

description: PWS,obese


title: nonexpanded mice at time point PI-14, repeats 1

city: Baltimore

first: Sam

last: Lee

state: MD

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Xenium in situ

scan_protocol: Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions.

data_processing: Raw sequencing data was processed using the 10X Genomics Ranger  and Vignette from Satija Lab for data analysis was followed. Cells from two repeated samples were combined.

extract_protocol: Skin tissue samples were fixed with 4% PFA and embedded in paraffin. Sectioned slides amounted to xenium slides for downstream analysis.

value: skin


title: Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp1


title: LiAcet_rep1

description: Library name: Sample 13


title: Gr0_4

description: PWS,not obese


title: Gr2_1

description: PWS,not obese


title: anaerobic_rep1

description: Library name: Sample 11


title: Gr1_1

description: PWS,obese


title: TB_rep2

description: Library name: Sample 10

value: Cultured in TB media


title: Gr0_3

description: PWS,not obese


title: Primary-activated-CD4-HIV-m6A-SAC-seq-label-rp2


title: Gr0_2

description: PWS,not obese


title: TB_rep1

description: Library name: Sample 9


title: 403L cells, Biological replicate 1


title: 403H cells, Biological replicate 3

value: Astrocytoma, WHO grade 4, patient derived cell line


title: Gr0_1

description: PWS,not obese


title: stationary_rep2

description: Library name: Sample 8

value: Cells harvested at OD600=2.0


title: bovine,ATAC-seq,Sperm,rep2

city: Yangling

first: zhang

last: yong

state: Shanxi

address: No.3 Taicheng Road

institute: Northwest A&F University

data_processing:
Initially, all reads underwent processing through TrimGalore (v.0.6.4) to eliminate reads with a minimum mapping quality of 20 and remove adapters. Subsequently, Bowtie2 (v2.3.4) (Langmead,2013)  was employed to map the filtered reads onto the genome (bovine, bosTau9). Removal of multiple mapped reads and duplicates was accomplished using MarkDuplicates.jar. The downstream calculation of Reads Per Kilobase Per Million of sequenced reads (RPKM) was performed exclusively on uniquely mapped reads. To mitigate batch and cell type variations in comparisons, RPKM values underwent further normalization via z-score transformation.
Assembly: bosTau9
Supplementary files format and content: BigWig files of each stage

organism: Bos grunniens

source_name: Sperm

extract_protocol:
Bovine ovaries, sourced from Holstein cows at a local abattoir, were preserved in pre-warmed saline solution. Cumulus oocyte complexes (COCs) were aspirated from antral follicles ranging from 2 to 10 mm, utilizing a 21-G needle connected to a vacuum pump. The COCs with uniform oocyte cytoplasm and at least three closed layers of cumulus cells were selected and washed in the collection medium: modified M199 medium (Sigma-Aldrich, M2520) supplement with 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, and 1 mg/mL PVA. Then, the washed COCs were transferred to oocyte maturation medium: modified M199 medium (Sigma-Aldrich, M2154) was supplemented with 2 mM Ala-glutamine, 0.22 mM sodium pyruvate, 10 μg/mL gentamicin, 50 ng/mL EGF, 40 ng/mL FGF, 0.01 IU/mL pFSH, 0.01 IU/mL pLH, β-estradiol 1μg/mL, 3.10 mM L-carnitine, 2.77 mM myo-inositol, 0.1 mM cysteamine, and 6 mg/mL fatty acid-free bovine serum albumin (BSA). The maturation process occurred in a humidified atmosphere containing 5% CO2 at 38.8°C.   Approximately 0.8 ×106 bovine sperm were purified employing a Puresperm 40/80 gradient18 column (Nidacon).  Bovine IVF embryos at various stages were collected at defined time points: 18-20 hpi (zygote), 30-32 hpi (2-cell), 42-44 hpi (4-cell), 72 hpi (8-cell), 132 hpi (morula). The zona pellucida of all oocytes and embryos underwent a brief incubation in 0.5% pronase (Sigma- Aldrich, P8811). Polar bodies of zygotes and early cleavage-stage embryos were eliminated by repeated pipetting using a fire-polished glass needle in DPBS supplemented with 0.01 mg/mL BSA (DPBS-0.001% BSA). The ICMs or TEs of bovine blastocysts were mechanically separated with a laser assistant.  The lysed outer cells (mostly trophectodermal cells) were manually removed using a finely pulled pipette. Isolated TEs and ICMs were washed two times with DPBS-0.001% BSA.
We prepared libraries of oocytes and early embryos utilizing the TruePrep DNA Library Prep Kit V2 from Illumina (Vazyme Biotech, TD502), with slight modifications (Wu, J. et al. ,2018). Briefly, oocytes or embryos without zona pellucida were transferred into a 0.2-mL conventional, low-binding tube (Axygen, PCR-02D-L-C) with a small volume of DPBS-0.001% BSA. After incubation with 6 μL lysis buffer (10 mM Tris-HCl pH = 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.5% IGEPAL CA-630) on ice for 10-30 min, 4 μL ddH2O, 4 μL 5 × TTBL, and 5 μL TTE mix V5 were added to the sample. The mixture was incubated at 37°C for 30 min, followed by mixing with 5 μL of 5 × TS stop buffer and further incubation at room temperature for 5 min. The sample was then mixed with 103 μL nuclease-free water and 2 μL of 20 ng/μL carrier RNA (Qiagen, 1068337) and transferred to a phase-lock tube (Qiagen,129056), containing 130 μL of phenol: chloroform: isoamyl alcohol (25:24:1). After centrifugation, the supernatant was transferred to a new low-binding 1.5-mL tube containing 1 μL glycogen, 13 μL of 3 M sodium acetate, and 130 μL isopropanol for DNA precipitation at -20°C overnight. Following centrifugation, the precipitated DNA was washed twice with 500 μL ice-cold 80% ethanol and dissolved in 20 μL of nuclease-free H2O. PCR was performed to amplify the libraries, which were then purified with 1.3 × AMPure beads (Beckman, A63882). Subsequently, all miniATAC-seq libraries were sequenced using Illumina Novaseq-6000 with paired-ended 150-bp reads.

value: Sperm


title: Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp2

value: Mock


title: acetate_rep2

description: Library name: Sample 6

value: K-12 substr. MG1655

value: WT

value: Carbon source:4g/L acetate


title: 403H cells, Biological replicate 1


title: Gr2_3

description: PWS,not obese


title: Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp3


title: tdTomato+ cDCs from naïve Il7r-cre; rosa26-lsl-tdTomato mice

city: Bunkyo-ku

first: Masashi

last: Kanayama

state: Tokyo

address: 1-5-45 Yushima

department: Department of Biodefense Research

country: Japan

institute: Medical Research Laboratory, Institute of Science Tokyo

description: MGI tech

library_source: transcriptomic single cell

data_processing:
FASTQ files containing sequence reads were processed into a Cell Ranger pipeline (10x Genomics), in which mapping, gene expression count, cell calling and clustering analyses were performed. Gene expression profiles in classified cells were analyzed by Loupe Browser (10x Genomics).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Cell Ranger Feature Barcode Matrices

source_name: Spleen

growth_protocol: SPF condition. 7-9 weeks-old mice were used for the experiments.

extract_protocol:
Spleens were harvested from naïve Il7r-cre; Rosa26-lsl-tdTomato mice and cDCs were enriched by using magnetic cell sorting with APC-labeled anti-CD11c antibody and anti-APC microbeads. Then, cells were stained and L-cDCs and M-cDCs were isolated by FACS sorting. Cells were washed and re-suspended in PBS.
Single cell gene expression analysis was conducted by GENEWIZ from Azenta Life Sciences (Tokyo, Japan). Approximately 10,000 cells with a 90% survival rate were applied to GEM (Gel Bead-in-Emulsion) generation using Chromium Controller (10x Genomics, Pleasanton, CA, USA), where individual cells were captured into single oil emulsions with reverse transcription reagent and a Gel Bead containing barcoded oligonucleotides. The reverse transcription reaction enables individual cDNAs to be labeled by unique cell barcodes with unique molecular tags in each single cell emulsion. cDNA amplification followed by library construction for single cell gene expression was performed using a Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10x Genomics). The resulting double-stranded libraries were quantified by Qubit dsDNA Assay (Thermo Fisher Scientific) and TapeStation D1000 ScreenTape (Agilent Technologies), then converted and processed into the form of single-stranded circular DNA (sscDNA) in order to be analyzed on a MGI sequencing platform.

