title: Tc9-day5

description:
yi-q16002
Gene expression data from in vitro polarized Tc9 cells on day 5

hyb_protocol: GeneChip Hybridization

scan_protocol: AGCC

data_processing: Affymetrix GeneChip Command Console (AGCC) Software

label: biotin

source_name: in vitro polarized Tc1 cells

label_protocol: WT Sense Target Labeling

growth_protocol: Isolated CD8+ T Cells were primed with platebound anti-CD3 and soluble anti-CD28 antibodies under Tc1- or Tc9-polarizing conditions. After 3 days of polarization, cells were transferred to new wells and cultured in standard T cell medium (RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum, 100 U/mL penicillin-streptomycin, 2 mM L-glutamine, and 50 μM 2-mercaptoethanol) with rhIL-2 (10 ng/mL) for another 2 days.

treatment_protocol: Tc9 cells were polarized in T cell medium supplemented with IL-4 (10 ng/mL), TGF-β (1 ng/mL), and anti–IFN-γ monoclonal antibody (clone XMG1.2, 20 μg/mL), while Tc1 cells were polarized in T cell medium supplemented with 10ng/mL recombinant human IL-2 (rhIL-2).

tag: develop stage

value: on day 5 after in vitro polarization

value: spleen and lymph node


title: Week4.DP.NPFic.1.RNA

status: Public on Jan 07 2024

type: SRA

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

country: USA

institute: University of Pittsburgh

description: Balb/c transfer system. Week 4.

library_source: transcriptomic

data_processing:
Raw reads quality and adapter sequences were checked using fastqc (v. 0.11.5).
Filtered adaptor and poor quality sequences respectively, using cutadapt (v. 1.8.3) (minimum phred quality score = 20).
The reference genome (mm10) based alignment of clean reads were performed using STAR (v. 2.6.0c) (Dobin et al., 2013).
Gene-level counts were determined using featureCounts packgae by subread/1.6.2 (Liao et al. 2014).
Raw counts were analyzed for differential expression using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10).
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Spleen

extract_protocol:
RNA purification was performed using the Qiagen RNeasy Micro Plus Kit. Libraries were generated using the SMART-Seq v4 Ultra Low Input RNA kit followed by Nextera FLEX using UDI set B indexes. Samples were sequenced using NovaSeq 6000 or NextSeq 2000 flowcells to obtain 20M 2x75 bp reads. Some samples were sequenced as 2x101 bp reads. Cells were collected via FACS, washed twice in PBS + 1% FCS, resuspended in 350 ul RLT Plus Buffer (Qiagen) with 1% 2-Me, and frozen at -80 ⁰C. RNA purification was performed using the Qiagen RNeasy Micro Plus Kit.
Libraries were generated using the SMART-Seq v4 Ultra Low Input RNA kit followed by Nextera FLEX using UDI set B indexes. Samples were sequenced using NovaSeq 6000 or NextSeq 2000 flowcells to obtain 20M 2x75 bp reads. Some samples were sequenced as 2x101 bp reads.

treatment_protocol: Cells were surfaced stained using antibodies for flow cytometry and sorted on BD FacsAria

tag: strain

value: Balb/c

tag: tissue

value: Spleen

tag: cell type

value: DP NP-Ficoll MBC


title: 769-P sihnRNPA2B1-2

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

country: China

institute: Southeast University

description: hnRNPA2B1 count

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were assemblyed by stringtie
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: exprSet.csv, csv format, containing the raw counts.

organism: Homo sapiens

source_name: clear cell Renal Carcinoma

growth_protocol: 769-P cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RNA-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

value: clear cell Renal Carcinoma

tag: cell line

tag: genotype


title: Week4.DP.NPFic.2.ATAC

library_source: genomic

data_processing:
Filtered adaptor and poor quality sequences respectively, using trimgalore(v.0.6.5 )
ATAC-seq reads were aligned to thereference genome assembly mm10 using Bowtie2 v2.3.3.
Mitochondrial reads, ummapped reads and low mappability (<30) reads were filtered out using the samtools view function. PCR duplicates were removed using Picard (v 2.18.12)
Peaks and peaks summit were called using MACS2  (with parameter -q 0.05 -B --nomodel --shift -75 --extsize 150) after merging filtered reads from replicate 1 and replaictes 2  from all sampels into two files.  These mereged replicates peak file was accessed using IDR and significnat peaks (Soft IDR threshold  < 0.1) was kept as true peaks.
Raw counts overlapping each peaks were quantified using bwtool summary (v.1.0.0) and normalised using the “voom” method (Law et al. 2014) in the “limma” R package (Ritchie et al. 2015).
Assembly: Mus musculus reference genome (mm10)
Supplementary files format and content: tab-delimited text files include log2 normalized expression values for each Sample.

molecule: genomic DNA

source_name: Balb/c transfer system Week 4

extract_protocol:
The protocol was adapted from Corces, et al. Resuspension buffer (RSB) was made at a final concentration of 10 mM Tris-HCl pH 7.5 (Thermo Fisher #15567027), 3 mM MgCl2 (Thermo Fisher #AM9530G), and 2 mM NaCl (Thermo Fisher #AM9760G) in molecular grade H20. 20,000-50,000 viable cells were pelleted in low-bind 1.5 ml microcentrifuge tubes (Eppendorf # 022431021), and washed once with PBS supplemented with 1% fetalplex and protease inhibitor (Sigma #P8340, stock at 100x). Supernatant was vacuum aspirated, and 50 µl of cold lysis buffer containing 0.1% IGEPAL CA-360 (Sigma #I8896, 0.01% Digitonin (Promega #G9441) , and 0.1% Tween-20 (Sigma #11332465001) in RSB was added to each sample by gently pipetting. Samples were incubated on ice for 3 minutes to isolate nuclei, then washed with 950 ul of 0.1% Tween-20 in RSB and pelleted at 500 x g for 10 minutes at 4⁰ C. Supernatant was aspirated using p1000 and p200 pipets, followed by addition of 50 ul transposition mix containing 25 ul TD buffer, 2.5 ul TDE1 Tagment DNA Eznyme (Illumina #20034197), 16.5 µl PBS, 0.01% Digitonin, 1% Tween-20, brought to 50 µl with molecular grade H20. Samples were incubated at 37⁰ C for 30 minutes, with mixing every 10 minutes by flicking the tube. Transposed DNA was then purified using the Qiagen MinElute PCR purification kit (Qiagen #28004).
To generate libraries, adapters (IDT for Illumina Nextera DNA Unique Dual Indexes, Illumina, #20027215) were added during amplification using 2X Phusion High Fidelity Mastermix with HF Buffer (ThermoFisher #F531L).  Libraries were cleaned up with Zymo DNA Clean & Concentrator-5 columns (Zymo Research #D4004) and assessed with a Qubit Flex Fluorometer (ThermoFisher $Q33327) and a TapeStation 4200 (Agilent #G2991BA).

value: spleen

value: GK1.5 + NP-Ficoll derived DP MBC


title: Week4.DN.NPFic.1.ATAC

value: GK1.5 + NP-Ficoll derived DN MBC


title: Tc1-day5

type: RNA

city: Houston

first: Liuling

last: Xiao

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description:
yi-q16001
Gene expression data from in vitro polarized Tc1 cells on day 5

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


title: Control-1

city: Suita

first: Junjun

last: Li

address: 2-2 Yamadaoka

country: Japan

institute: Osaka University

data_processing:
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks ver. 2.2.1.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw count for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

extract_protocol:
RNA was harvested using TRIzol™ Reagent ((Invitrogen, USA)) according to the manufacturer’s protocol.
Library preparation was performed using the TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Human iPSC-derived cardiomyocytes

value: WT

tag: treatment


title: Week4.DP.NPFic.2.RNA

description: Balb/c transfer system. Week 4.


title: Week4.DP.FGK.2.RNA

description: Balb/c transfer system. Week 4.

value: DP FGK MBC


title: Week4.DP.FGK.1.RNA

description: Balb/c transfer system. Week 4.


title: Week4.DN.NPFic.2.RNA

description: Balb/c transfer system. Week 4.

value: DN NP-Ficoll MBC


title: MCF7 A-DCCs_2 [A_2]

city: Hangzhou

first: Yao-Shun

last: Yang

state: Zhejiang Province

address: 866 Yuhangtang Rd

institute: Zhejiang University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include gene_count for each Sample

source_name: MCF7 A-DCCs

extract_protocol:
Cells were freezed and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: A-DCCs


title: 769-P sihnRNPA2B1-1

description: hnRNPA2B1 count


title: Week4.DN.FGK.2.ATAC

value: FGK + GK1.5 treated DN MBC


title: Week4.DN.FGK.1.ATAC


title: Week4.DN.NPFic.1.RNA

description: Balb/c transfer system. Week 4.


title: Week4.DN.aCD40L.2.ATAC

value: MR1 treated DN MBC


title: Week4.DN.FGK.2.RNA

description: Balb/c transfer system. Week 4.

value: DN FGK MBC


title: 769-P sihnRNPA2B1-NC2

description: hnRNPA2B1 count


title: 769-P sihnRNPA2B1-NC3

description: hnRNPA2B1 count


title: Week4.DN.FGK.1.RNA

description: Balb/c transfer system. Week 4.


title: Week4.aCD40L.DP.1.ATAC

value: MR1 treated DP MBC


title: Week4.CD80SP.NPFic.2.RNA

description: Balb/c transfer system. Week 4.

value: CD80SP NP-Ficoll MBC


title: Week4.CD80SP.NPFic.1.RNA

description: Balb/c transfer system. Week 4.

value: Balb/c


title: 769-P sihnRNPA2B1-NC1

description: hnRNPA2B1 count


title: Week4.CD80SP.FGK.2.RNA

description: Balb/c transfer system. Week 4.

value: Spleen

value: CD80SP FGK MBC


title: 769-P siDRAIC-3

description: DRAIC count

value: clear cell Renal Carcinoma

value: siDRAIC


title: Week4.CD80SP.FGK.1.RNA

description: Balb/c transfer system. Week 4.


