title: BE2C-KDM4B-002

data_processing:
Raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked/removed with Picard (version 1.65). Only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) for downstream analysis.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using 'macs2 callpeak  -t cut_tag_file -f BEDPE -q 0.05 --keep-dup all' .
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig.
Assembly: hg19(GRCh37.p13)
Supplementary files format and content: bigwig, narrowPeak file
Library strategy: CUT&Tag

source_name: BE2C cell line

growth_protocol: BE2C cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
CUT&Tag DNAs of BE2C cells were prepared by following the protocol as described previously (Kaya-Okur et al. 2019 and https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6?step=1 ) with minor modifications. BE2C approximately 500,000 cells were washed with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). Nuclei were isolated with cold NE1 buffer (20 mM HEPES–KOH, pH 7.9; 10 mM KCl 0.1%; Triton X-100; 20% Glycerol, 0.5 mM Spermidine; 1x Protease Inhibitor) for 10 min on ice. Nuclei were collected by 600 x g centrifuge and resuspended in 1ml washing buffer containing with 10 µL of activated concanavalin A-coated beads (Bangs laboratories, BP531) at RT for 10 min.  Bead-bound nuclei were collected with placing tube on magnet stand and removing clear liquid. The nuclei bound with bead were resuspended in 50 µL Dig-150 buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2 mM EDTA) and incubated with a 1:50 dilution of KDM4A (Sigma, HPA007610), KDM4B (Active motif, 61221, AB_2615033) and KDM4C (Sigma, HPA069357) antibodies overnight at 4 °C. The unbound primary antibody was removed by placing the tube on the magnet stand and withdrawing the liquid. The primary antibody bound nuclei bead was mixed with Dig-150 buffer 100µL containing guinea pig anti-Rabbit IgG antibody (Antibodies, ABIN101961) 1:100 dilution for 1 hour at RT. Beads bound nuclei were washed using the magnet stand 3× for 5 min in 1 mL Dig-150 buffer to remove unbound antibodies.  A 1:100 dilution of pA-Tn5 adapter complex was prepared in Dig-300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail).  After removing the liquid on the magnet stand, 100 µL mixture of pA-Tn5 and Dig- 300 buffer was added to the nuclei bound beads with gentle vortex and incubated at RT for 1 h. After 3× 5 min in 1 mL Dig-300 buffer to remove unbound pA-Tn5 protein, nuclei were resuspended in 250 µL Tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. EDTA 10 µL of 0.5 M, 3 µL of 10% SDS and 2.5 µL of 20 mg/mL Proteinase K were added to stop tagmentation and incubated at 55 °C for 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in water.
Sequencing libraries were prepared using NEBNext HiFi 2× PCR Master Mix (NEB, M0541L) according to the manufacturer's instructions. The PCR products were cleaned up with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Agilent Technologies). The libraries were sequenced on a HiSeq2500 with paired-end 50-bp reads (Illumina).


title: BE2C_siKDM4C90_1

status: Public on Mar 02 2024

type: SRA

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

country: USA

institute: St Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to human genome assembly (hg38) (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (r31, GRCh38.p12) .
Assembly: GRCh38(hg38)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: BE2C, KELLY and SKNAS cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
For siRNA knockdown, cells were treated with siCtrl or siKDM6B for 72h.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

tag: cell line

tag: treatment

value: siKDM4C #90


title: BE2C-KDM4C-002

library_source: genomic

molecule: genomic DNA

tag: antibody


title: BE2C_siCtrl2_1

value: siCtrl


title: BE2C-KDM4B-001


title: BE2C-KDM4A-002


title: SKNAS_siKDM4A36_2

value: SKNAS

value: siKDM4A #36


title: BE2C-KDM4A-001


title: CutTag_BBE2C-QC-KDM4BAM-002

data_processing:
Library strategy: CUT and Tag
Raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked/removed with Picard (version 1.65). Only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) for downstream analysis.
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using 'macs2 callpeak  -t cut_tag_file -f BEDPE -q 0.05 --keep-dup all' .  For calling broad peaks, we used SICER (version 1.1) with parameters of redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp and E 0.00001.
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig,peak