value: Spleen

value: Conventional dendritic cell

value: Il7r-cre; Rosa26-lsl-tdTomato

value: L-cDC


title: 403H cells, Biological replicate 2


title: tdTomato- cDCs from naïve Il7r-cre; rosa26-lsl-tdTomato mice

description: MGI tech

value: M-cDC


title: Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp3

value: Peripheral blood

value: T-lymphoblast


title: CAGEseq_501mel shNIPBL_#2 6D rep2

city: New York

first: Elissa

middle: WP

last: Wong

state: NY

address: 1275 York Avenue

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

data_processing:
CAGE-seq reads were analyzed based on the Nextflow CAGE-seq analysis pipeline.
Index sequences, EcoP15I recognition site and the first G following the EcoP15I site at the 5’-end from reads were removed using Cutadapt (v2.6).
rRNA sequences were filtered out using SortMeRNA (v4.2.0) and filtered reads were aligned to the hg19 genome using STAR (v2.7.1a).
At this step, two sets of BAM files were created for each sample: one with uniquely mapped reads (adding --outFilterMultimapNmax 1 to STAR command) and one with multi-mapped reads (adding --outFilterMultimapNmax 10 to STAR command). Unmapped reads from BAM files were removed.
BAM files were converted to BED files with the summed up 1 bp unclustered CAGE tags using SAMtools (v1.9) and bamtobed (v.2.26.0). We pooled CAGE tags across samples, filtered them by TPM threshold of 0.5 and then clustered them with paraclu to generate a BED file with the clustered CAGE transcription start sites (CTSSs). CAGE tags were intersected with the clusters identified by paraclu and a raw count table with columns for each sample and rows for each tag cluster was generated. DESeq2 (v1.30.1) was used to perform differential CAGE expression using the raw count table. CTSS clusters were annotated using R/Bioconductor packages ChIPseeker (v1.26.2) and AnnotationDbi (v1.52) using GENCODE (v19) gene annotations.
Assembly: hg19
Supplementary files format and content: Differential expression analysis by DESeq2

source_name: skin

growth_protocol: All cells lines were cultured in media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin. All cells were cultured at 37 ºC in 5% CO2.

extract_protocol:
Cells were lyzed directly on culture dish with TRIzol RNA isolation reagent (Thermo fisher scientific). Total RNA was extracted by thorough mixing with chloroform and isopropanol precipitation of upper aqueous phase. 5 µg total RNA was reverse transcripted using a primer that carried a 15-nt random region and EcoP15I recognition sequence and SuperScriptIII RNase H- reverse transcriptase (Thermo fisher scientific) in the presence of trehalose/sorbitol to increase efficiency of reverse transcription. Diol groups on RNA/cDNA duplex were oxidated and labelled with biotin hydrazide (Vector laboratories). RNase I (Promega) treatment was performed to cleave single-stranded RNA regions that were not hybridized with first-strand cDNA. tRNA-coated streptavidin beads (Thermo fisher scientific) were used to capture biotinylated RNA/cDNA duplex. Sample was washed three times with wash buffer A [4.5 M NaCl, 50 mM EDTA (pH 8.0) and 0.1 % Tween20], once with wash buffer B [10 mM Tris–HCl (pH 8.5), 1 mM EDTA (pH 8.0), 0.5 M NaOAc (pH 6.1) and 0.1 % Tween20] and once with wash buffer C [0.3 M NaCl, 1 mM EDTA (pH 8.0) and 0.1 % Tween20]. Single-stranded cDNAs were released from streptavidin beads by heating at 95 °C for 5 min. Released cDNA was treated with RNase H (Thermo fisher scientific) and RNase I (Promega) at 37 °C for 45 min and proceed for library construction.
Library was constructed with modified primers for compatible sequencing on Illumina Nextseq 500 sequencer. Ligation of bar-coded 5’ linker was performed. Second-strand cDNA was synthesized using Deep Vent (exo-) DNA polymerase (NEB) and biotinylated second-strand primer. cDNA was treated with shrimp alkaline phosphatase (Thermo fisher scientific) to remove phosphate group from 5’ linker. EcoP15I (NEB) was used to cleave 27 nt downstream of the recognition site at the 5’ linker. 3’ linker was ligated to the 27-nt-long tags, purified with tRNA-coated streptavidin beads and amplified with 2x Phusion high-fidelity PCR mix (NEB). CAGE libraries were treated with Exonuclease I (NEB) to degrade any single-stranded DNA before sequencing.
Libraries were sequenced on NextSeq 500 using SR50 to obtain around 40 M reads for each library.

treatment_protocol: Cells that were transduced with lentivirus carrying puromycin-resistant shRNA plasmids were treated with 2 µg/ml puromycin.

value: melanoma


title: stationary_rep1

description: Library name: Sample 7


title: CAGEseq_501mel shNIPBL_#2 6D rep1

value: skin


title: bovine,ATAC-seq,Sperm,rep1


title: sorbital_arginine_rep1

description: Library name: Sample 3

value: Carbon source:4g/L sorbitol, supplemented with 5mM L-arginine


title: Primary-activated-CD4-Mock-m6A-SAC-seq-label-rp1

value: pseudodiploid


title: acetate_rep1

description: Library name: Sample 5


title: sorbital_arginine_rep2

description: Library name: Sample 4


title: M.cDC2_LPS.M2.3

data_processing:
Obtained raw reads were trimmed and quality-filtered using Trim Galore! (version 0.6.7), Trimmomatic (version 0.39) and cutadapt (version 3.7) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.9a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.

growth_protocol: WT C57BL/6J mice were maintained in SPF condition and used for the study at 7-8 weeks of age.

extract_protocol:
RNA was extracted using Rneasy micro kit (Qiagen)
Double-stranded cDNA libraries (RNA-seq libraries) were prepared using a SMART Seq HT Kit (Clontech, 634455) and a Nextera XT DNA Library Preparation Kit (Illumina, FC 131 1096) according to the manufacturer’s instructions.

treatment_protocol: For CLP-cDC2s and CDP-cDC2s, CLPs or CDPs were directly injected into the BM of recipient mice. LPS (5 mg/kg) was intraperitoneally administarated and cDC2s were isolated from the spleen 4 days after the LPS-treatment.

value: Conventional dendritic cells

value: LPS-administration day 4


title: CAGEseq_501mel shLuc 6D rep2

value: shLuc


title: Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp2


title: Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp2

value: Mock


title: CAGEseq_501mel shNIPBL_#1 6D rep2


title: M.cDC2_LPS.M2.2


title: Primary-activated-CD4-HIV-m6A-SAC-seq-input-rp1


title: M.cDC2_LPS.M2.1


title: M9_glucose_rep2

description: Library name: Sample 2

value: K-12 substr. MG1655

value: WT

value: Carbon source:4g/L glucose


title: L.cDC2_LPS.L2.1

value: Spleen


title: Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp3


title: Caco2 cells, 3-ABA-treated, biol rep3

city: Tokyo

first: Takahiko

last: Toyonaga

address: 3-19-18 Nishishinbashi, Minato-ku

department: Gastroenterology and Hepatology

institute: The Jikei University School of Medicine

data_processing:
RaNA-seq vesrion 1.0
Assembly: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

source_name: colon

extract_protocol:
RNA was harvested using Total RNA Purification Kit.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA library prep kit following  manufacturer's protocol.

value: colon

value: epithelial cells


title: ɑBAX1, sort 1 specificity

city: Seattle

first: David

last: Baker

state: WA

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

data_processing:
Reads aligned (software developed in-house)
Counts determined for unmutated sequence and all single-position mutants (scripts developed in-house)
Enrichment ratios calculated based on counts in naïve library and sorted population
Assembly: BAK-CDP02 (BB02):  GADPKKVLDKAKDQAENVVRKLKQILEELYKEARKLDLTQDEKIELILRYIAAMLAAIGDILEAIRQAKEEADKLKKAGLVNSQQLDELKRRLEELRKEAARKARDYAEEFRNKLEYG
Assembly: aBAK1 (BB02G): GADPKKVLDKAKDQMENVVRKLKQILEELAKEARKLDLTQDEKIELILRYIVAHLAAIGDIEEAIREAKEEADKLKKAGLVNSQQLDEFKRRLEELHKEADRKRRDYAEEFRNKLEYG
Assembly: BAX-CDP01 (BB13): GADPKKVLDKARDQAENRVRELAQKLEELYKEARKLDLTQEERRKLEKRYKAAMEEAIKDIREAIRQAKQEADKLKKAGLVNSQQLKELKQRLNELAIAAALRAIGDAIEFRRKLQYG
Assembly: aBAX1 (BB13B): GADPKKVLDKARDQAENRVRELAQKLEELYKEARKLDLTQEERRKLEKRYKAAMEEAIKDIHEAIEQAKEEADKLKDAGLVNEQQLKELKQRLNELAIAAAFRASGDTIEFRRKLQYG
Supplementary files format and content: The processed data file in Excel format (.xlsx) contains enrichment ratios per variant per selection pool normalized to the enrichment ratio of the unmutated sequence.