title: 769-P siDRAIC-2

description: DRAIC count


title: Week4.aCD40L.DN.1.ATAC

value: spleen


title: Week10.CD80SP.NPCGG.3.RNA

description: Balb/c transfer system. Week 10.

value: CD80SP MBC


title: Week10.CD80SP.NPCGG.1.RNA

description: Balb/c transfer system. Week 10.


title: Week10.PDL2SP.NPCGG.2.ATAC

source_name: Balb/c transfer system Week 10

value: SP MBC


title: Week10.PDL2SP.NPCGG.1.ATAC


title: Week10.CD80SP.NPCGG.2.RNA

description: Balb/c transfer system. Week 10.


title: Day2-5.GL7.PreC.3.RNA

source_name: Balb/c transfer system. Day 2.5.


title: 769-P siDRAIC-1

description: DRAIC count


title: Day2-5.GL7.PreC.2.RNA


title: 769-P siDRAIC-NC3

description: DRAIC count

value: siDRAIC-NC


title: Day14.LZ.GC.3.RNA

source_name: Balb/c transfer system. Day 14.


title: Week10.DP.NPCGG.2.ATAC

value: DP MBC


title: Day2-5.GL7.PreC.1.RNA


title: Week10.DP.NPCGG.1.ATAC


title: Day14.LZ.GC.2.RNA


title: 769-P siDRAIC-NC2

description: DRAIC count


title: Day14.LZ.GC.1.RNA


title: Week10.DN.NPCGG.2.ATAC

value: DN MBC


title: Day14.DZ.GC.2.RNA


title: Day14.DZ.GC.3.RNA


title: 769-P siDRAIC-NC1

description: DRAIC count


title: Week10.DN.NPCGG.1.ATAC


title: Week10.DP.NPCGG.3.RNA

source_name: Balb/c transfer system. Week 10.


title: Human Fetal Astrocyte (Lonza:CC-2565)

city: DARLINGTON

first: Andre

last: Mckenzie

state: New South Wales

address: J03 Level 1 Mylab HubElectrical Engineering buildi

country: Australia

institute: University of Sydney

description:
Fetal Astro
Illumina NovaSeq X

data_processing:
Read Qaulity was assesed using FastQC
Reads were mapped to Ensembl GRCH37.70 using Star Aligner
Read count was extracted using FeatureCounts from aligned reads to human genome
Assembly: Ensembl GRCH37.70
Supplementary files format and content: tab-deliminted text file includes raw counts of all sample

source_name: Fetal Astrocyte

growth_protocol: Cells were grown on matrigel (0.08 mg/well) coated 6-well platesNPCs were maintained in media containing DMEM/F12, 1x N2 (Invitrogen), 1x B27-RA (Invitrogen) and 20 ng/ml FGF2 (Abcam) and changed daily.Astrocytes were maintained in astrocyte medium (astrocyte basal medium (ScienCell), 2 % fetal bovine serum, astrocyte growth supplement and 10 U/mL penicillin/streptomycin solution) and were fed every other day. All cells were incubated at 37C with 5% CO2.

extract_protocol:
RNA was extracted using Rneasy kit from Qiagen. Greater than 500 ng of RNA was collected per sample with a RIN score grater than 9.
RNA-seq data was collected by the Australian Genome Research Facility via the Illumina Novaseq X system. Samples were run on the 10B 300 cycle (2 x 150 bp) lane.

treatment_protocol: Human control iPSC-derived astrocytes and human fetal astrocytes (Lonza:CC-2565) were plated at 12x104 cells/well of a 6-well plate. Human control iPSC-derived neural precursor cells (NPCs) were plated at 48x104 cells/well of a 6-well plate. Cells were then incubated from 24-48 h.

value: Fetal Astrocyte

tag: gender

value: M


title: Day2-5.GL7.PreC.3.ATAC

source_name: Balb/c transfer system Day 25

value: Early memory precursor


title: Week10.DP.NPCGG.2.RNA


title: Week10.DP.NPCGG.1.RNA


title: 88 Ctrl iPSC-derived astrocyte

description:
88 iAstro
Illumina NovaSeq X

source_name: iPSC-derived Astrocyte

value: iPSC-derived Astrocyte


title: Week10.PDL2SP.NPCGG.3.RNA


title: Day2-5.GL7.PreC.2.ATAC


title: 88 Ctrl iPSC-derived neural precursor cell

description:
88 NPC
Illumina NovaSeq X

source_name: iPSC-derived Neural precursor cell

value: iPSC-derived Neural precursor cell


title: Week10.PDL2SP.NPCGG.2.RNA


title: Normal group rat, No.68

city: Shanghai

first: Ming-Shu

last: Xu

address: No. 650 South Wanping Road, Xuhui District

department: Shanghai Research Institute of Acupuncture and Meridian

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to Rnor_6.0 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Rattus norvegicus

source_name: motor cortex

extract_protocol:
Total RNA was extracted following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

tag: time

value: 8 weeks

value: motor cortex

value: Sprague-Dawley

tag: Sex

value: male


title: 71 Ctrl iPSC-derived astrocyte

description:
71 iAstro
Illumina NovaSeq X

value: F


title: Normal group rat, No.39


title: Day14.LZ.GC.2.ATAC

source_name: Balb/c transfer system Day 14

value: Balb/c

value: Light zone germinal center


title: 71 Ctrl iPSC-derived neural precursor cell

description:
71 NPC
Illumina NovaSeq X


title: Day14.LZ.GC.1.ATAC

value: spleen


title: Week10.PDL2SP.NPCGG.1.RNA

value: Spleen


title: Week10.DN.NPCGG.3.RNA


title: Normal group rat, No.32


title: SRSF6_rep1

status: Public on Jan 08 2024

city: Berlin

first: IBRAHIM

middle: AVSAR

last: ILIK

state: Berlin

address: Ihnestraße 63-73

country: Germany

institute: Max-Planck-Institut für molekulare Genetik

data_processing:
library strategy: FLASH-seq (Ilik et al., 2020)
Illumina base calling, demultiplexing and FASTQ conversion
Merging with bbmerge v. 38.72
Demultiplexing with flexbar v. 3.5.0
UMI extraction with umi_tools extract v. 1.0.0
Alignment to human (hg38), mouse (mm10) or Drosophila genomes (dm6) with bowtie2 v. 2.3.5 and bbmap v. 38.72
bigWigs generation using bamCoverage 3.3.1
Assembly: hg38, mm10, dm6
Supplementary files format and content: Raw RNA-seq coverage in bigWig format, separate files for plus and minus strands

source_name: Flp-In T-Rex HEK293

extract_protocol:
Cells were crosslnked with 0.199 mj/cm2 UV-C light,  lysed with 1xNLB buffer, protein-of-interest purified with streptavidin beads, co-purifying RNA isolated with proteinase K digestion and purified with Oligo clean and concentrator-5 columns (Zymo).
Custom library prep, described in Ilik et al., 2020. Isolated RNA is ligated to s-oligo on beads, reverse-transcribed, RNaseH digested, circularized with CircLigase and PCR amplified.

value: Flp-In T-Rex HEK293

tag: molecule subtype

value: RNAseI digested RNA


title: MCF7 A-DCCs-input DNA

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the hg18 genome assembly using BWA version 0.7.12-r1039
Peak calling using MACS2 (version: 2.1.0)
Genome_build: hg18
Supplementary_files_format_and_content: peak files

source_name: MCF7 A-DCCs-input DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: A-DCCs

tag: chip antibody


title: Day14.DZ.GC.2.ATAC

value: Dark zone germinal center


title: Day14.DZ.GC.1.RNA


title: 06 Ctrl iPSC-derived neural precursor cell

description:
06 NPC
Illumina NovaSeq X


title: Week10.DN.NPCGG.1.RNA


title: Week10.DN.NPCGG.2.RNA


title: Low EV secretor scRNAseq

city: Los Angeles

first: Dino

last: Di Carlo

address: 420 Westwood plaza

institute: University of California, Los Angeles

description: scRNA-seq

data_processing:
Data was demultiplexed and output as fastq.gz in Basespace using library indexes
fastq.gzs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Data was analyzed using 10X Cell Ranger and Loupe browsers.
Assembly: GRCh38 (human)
Supplementary files format and content: Data was filtered based on Cell Ranger Multi analysis.

source_name: adipose

growth_protocol: Immortalized human adipose-derived MSCs (ATCC SCRC-4000) were cultured in MSC Basal Medium supplemented with Low Serum MSC Growth Kit for adipose MSCs.

extract_protocol:
Nanovials were loaded directly into the cell mix at a concentration of 500 nanovials per ul for use in the 10x Chromium workflow.
Libraries were constructed as described in the Chromium Single Cell 3' Reagent Kits User Guide (v3.1 Chemistry Dual Index)
scRNAseq libraries were constructed as typically described in the guide above.

treatment_protocol: MSCs were cultured and loaded onto gelatin coated nanovials for 2 hours before straining excess cells. Cells were bound and allowed to secrete for a 24 hour incubation. Nanovials are then collected and incubated with anti-CD9 BV650 antibody for 30 minutes. Nanovials containing single cells were isolated by FACS using calcein stain and anti-CD9 fluorescent signal as high and low secretors. Cell-loaded nanovials were then diluted and added directly to the single cell RNA-seq workflow.