extract_protocol:
KDM4B CUT&Tag DNAs of BE2C cell with and without QC6352 treatment were prepared by following the protocol as described previously (Kaya-Okur et al. 2019 and https://www.protocols.io/view/bench-top-cut-amp-tag-bcuhiwt6?step=1 ) with minor modifications. BE2C cells approximately 500,000 with and without QC6352 200nM treatment were washed with wash buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail). Nuclei were isolated with cold NE1 buffer (20 mM HEPES–KOH, pH 7.9; 10 mM KCl 0.1%; Triton X-100; 20% Glycerol, 0.5 mM Spermidine; 1x Protease Inhibitor) for 10 min on ice. Nuclei were collected by 600 x g centrifuge and resuspended in 1ml washing buffer containing with 10 µL of activated concanavalin A-coated beads (Bangs laboratories, BP531) at RT for 10 min.  Bead-bound nuclei were collected with placing tube on magnet stand and removing clear liquid. The nuclei bound with bead were resuspended in 50 µL Dig-150 buffer (20 mM HEPES pH 7.5; 150 mM NaCl; 0.5 mM Spermidine; 1× Protease inhibitor cocktail; 0.05% Digitonin; 2 mM EDTA) and incubated with a 1:50 dilution of KDM4B antibody (KDM4B, Active Motive, 61221) overnight at 4 °C. The unbound primary antibody was removed by placing the tube on the magnet stand and withdrawing the liquid. The primary antibody bound nuclei bead was mixed with Dig-150 buffer 100uL containing guinea pig anti-Rabbit IgG antibody (Antibodies, ABIN101961) 1:100 dilution for 1 hour at RT. Beads bound nuclei were washed using the magnet stand 3× for 5 min in 1 mL Dig-150 buffer to remove unbound antibodies.  A 1:250 dilution of pA-Tn5 adapter complex was prepared in Dig-300 buffer (20 mM HEPES, pH 7.5, 300 mM NaCl, 0.5 mM Spermidine, 0.05% Digitonin, 1× Protease inhibitor cocktail).  After removing the liquid on the magnet stand, 100 µL mixture of pA-Tn5 and Dig- 300 buffer was added to the nuclei bound beads with gentle vortex and incubated at RT for 1 h. After 3× 5 min in 1 mL Dig-300 buffer to remove unbound pA-Tn5 protein, nuclei were resuspended in 250 µL Tagmentation buffer (10 mM MgCl2 in Dig-300 buffer) and incubated at 37 °C for 1 h. EDTA 10 µL of 0.5 M, 3 µL of 10% SDS and 2.5 µL of 20 mg/mL Proteinase K were added to stop tagmentation and incubated at 55 °C for 1 hour. DNA was then precipitated by phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in water.
Sequencing libraries were prepared using NEBNext HiFi 2× PCR Master Mix (NEB, M0541L) according to the manufacturer's instructions. The PCR products were cleaned up with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Agilent Technologies). The libraries were sequenced on a HiSeq2500 with paired-end 50-bp reads (Illumina).

treatment_protocol: BE2C cells were treated with QC6352 200nM for 48h.

value: QC6352 200nM treatment

tag: chip antibody


title: CutTag_BBE2C-DMSO-KDM4BAM-001

value: DMSO 0.1% treatment


title: CutTag_BBE2C-DMSO-KDM4BAM-002


title: CutTag_BBE2C-QC-KDM4BAM-001


title: SH_SY5Y_QC6352_2

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60).  GEMM mouse samples were mapped to mm10 and other samples were mapped to hg38 (STAR v2.7).
The gene level expression values were quantified (RSEM v1.31) based on GENCODE annotation (  M22 for GEMM mouse samples; r31, GRCh38.p12 for other samples).
Assembly: GRCh38 (hg38) or GRCm38 (mm10)
Supplementary files format and content: gene-level RSEM raw count, TPM, FPKM txt files

growth_protocol: The cells were cultured in RPMI 1640 supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2. Transgenic TH-Mycn/AlkF1178L mice were housed with temperature and 12h light /12h dark cycle controlled under specific-pathogen-free conditions (SPF) at the St Jude Children’s Research Hospital mouse facility.