organism: Saccharomyces cerevisiae

growth_protocol: Please see our corresponding publication for the yeast protocols for growth and induction of protein expression.

extract_protocol:
Yeast were lysed with 125 U/ml Zymolase at 37 ºC for 5 h, and DNA was harvested (Zymoprep kit from Zymo Research). Genomic DNA was digested with 2 U/µl Exonuclease I and 0.25 U/µl Lambda exonuclease (New England Biolabs) for 90 min at 30 ºC, and plasmid DNA purified with a QIAquick kit (Qiagen).
In some instances, gene sequences were diversified by overlapping PCR for site-directed mutagenesis libaries as described in Procko et al. J Mol Bio 2013. In other instances, gene sequences were commercially synthesized. Genes were prepared with 5’ and 3’ overhangs >20 bp to enable homologous recombination with the plasmid backbone (pETCON) for yeast expression and surface display via fusion to Aga2p.
DNA amplicon sequencing

treatment_protocol: Please see our corresponding publication for library treatments prior to FACS selection


title: ɑBAX1, sort 2 specificity


title: Primary-activated-CD4-Mock-m6A-SAC-seq-input-rp1


title: L.cDC2_LPS.L2.2

value: Il7r-cre; Rosa26-lsl-tdTomato


title: np10

city: Leicester

first: Izabella

middle: Zofia Anna

last: Pawluczyk

address: University Road

department: Cardiovascular Sciences

country: United Kingdom

institute: University of Leicester

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using bcl2fastq software (Illumina inc). FASTQ data were checked using FastQC tool.
The data were filtered, mapped, normalised and underwent unsupervised analysis.
data were analysed for differential expression including statistics.
Data were also analysed for novel microRNA and isomiRs
Assembly: not provided
Supplementary files format and content: Excel: raw data, tpm, comparisons: M v H, M v NP, NP v H, NP v P, P v H, P v M

source_name: serum

extract_protocol:
RNA was isolated from 500μl serum using proprietory protocol optimised for serum/plasma. RNA was eluted in ultra-low volume followed by QC analysis of RNA
Library preparation done using QIAseq miRNA library Kit. 5μl total RNA was converted into microRNA NGS libraries. Adapters containing UMI were ligated to RNA, then RNA converted to cDNA. cDNA was amplified using PCR an indices were added. After PCR samples were purified
Library preparation QC performed using Bioanalyser 2100(Agilent) or TapeStation 4200 (Agilent). Library pools were quantified using PCR.
microRNA library pools were then sequenced using NextSeq500 sequencing instrument acording to manufacturer's instructions.

value: serum

value: IgAN non prog


title: ɑBAX1, sort 2 affinity


title: m1

value: membranous nephropathy


title: m4


title: CAGEseq_501mel shNIPBL_#1 6D rep1

value: skin

value: melanoma


title: ɑBAX1, naïve


title: CLP.cDC2_CLP.3


title: p4

value: IgAN prog


title: Caco2 cells, 3-ABA-treated, biol rep2


title: ɑBAX1, sort 1 affinity


title: CAGEseq_501mel shLuc 6D rep1


title: CLP.cDC2_CLP.1

value: Conventional dendritic cells


title: CLP.cDC2_CLP.2

value: LPS-administration day 4


title: Caco2 cells, non-treated control, biol rep2


title: p10


title: BAX-CDP01, sort 2 affinity


title: CDP.cDC2_CDP.2


title: L.cDC2_LPS.L2.3


title: Caco2 cells, 3-ABA-treated, biol rep1


title: Caco2 cells, non-treated control, biol rep3


title: h10

value: healthy subject


title: M9_glucose_rep1

description: Library name: Sample 1


title: Caco2 cells, non-treated control, biol rep1


title: CDP.cDC2_CDP.3


title: CDP.cDC2_CDP.1


title: BAX-CDP01, sort 1 specificity


title: BAX-CDP01, sort 2 specificity


title: WT8

city: Charlestown

first: Erik

last: Abels

state: Massachusetts

address: 149 13th Street

department: Neurology

institute: Massachusetts General Hospital

data_processing:
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Sequencing was done using an Illumina MiniSeq and bioinformatic analysis was performed using DESeq2 in R
Duplicate reads were marked using the MarkDuplicates tool in picard-tools-1.8.4 and removed.
The uniquely aligned reads were then counted against Gencode’s GRCm38.p3 GTF annotations using htseq-count in the intersection-strict mode
Data analysis of mapped counts was performed in R 3.2.3 using the DESeq2 package
Samples with less than 6000 genes with at least 5 mapped reads were excluded from analysis; no samples were excluded from this analysis
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: tab-delimited text file with read counts per sample

source_name: Female WT microglia

extract_protocol:
Microglia are isolated from mouse brain following protocol described in Hickman et al. 2013. Total RNA was isolated using RNeasy Plus Micro kit (Qiagen) using the total RNA isolation protocol.
Total RNA was isolated and sequencing libraries were made using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) . Sequencing was done using an Illumina MiniSeq

treatment_protocol: Injection protocol: rAPOE (reconstituted in PBS) is injected in the left hemisphere. Sixteen hours post injection, mice are euthanized and injected and contralateral hemispheres collected. Hemispheres are dissociated and microglia isolated and processed as described.

value: brain

tag: strain

value: female

tag: injected with

value: not injected

tag: age

value: 12 -18 weeks

value: microglia


title: BAX-CDP01, sort 1 affinity


title: BAX-CDP01, naïve


title: m2


title: h8


title: WT7

value: WT


title: Kidney PH70% 7d - 2

city: Moscow

first: Evgeny

last: Karpulevich

address: Alexandra Solzhenitsina

department: Information Systems

country: Russia

institute: ISP RAS

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads
STAR+salmon+DE+Hobotnica
Assembly: GRCm39
Supplementary files format and content: comma delimeted text files for each Sample

source_name: Kidney

extract_protocol:
Processing of the biomaterial was carried out under aseptic conditions using sterile tools. Total RNA was isolated from snap-frozen tissue after removal after homogenization with Teflon beads in QIAZOL (Qiagen), followed by purification and concentration with RNA Clean & Concentrator kit (Zymo Research), quantity was estimated using Qubit 2.0 device (Invitrogen, Life Technologies).
After isolating total RNA from 1 μg, samples were prepared for sequencing on the Illumina platform. libraries using the TruSeq RNA kit Sample Prep Kit v2 with 10 cycle enrichment step in accordance with the manufacturer's recommendations. The quality of RNA and resulting libraries was checked using an Agilent 2100 Bioanalyzer capillary electrophoresis system (Agilent Tec. Inc., USA). The RIN parameter for RNA was at least 7. The concentration of the libraries was assessed using real-time polymerase chain reaction on the CFX96 Touch Real-Time PCR Detection System device (Bio-Rad, USA). The final libraries were pooled in equimolar proportions before sequencing on the Illumina HiSeq 2500 platform using 50-base paired-end reads.