value: adipose

value: ATCC SCRC-4000

value: Mesenchymal Stromal Cell


title: Day14.DZ.GC.1.ATAC


title: MCF7 A-DCCs-DEK_2

source_name: MCF7 A-DCCs-DEK


title: Day0.FO.3.RNA


title: Day2-5.GL7.PreC.1.ATAC

value: Early memory precursor


title: Day0.FO.2.ATAC

source_name: B18+/- JK-/- mice Day 0

value: Follicular Naive


title: High EV secretor scRNAseq

description: scRNA-seq


title: MCF7 A-DCCs-DEK_1


title: Day0.FO.1.ATAC


title: Day0.FO.2.RNA


title: MCF7 A-DCCs_ATAC-seq_3

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2).
These reads were aligned to a reference genome using BWA, with standard parameters.
These reads were then filtered for high quality (MAPQ ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel -- keepdup all --call-summits’.
Genome_build: hg18
Supplementary_files_format_and_content: peak files

extract_protocol:
Nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix. The transposition reaction was incubated at 37°C for 30 min.
Equimolar Adapter1 and Adatper 2 were added after transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: transposase-accessible DNA


title: M509CD45pos

first: Ronald

middle: J

last: Buckanovich

state: Pennsylvania

address: 204 Craft Avenue

department: Department of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell cDNA libraries were processed for RNA sequencing using an Illumina NovaSeq 6000 platform. CellRanger (v3.1.0) was used to perform read alignment, barcode filtering and unique molecular identifier quantification using the 10x GRCh38 transcriptome (v3.0.0) for inhouse FASTQ inputs with the default settings. The count matrices of the four reads were then aggregated using cellrange aggr.
Inhouse CellRanger-filtered matrices were loaded into an individual Seurat object using Seurat (v4.0.1). A total of 18 samples were selected from the public datasets.  For each sample, the resulting gene-by-cell matrix was normalized and scaled. Cells retained for analysis had a minimum of 500 expressed genes and 1,000 UMI counts and had less than 25% mitochondrial gene expression. Cell cycle phase was assigned using the Seurat CellCycleScoring function. Scrublet (v0.2.1) was used to calculate and filter cells with a doublet score greater than 0.25. Sample matrices were merged by patient and subsequently renormalized and scaled using default Seurat functions. Sample matrices were merged by patient and subsequently renormalized and scaled using default Seurat functions.
The resulting gene-by-cell matrix as described above was loaded as a Seurat object via the CreateSeuratObject function to include features detected in at least 3 cells and cells with at least 400 detected features. Cells retained for analysis had a minimum of 500 expressed genes and 1,000 UMI counts and had less than 30% mitochondrial gene expression. DoubletFinder (v2.0.3) was used to calculate and filter cells, where the SCTransform normalization was used and the doublet formation rate was set to be 5%. Sample matrices were merged by patient and subsequently renormalized and scaled using log-normalization with scale factor 1e4.
We scaled and centered 2,000 variable features, detected with the vst method, and regressed out mitochondrial read percentage. Principal component analysis was performed on the filtered feature-by-barcode matrix. UMAP embeddings were based on the first 30 principle components. Subsequently, data integration was performed using Harmony (v0.1.0) using the function RunHarmony to remove the batch effects among samples. The integrated data contained a total of 33,718 genes across 111,062 cells.
Assembly: GRCh38-3.0.0
Supplementary files format and content: a h5 files which contains a gene expression matrix

source_name: Ovary

extract_protocol:
We selected two treatment-naïve high-grade ovarian serous cancer samples, one high-stromal and one low-stromal, and generated inhouse scRNA-seq data. We used FACS to sort immune cells (CD45+) and non-immune cells (CD45-) of each tumor sample. Each of the two compart was subjected to scRNA-seq as a separate library. Single-cell libraries were generated from sorted live CD45+ cells using the Chromium Single Cell 30 Reagent (5PrimeV1 and Next GEM 5PrimeV1.1 Chemistry).
Sorted cells were resuspended in PBS with 0.04% bovine serum albumin (BSA; Sigma) and were counted using the Cellometer Auto2000 (Nexcelom). Cells were then loaded into the Single Cell Chip and processed through the 10X controller for droplet generation (targeting a recovery of 10,000 cells per sample), resulting in droplets containing a single cell and bead per droplet. After droplet generation, cells were subjected to in-drop lysis and reverse transcription, resulting in single-cell transcriptomes bearing bead-speciﬁc sequences to identify the cell of origin. Following reverse transcription, cDNA was isolated and ampliﬁed by 13 cycles of PCR. Ampliﬁed cDNA was then size-selected by SPRISelect Beads, and was subjected to enzymatic fragmentation, end repair, and A-tailing. Adaptors were then ligated, and sample indices were added by PCR. Samples were then size-selected by SPRISelect, and the concentration was determined by KAPA DNA Quantiﬁcation. The end result of this process is library constructs containing P5 and P7 Illumina sequencing adaptors, a 16 base pair cell barcode, 10 base pair unique molecular identiﬁer (UMI), a gene insert and an i7 sample index.

value: Ovary


title: Day0.FO.1.RNA


title: LysM_d21

city: Beijing

first: Siwei

last: Feng

address: No.30,Shuangqing street

institute: Siwei Feng

description: 3’ Gene Expression

data_processing:
Quality control, Cell Ranger Single Cell Software Suite (v4.0).
Sample de-multiplexing, Cell Ranger Single Cell Software Suite (v4.0).
Barcode processing, Cell Ranger Single Cell Software Suite (v4.0).
Single-cell 3′ gene counting, Cell Ranger Single Cell Software Suite (v4.0).
Alignment, Cell Ranger Single Cell Software Suite (v4.0).
Assembly: mm10 (GRCm38)
Supplementary files format and content: Filtered matrix of gene by cell expression (matrix.mtx), file with barcodes (barcodes.tsv) and file with expressed genes (genes.tsv). Files are ready to be imported to Seurat package.

source_name: Lung

extract_protocol:
Lung cells were harvested PBS perfusion, placed in DMEM containing 10% FBS, minced finely, and digested at 37 ⁰C for an hour with mechanical disruption with a stir bar and enzymatic digestion with Liberase Blendzyme III (Roche), hyaluronidase (Sigma), and DNase I (Sigma).
Single cells from naïve or infected lungs were enriched for live cells using dead-cell depletion kit (Milteny). Then single cell suspensions were subjected to droplet-based massively parallel scRNA-seq using Chromium Single Cell 3′ (v3) Reagent Kit in the BSL-3 laboratory as per manufacturer’s instructions (10x Genomics). Cell suspensions were loaded at 1,000 cells/μl to capture 10,000 cells/lane. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript was labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA was isolated and removed from the BSL-3 space for library generation. The cDNA underwent 11 cycles of amplification, followed by fragmentation, end repair, A-tailing, adaptor ligation, and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (Illumina), targeting 50,000 read pairs/cell.

value: Lung, left lobe

value: Mycobacterium tuberculosis infection, day 21


title: 06 Ctrl iPSC-derived astrocyte

description:
06 iAstro
Illumina NovaSeq X

value: iPSC-derived Astrocyte

value: F


title: M509CD45neg

description: 10x Genomics


title: young control

city: Durham

first: Daniel

last: Saban

state: NC

address: 2351 Erwin Rd, Duke Eye Center

institute: Duke University

description: barcodes 4

data_processing:
Raw sequencing data were initially processed with Cell Ranger pipelines (10x Genomics).
FASTQ files were generated by demultiplexing BCL files and further aligned with STAR aligner to the mouse genome reference mm10.
Feature barcode processing and unique molecular identifier counting were then performed according to the standard workflow.
Genome_build: mm10
Supplementary_files_format_and_content: expression matrix in mtx format with tsv files of barcodes and features

molecule: polyA RNA

source_name: retina

extract_protocol:
Retinas were dissected and digested to generate single cell suspension. Viable CD45+ single cells were sorted using FACS.
Libraies were constructed using 10x Genomics Chromium platform with Chromium Single Cell 3′ chemistry reagent kit.
scRNA-seq

value: retinal immune cells

value: retina

value: WT

tag: age

value: post natal 60 days


title: M419CD45pos

description: 10x Genomics


title: MCF7 A-DCCs_ATAC-seq_2

source_name: MCF7 A-DCCs

value: A-DCCs


title: MCF7 A-DCCs_ATAC-seq_1


title: CD11c_d21

description: 3’ Gene Expression


title: Flox_d21

description: 3’ Gene Expression


title: aging model

description: barcodes 3

value: post natal 2 years


title: M419CD45neg

description: 10x Genomics


title: MCF7 A-DCCs-DEK_3


title: MCF7 DCCs ATAC-seq_3

source_name: MCF7 DCCs

value: dormant cancer cells (DCCs)


title: LysM_Naive

description: 3’ Gene Expression

value: Naive


title: P23H model

description: barcodes 2


title: NR

description:
SampleTag01_NR
SampleTag02_NR
SampleTag03_NR
SampleTag04_NR
SampleTag05_NR
SampleTag06_NR
SampleTag07_NR
SampleTag08_NR
SampleTag08_hs had low viability. No cells were detected.

data_processing:
Raw sequencing data were initially processed with BD Rhapsody™ Analysis pipelines on the Seven Bridges Genomics platform
FASTQ files, the human genome reference GRCh38 and the transcriptome annotation file were used for alignment and annotation of WTA analysis.
Read quality filtering,cell ID and molecule ID identification, and mRNA alignment were perfromed. UMI errors were adjusted using recrusive substitution erroro correction.
Putative cells and sample origins were determined according to the standard pipline.
Assembly: GRCh38
Supplementary files format and content: csv files of expression counts and sample tags

source_name: neuroretina

extract_protocol:
Retinas were dissected and digested to generate single cell suspension. Samples were immuno-labelled with BD single-cell multiplexing antibodies. Viable CD45+CD11B+ single cells were sorted using FACS.
Tow libraies of RPE/choroid and neuroretinas were constructed using BD Rhapsody™ Single-Cell Analysis System with Whole Transcriptome Analysis (WTA) Amplification Kit.