extract_protocol:
Total RNA extraction from cells and tumor tissues was performed using the RNeasy Mini Kit (74106, Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: The generation of QC6352-resistant BE2C cells was established by exposing the parental BE2C cells to QC6352 in sequential, increasing concentrations of QC6352 (0.1, 0.2, 0.5, 1, 2, and 2.5 µM; each concentration was incubated for 5-7 days). The final concentration of QC6352 was 2.5 µM. GIMEN and SH-SY5Y cells were treated DMSO or QC6352 100 nM for 48 hours. GIMEN cells were overexpressing MYCN or vector. For the tumor samples from TH-MYCN/ALKF1178L mouse model, the tumors were either treated with vehicle or QC6352 25 mg/kg.

tag: cell type

value: neuroblastoma


title: CutTag_BBE2C-QC-H3K27me3-002


title: BE2C_siKDM4B_67


title: CutTag_BBE2C-QC-H3K27me3-001


title: BE2C-KDM4C-001


title: ChIP-seq_BE2C-QC6352-H3K36me3-002

data_processing:
ChIP-seq raw reads were first trimmed low-quality ends using trim-galore (0.4.4; default parameter) and then aligned to the human reference genomes (hg19) using BWA (version 0.7.12; default parameter) and duplicated reads were then marked with Picard (version 1.65), with only nonduplicated reads kept by samtools (version 1.3.1, parameter ‘‘-q 1 -F 1024’’. For data quality control and to estimate the fragment size, the nonduplicated version of SPP (version 1.11) was used to calculate the relative strand correlation value with support of R (version 3.6.1). To visualize ChIP-seq data on the integrated genome viewer (IGV) (version 2.3.82).
MACS2 (version 2.1.1 20160309) was used to call narrow peaks  using macs2 callpeak -f BEDPE --keep dup all -p 0.05 with IP library file  and IGG file.
SICER (version 1.1) was used to call broad peaks with parameters of redundancy threshold 1, window size 200bp, effective genome fraction 0.86, gap size 600bp, FDR 0.00001 with fragment size defined above).
Filtered out peaks overlapping with regions on the ENCODE blacklist.
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
To visualize global change of H3K9me3 and H3K36me3 ChIPseq data, ChIPseqSpikeInFree(version 1.2.3) was used to calculate scaling factor to adjust the effective ChIP-seq library size.
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: bigwig, peak