value: Kidney


title: ɑBAK1, sort 2 specificity


title: WT4


title: ɑBAK1, sort 2 affinity


title: p1


title: Kidney PH70% 7d - 1


title: WT3


title: Kidney intact 3

value: intact


title: Kidney PH70% 7d - 3


title: h5

value: serum


title: WT2


title: h2


title: ɑBAK1, sort 1 specificity


title: Kidney intact 2


title: p6


title: ɑBAK1, sort 1 affinity


title: Kidney intact 1


title: WT1


title: np9

value: IgAN non prog


title: ɑBAK1, naïve


title: PBS5

source_name: Male ApoE KO injected with PBS microglia

value: ApoE KO

value: male

value: PBS microglia


title: m3

value: membranous nephropathy


title: Kidney PH70% 3d - 3


title: BAK-CDP02, sort 2 specificity


title: PBS4


title: h9


title: WT6


title: Kidney PH70% 3d - 2


title: h6


title: BAK-CDP02, sort 2 affinity


title: Kidney PH70% 3d - 1


title: h3


title: PBS2


title: Kidney PH70% 1d - 3


title: BAK-CDP02, sort 1 specificity


title: BAK-CDP02, naïve


title: PBS1


title: np7


title: F4

source_name: Female ApoE KO microglia


title: M-cDC2_sample3

data_processing:
Obtained raw reads were trimmed and quality-filtered using Trim Galore! (version 0.6.7), Trimmomatic (version 0.39) and cutadapt (version 3.7) software.
Trimmed reads were then mapped to the human GRCh38 genome using STAR (version 2.7.9a).
Reads on annotated genes were counted using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript. Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

value: Spleen

value: Conventional dendritic cells

value: Il7r-cre; Rosa26-lsl-tdTomato


title: np1


title: h1

value: healthy subject


title: F3

value: brain

value: female


title: M-cDC2_sample2


title: F2

value: not injected

value: 12 -18 weeks


title: m9


title: M-cDC2_sample1


title: m7


title: F1

value: microglia


title: Apoe5

source_name: Male ApoE KO injected with rAPOE microglia

value: rAPOE microglia


title: PBS3


title: m6


title: M-cDC1_sample3


title: Kidney PH70% 1d - 2

value: Kidney


title: np6

value: serum


title: Apoe4


title: np5

value: IgAN non prog


title: M-cDC1_sample2


title: M-cDC1_sample1


title: Kidney PH70% 1d - 1


title: Apoe3

value: ApoE KO


title: p3

value: IgAN prog


title: L-cDC2_sample3


title: Apoe2

value: male


title: m8

value: membranous nephropathy


title: L-cDC2_sample2

value: Spleen


title: Apoe1


title: L-cDC2_sample1

value: Conventional dendritic cells


title: p9


title: p2


title: L-cDC1_sample3

value: Il7r-cre; Rosa26-lsl-tdTomato


title: h4

value: healthy subject


title: L-cDC1_sample2


title: np8


title: L-cDC1_sample1


title: m10


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 6 [FP20_WARS6]

city: Lausanne

first: Francesca

last: Pontanari

address: Route Cantonale

department: SV

country: Switzerland

institute: EPFL

data_processing:
After sequencing on the DNBSEQ platform, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality (phred quality < 20) reads from raw reads.
Sequenced reads were mapped to the GRCm38   mm10   primary   assembly  of the mouse genome using ensembl release 95 gene annotation with STAR aligner version 2.7.3a
Reads were counted using STAR aligner
Assembly: Mus_musculus.GRCm38.95
Supplementary files format and content: xlsx file with counts per gene per sample

source_name: Liver

extract_protocol:
RNA was extracted in Trizol from frozen liver tissue
RNA libraries were prepared for sequencing using standard DNBSEQ protocols with polyA enrichment

value: Liver


title: np2


title: TC71_ENG_wild_type_rep3

city: Seville

first: Pilar

last: Puerto-Camacho

state: Seville

address: Avda. Manuel Siurot s/n

department: Oncohematology

country: Spain

institute: Institute of Biomedicine of Seville

description: Gene expression data from WT TC71 cells seeded

hyb_protocol: The amplified cDNA was quantified, fragmented, and labeled in preparation for hybridization to GeneChip® Clariom S Human Array (Thermo Fisher Scientific, Inc.) using 5.5 μg of single-stranded cDNA product and following protocols outlined in the user manual.

scan_protocol: Washing, staining (GeneChip® Fluidics Station 450, Thermo Fisher Scientific, Inc.), and scanning (GeneChip® Scanner 3000, Thermo Fisher Scientific, Inc.) were performed following protocols outlined in the user manual for cartridge arrays.

data_processing: Array data were quantile normalized through Robust Multichip Average (RMA) method, using the oligo package from R/Bioconductor. Custom ClariomSHuman_Hs_ENSG CDF files from Brainarray were employed to discard unspecific and bad quality probesets.

source_name: Ewing sarcoma cell line, wild type

label_protocol: RNA was amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.). Amplification was performed with 100 ng of total RNA input following procedures described in the WT PLUS Reagent Kit user manual.

growth_protocol: 10% FBS 1%P/S RPMI on 1 µg/mL gelatin pre-treated plates

extract_protocol: miRNeasy Mini Kit from QIAGEN without DNAse treatment following manufacturer's instructions

tag: cancer type

value: Ewing sarcoma

tag: shRNA transfection

value: WT


title: TC71_ENG_wild_type_rep2


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 5 [FP20_WARS5]


title: TC71_ENG_wild_type_rep1


title: p7


title: TC71_ENG_control_rep3

description: Gene expression data from pEMPTY TC71 cells seeded in vitro

source_name: Ewing sarcoma cell line, ENG control

value: pEMPTY


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 4 [FP20_WARS4]


title: TC71_ENG_control_rep2


title: m5


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 3 [FP20_WARS3]


title: Cancer associated fibroblast from NSCLC patient 20160322

type: genomic

city: Taipei

first: Chao-Chi

last: Ho

address: 1 Jen Ai Road, Section 1

department: Department of Internal Medicine

country: Taiwan

institute: National Taiwan University Hospital and National Taiwan University College of Medicine

description: DNA methylation data of cancer associated fibroblast from NSCLC patient

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: Cancer associated fibroblast

label_protocol: Standard Illumina Protocol

growth_protocol: 800 cells per well were seeded to ultra-low adherent 24-wel plates (Corning) with MCDB201 medium (Invitrogen), and exposed to condition medium from cultured NFs and CAFs.

extract_protocol: genomic DNA was extracted and purified from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: The medium was supplemented with epidermal growth factor (20ng/ml, Sigma) and bFGF (20ng/ml, Invitrogen).

value: Cancer associated fibroblast

tag: smoking

value: Ever

tag: gender

value: Male

tag: histology

value: LUAD

tag: Stage

value: Early


title: p5

value: serum


title: Cancer associated fibroblast from NSCLC patient 20151014

tag: cell type

value: LUSC

value: Late


title: TC71_ENG_control_rep1

tag: cell line


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 2 [FP20_WARS2]

tag: treatment


title: TC71_ENG_upregulatd_clone2_rep3

description: Gene expression data from pENG TC71 cells seeded in vitro

source_name: Ewing sarcoma cell line, ENG downregulation

value: pENG


title: h7


title: Slc25a47-Wars1lox/lox injected with Cre+Wars1, 18 weeks old, 6h fasting - biological replicate 1 [FP20_WARS1]


title: Cancer associated fibroblast from NSCLC patient 20151104


title: Cancer associated fibroblast from NSCLC patient 20160921


title: np4

value: IgAN non prog


title: TC71_ENG_upregulatd_clone2_rep2


title: TC71_ENG_upregulatd_clone1_rep3


title: TC71_ENG_upregulatd_clone2_rep1


title: Cancer associated fibroblast from NSCLC patient 20150811


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 6 [FP20_SLC6]


title: Cancer associated fibroblast from NSCLC patient 20160509

value: Never

value: Female


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 5 [FP20_SLC5]


title: Cancer associated fibroblast from NSCLC patient 20160127


title: Cancer associated fibroblast from NSCLC patient 20160531


title: p8

value: IgAN prog


title: Cancer associated fibroblast from NSCLC patient 20160913


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 4 [FP20_SLC4]

value: Liver


title: np3


title: Cancer associated fibroblast from NSCLC patient 20161227


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032230]

city: Oviedo

first: Guillermo

middle: M

last: Albaiceta

address: Avenida de Roma s/n

institute: Instituto de Investigación Sanitaria del Principado de Asturias

data_processing:
Basecalling data from NextSeqs was demultiplexed using bcl2fastq to obtain FastQ files.
FASTQ files were analyzed with HTG EdgeSeq parser software to generate raw counts
Abundances were calculated by adjusting raw counts to  total counts
Genome_build: miRBase 22.1
Supplementary_files_format_and_content: Csv file with raw counts for the identified micro-Rnas in each sample

extract_protocol:
Bronchoalveolar lavage fluid (BALF) recovered after intratracheal instillation of 10 ml of sterile saline. Recovered fluid was filtered and centrifuged, and supernatants immediately frozen.
EdgeSeq miRNA whole transcriptomic assay, HTG Molecular Diagnostics Inc, USA

tag: subject status

tag: patient id

tag: tidal volume (ml/kg)

tag: lung strain

tag: sample type

value: Bronchoalvelar lavage fluid

tag: molecule type

value: micro-RNA


title: TC71_ENG_upregulatd_clone1_rep2

value: Ewing sarcoma


title: Cancer associated fibroblast from NSCLC patient 20161213

value: Cancer associated fibroblast


title: Cancer associated fibroblast from NSCLC patient 20151208


title: Normal fibroblast from NSCLC patient 20151104

description: DNA methylation data of normal fibroblast from NSCLC patient

source_name: Normal fibroblast

value: Normal fibroblast

value: Ever


title: Cancer associated fibroblast from NSCLC patient 1227

value: Male


title: TC71_ENG_upregulatd_clone1_rep1


title: Cancer associated fibroblast from NSCLC patient 20161115

value: LUAD

value: Early


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 3 [FP20_SLC3]

tag: tissue

tag: genotype


title: Normal fibroblast from NSCLC patient 20150811

tag: age

value: LUSC


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1702-A032229]