value: neuroretina

value: myeloid cells

tag: donor id

value: Donor1 -  Donor8

tag: sample tag id

value: SampleTag01_hs - SampleTag08_hs

value: over 70


title: MCF7 DCCs ATAC-seq_2

value: transposase-accessible DNA


title: NaIO3 model

description: barcodes 1


title: CD11c_Naive

description: 3’ Gene Expression

value: Lung, left lobe


title: RPE_CH

description:
SampleTag01_RPE_CH
SampleTag02_RPE_CH
SampleTag03_RPE_CH
SampleTag04_RPE_CH
SampleTag05_RPE_CH
SampleTag06_RPE_CH
SampleTag07_RPE_CH
SampleTag08_RPE_CH

source_name: RPE/choroids

value: RPE/choroids


title: Flox_Naive

description: 3’ Gene Expression


title: MCF7 DCCs ATAC-seq_1


title: siTRUB1_input_rep1

status: Public on Jan 06 2024

city: Chicago

first: Tao

last: Pan

state: Illinois

address: 929 E. 57th Street

department: Biochemistry and Molecular Biology

institute: University of Chicago

description: Nanopore RNA direct sequencing

data_processing:
Base calling was performed by guppy base caller (version 3.2.2+9fe0a78).
Then the reads were aligned to human genome (GRCh38.p13) by minimap2 (version 2.18-r1015) with parameters -ax splice -uf -k14.
The mapped reads were piled up by samtools (v1.11).
The expression counts of genes were calculated as the maximum peak height of the reads piled at the gene regions.
Assembly: GRCh38.p13
Supplementary files format and content: Sample 1 (HeLa): csv files containing genome positions of A and m6A sites used for model training
Supplementary files format and content: Sample 2-13 (HEK 293T): csv files containing gene expression levels

growth_protocol: Human embryonic kidney (HEK) HEK293T/17 cells (CRL11268) and HeLa cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose and L-glutamine, without sodium pyruvate (HyClone, SH30022.01) and with 10% FBS in a 37°C incubator at 5% CO2 to seed for reverse transfection by RNAiMax (Sigma 13778150). HeLa cells (ATCC) were cultured in  Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose and L-glutamine, without sodium pyruvate (HyClone, SH30022.01) with 10% FBS and 1% Pen–Strep(Penicillin–Streptomycin). ~3.5 x 106 cells were seeded into three 150 mm plates with the same media without 1% Pen–Strep(Penicillin–Streptomycin).

extract_protocol:
Input and polysome RNA samples were made to 150 μL in dH2O and cleaned by adding 280 μL Beckman RNAClean XP beads. Samples were mixed by pipetting up and down, incubated at room temperature for 5 minutes, pelleted on a magnetic rack for 5 minutes, washed with 1000 μL 70% EtOH three times, and air dried for ten minutes before eluting into 150 μL dH2O. Poly(A)-selection of cleaned RNA samples was then done using Promega PolyATract mRNA Isolation System IV per the manufacturer’s protocol. Briefly, RNA samples were made to 500 μL and incubated at 65°C for 10 minutes before addition of 3 μL Biotin-dT and 1x SSC. Once cooled, this sample was added to 100 μL of washed poly(A) magnetic beads in 0.5x SSC. Following a 10-minute incubation at room temperature, RNA-bound beads were captured using a magnetic rack, washed in 0.1X SSC, and eluted in a total of 250 μL dH2O.
RNA libraries for Nanopore direct RNA seq were prepared with Oxford Nanopore technology SQK-RNA-002 kit following manufacturer's protocols.

treatment_protocol:
For each knockdown condition, 75 μL Lipofectamine RNAiMax was added to three separate 150 mm plates containing 300 pmol siRNA (siCtrl, MISSION® siRNA Universal Negative Control #1; siMETTL3, SASI_HS_00044317; siTRUB1, SASI_Hs02_0036419) in 5 mL Opti-MEM™ I Reduced Serum Medium (31985070) and incubated at 37°C with 5% CO2 for 20 minutes.
5-50% sucrose gradient (20 mM HEPES, pH 7.6, 100mM KCl, 5 mM MgCl2, 100 ug/mL CHX supplemented with fresh 1x Roche protease inhibitor and 1% SUPERase Inhibitor) was prepared in SETON 7042 tubes using a Biocomp Gradient Station. 600 μL sucrose gradient was removed from the top of each balanced sucrose gradient tube and then replaced by gently pipetting 600 μL of the respective knockdown cell lysate on top the gradient. Sucrose gradients were centrifuged for 3 hours at 28,000 RPM in an Optima L-100XP centrifuge using a Beckman SW28 rotor. Sucrose gradient fractions were collected and absorbances continuously measured using a Biocomp gradient station.

value: TRUB1 KD

value: input


title: siTRUB1_polysome_rep1

description: Nanopore RNA direct sequencing

value: polysome


title: siMETTL3_polysome_rep2

description: Nanopore RNA direct sequencing

value: METTL3 KD


title: siTRUB1_input_rep2

description: Nanopore RNA direct sequencing


title: siMETTL3_polysome_rep1

description: Nanopore RNA direct sequencing


title: siMETTL3_input_rep2

description: Nanopore RNA direct sequencing


title: siCtrl_polysome_rep1

description: Nanopore RNA direct sequencing

value: WT


title: siCtrl_input_rep2

description: Nanopore RNA direct sequencing


title: siMETTL3_input_rep1

description: Nanopore RNA direct sequencing


title: siCtrl_polysome_rep2

description: Nanopore RNA direct sequencing


title: siCtrl_input_rep1

description: Nanopore RNA direct sequencing


title: HeLa_WT

description: Nanopore RNA direct sequencing

source_name: HeLa (ATCC)

value: HeLa (ATCC)

value: untreated


title: Liver-FFPE-5mC-2

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican St

department: Medicine

institute: University of Washington

description: 03-03-22 ChIP755MeDIP-Seq

data_processing:
Fastqs were processed using Fastp all-in-one processing tool.
Files were then converted to BAM using Bowtie2 tool, and into bigwig format using Bamcompare tool (treatment = 5mC, control = input).
Read counts were obtained from the BAM files using featureCounts, and then PCA plots and normalized count tables were generated using the Limma tool.
Spearman correlation scatterplots were generated by running multiBigwigSummary tool on the bigwig files to be compared, and then running plotCorrelation on the resulting files.
Assembly: mm10
Supplementary files format and content: tabular - normalized read counts

source_name: liver

extract_protocol: none provided

treatment_protocol: Organs harvested from mice and either flash frozen (Frozen) or fixed in 10% formalin and then embedded in paraffin (FFPE).

value: liver

tag: nucleic acid_type

value: ssDNA

tag: medip antibody

value: FFPE


title: Kidney-Frozen-RT

description: 01-15-22 RT-Seq3

data_processing:
Fastqs were processed using Fastp all-in-one processing tool.
Files were then converted to BAM using HISAT2.
Read counts were obtained from the BAM files using featureCounts, and then PCA plots and normalized count tables were generated using the Limma tool.
Spearman correlation scatterplots were generated by running Multibamsummary tool on the BAM files to be compared, and then running plotCorrelation on the resulting files.
Genomic Expression figures were generated by uploading the BAM files to IGV and visualizing expression at a given genomic location.
Assembly: mm10
Supplementary files format and content: tabular - normalized read counts

source_name: kidney

extract_protocol: RNA isolated using deparaffinization protocol developed by Bomsztyk lab (FFPE only) and Trizol and PIXUL sheared for 6min.

value: kidney

value: Frozen


title: Kidney-FFPE-RT

description: 01-15-22 RT-Seq3


title: Liver-FFPE-RT

description: 01-15-22 RT-Seq3


title: Heart-FFPE-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq

source_name: heart

value: heart


title: Heart-FFPE-RT

description: 01-15-22 RT-Seq3


title: Brain-FFPE-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq

source_name: brain

value: brain


title: Liver-Frozen-RT

description: 01-15-22 RT-Seq3


title: Kidney-FFPE-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Brain-Frozen-RT

description: 01-15-22 RT-Seq3


title: Liver-Frozen-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Heart-Frozen-RT

description: 01-15-22 RT-Seq3


title: Kidney-Frozen-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Heart-Frozen-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq


title: siTRUB1_polysome_rep2

description: Nanopore RNA direct sequencing


title: Brain-Frozen-5mC-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Liver-FFPE-Input-2

description: 03-03-22 ChIP755MeDIP-Seq

value: Input


title: Kidney-FFPE-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Brain-FFPE-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Heart-FFPE-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Kidney-Frozen-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Liver-Frozen-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Brain-Frozen-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Heart-FFPE-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-FFPE-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Kidney-FFPE-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Liver-Frozen-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-FFPE-RT

description: 01-15-22 RT-Seq3


title: Heart-Frozen-Input-2

description: 03-03-22 ChIP755MeDIP-Seq


title: Heart-Frozen-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Heart-FFPE-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Liver-FFPE-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-FFPE-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-Frozen-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-Frozen-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Kidney-Frozen-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Kidney-FFPE-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Heart-Frozen-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-FFPE-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD

data_processing:
Fastqs were processed using Fastp all-in-one processing tool.
Files were then converted to BAM using Bowtie2 tool, and into bigwig format using Bamcompare tool (treatment = antibody, control = input).
Read counts were obtained from the BAM files using featureCounts, and then PCA plots and normalized count tables were generated using the Limma tool.
Spearman correlation scatterplots were generated by running multiBigwigSummary tool on the bigwig files to be compared, and then running plotCorrelation on the resulting files.
Assembly: mm10
Supplementary files format and content: tabular - normalized read counts

extract_protocol:
Frozen: tissue core harvested using CryoCore, 1% formaldehyde crosslink for 30min, 125mM glycine quench for 5min, PBS wash, then PIXUL shear 4minx4 and centrifuge. FFPE:  deparaffinization with SafeClear at 50oC for 3min, then serial 10min incubations in EtOH (100%, 50%, and 10%), extraction at 95oC for 20min in extraction buffer, then addition of protease inhibitors and PIXUL shear 4min x4 and centrifuge. The obtained chromatin is then immunoprecipitated with Pol II CTD antibody using the Matrix ChIP protocol developed by the Bomsztyk lab.
Libraries were generated using the Low Cell Chip Seq, Next Gen Library, and Next Gen Indexing kits by Active Motif OR Twist NGS Mechanical Fragmentation kit by Twist Biosciences
ChIP-Seq using Pol II CTD antibody