extract_protocol:
BE2C 1 x 10e7 of  cells treated with DMSO control or 200 nM of QC6352 for 48 h were cross-linked with freshly prepared 1% formaldehyde (final concentration) for 10 min and quenched with 125 mM glycine (final concentration) for 5 min at room temperature. Cells were washed once with Dulbecco's Phosphate-Buffered Saline (DPBS). 5-8 ml of ice-cold cell lysis buffer (5 mM PIPES pH 8.0, 85 mM KCl and 0.5% NP-40 supplemented with 1 tablet protease inhibitor cocktail) were added to cells. The cells were recovered with a cell scraper and transferred to 50-ml conical tubes on ice. Cell pellets were collected by centrifugation at 2,000 rpm for 5 minutes at 4 °C. The pellets were resuspended in cell lysis buffer and incubated on ice for 10 min. Cells were passed 20 times through a 20-gauge needle. The nuclei were collected by centrifugation at 2,000 rpm at 4 °C for 5 minutes. The nuclear pellets were resuspended and lysed with 250 μl RIPA buffer (1X PBS, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS with 1 tablet protease inhibitor cocktail). The lysates were sonicated for at least 30 min (30 sec on/30 sec off) using Bioruptor Pico (Diagenode, Inc., Denville, NJ) and centrifuged at 14,000 rpm in a microfuge for 15 minutes at 4 °C. The supernatant was collected, and the sonicated DNA fragments were examined by electrophoresis on a 1% agarose gel. The sonicated samples with enrichment of fragments between 100 to 500 bp range were used for the chromatin immunoprecipitation (ChIP) after removing 50 μL from each sample as input. The primary antibodies H3K36me3 (RevMab, 31-1051-00), H3K4me1 (Abcam, ab8895) and H3K27ac (Abcam, ab4729) were coupled with 25 μL magnetic beads (Dynabeads M-280 Sheep Anti-Rabbit IgG, Invitrogen 11203D) and H3K9me3 (Absolute antibody, 309M3-B ) was coupled with 100 μL magnetic beads (Dynabeads M280 Streptavidin, Invitrogen 11205D)  overnight in the cold room at 4 °C, washed three times with PBS/BSA (1X PBS/5 mg/ml BSA (fraction V)) at 4°C, then incubated with sonicated DNA chromatin samples overnight in the cold room at 4°C. The beads containing immuno-bound chromatin were collected by placing the microfuge tube on a magnet rack. The beads were extensively washed with LiCl washing buffer (100 mM Tris pH 7.5/500 mM LiCl/1% NP-40/1% sodium deoxycholate) 5 times and TE buffer (10 mM Tris-HCl pH 7.5 and 0.1 mM Na2EDTA) once. Bound chromatin was recovered by IP elution buffer (1% SDS and 0.1 M NaHCO3) and reverse-crosslinked at 65°C overnight. DNAs were purified using the Mini-Elute PCR Purification Kit (Qiagen, Valencia, CA) after treatment with RNase A and proteinase K. ChIP enriched DNAs were submitted for library preparation and sequencing.
5-10 ng of DNA was using to prepare libraries by the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext Q5 Hot Start HiFi PCR Master Mix according to the manufacturer’s instructions (New England Biolabs). Completed ChIP-seq libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (Perkin Elmer). All libraries were quantified using the Quant-iT PicoGreen dsDNA assay (Life Technologies), Kapa Library Quantification kit (Kapa Biosystems).


title: ChIP-seq_BE2C-ctrl-H3K36me3-002


title: ChIP-seq_BE2C-QC6352-H3K36me3-001


title: CutTag_BBE2C-DMSO-H3K27me3-002


title: ChIP-seq_BE2C-ctrl-H3K4me1-002

value: H3K4me1, Abcam, ab8895


title: ChIP-seq_BE2C-QC6352-H3K4me1-002


title: ChIP-seq_BE2C-ctrl-H3K9me3-001

value: H3K9me3, Absolute antibody, 309M3-B


title: ChIP-seq_BE2C-ctrl-H3K9me3-002


title: ChIP-seq_BE2C-QC6352-H3K27ac-002

value: H3K27Ac, Abcam,ab4729


title: ChIP-seq_BE2C-ctrl-H3K4me1-001


title: ChIP-seq_BE2C-ctrl-H3K36me3-001


title: ChIP-seq_BE2C-QC6352-input-002


title: CutTag_BE2C-DMSO-H3K27me3-001


title: ChIP-seq_BE2C-QC6352-input-001


title: ChIP-seq_BE2C-QC6352-H3K4me1-001


title: ChIP-seq_BE2C-ctrl-H3K27ac-002


title: ChIP-seq_BE2C-ctrl-input-002


title: ChIP-seq_BE2C-ctrl-H3K27ac-001


title: ChIP-seq_BE2C-ctrl-input-001


title: ATAC-seq_SIMA-QC-002

data_processing:
The ATAC-seq raw reads were aligned to the human reference genome (hg19) using BWA (version 0.7.12-r1039) to and then removed duplicated reads with Picard (version 1.65), with only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) .  Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the  – strand.
Nucleosome free reads was used  to generate bigwig files and call eanriched regions. MACS2 (version 2.2.7.1) parameters are  “-q 0.01 –nomodel –extsize 200 –shift 100 -f BEDPE --keep-dup all”.
genomeCoverageBed (bedtools 2.25.0) was used to produce genome-wide coverage in BEDGRAPH file and then converted it to bigwig file by bedGraphToBigWig. The bigwig files were scaled to 15 million reads to allow comparison across samples.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak

source_name: SIMA

growth_protocol: BE2C and SIMA cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum.All cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Fresh cultured BE2C and SIMA (100,000 per sample) with or without treatments were harvested and washed with 150ml cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.

treatment_protocol: BE2C and SIMA cells were treated with DMSO 0.1% or QC6352 200nm  for 72 hours.

value: SIMA


title: ATAC-seq_SIMA-ctrl-002


title: ChIP-seq_BE2C-QC6352-H3K9me3-002


title: ATAC-seq_SIMA-QC-001


title: ATAC-seq_BE2C-QC-001


title: ATAC-seq_BE2C-ctrl-002


title: ChIP-seq_BE2C-QC6352-H3K27ac-001


title: ATAC-seq_BE2C-ctrl-001


title: Monocytes, anti-Ly6G, biol rep 3

city: Shanghai

first: Shicheng

last: Wang

address: 1954 Huashan Road, Xuhui District, Shanghai

country: China

institute: Shanghai Jiao Tong University

description:
anti_Mono3
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt

data_processing:
Raw reads of fastq format were firstly processed using fastp1 and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm10
Supplementary files format and content: raw counts for each sample
Supplementary files format and content: FPKM for each sample

organism: Mus musculus

source_name: Spleen

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: tissue

value: Spleen

value: Monocytes

tag: genotype

value: WT


title: Monocytes, anti-Ly6G, biol rep 2

description:
anti_Mono2
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt


title: Serum-NegativeControl-rep55-Phase II

type: protein

city: Foshan

first: He

middle: Yan

last: Bin

state: GUANGDONG

address: Sino-European Center A, 2 Lingnan Avenue South, Shunde, Foshan, Guangdong, China

institute: BCBIO

description: Phase II of the experimental design

hyb_protocol: The microarray was taken out from − 80°C and then incu-bated in blocking buffer (3% BSA in PBS) at RT for 3h.Then a serum sample diluted at 1:200 in binding buffer (1%BSA in PBST) was added to the microarray and incubatedat 4°C overnight

scan_protocol: The micro-array was scanned with the LuxscanTM 10K-A (CapitalBio Corporation, Beijing, China).

data_processing: Data analysis was carried out using The GenePix Pro 6.0 (Axon Instruments, Foster City, CA). The signal for each spot (SNR) was defined as the ratio of the fore-ground to the background median intensity and normalized using the median value.

molecule: protein

source_name: Serum,NegativeControl,Phase II

label_protocol: After washing with PBST, the microarray was incubated with 1:1000 diluted Fluor conjugated goat anti-human IgG (532nm) and donkey anti-human IgM (635nm) (Jackson ImmunoResearch, West Grove, PA) at RT for 1h in the dark. After washing with PBST, the microarray was rinsed with dd H2O and dried

extract_protocol: standard protocol

tag: gender

value: male

tag: age

tag: sampletype

value: Serum

tag: cancertype

value: NegativeControl

tag: designphase

value: Phase II

tag: molecule

value: Serum autoantibody proteins IgG

value: Serum autoantibody proteins IgM


title: Serum-NegativeControl-rep57-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep56-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep60-Phase II

description: Phase II of the experimental design

value: female


title: Serum-NegativeControl-rep59-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep53-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep51-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep54-Phase II