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 2 [FP20_SLC2]


title: SKNMC_ENG_control_rep3

description: Gene expression data from shNT SKNMC cells seeded

tag: cancer type

value: SKNMC

tag: shRNA transfection

value: shNT


title: Normal fibroblast from NSCLC patient 20151208

tag: smoking

tag: gender


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1702-A032226]


title: Slc25a47-Wars1lox/lox injected with Cre+Slc25a47, 18 weeks old, 6h fasting - biological replicate 1 [FP20_SLC1]


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032225]


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 6 [FP20_CRE6]

value: Cre+Gfp


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032224]


title: Normal fibroblast from NSCLC patient 20161227

value: Never

tag: histology

tag: Stage

value: Late


title: Normal fibroblast from NSCLC patient 20151014

tag: cell type


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 5 [FP20_CRE5]

tag: treatment


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032223]

tag: subject status


title: SKNMC_ENG_control_rep2

tag: cell line


title: Normal fibroblast from NSCLC patient 20160322


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032222]

tag: patient id

tag: tidal volume (ml/kg)


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 3 [FP20_CRE3]


title: SKNMC_ENG_control_rep1


title: SKNMC_ENG_downregulatd_clone2_rep2

description: Gene expression data from shENG SKNMC cells seeded

value: shENG


title: SKNMC_ENG_downregulatd_clone2_rep3


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032221]

tag: lung strain

tag: sample type


title: SKNMC_ENG_downregulatd_clone2_rep1


title: SKNMC_ENG_downregulatd_clone1_rep3


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 2 [FP20_CRE2]

tag: tissue

value: Liver


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1702-A032220]

value: Bronchoalvelar lavage fluid

tag: molecule type


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 1 [FP20_CRE1]

tag: genotype


title: Normal fibroblast from NSCLC patient 20160127

tag: age

value: Female


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 6 [FP20_GFP6]

value: Gfp


title: SKNMC_ENG_downregulatd_clone1_rep2

tag: cancer type

value: Ewing sarcoma

tag: shRNA transfection


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032218]

value: micro-RNA


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1702-A032219]


title: Normal fibroblast from NSCLC patient 20160531

value: Normal fibroblast

tag: smoking

tag: gender


title: SKNMC_MMP14_control_rep4

description: Gene expression data from sgNT SKNMC cells seeded in vitro

source_name: Ewing sarcoma cell line, MMP14 control

value: sgNT


title: Cancer associated fibroblast from NSCLC patient 20151006

value: Cancer associated fibroblast

tag: histology

value: LUAD

tag: Stage


title: Normal fibroblast from NSCLC patient 20161115

tag: cell type

value: Early


title: SKNMC_MMP14_control_rep3

value: SKNMC


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032217]

tag: subject status


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 4 [FP20_GFP4]

tag: treatment


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 5 [FP20_GFP5]


title: Normal fibroblast from NSCLC patient 20160921

value: Ever

value: Male


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1701-A032216]

tag: patient id


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 3 [FP20_GFP3]


title: Bronchoalveolar lavage fluid from mechanically ventilated patient with cardiogenic shock [1702-A032215]

tag: tidal volume (ml/kg)


title: SKNMC_MMP14_control_rep2

tag: cell line


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 2 [FP20_GFP2]


title: SKNMC_MMP14_control_rep1

description: Gene expression data from sgNT sknmc cells seeded in vitro


title: Cancer associated fibroblast from NSCLC patient 20150707


title: Slc25a47-Wars1lox/lox injected with Gfp alone, 18 weeks old, 6h fasting - biological replicate 1 [FP20_GFP1]


title: SKNMC_ENG_downregulatd_clone1_rep1


title: SKNMC_MMP14_knockout_clone2_rep1

description: Gene expression data from sgMMP14 SKNMC cells seeded in vitro

source_name: Ewing sarcoma cell line, MMP14 downregulation


title: Normal fibroblast from NSCLC patient 20160913

value: Never


title: Zebrafish, BG, rep3

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

institute: East China University of Science and Technology

description: Library name: Sample 9

data_processing:
Constructing an index of the reference genome using HISAT2 (v2.1.0)
Assembly: GRCz21
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

organism: Danio rerio

source_name: Intestine

growth_protocol: Three-to six-month-old AB line zebrafish were maintained at 27 ± 1 °C and under a controlled light/dark cycle (14 h light/10 h dark).

extract_protocol:
The RNA of each individual sample was isolated by Trizol (Invitrogen) and chloroform.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

treatment_protocol: 10 µL yeast-derived β-glucan (10 mg/mL) was intraperitoneally injected (i.p.), and after resting for 5 days, 5 µL E. piscicida(2 × 106 CFU/mL) was challenged with through rectal injection

value: Intestine

tag: strain

value: AB

value: WT

value: Beta-Glucan training and E. piscicida infection

tag: time

value: Day 7


title: Zebrafish, BG, rep2

description: Library name: Sample 8

tag: tissue


title: Slc25a47-Wars1lox/lox injected with Cre+Gfp, 18 weeks old, 6h fasting - biological replicate 4 [FP20_CRE4]

value: Liver

tag: genotype

value: Cre+Gfp


title: Zebrafish, BG, rep1

description: Library name: Sample 7


title: Normal fibroblast from NSCLC patient 20160509

tag: age

value: Female


title: Normal fibroblast from NSCLC patient 1227

value: Normal fibroblast

value: LUSC

value: Late


title: sample15, pigBAL, ISU1, DPI20, biol rep3

city: Pirbrigh

first: liu

last: yang

address: Ash Rd

institute: The Pirbright Institute

description:
Library name: sample_15
10x Genomics

data_processing:
Bcl files were demultiplexed using ‘cellranger mkfastq’ and aligned/counted using ‘cellranger count’ (cellranger-7.1.0) using default parameters and Sus scrofa genome (genome assembly 11.1, Ensembl release 108).
Assembly: Sscrofa11.1
Supplementary files format and content: 10X unfiltered (raw) feature h5 matrix files

organism: Sus scrofa

source_name: bronchoalveolar lavage

extract_protocol:
Cryopreserved BAL cells were thawed, washed and resuspended in PBS. Cells were incubated with antibodies against CD4 (clone 74-12-4, PerCP-Cy5.5-conjugated, BD Biosciences), CD8β (clone PPT23, FITC-conjugated, Bio-Rad), CD3 (clone PPT3, APC-conjugated, Southern Biotech), CD16 (clone G7, AF647-conjugated, Bio-Rad), CD172a (clone 74-22-15, PE-conjugated, Bio-Rad) and Fixable Viability Dye eFluor780 (ThermoFisher). After two washes in PBS, cells were fixed, washed again and sorted on a FACSAria UIII (BD Biosciences), equipped with 405, 488, 561 and 640nm lasers and BD FACSDiva 8 software. After gating on FSC-AdimSSC-Adim cells and exclusion of doublets and dead cells, CD4+, CD8β+ and CD3-CD16- (to enrich for B cells) cells were sorted (12,000 cells per population). In addition, after gating on FSC-AbrightSSC-Abright cells, doublet and dead cell exclusion and gating on CD16+CD172a+ cells, 12,000 macrophages were sorted. Cells from each fraction were pooled and subjected to partitioning and barcoding on a 10x Genomics Chromium iX Controller.
Single cells were processed using the Chromium iX Controller with the Next GEM chip G and the single cell 3’ kit v3.1 library preparation kit from 10x Genomics (Pleasanton, CA). For each of the BAL samples, approximately 10,000 cells were targeted for recovery during partitioning. The samples were grouped randomly and run in pairs, using three NextSeq High Output 150 cycle reagent kits (Illumina, San Diego, CA), with 1% PhiX, aiming for about 200 million reads per sample, with the run format aligning with 10X guidelines. The sequencing was performed on an Illumina NextSeq 550, using 3 high output 200 cycle reagent kit and flow cells.