value: dsDNA

value: Pol II CTD


title: Kidney-FFPE-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Kidney-Frozen-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-FFPE-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-Frozen-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Heart-FFPE-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Heart-Frozen-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-FFPE-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-FFPE-5mC-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Brain-FFPE-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-Frozen-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Heart-Frozen-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Kidney-Frozen-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Brain-Frozen-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Liver-FFPE-Pol-II-1

description: 11-19-21 ChIP750-751Seq LCCS - Pol II CTD


title: Kidney-Frozen-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Liver-Frozen-Input-1

description: 02-15-22 ChIP753MeDIP-Seq


title: Liver-Frozen-Pol-II-1


title: Brain-Frozen-Pol-II-1


title: Heart-FFPE-Pol-II-1


title: Brain-FFPE-Pol-II-1


title: Kidney-FFPE-PolII-Input-1


title: Liver-FFPE-PolII-Input-1


title: Kidney-FFPE-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Heart-Frozen-Pol-II-1


title: Liver-Frozen-PolII-Input-1


title: Kidney-Frozen-PolII-Input-1


title: Brain-FFPE-PolII-Input-1


title: Heart-FFPE-PolII-Input-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Brain-Frozen-Pol-II-2

description: 01-21-22 ChIP752Seq TWIST - Pol II CTD


title: Heart-FFPE-PolII-Input-1


title: Brain-Frozen-PolII-Input-1


title: Kidney-FFPE-H3K4m3-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3

extract_protocol:
Frozen: tissue core harvested using CryoCore, 1% formaldehyde crosslink for 30min, 125mM glycine quench for 5min, PBS wash, then PIXUL shear 4minx4 and centrifuge. FFPE:  deparaffinization with SafeClear at 50oC for 3min, then serial 10min incubations in EtOH (100%, 50%, and 10%), extraction at 95oC for 20min in extraction buffer, then addition of protease inhibitors and PIXUL shear 4min x4 and centrifuge. The obtained chromatin is then immunoprecipitated with H3K4m3 antibody using the Matrix ChIP protocol developed by the Bomsztyk lab.
Libraries were generated using the Low Cell Chip Seq, Next Gen Library, and Next Gen Indexing kits by Active Motif OR Twist NGS Mechanical Fragmentation kit by Twist Biosciences
ChIP-Seq using H3K4m3 antibody


title: Heart-Frozen-PolII-Input-1


title: Brain-FFPE-H3K4m3-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K4m3-Input-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-FFPE-H3K4m3-Input-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Heart-FFPE-H3K4m3-Input-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K4m3-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-FFPE-H3K4m3-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Heart-FFPE-H3K4m3-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-FFPE-Pol-II-1


title: Heart-FFPE-H3K4m3-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Brain-FFPE-H3K4m3-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-Frozen-Pol-II-1


title: Kidney-FFPE-H3K4m3-Input-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-Frozen-H3K4m3

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Heart-Frozen-H3K4m3

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K4m3-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Brain-Frozen-H3K4m3

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K4m3-Input-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Brain-FFPE-H3K4m3-Input-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Heart-FFPE-H3K4m3-Input-1

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Heart-Frozen-Input

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Kidney-Frozen-Input

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Heart-FFPE-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac

extract_protocol:
Frozen: tissue core harvested using CryoCore, 1% formaldehyde crosslink for 30min, 125mM glycine quench for 5min, PBS wash, then PIXUL shear 4minx4 and centrifuge. FFPE:  deparaffinization with SafeClear at 50oC for 3min, then serial 10min incubations in EtOH (100%, 50%, and 10%), extraction at 95oC for 20min in extraction buffer, then addition of protease inhibitors and PIXUL shear 4min x4 and centrifuge. The obtained chromatin is then immunoprecipitated with H3K27Ac antibody using the Matrix ChIP protocol developed by the Bomsztyk lab.
Libraries were generated using the Low Cell Chip Seq, Next Gen Library, and Next Gen Indexing kits by Active Motif OR Twist NGS Mechanical Fragmentation kit by Twist Biosciences
ChIP-Seq using H3K27Ac antibody


title: Kidney-FFPE-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Brain-Frozen-Input

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Brain-FFPE-H3K4m3-Input-2

description: 12-07-21 ChIP749Seq LCCS - H3K4m3


title: Brain-FFPE-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Kidney-Frozen-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Heart-Frozen-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Liver-Frozen-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Brain-Frozen-H3K27Ac-2

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Liver-FFPE-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Kidney-FFPE-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Heart-FFPE-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Brain-FFPE-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Liver-Frozen-H3K27Ac-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Kidney-Frozen-H3K27Ac-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Heart-Frozen-H3K27Ac-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Brain-Frozen-H3K27Ac-Input

description: 08-25-21 ChIP746Seq LCCS - H3K27Ac


title: Liver-Frozen-H3K4m3

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Liver-FFPE-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Liver-Frozen-Input

description: 11-13-21 ChIP749Seq LCCS - H3K4m3


title: Brain-FFPE-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Liver-Frozen-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Kidney-FFPE-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Kidney-Frozen-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Heart-Frozen-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Brain-Frozen-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: Br-FFPE-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP

data_processing:
Fastqs were processed using Fastp all-in-one processing tool.
Files were then converted to BAM using HISAT2.
Read counts were obtained from the BAM files using featureCounts, and then PCA plots and normalized count tables were generated using the Limma tool.
Spearman correlation scatterplots were generated by running multiBamSummary tool on the BAM files to be compared, and then running plotCorrelation on the resulting files.
Genomic Expression figures were generated by uploading the BAM files to IGV and visualizing expression at a given genomic location.
Assembly: mm10
Supplementary files format and content: tabular - normalized read counts

extract_protocol:
RNA isolated using deparaffinization protocol developed by Bomsztyk lab (FFPE only) and Trizol and PIXUL sheared for 20min, then immunoprecipitated with MeRIP antibodies (m6A, 5mC) using the MeRIP protocol developed by the Bomsztyk lab.
RNA libraries were generated using the Zymo-Seq RiboFree Total RNA Library Kit from Zymo Research.

tag: merip antibody


title: H-FFPE-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: K-Frozen-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-Frozen-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-FFPE-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: H-Frozen-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-FFPE-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: H-FFPE-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-Frozen-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-FFPE-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: K-Frozen-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Br-Frozen-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: K-FFPE-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: H-Frozen-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: H-FFPE-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: K-FFPE-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: Br-FFPE-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: Li-Frozen-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: Heart-FFPE-H3K27Ac-1

description: 03-23-21 ChIP722-723Seq LCCS - H3K27Ac


title: DMSO_2

city: Cambridge

first: Byron

last: Andrews

state: Choose County

address: Storm Therapeutics, Moneta Building, Babraham Research Campus

country: United Kingdom

institute: Storm Therapeutics

description: out_nanocompore_results_DMSO-vs-2457; out_nanocompore_results_DMSO-vs-3006

data_processing:
A GridION instrument controlled by MINKNOW software (v20.10.6) was loaded with four flowcells and four channel libraries were run separately and simultaneously. Readfish (v3.0.0) selective sequencing32 was used during the GridION run to eject abundant and irrelevant transcripts. Briefly, the accessions of 81 mouse transcripts comprising mitochondrial transcripts and cytoplasmic ribsomal protein-encoding transcripts were used to generate an exclude list
Reads were basecalled in real time using Guppy (v4.2.3). FAST5 files were recorded for later processing by Nanopolish (v0.11.2)
Basecalled reads and Fast5 signal files were processed to prepare for Nanocompore (v1.0.3) comparison analysis
Briefly, fastq files were aligned to a mouse transcriptome version M20 with minimap2 (v2.2.0)34 to obtain bam alignment files, then Nanopolish's eventalign module was used to estimate kmer pore transition ('dwell') times from the alignment and the Fast5 signal files. The Nanopolish-compress tool was used to average nanopolish output by kmer
Nanocompore was used to discern significant differences in signal current intensity and dwell time between the control and treatment replicate pairs, using the GMM-logit option to use Gaussian Mixture Modelling to discern the presence of two different nucleotide modification states, and logit regression analysis to calculate the difference in site characteristics between the samples.
Assembly: GRCm38
Supplementary files format and content: unfiltered output from nanocompore in .tsv format

source_name: breast

growth_protocol: Murine AT3 cells were cultured in DMEM (Gibco) supplemented with 10% FBS, 100 IU/ml penicillin, 100µg/ml streptomycin, 2mM Glutamax, 15mM HEPES and MEM Non-Essential Amino Acids (Gibco). All cell lines were incubated at 37°C and 5% CO2 and were regularly tested and verified to be negative for mycoplasma contamination by PCR analysis through in-house genotyping.

extract_protocol:
Total RNA was isolated using TRIzol LS reagent (Invitrogen) according to manufacturer’s instructions and ethanol precipitation. RNA concentration was quantified with a Qubit Fluorometer (Thermo Fisher Scientific). Extracted total RNA was processed to obtain polyA-tailed transcripts with Dynabeads (Invitrogen) according to the manufacturer's instructions.
A target amount of 200ng was used to create a readable transcript library for a single flowcell (type FLO-MIN106) using a protocol based on Oxford Nanopore Technology's DirectRNA SQK-RNA002 kit protocol. Each sample was sequenced on a single flowcell with version R9.4.1 chemistry.

treatment_protocol: AT3 cells were treated with DMSO, 20µM STM2457 or 2µM STM3006 in duplicate for 24 and 48 hours.