description: Phase II of the experimental design


title: ATAC-seq_BE2C-QC-002

value: QC6352 200nM treatment


title: Monocytes, anti-Ly6G, biol rep 1

description:
anti_Mono1
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt


title: Serum-NegativeControl-rep50-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep49-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep52-Phase II

description: Phase II of the experimental design


title: Monocytes, CTT, biol rep 3

description:
A_Mono3
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt

value: CTT


title: ATAC-seq_SIMA-ctrl-001

value: DMSO 0.1% treatment


title: Serum-NegativeControl-rep48-Phase II

description: Phase II of the experimental design


title: Neutrophils, CTT, biol rep 3

description:
A_Neu3
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt

value: Neutrophils


title: Monocytes, CTT, biol rep 2

description:
A_Mono2
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt


title: Serum-NegativeControl-rep46-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep47-Phase II

description: Phase II of the experimental design


title: Monocytes, CTT, biol rep 1

description:
A_Mono1
Monocyte counts_anno.txt
Monocyte FPKM_anno.txt


title: Serum-NegativeControl-rep45-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep43-Phase II

description: Phase II of the experimental design


title: Neutrophils, CTT, biol rep 2

description:
A_Neu2
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt


title: Serum-NegativeControl-rep44-Phase II

description: Phase II of the experimental design


title: ChIP-seq_BE2C-QC6352-H3K9me3-001

value: H3K9me3, Absolute antibody, 309M3-B


title: Serum-NegativeControl-rep42-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep58-Phase II

description: Phase II of the experimental design


title: Neutrophils, control, biol rep 2

description:
C_Neu2
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt

value: control


title: Neutrophils, CTT, biol rep 1

description:
A_Neu1
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt


title: Neutrophils, control, biol rep 1

description:
C_Neu1
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt


title: GEMM_QC6352_3

source_name: Tumor

value: Tumor

value: QC6352 treatment


title: Serum-NegativeControl-rep41-Phase II

description: Phase II of the experimental design


title: GEMM_QC6352_1


title: Serum-NegativeControl-rep39-Phase II

description: Phase II of the experimental design


title: GEMM_CTRL3

value: Vehicle treatment


title: GEMM_CTRL2


title: Serum-NegativeControl-rep37-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep36-Phase II

description: Phase II of the experimental design


title: GEMM_QC6352_2


title: Serum-NegativeControl-rep38-Phase II

description: Phase II of the experimental design


title: GEMM_CTRL1


title: Serum-NegativeControl-rep40-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep35-Phase II

description: Phase II of the experimental design


title: Mutant iWAT RNA biol rep2

city: Daejon city

first: Ju Gyeong

last: Kang

address: Daehak-Ro 291

department: Biological sciences

country: South Korea

institute: KAIST

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (100bp reads)
Reads were mapped to the mouse transcriptome(mm10) and quantified using salmon v1.9.0 with option --numBootstraps 30.
Transcript-level quantification result from each samples were imported and summarized to gene-level using Tximeta v1.12.4.
Differential expression analysis was performed using DEseq2 v1.34.0 using lfcShrink function.
Assembly: mm10
Supplementary files format and content: Table of transcript-level quantification result (TPM) from each samples

source_name: adipose (iWAT)

extract_protocol:
Total tissue RNA was purified using Trizol Reagent
Sequencing libraries were constructed with the use of a TruSeq stranded Total RNA Library Kit

value: adipose (iWAT)