value: bronchoalveolar lavage

value: leukocytes

value: wild-type

tag: Sex

value: female


title: Zebrafish, EIB202, rep3

description: Library name: Sample 6

value: E. piscicida infection


title: Cancer associated fibroblast from NSCLC patient 20150930

value: Cancer associated fibroblast

value: Never

value: LUAD


title: sample14, pigBAL, ISU1, DPI20, biol rep2

description:
Library name: sample_14
10x Genomics


title: Normal fibroblast from NSCLC patient 20161213

value: Early


title: SKNMC_MMP14_knockout_clone1_rep2

tag: cancer type

value: Ewing sarcoma

value: SKNMC

tag: shRNA transfection


title: cell_ENG_wild_type_rep3

description: Gene expression data from WT RM82 cells seeded

value: WT


title: Cancer associated fibroblast from NSCLC patient 20150826

tag: smoking

tag: gender


title: cell_ENG_wild_type_rep2


title: Cancer associated fibroblast from NSCLC patient 20150630

value: Ever

value: Male

tag: histology

tag: Stage


title: sample13, pigBAL, 135, DPI20, biol rep4

description:
Library name: sample_13
10x Genomics

tag: cell type


title: Zebrafish, EIB202, rep1

description: Library name: Sample 4

value: Intestine

value: AB

tag: treatment

value: Day 7


title: sample12, pigBAL, 135, DPI20, biol rep3

description:
Library name: sample_12
10x Genomics

value: bronchoalveolar lavage


title: Zebrafish, mock, rep3

description: Library name: Sample 3

value: no


title: Zebrafish, mock, rep2

description: Library name: Sample 2


title: Zebrafish, EIB202, rep2

description: Library name: Sample 5


title: Cancer associated fibroblast from NSCLC patient 1213

value: Female


title: sample11, pigBAL, 135, DPI20, biol rep2

description:
Library name: sample_11
10x Genomics

value: leukocytes

value: wild-type

value: female


title: sample10, pigBAL, 135, DPI20, biol rep1

description:
Library name: sample_10
10x Genomics


title: Cancer associated fibroblast from NSCLC patient 20150812

value: Cancer associated fibroblast

value: Never


title: sample16, pigBAL, ISU1, DPI20, biol rep4

description:
Library name: sample_16
10x Genomics


title: Zebrafish, mock, rep1

description: Library name: Sample 1


title: SKNMC_MMP14_knockout_clone1_rep1


title: sample9, pigBAL, ISU1, DPI20, biol rep1

description:
Library name: sample_09
10x Genomics


title: cell_ENG_wild_type_rep1


title: cell_ENG_control_rep3

description: Gene expression data from shNT RM82 cells seeded

value: shNT


title: SKNMC_MMP14_knockout_clone2_rep2

value: Ewing sarcoma


title: cell_ENG_control_rep2


title: cell_ENG_control_rep1


title: ATAC_CD8_Day35_m38_Rep3

first: Endi

middle: K

last: Santosa

state: New York

address: 417 E 68th St

department: Immunology

description:
Library name: ATAC_CD8_Day35_m38_Rep3
ATAC_rawCounts.txt
ATAC_peaks.txt

data_processing:
For all sequenced data, paired-end reads were trimmed for adaptors and removal of low-quality reads using Trimmomatic (v.0.36). Trimmed reads were mapped to the Mus musculus genome (mm10 assembly) using Bowtie2 (v2.2.9). Read counts for features (peak regions for ATAC-seq and exons for RNA-seq) were generated using the summarizeOverlaps function from the GenomicAlignments package (v1.10.1). Differential analyses were executed with DESeq2 (v1.14.1) using the UCSC Known Gene models as reference annotations. Features were considered differential if they showed a P value (Padj) < 0.05, adjusted for multiple hypothesis correction.
For peak calling, all positive-strand reads were shifted 4 bp downstream and all negative-strand reads were shifted 5 bp upstream to center the reads on the transposon binding event. Shifted, concordantly aligned paired mates were used for peak calling by MACS2 at a P value of 0.01. IDR calculations using scripts provided by the ENCODE project were performed on all pairs of replicates using an oracle peak list called from merged replicates for each condition, keeping only reproducible peaks showing an IDR value of 0.05 or less. Overlapping peaks from different conditions were merged using the following conditions: if a peak overlapped with more than one other peak, the peak with the highest overlap (calculated as the percentage of overlap width out of the total width of the narrower peak) was merged; if the overlap of two peaks was > 75%, non-overlapping portions were removed; if the overlap was 75% or less, then both peaks were merged to create a single peak encompassing both peak ranges. A union of both merged overlapping peaks and unique reproducible peaks for each condition was used to generate the final atlas and was used for further analysis.
Assembly: mm10
Supplementary files format and content: RNA_rawCounts.txt
Supplementary files format and content: ATAC_rawCounts.txt
Supplementary files format and content: ATAC_peaks.txt

source_name: Spleen

extract_protocol:
For RNA-seq: We isolated 20,000–50,000 sorted splenic lymphocytes for RNA-sequencing. CD8+ T cells were sorted from wild-type mice at d0 (naive: TCRβ+CD8+CD62LhiCD44lo), d7, or d35 PI (effector and memory: TCRβ+CD8+CD62LloCD44hiTetramer+). For ATAC-seq, 7,000-50,000 cells were collected. Fresh cells were washed in cold PBS and lysed. Transposition occurred at 42 °C for 45 min.
For RNA-seq: RNA was isolated from sorted cell populations using Trizol (Invitrogen), and total RNA was amplified using the SMART-seq V4 Ultra Low Input RNA kit (Clontech). Subsequently, 10 ng of amplified cDNA was used to prepare Illumina HiSeq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using eight cycles of PCR. For ATAC-seq: DNA was purified using the MinElute PCR purification kit (Qiagen) and amplified for five cycles. Additional PCR cycles were evaluated by real-time PCR. The final product was cleaned by Ampure Beads at a 1.5 × ratio.

value: Spleen

tag: epitope

value: CD8 +T

value: MCMV

tag: day


title: ATAC_CD8_Day35_m38_Rep2

description:
Library name: ATAC_CD8_Day35_m38_Rep2
ATAC_rawCounts.txt
ATAC_peaks.txt

value: WT


title: sample8, pigBAL, 135, DPI1, biol rep4

description:
Library name: sample_08
10x Genomics


title: Cancer associated fibroblast from NSCLC patient 20100510

value: LUSC

value: Late


title: Cancer associated fibroblast from NSCLC patient 20150818

value: Ever

value: Male

value: LUAD


title: Cancer associated fibroblast from NSCLC patient 0304

value: Female

value: Early


title: sample6, pigBAL, 135, DPI1, biol rep2

description:
Library name: sample_06
10x Genomics

value: bronchoalveolar lavage

value: leukocytes

value: wild-type


title: ATAC_CD8_Day35_m38_Rep1

description:
Library name: ATAC_CD8_Day35_m38_Rep1
ATAC_rawCounts.txt
ATAC_peaks.txt


title: sample7, pigBAL, 135, DPI1, biol rep3

description:
Library name: sample_07
10x Genomics

value: female


title: Cancer associated fibroblast from NSCLC patient 20150902

value: Cancer associated fibroblast

value: Never


title: ATAC_CD8_Day7_m38_Rep2

description:
Library name: ATAC_CD8_Day7_m38_Rep2
ATAC_rawCounts.txt
ATAC_peaks.txt

value: Spleen


title: cell_ENG_downregulatd_clone2_rep3

description: Gene expression data from shENG RM82 cells seeded

value: Ewing sarcoma

tag: cell line

value: shENG


title: sample4, pigBAL, ISU1, DPI1, biol rep4

description:
Library name: sample_04
10x Genomics


title: Cancer associated fibroblast from NSCLC patient 20150428


title: sample5, pigBAL, 135, DPI1, biol rep1

description:
Library name: sample_05
10x Genomics


title: cell_ENG_downregulatd_clone2_rep2


title: cell_ENG_downregulatd_clone1_rep1


title: cell_ENG_downregulatd_clone1_rep3


title: cell_ENG_downregulatd_clone1_rep2


title: sample3, pigBAL, ISU1, DPI1, biol rep3

description:
Library name: sample_03
10x Genomics


title: ATAC_CD8_Day7_m38_Rep1

description:
Library name: ATAC_CD8_Day7_m38_Rep1
ATAC_rawCounts.txt
ATAC_peaks.txt