value: breast

value: Mouse mammary carcinoma

value: DMSO


title: K-FFPE-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: K-Frozen-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: STM2457_1


title: Br-Frozen-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: Br-Frozen-m6A-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Li-FFPE-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: Br-FFPE-Input-MeRIP-Seq4

description: 08-30-22 MeRIP-Seq4 from ChIP773MeRIP


title: Br-FFPE-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: H-FFPE-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: K-FFPE-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: STM3006_2


title: BASCsTracer, bleo injuryed, scRNAseq

first: zixin

last: liu

address: 320 Yueyang road, Life Science Research Building A2112

institute: Center for Excellence in Molecular Cell Science

description: 10x Genomics

data_processing:
Each single-cell RNA sequencing (scRNA-seq) dataset was processed using the CellRanger pipeline (v6.1.1) for alignment to the customized mouse reference genome (mm10), alignment filtering, barcode counting, and UMI counting.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: whole lung

extract_protocol:
After the mice were killed, the lungs were perfused using cold PBS through the right ventricle to wash out the blood cell and then the protease solution (collagenase type I (500U ml−1; Gibco 17100–017), elastase(4U ml−1; Worthington Biochemical Corporation LS002279), dispase (5 U ml−1; BD Biosciences 354235) and DNase I (0.33 U ml−1; Worthington Biochemical Corporation LS002139) in DMEM (Gibco, 11965092)) was injected into the lungs through the trachea to the lung. After that, the lungs were minced into small pieces and incubated in 4 ml protease solution for 30 min at a 37°C shaker with frequent agitation. Subsequently, the tissue pieces were dissociated by pipetting and centrifuged at 1000 x g for 5 min at 4°C. After washing with DMEM, the pellet was resuspended in 3 ml 0.1% Trypsin-EDTA (Gibco, 25200072) with DNase I and incubated for 20 minutes at a 37 °C shaker with agitation and pipetting. Then the DMEM with 10% FBS was added to terminate the digestion and the cells were filtered sequentially through 100 μm strainers and centrifuged at 1000 x g for 5 min at 4°C.
The cells isolated from bleomycin-treated mice were sorted using Fluorescence-Activated Cell Sorting (FACS) based on their cell lineage, relying specifically on fluorescent signals (AT2-Tracer: ZsGreen+; BASCs-Tracer: ZsGreen+, tdTomato+; Club-Tracer: tdTomato+). Cells with distinct lineages were loaded into the 10x Chromium controller to generate GEMs respectively, which were subsequently processed into single-cell 5ʹ gene expression libraries using the Chromium Single Cell 5ʹ Library Kit (v2 Chemistry). All samples were pooled for sequencing on the Illumina NovaSeq 6000 PE150 platform.

value: whole lung

value: lung epithelial cells

value: bleo injuryed


title: Li-Frozen-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: STM2457_2

value: WT


title: ClubTracer, bleo injuryed, scRNAseq

description: 10x Genomics


title: STM3006_1


title: H-Frozen-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: K-Frozen-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP


title: allograft

city: Wuhan

first: Jie

last: Wu

state: Hubei

address: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Road 1277

department: Department of Cardiovascular Surgery

data_processing:
We obtained H5 files after fastq files were processed by software Cell Ranger
Seruat (version 4.0.1) was used to filter the clusters
clusters were identified by characteristic genes combined with SingleR (version 1.4.1) annotation
CellChat (version 1.0.0) was used for cell communication analysis.
Assembly: mm10
Supplementary files format and content: h5(Filtered feature-barcode matrices HDF5)

extract_protocol:
Cardiac allografts normally arrest at day 7 after transplantation because of acute transplantation rejection. Therefore, we harvested spleens and cardiac allografts of allograft group recipients at day 6 before cardiac allografts arrest. At the same time, spleens and cardiac isografts of isograft group recipients were harvested. CD45+ cells were respectively isolated from cardiac allografts, allograft group recipients’ spleen, cardiac isografts and isograft group recipients’ spleen after digestion, centrifugation and flow sorting. In brief, cardiac grafts were cut into pieces and digested with 1 mg/mL of collagenase B (Roche 11088815001) in HEPES buffer for 45 min at 37°C. After digestion, cell suspensions were collected and filtered with 70-μm cell strainers (BIOFIL), Percoll (Beijing Solarbio Science & Technology Co., Ltd.) was used to purify mononuclear cells through density centrifugation with 600g 25min RT not-brake. Splenocytes were prepared through grinding, erythrocyte lysis, washing and centrifugation (600g, 3min). CD45+ live cells were then sorted by FACSAria flow cytometer after Cardiac graft infiltrating cells and splenocytes stained with CD45-APC (Biolegend 103112) and Zombie GreenTM Fixable Viability Kit (Biolegend 423112).
Single cell Gel Bead-In-Emulsions (GEMs) were constructed using Chromium Single Cell 5’ Library and Gel Bead Kit following the manufacturer’s instruction. Briefly, Briefly, FACS-sorted cells were washed with 0.04% BSA PBS for three times and were resuscitated to a concentration of 700~1200 cells/uL (Viability≥85%) as determined by Countess™ II Automated Cell Counter. Cells were captured in droplets at a targeted cell recovery of cells. Single cell GEMs was consisted of single cell and specific 16nt 10× Barcodes, 10nt unique molecular identifiers (UMI). In single cell GEMs, tagged cells lysed and released mRNA was barcoded in GEMs. Reverse transcription was performed in GEMs. After the RT step, the amplification of 10× Barcoded cDNA was completed after emulsion broken. Amplified cDNA was then used for both 5’ gene expression library construction and TCR enrichment. Library was sequenced on NovaSeq platform (Illumia). Sequencing depth was set to be 30 million per cell.

treatment_protocol: 8-10 weeks male C57BL/6 (H-2b) and BALB/c(H-2d) were purchased from Charles River (Beijing, China). All mice experiments were performed in a specific pathogen-free facility according to the guidelines of the animal care and use committee of Huazhong University of Science and Technology. We established the murine heterotopic heart transplantation model as previously described . Allograft group: BALB/c (H2d) hearts were transplanted into fully MHC-mismatched C57BL/6 (H2b) recipients. Isograft group: C57BL/6 (H2b) hearts were transplanted into MHC-matched C57BL/6 (H2b) recipients.

tag: strain

tag: library type


title: Panc1-JTE607-R3

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

data_processing:
Basecalls performed using bcl2fastq2 version 2.20
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v38) using STAR (v2.7.9a)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE r38
Supplementary files format and content: Comma-separated file with raw counts

source_name: pancreas

extract_protocol:
QiagenmiRNeasy
KAPA RNA HyperPrep Kit with RiboErase (HMR)

tag: tissue

value: pancreas

tag: group

value: drug treatment

tag: cell type

value: PDAC


title: iso_spleen_TCR

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology


title: Br-Frozen-Input-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP

tag: treatment


title: tRNA-TR3

first: Xujia

address: 5117 Centre Avenue

department: Hillman Cancer Center

institute: University of Pittsburgh

description: Please add these samples to GSE229673 as a new SubSeries

data_processing:
Sequencing quality was examined by FastQC software and trimmed reads (trimmed 3’-adaptor bases by Cutadapt) were aligned to the cytoplasmic mature-tRNA sequences getting from GtRNAdb and the mitochondrial tRNA sequences getting from mitotRNAdb using BWA software with 2 maximum mismatches. Uniquely mapped reads for each isodecoder were kept.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample.

growth_protocol: All GSCs in control media were cultured in Neurobasal media (#21103049; Gibco) supplemented with B27 without vitamin A (#12587010; Gibco), 20 ng/ml recombinant human EGF (#236-EG-01M; R&D Systems), and 20 ng/ml recombinant human bFGF (#4114-TC-01M; R&D Systems), sodium pyruvate (#11360070; Gibco), GlutaMAX (#35050061; Gibco) and streptomycin/penicillin (#15140122; Gibco) at 37 °C with 20% oxygen and 5% carbon dioxide. Media contain 800 μM L-threonine. All GSCs in threonine-restricted media were cultured in the customized media with low threonine concentration (4 μM), of which all the other components are the same as the complete Neurobasal media.

extract_protocol:
For tRNA-seq, total RNA was extracted using TRIzol Reagent (#15596018; Life Technologies) and chloroform/isopropanol precipitation method. Next, tRNA was isolated from total RNA using denaturing urea polyacrylamide gel electrophoresis (Urea PAGE) and then subjected to m1A & m3C demethylation using rtStarTM tRF&tiRNA Pretreatment Kit (#AS-FS-005; Arraystar). Demethylated tRNA was purified and then partially hydrolysed according to Hydro-tRNAseq method.
Small RNA sequencing libraries were constructed using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® kit (E7300L/E7850L; New England Biolabs) by Arraystar. Size selection of ~140-155 bp PCR amplified fragments (corresponding to ~19-35 nt tRNA fragments size range) was performed. The produced tRNA-seq libraries were qualified and absolutely quantified and sequenced on Illumina sequencer.

treatment_protocol: YRDC deprivation was conducted by shRNA. Threonine restriction was performed by replacing media for 72 h.