value: CD8 +T

value: WT

value: MCMV


title: RNA_CD8_Day35_m38_Rep2

description:
Library name: RNA_CD8_Day35_m38_Rep2
RNA_rawCounts.txt


title: RNA_CD8_Day35_m38_Rep1

description:
Library name: RNA_CD8_Day35_m38_Rep1
RNA_rawCounts.txt


title: sample2, pigBAL, ISU1, DPI1, biol rep2

description:
Library name: sample_02
10x Genomics


title: RNA_CD8_Day7_m38_Rep2

description:
Library name: RNA_CD8_Day7_m38_Rep2
RNA_rawCounts.txt


title: Cancer associated fibroblast from NSCLC patient 0330

description: DNA methylation data of cancer associated fibroblast from NSCLC patient

value: Late


title: cell_MMP14_wild_type_rep3


title: cell_ENG_downregulatd_clone2_rep1


title: ATAC_CD8_Day7_m38_Rep3

description:
Library name: ATAC_CD8_Day7_m38_Rep3
ATAC_rawCounts.txt
ATAC_peaks.txt


title: Gsdme global deletion model,KO-AAA

city: 上海

first: Zhen

last: Zhang

state: 上海

address: 延长中路

department: Pharmacy

institute: Shanghai Tenth People's Hospital Tongji University School of Medicine

description: BD Rhapsody

data_processing:
Basecalls performed using CASAVA version 1.8
Thedemultiplexing,barcodeprocessing,genecountingweremadeusingthe STARsolo
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: aorta

extract_protocol:
samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with xx U/mL collagenase I (Worthington) and xx U/mL DNase I (Worthington) for 45 min at 37°C, with agitation. After digestion, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.04% BSA, the cell pellets were re-suspended in PBS containing 0.04% BSA and re-filtered through a 35μm cell strainer
Sequencing libraries were conducted using the BD Rhapsody Single-Cell Analysis System (BD Biosciences), following the manufacture's protocol.

value: aorta

value: PPE induced AAA


title: Cancer associated fibroblast from NSCLC patient 20150303

value: Female

value: Other


title: Cancer associated fibroblast from NSCLC patient 20150318

value: LUAD

value: Early


title: Cancer associated fibroblast from NSCLC patient 20150505

value: Ever

value: Male


title: cell_MMP14_wild_type_rep1


title: cell_MMP14_control_rep3

description: Gene expression data from sgNT RM82 cells seeded in vitro

value: sgNT


title: Cancer associated fibroblast from NSCLC patient 20150519

value: Cancer associated fibroblast

value: Never


title: cell_MMP14_wild_type_rep2

value: Ewing sarcoma


title: Cancer associated fibroblast from NSCLC patient 20150203_2


title: head and neck tumor after proton therapy mouse 3

data_processing:
nf-core/rnaseq
Assembly: hg38, mm39
Supplementary files format and content: comma delimeted text files include gene count values for each Sample

source_name: laryngeal tumor

value: laryngeal tumor

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, implanted subcutaneously in an immunodeficient mouse, after neutron therapy

value: Phenotype:CD44+, KRT17+

value: neutron therapy (10 Gy)


title: Cancer associated fibroblast from NSCLC patient 20100426_1


title: sample1, pigBAL, ISU1, DPI1, biol rep1

description:
Library name: sample_01
10x Genomics

value: bronchoalveolar lavage

value: leukocytes

value: wild-type

value: female


title: d14_t3

city: Zhengzhou

first: Jiqi

last: Shan

state: Henan

address: 1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: The First Affiliated Hospital of Zhengzhou University, Zhengzhou,

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster.
Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster.
Deduplicated Reads were mapped to the reference genome ofMus_musculus.GRCm38 using STRA software (version 2.5.3a) with default parameters.Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited excel file includes RPKM values for each Sample

source_name: T cell

growth_protocol: B16 tumor-bearing mice

extract_protocol:
Total RNAs were extracted using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999).
2 μg total RNAs were used for stranded RNA sequencing library preparation KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.
UID-mRNA-seq PE-150

treatment_protocol: CD8+ T cells in TILs from B16 tumor-bearing mice were sorted on day 7 and day 14 using mouse CD8a microbeads (Miltenyi Biotec, 130-117-044) according to the manufacturer’s protocol.

value: B16 tumor


title: head and neck tumor before proton therapy mouse 3

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, implanted subcutaneously in an immunodeficient mouse, before neutron therapy


title: wild type AAA model ,WT-AAA

description: BD Rhapsody

value: aorta

value: PPE induced AAA


title: Cancer associated fibroblast from NSCLC patient 20150203_1

value: Male

value: LUAD

value: Early


title: head and neck tumor after proton therapy mouse 2

value: head and neck tumor


title: d14_t1


title: Cancer associated fibroblast from NSCLC patient 20150331_1

value: Cancer associated fibroblast

value: Ever


title: d14_t2


title: head and neck tumor before proton therapy mouse 2

value: laryngeal tumor


title: Cancer associated fibroblast from NSCLC patient 20100315

value: Never


title: Cancer associated fibroblast from NSCLC patient 20140411

value: Other


title: head and neck tumor after proton therapy mouse 1

value: continuous cell culture obtained from a patient with a laryngeal tumor, passage 4, implanted subcutaneously in an immunodeficient mouse, after neutron therapy

value: Phenotype:CD44+, KRT17+

value: neutron therapy (10 Gy)


title: head and neck tumor before proton therapy mouse 1


title: d7_t2


title: d7_t3


title: cell_MMP14_knockout_clone2_rep3

description: Gene expression data from sgMMP14 RM82 cells seeded in vitro

value: Ewing sarcoma


title: cell_MMP14_knockout_clone2_rep2


title: cell_MMP14_control_rep1

value: sgNT


title: cell_MMP14_knockout_clone2_rep1


title: cell_MMP14_control_rep2


title: d7_t1

value: B16 tumor


title: cell_MMP14_knockout_clone1_rep3


title: Cancer associated fibroblast from NSCLC patient 20101228

value: LUSC


title: Intestinal epithelia , Embryo day 15.5

city: Portland

first: Guanming

last: Wu

state: OR

address: 3181 S.W. Sam Jackson Park Road

institute: OHSU

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: intestine

extract_protocol:
Freshly collected DC and Si8 from RedMUC298trTg mice were flushed with ice-cold HBSSwo (Mg2+/Ca2+ free supplemented with 10mM HEPES, pH 7.2) to remove luminal content. The tissue was inverted and inflated by injection of HBSSwo. Epithelial isolation was performed by incubation of tissue with pre-digestion buffer (HBSSwo, 5 mM EDTA, 5% v/v FCS, 1 mM DTT) in a shaking incubator. The isolated epithelial cells were resuspended in digestion buffer (HBSS with Mg2+/Ca2+ supplemented with 2 mg/ml collagenase type I and 40 U/ml DNase I) and incubated at 37 °C for 30 min. Cells were washed and re-suspended in PBS and stained with a Viability Dye, washed and resuspended in FACS buffer (HBSSwo, 2% v/v FCS, 5mM EDTA). Alive GCs were sorted using a FACS Jazz (Becton Dickinson) according to the presence or absence of mCherry signal using a C57Bl6 mouse as negative control. Goblet cells were washed in HBSS-/- and resuspended in HBSS-/- supplemented with 0.04% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: intestine

value: embryonic (E15.5) intestinal epithelia, expressing Bmi1


title: NC_3

first: Chuandong

last: Wang

address: 320 Yueyang Road

institute: SJTU

data_processing:
Trimmomatic and Cutadapt software were used to remove the sequencing connections and low-quality sequences from the original sequencing data to obtain clean data.
Blastn (2.9.0+) was used for comparison and the read count number was obtained based on the quantitative result.
miRDeep2 software was used to normalize reads counts and obtain CPM (Reads Count Per Million) values.
Assembly: mm10
Supplementary files format and content: raw_counts includes raw counts for each sample

source_name: Cartilage

growth_protocol: Chondrocyte were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and 1% antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Tissue RNA Purification Kit PLUS kit (#EZB-RN001-plus) was used to extract total RNA from the cell.
Perform 3 'end connector connections, reverse transcription primer hybridization, 5' end connector connections, cDNA single strand synthesis, library amplification, and other processing on the sample. After quality inspection and purification, a library that meets the Illumina platform sequencing requirements was finally obtained.