tag: cell line

value: glioblastoma stem cell

tag: genotype

value: threonine restriction (4 μM thr)


title: Panc1-JTE607-R2


title: H-Frozen-m6A-MeRIP-Seq3

description: 08-16-22 MeRIP-Seq3 from ChIP772MeRIP

value: heart

value: Frozen


title: DMSO_1


title: allograft_TCR


title: AT2Tracer, bleo injuryed, scRNAseq

description: 10x Genomics


title: tRNA-TR2

value: brain


title: tRNA-TR1


title: iso_spleen


title: tRNA-KD3

value: YRDC knockdown

value: control media (800 μM thr)


title: Panc1-JTE607-R1


title: Panc1-DMSO-R3


title: tRNA-KD1


title: allo_spleen_TCR


title: Panc1-DMSO-R2


title: tRNA-NT3


title: Panc1-DMSO-R1


title: tRNA-NT2


title: TCMK1 cells,YOD1+Ang II 3

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: TCMK1 cell

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TCMK1 cell

value: Renal tubular epithelial cells

value: YOD1 overexpression

value: Ang II


title: tRNA-NT1

city: Pittsburgh


title: Panc1-sh1CPSF3-R2

value: knockdown experiment

value: CPSF3 knockdown


title: patient13

city: Be'er Sheva

first: Nataly

last: Makarenkov

address: David Ben Gurion Blvd 1

country: Israel

institute: Ben Gurion University

data_processing:
adapter trimming with cutadapt AACTGTAGGCACCATCAAT - leaving only reads above 17 bp
running miRGE3

source_name: small RNA from plasma

extract_protocol:
small RNA was extracted from the plasma using mirneasy serum/plasma advanced kit (Qiagen) (Cat No. 217204)
libraries were constructed using QIAseq™ miRNA Library Kit (Qiagen, Cat # 331505)

tag: subject

tag: disease state

value: non-alcoholic fatty liver disease

value: plasma


title: TCMK1 cells, YOD1+Ang II 1


title: patient12


title: Panc1-sh1CPSF3-R1

value: pancreas


title: tRNA-KD2


title: patient11


title: TCMK1 cells, Ctrl+Ang II 3

value: control


title: Panc1-shNTC-R3

value: PDAC

value: shNTC


title: Panc1-shNTC-R2


title: TCMK1 cells, Ctrl+Ang II 2


title: allo_spleen


title: Panc1-shNTC-R1


title: patient10


title: TCMK1 cells, Ctrl+Ang II 1


title: pHBEC_CTRL_Zn_rep4

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from human bronchial epithelial cells from control treated with Zn, biological replicate 4

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol (GeneChip Scanner 3000 7G)

data_processing: Transcriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific) was used for quality control and to obtain annotated normalized SST-RMA gene-level data

source_name: Human bronchial epithelial cells

label_protocol: WT PLUS Reagent Kit (Thermo Fisher Scientific).

growth_protocol: As described in the paper. Briefly, isolated pHBECs seeded on CollagenIV-coated transwell inserts were cultured in PneumaCultTM - Ex Plus Media (STEMCELL Technologies, REF:05041) until 95% cell confluency before airlift (ALId0; basal medium PneumaCultTM with 100x PneumaCultTM - ALI Maintenance Supplement, STEMCELL Technologies, REF:05006). Basal medium was changed every second day; ALI apical side was washed 1/week (HBSS Ca2+/Mg2+, Gibco Life Technologies, REF:14065-049). Cellular frequencies in main stem bronchi were in line with previously reported data for multi-ciliated cells (47-49% [31–33]) and secretory cells (6-21% [32, 33]) on ALI cultures.

extract_protocol: Total RNA was isolated by RNeasy Plus Mini Kit (Qiagen, Hilden, Germany)

treatment_protocol: As described in the paper. Briefly, ALI-cultured pHBECs were exposed to aerosolized carbon nanoparticles (NP) CNPs (Printex 90; primary particle diameter: 14nm; Degussa, Germany), zinc oxide NPs (ZnO; JRC reference material NM110; primary particle diameter: 158nm) or LPS (Lipopolysaccharides from Escherichia coli O55:B5, Sigma-Aldrich, REF:2974730) using the ALICE CLOUD technology (VITROCELL® CLOUD 12, VITROCELL Systems, Waldkirch, Germany). The VITROCELL® CLOUD 12 system provides uniform aerosol deposition onto the cells in approx. 3-5min, taking advantage of effects related cloud dynamics. After nebulization of 200µl of a NP suspension, the cell deposited NP dose is measured by an integrated quartz crystal microbalance (QCM), which provides accurate NP dosimetry. NP exposure was performed at 37°C applying the following doses: Sham controls (saline solution 0.9%), CNP 10.8cm2/cm2, ZnO low dose 0.14cm2/cm2 at ALId30±2 after air-lift. NP suspensions of 5.1mg/ml (CNP) and 1.8mg/ml for ZnO low dose were prepared in 1:100 diluted saline (saline solution/ NaCl 0.009% in water) using a probe sonicator (Bachofer GmbH, Reutlingen, Germany; 30% output energy, 30s for CNP (37J/mL sonication energy) and 160s for ZnO (195J/mL)) obtaining NP agglomerates with 160nm and 260nm (volumetric median) diameter for CNP and ZnO NPs as confirmed by DLS (Dynamic Light Scattering; Zetasizer, Malvern Instruments, GBR). LPS was nebulized (200μl; 1mg/ml; 0.699µg/cm2) as an inflammation reference.

value: Zn


title: patient9


title: Panc1-sh1CPSF3-R3


title: pHBEC_CTRL_Zn_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with Zn, biological replicate 1


title: DT_Replicate3

data_processing:
TCR sequencing library using KC-DigitalTM Stranded TCR-seq Library Prep Kit  (Seqhealth Technology) for Illumina NovaSeq 6000 pair-ended 150bp sequencing following the manufacturer’s instruction.
the raw data correction using kcUID after quality control and deduplication
The de-duplicated consensus sequences were used for TCR-seq analysis.
Alignment of raw sequences, extraction of clonotypes were performed by MiXCR v4.1.0 Immune Repertoire Analyzer software (milaboratory)
Abundance measurements and statistical analysis of the resultant clonotype sets was analyzed using the immunArch R package v0.7.0 (ImmunoMind Team)
Assembly: mm10
Supplementary files format and content: Comma-Separated Row counts for each sample
Supplementary files format and content: text file of the number and proportion of cloned TRB sequences
Library strategy: TCR-Seq

source_name: lymph nodes

extract_protocol:
T cells were isolated from the draining lymph nodes with Pan T Cell Isolation Kit (Miltenyi Biotec). Total cellular RNA was extracted with RNAiso Plus (TaKaRa) .About 2μg total RNA of each sample were used for TCR sequencing library.
TCR sequencing library using KC-DigitalTM Stranded TCR-seq Library Prep Kit  (Seqhealth Technology)

value: lymph nodes

value: DT

value: T cells

value: C57BL/6 background PD-1DTR

value: established the murine skin transplantation model and obtained the draining lymph nodes (dLNs) T cells from recipients


title: pHBEC_CTRL_Zn_rep3

description: Gene expression data from human bronchial epithelial cells from control treated with Zn, biological replicate 3


title: patient8


title: pHBEC_COPD-IV_Zn_rep3

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Zn, biological replicate 3

value: COPD-IV


title: TCMK1 cells, YOD1+Ang II 2

value: TCMK1 cell

value: Renal tubular epithelial cells

value: YOD1 overexpression


title: DT_Replicate2


title: pHBEC_COPD-IV_Zn_rep2

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Zn, biological replicate 2


title: pHBEC_COPD-IV_Zn_rep4

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Zn, biological replicate 4


title: pHBEC_COPD-IV_Zn_rep1

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Zn, biological replicate 1


title: RIBO-TR_1

data_processing:
For RNA-seq, raw FASTQ reads were trimmed using Trim Galore, followed by transcript mapping with Hisat2 to human reference genome (hg38). Samtools was used for sorting, indexing and format conversion from SAM files. Quantification were performed using FeatureCounts.
For ribosome profiling, raw sequencing data were pre-processed to remove low-quality reads and adapter contamination. Reads were then aligned to human rRNA and tRNA sequences (downloaded form NCBI) using Bowtie (v.1.3.1) to remove rRNA and tRNA contamination.Unaligned reads were then aligned to the homo sapiens genome (GRCh38) using Bowtie (v.1.3.1) with default parameters. Ribosome footprints (RFPs) were counted as the number of reads aligned to CDS region for each gene using FeatureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample.
Supplementary files format and content: tab-delimited text files include raw ribosome footprint counts for each sample.

extract_protocol:
For RNA-seq, cellular total RNA was extracted using TRIzol Reagent (#15596018; Life Technologies) and Direct-zol RNA Miniprep kit (#R2052; Zymo Research). For Ribosome profiling, ribosome footprint extraction and library construction were conducted in TB-Seq. Briefly, cell pellets were resuspended in ice cold lysis buffer (20 mM Tris-HCl, pH 7.4, 100 mM NaCl, 5 mM MgCl2, 1% Triton X-100, 1 mM DTT, 20 U/ml Turbo DNase I, 0.1 % NP-40, 100 µg/ml cycloheximide) and the soluble cytoplasmic fraction was isolated by centrifugation at top speed in a microcentrifuge for 20 min at 4 °C. Supernatants were collected and clarified lysates were digested with RNase I for 45 min at room temp. Digestion was stopped with SuperaseIN and monosomes were purified by size exclusion chromatography on MicroSpin S-400 HR columns (GE Healthcare). Size selection of footprints with length 25-33 nt was performed by electrophoresis on 15% TBE-urea gels.
For RNA-seq, total RNA was extracted for library construction using Illumina TruSeq Stranded Total RNA Library Prep Kit in Novogene. For ribosome profiling, libraries were prepared using a SMARTer smRNA-seq kit (TakaraBio) in TB-Seq.

value: brain

value: glioblastoma stem cell

value: WT

value: threonine restriction (4 uM thr)


title: RIBO-TR_2


title: patient7

value: non-alcoholic fatty liver disease

value: plasma


title: DT_Replicate1


title: pHBEC_CTRL_Zn_rep2

description: Gene expression data from human bronchial epithelial cells from control treated with Zn, biological replicate 2

value: control


title: RIBO-KD_2

value: YRDC knockdown

value: control media (800 uM thr)


title: pHBEC_CTRL_Sham_72h_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with Sham for 72h, biological replicate 1

value: Sham for 72h


title: patient6


title: PBS_Replicate3

value: lymph nodes

value: PBS

value: T cells


title: RIBO-KD_1


title: patient5


title: PBS_Replicate2

value: C57BL/6 background PD-1DTR

value: established the murine skin transplantation model and obtained the draining lymph nodes (dLNs) T cells from recipients


title: patient4


title: RIBO-NT_2


title: pHBEC_CTRL_Sham_rep2

description: Gene expression data from human bronchial epithelial cells from control treated with Sham, biological replicate 2

value: Sham


title: PBS_Replicate1


title: pHBEC_CTRL_Sham_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with Sham, biological replicate 1


title: pHBEC_CTRL_Sham_rep3

description: Gene expression data from human bronchial epithelial cells from control treated with Sham, biological replicate 3


title: RIBO-NT_1


title: ISO_Replicate3

source_name: S

value: S

value: ISO


title: KDTR_3

value: brain

value: glioblastoma stem cell


title: patient3


title: patient2


title: ISO_Replicate2


title: patient1


title: KDTR_2

value: threonine restriction (4 uM thr)


title: ALLO Rep3

data_processing:
Clean reads were mapped to the mm10 (UCSC) mouse genome with  subjunc (subread v2.0.1) with default parameters.
Transcripts were assembled Expression quantitation using featureCounts (subread v2.0.1) with mouse annotation (release_M20) from Gencode
Differential gene expression was calculated using the DESeq2 package (v1.30.1) package of the R (version 4.0.4) software
Assembly: mm10
Supplementary files format and content: Comma-Separated Row counts for each sample

source_name: TEa cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
DNase I was used to digest double-stranded and single-stranded DNA in total RNA, then, magnetic beads were purified to recover the reaction products, RNase H or Ribo-Zero method (human, mouse, plants) (Illumina, USA) was used to remove the rRNA. Purified mRNA from previous steps was fragmented into small pieces with fragment buffer at appropriate temperature. Then, First-strand cDNA was generated in First Strand Reaction System by PCR, and the second-strand cDNA was generated as well. The reaction product was purified by magnetic beads, afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to carry out end repair. The cDNA fragments with adapters were amplyfied by PCR, and the products were purified by Ampure XP Beads. Library was validating on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products above were heated denatured and circularized by the splint oligo sequence. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29(Thermo Fisher Scientific, MA, USA) to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on NovaSeq 6000 platform .

value: allograft

value: TEa cells

value: established the adoptive transfer murine heterotopic heart transplantation model and isolated TEa cells from spleens


title: Stool microbiota from the sample M16

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
KO3
16s rRNA v3-v4 sequencing of mice stool

data_processing:
demultiplexing from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming qiime cutadapt trim-paired  --i-demultiplexed-sequences demux-paired-end.qza --p-adapter-f  CCTACGGGNGGCWGCAG   --p-adapter-r  GACTACNVGGGTWTCTAATCC  –o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose
quality check qiime demux summarize  --i-data trimmed-seqs.qza --o-visualization demux.qzv
quality trimming, pair merging and ASV table creation qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 283 --p-trunc-len-r 168 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
taxonomic assignment qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
further analyses R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: feature_table.csv: CSV text file containing the abundance table
Supplementary files format and content: dna-sequences.fasta: text containing every processed reference-sequence code and sequence
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16s rRNA v3-v4 sequencing of mice stool

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

tag: time point

tag: condition

value: KO


title: ISO_Replicate1


title: KDTR_1

value: YRDC knockdown


title: TR_3

value: WT


title: Stool microbiota from the sample M15

description:
KO2
16s rRNA v3-v4 sequencing of mice stool


title: ALLO Rep2


title: Stool microbiota from the sample M14

description:
KO1
16s rRNA v3-v4 sequencing of mice stool


title: TR_2


title: pHBEC_COPD-IV_Sham_rep4

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Sham, biological replicate 4

value: COPD-IV


title: TR_1


title: pHBEC_COPD-IV_Sham_rep3

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Sham, biological replicate 3


title: pHBEC_COPD-IV_Sham_rep1

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Sham, biological replicate 1


title: KD_3

value: control media (800 uM thr)


title: ISO Rep3

value: isograft


title: ALLO Rep1


title: ISO Rep2


title: Stool microbiota from the sample M12

description:
WT3
16s rRNA v3-v4 sequencing of mice stool


title: KD_2


title: pHBEC_CTRL_Printex_72h_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with Printex for 72h, biological replicate 1

value: control

value: Printex for 72h


title: Stool microbiota from the sample M11

description:
WT2
16s rRNA v3-v4 sequencing of mice stool


title: KD_1


title: ISO Rep1


title: Stool microbiota from the sample M10

description:
WT1
16s rRNA v3-v4 sequencing of mice stool


title: pHBEC_COPD-IV_Sham_rep2

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Sham, biological replicate 2

value: Sham


title: Stool microbiota from the sample M9

description:
WT0
16s rRNA v3-v4 sequencing of mice stool


title: pHBEC_CTRL_Printex_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with Printex, biological replicate 1

value: Printex


title: pHBEC_CTRL_Printex_rep3

description: Gene expression data from human bronchial epithelial cells from control treated with Printex, biological replicate 3


title: NT_3


title: Macrophage,  Mac-GsαKO5

city: Jinan

first: Chang

last: Ma

state: Shandong

address: Wenhuaxi Road107#

institute: Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
Paired-end sequence files (fastq) were mapped to the reference genome GRCm39.108 using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance measurements were generationed and normalized  using Cufflink version 2.0.2.Linux_x86_64 ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression analysis for mRNA was performed using R package edgeR.
Assembly: GRCm39.108
Supplementary files format and content: tab-delimited text file includes normalized FPKM values and raw fragment counts for each Sample

source_name: Macrophage

growth_protocol: Peritoneal macrophages were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin (P/S) at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Standard cell culture conditions are applied, with no additional treatments.

value: Macrophage

value: Mac-Gs{alpha}KO


title: Macrophage,  Mac-GsαKO4


title: NT_2

value: brain

value: glioblastoma stem cell


title: Stool microbiota from the sample M13

description:
KO0
16s rRNA v3-v4 sequencing of mice stool


title: pHBEC_CTRL_Printex_rep2

description: Gene expression data from human bronchial epithelial cells from control treated with Printex, biological replicate 2


title: Stool microbiota from the sample M8

value: Healthy


title: Macrophage,  Mac-GsαKO3


title: pHBEC_CTRL_Printex_rep4

description: Gene expression data from human bronchial epithelial cells from control treated with Printex, biological replicate 4


title: pHBEC_COPD-IV_Printex_rep2

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Printex, biological replicate 2


title: pHBEC_COPD-IV_Printex_rep3

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Printex, biological replicate 3


title: NT_1


title: Macrophage,  Mac-GsαKO2


title: pHBEC_COPD-IV_Printex_rep4

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Printex, biological replicate 4


title: Stool microbiota from the sample M6

description:
KO1
16s rRNA v3-v4 sequencing of mice stool


title: human heart organoid, rsPIBF1 treated, rep3

city: Seoul

first: In-Jeoung

last: Baek

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan Institute for Life Sciences

data_processing:
Raw sequence reads produced by the sequencer were cleaned using Trim Galore version 0.6.5.
The cleaned reads were aligned on human reference genome (GRCh38.p13) and quantified using  Subread version 2.0.3.
Assembly: GRCh38.p13
Supplementary files format and content: csv, read counts

source_name: Heart

growth_protocol: Human iPSCs were cultured in mTeSR-TM1 medium (StemCell Technologies) containing 10 μM Y-27632 (1254, Tocris Bioscience) and 10% Matrigel (345277, Corning) for 3 days on a shaking incubator to form embryonic bodies (EBs). EBs were then cultured in RPMI1640 containing B27 supplement without insulin and 6 μM CHIR99021 (4423, Tocris Bioscience) for 2 days, and then in RPMI1640 containing B27 supplement without insulin and 2 μM C-59 (S7037, Selleckchem) for 2 days. On day 7, cells were cultured in Advanced MEM (AD-MEM) containing 1% GlutaMAX and 1% antibiotic-antimycotic (hHO medium).

extract_protocol:
Total RNA was isolated from EBs (day 3), control or sPIBF-treated hHOs (day 20) using Trizol Reagent kit (15596026, Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit v2 following manufacturer's protocols.

treatment_protocol: To verify the effect of rsPIBF on the development of hHO, on day 8 (one day after hHO induction), cells were cultured in the hHO medium (control group), or hHO medium containing 200 ng/ml sPIBF (sPIBF group), with the medium replaced every two days until day 19-21.

value: Heart

value: iPSC

value: organoid

value: wild-type


title: Macrophage,  Mac-GsαKO1


title: pHBEC_CTRL_LPS_rep3

description: Gene expression data from human bronchial epithelial cells from control treated with LPS, biological replicate 3

value: LPS


title: human heart organoid, rsPIBF1 treated, rep2


title: pHBEC_COPD-IV_Printex_rep1

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with Printex, biological replicate 1

value: COPD-IV


title: Stool microbiota from the sample M5

value: KO


title: Macrophage, CTR5

value: CTR


title: human heart organoid, rsPIBF1 treated, rep1


title: Macrophage, CTR4


title: Stool microbiota from the sample M4

description:
WT3
16s rRNA v3-v4 sequencing of mice stool

value: WT


title: Stool microbiota from the sample M3


title: pHBEC_COPD-IV_LPS_rep4

description: Gene expression data from human bronchial epithelial cells from COPD-IV patient treated with LPS, biological replicate 4


title: human heart organoid, control, rep3

value: control


title: pHBEC_CTRL_LPS_rep1

description: Gene expression data from human bronchial epithelial cells from control treated with LPS, biological replicate 1


title: human heart organoid, control, rep1


title: pHBEC_CTRL_LPS_rep2

description: Gene expression data from human bronchial epithelial cells from control treated with LPS, biological replicate 2


title: Stool microbiota from the sample M7

description:
KO2
16s rRNA v3-v4 sequencing of mice stool


title: Stool microbiota from the sample M2

description:
WT1
16s rRNA v3-v4 sequencing of mice stool


title: human heart organoid, control, rep2


title: Macrophage, CTR3


title: Stool microbiota from the sample M1

description:
WT0
16s rRNA v3-v4 sequencing of mice stool


title: Macrophage, CTR2