treatment_protocol: Chondrocyte stimulated with 10 ng/ml IL-1β for 24 hours

value: Cartilage

value: primary cell - chondrocyte

value: WT

value: untreated


title: uggtΔ mutant, cultured in YPD, rep2

city: Seoul

first: Catia

last: Mota

state: Seoul

address: Heukseok-ro 84

department: Life Science

institute: Chung-Ang University

data_processing:
Quality control of raw sequencing data was performed using FastQC
Adapter and low quality reads (<Q20) were removed using FASTX_Trimmer and BBMap
Trimmed reads were mapped to the reference genome using TopHat
The RC (Read Count) data were processed based on FPKM+Geometric normalization method using EdgeR within R
FPKM (Fragments Per kb per Million reads) values were estimated using Cufflinks
Assembly: ASM1180120v1
Supplementary files format and content: The files include readcount, RPKM and TPM values for each samples.
Supplementary files format and content: The files include annotations from GO, InterPro, Pfam, and NCBI DB.

organism: Cryptococcus neoformans

source_name: fungal cell

growth_protocol: Respetive C. neoformans strains were grown to an OD600 of 0.8 in YPD medium at 28°C.

extract_protocol:
Total RNA was isolated using the liquid nitrogen method, and purified using Rneasy mini kit (Qiagen). About 3~5 ug of total RNA was used for the construction of the sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA-Seq Kit (NEW ENGLAND BioLabs, Inc., UK).

tag: strain

value: fungal cell

value: MAT{alpha} CNAG_03648::NAT#159


title: BY4741 strain, WT, highty level  L-A virus, No2 isolate, polyA enriched

first: Tien-Hsien

last: Chang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

institute: Academia Sinica

description:
Library name: Fungi budding yeasts Saccharomycetes isolate17
Expression_counts: polyAEnrich_high level L-A virus_No2_isolate

data_processing:
Sequencing data were aligned to the yeast reference genome yeast_R64 by STAR read mapper (versionL2.1.11b).  Differential-expression analysis was done using HTseq/RSEM.
Assembly: Sequencing data were aligned to the yeast reference genome yeast_R64
Supplementary files format and content: text file includes raw counts for each sample

growth_protocol: Independent colonies from each of the  L-A-, L-A+, and L-A++ isolates were cultured in liquid YPD (2% dextrose, 2% peptone and 1% yeast extract) medium overnight.

extract_protocol:
Total RNA was isolated using MasterPureTM Yeast RNA Purification Kit (Lucigen) and treated with DNase I at 37˚C for 30 m.
For rRNA depleted method was using QIAseq FastSelect RNA Library kit (334215) and TruSeq Stranded mRNA sample prep kit (RS-122-2101) at the Genomics Core Facility, Institute of Molecular Biology, Academia Sinica, Taiwan. For the poly(A) RNA enriched approach, was using SureSelect XT HS2 mRNA Library Preparation Kit with Index Primer Pairs 97-192, 96 Reactions (G9997B) (Agilent, Santa Clara, CA, USA) and the SureSelect XT HS2 mRNA Library Preparation kit (Agilent, Santa Clara, CA, USA) was used for library construction, followed by HighPrep PCR clean-up system. (MagBio Genomics, Gaithersburg, MD, USA)(W3852001-1).done at Welgene Biotech Co., Ltd. (Taipei, Taiwan).


title: Cancer associated fibroblast from NSCLC patient 20101221

value: Cancer associated fibroblast

value: Never

value: Female

value: Early


title: NC_2


title: BY4741 strain, WT, highty level  L-A virus, No1 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate16
Expression_counts: polyAEnrich_high level L-A virus_No1_isolate


title: cell_MMP14_knockout_clone1_rep2


title: WT, cultured in YPD, rep2

value: MAT{alpha} (serotype A)


title: NC_1


title: BY4741 strain, WT, mid level  L-A virus, No3 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate15
Expression_counts: polyAEnrich_mid level  L-A virus_No3_isolate


title: Normal fibroblast from NSCLC patient 20151006

description: DNA methylation data of normal fibroblast from NSCLC patient

value: Normal fibroblast

value: LUAD


title: uggtΔ mutant, cultured in YPD, rep1


title: cell_MMP14_knockout_clone1_rep1

value: Ewing sarcoma


title: IL_1_3


title: Cancer associated fibroblast from NSCLC patient 20101231


title: Normal fibroblast from NSCLC patient 20150930

value: Late


title: BY4741 strain, WT, mid level  L-A virus, No1 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate13
Expression_counts: polyAEnrich_mid level  L-A virus_No1_isolate


title: BY4741 strain, WT, mid level  L-A virus, No2 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate14
Expression_counts: polyAEnrich_mid level  L-A virus_No2_isolate


title: BY4741 strain, WT, highty level  L-A virus, No3 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate18
Expression_counts: polyAEnrich_high level L-A virus_No3_isolate


title: IL_1_1


title: IL_1_2


title: BY4741 strain, WT, without L-A virus, No3 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate12
Expression_counts: polyAEnrich_without L-A virus_No3_isolate


title: HFD_hippocampus_3

city: Nanjing

first: jin

last: wang

address: No. 321 Zhongshan Road

department: Department of Endocrinology

institute: Drum Tower hospital affiliated to Nanjing university medical school

data_processing:
miRNA sequences, tRNA sequences and piRNA sequences were obtained from miRBase v21(Kozomara and Griffiths-Jones, 2014), GtRNAdb (Chan and Lowe, 2016) and piRNA bank (Lakshmi and Agrawal, 2008), respectively. Bowtie was used to align clean reads to these reference sequences for annotation.
Assembly: miRBase v21; GtRNAdb; piRNA bank
Supplementary files format and content: tab-delimited text files include readcount values for each Sample

source_name: brain

extract_protocol:
Adipose tissue derived EVs and hippocampus were extracted from male mice of the C57BL/6J backgrounds and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: male

value: brain

value: HFD diet


title: WT, cultured in YPD, rep1


title: Normal fibroblast from NSCLC patient 20150630

value: Ever

value: Male


title: HFD_hippocampus_2

value: WT


title: Normal fibroblast from NSCLC patient 20100510

value: LUSC


title: BY4741 strain, WT, without L-A virus, No2 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate11
Expression_counts: polyAEnrich_without L-A virus_No2_isolate


title: Brain arteries from SAH7d animal, rep. 5

city: Puerto Real

first: Maria del Carmen

last: González Montelongo

state: Cádiz

address: Calle Esparraguera 111

institute: University of Cádiz

description:
Gene expression data from SAH7d animals
H5

hyb_protocol: Hybridazation (GeneChip Hybridization Oven 654,Thermo Fisher Scientific, Inc.) and, washing and staining (GeneChip Fluidics Station 450, Thermo Fisher Scientific, Inc.), were performed following protocols outlined in the user manual for cartridge arrays

scan_protocol: Scanning with a GeneChip® Scanner 3000 7G system (Thermo Fisher Scientific, Inc.) was performed following protocols outlined in the user manual for cartridge arrays.

data_processing: CEL files were analyzed by Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific, Inc.)

label: Biotin

source_name: Brain rat arteries under SAH induction procedure

label_protocol: Total RNA was amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Thermo Fisher Scientific, Inc.)

growth_protocol: 13 samples or brain arteries were collected from experimental groups. Control (3), Sham7d (5) and SAH7d (5).

extract_protocol: The homogenization of the arteries was performed using the RNeasy® Micro Kit (Qiagen). The RNA isolation process was completed using the QIAcube platform (Qiagen)

treatment_protocol: Arteries were cleaned under a magnifying glass in ice-cold RNAses-free Hank’s solution, immediately frozen in liquid nitrogen and stored at -80 ºC.

value: Brain arteries cleaned from connective tissues

value: Wistar

value: six months old

value: under SAH induction procedure


title: BY4741 strain, WT, without L-A virus, No1 isolate, polyA enriched

description:
Library name: Fungi budding yeasts Saccharomycetes isolate10
Expression_counts: polyAEnrich_without L-A virus_No1_isolate


title: Normal fibroblast from NSCLC patient 1213

value: Never

value: Female

value: Early


title: Normal fibroblast from NSCLC patient 20150826

value: Normal fibroblast

value: LUAD


title: Normal fibroblast from NSCLC patient 20150812


title: HFD_hippocampus_1


title: Normal fibroblast from NSCLC patient 0304