value: Adipoq-Cre; Lats1fl/fl; Lats2fl/fl; Rosa-LSL-tdTomato


title: Mutant iWAT RNA biol rep3


title: Mutant iWAT RNA biol rep1


title: Control iWAT RNA biol rep3


title: Serum-NegativeControl-rep32-Phase II

description: Phase II of the experimental design

value: Serum


title: Serum-NegativeControl-rep29-Phase II

description: Phase II of the experimental design

value: male

value: NegativeControl


title: Neutrophils, control, biol rep 3

description:
C_Neu3
Neutrophil counts_anno.txt
Neutrophil FPKM_anno.txt

value: Spleen

value: WT


title: Control iWAT RNA biol rep2


title: Serum-NegativeControl-rep30-Phase II

description: Phase II of the experimental design

value: female

value: Phase II

value: Serum autoantibody proteins IgG

value: Serum autoantibody proteins IgM


title: Control iWAT RNA biol rep1


title: Serum-NegativeControl-rep28-Phase II

description: Phase II of the experimental design


title: Diff_C3H10T1/2_TAZ4SA, Input

data_processing:
Prepared libraries were sequenced on a NovaSeq 6000 with paired-end method. (150bp reads)
ChIP-seq reads were trimmed using Trimmomatic version 0.38 and aligned to the UCSC mm10 genome using Bowtie version 1.1.2.
Duplicates were removed using Picard MarkDuplicates version 0.118.
Peaks were called using MACS2 version 2.1.1 with q-value cut-off 0.05.
BedGraph files were generated from -B parameter of MACS2 and converted to bigWig files.
Assembly: mm10
Supplementary files format and content: BED file of ChIP-seq peaks (except for input sample)

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Chromatin was sonicated for 10 min and subjected to immunoprecipitation with TAZ antibody (bd560235)
Sequencing libraries were constructed with the use of a TruSeq ChIP-seq Library Preparation Kit

value: adipocyte


title: Serum-NegativeControl-rep27-Phase II

description: Phase II of the experimental design


title: Diff_C3H10T1/2_TAZ4SA, TAZ, rep2

value: ChIP with TAZ ab (bd560235)


title: Serum-NegativeControl-rep26-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep34-Phase II

description: Phase II of the experimental design


title: WWv SMC 5

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.2a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE vM19 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed file is a tab delimited matrix file with the first column representing the Ensembl gene name and subsequent columns raw gene counts generated by --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with an exon of only one gene on the appropriate strand.

source_name: Primary SMCs extracted from Aorta

extract_protocol:
RNA was extracted using Omega EZNA RNA isolation kit
Libraries were prepared for seuencing with the Nugen Universal Plus mRNA-Seq Library Preparation Kit

treatment_protocol: primary SMCs were extracted from the aortas of five KitW/WV mice and five Wild type mice through collagenase digestion then grown until passage 2

value: Primary SMCs

value: WWv


title: Serum-NegativeControl-rep31-Phase II

description: Phase II of the experimental design


title: WWv SMC 3


title: Serum-NegativeControl-rep33-Phase II

description: Phase II of the experimental design


title: WWv SMC 1


title: WWv SMC 4


title: Serum-NegativeControl-rep24-Phase II

description: Phase II of the experimental design


title: WWv SMC 2


title: Wild type SMC 5

value: Wild type


title: Serum-NegativeControl-rep22-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep19-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep20-Phase II

description: Phase II of the experimental design


title: Wild type SMC 4


title: Wild type SMC 3


title: Wild type SMC 2


title: Serum-NegativeControl-rep17-Phase II

description: Phase II of the experimental design


title: Diff_C3H10T1/2_TAZ4SA, TAZ, rep1


title: Serum-NegativeControl-rep25-Phase II

description: Phase II of the experimental design


title: Wild type SMC 1


title: Prototype TG

city: Stanford

first: Allan

last: Feng

state: CA

address: 269 Campus Dr

department: Imm/Rheum

institute: Stanford School of Medicine

description: Antibodies in samples bind to barcoded beads conjugated to antigens. Antibody reactivity was quantified by the fluorescence measured as MFI from the secondary antibody.

hyb_protocol: A fluorescent secondary antibody was added to a PBS solution containing conjugated beads bound to antibodies.

scan_protocol: A Luminex FlexMAP 3D instrument was used to quantify autoantibody levels in each sample by measuring fluorescence (in MFI) from each barcoded bead.

data_processing:
Barebeed MFI values were subtracted from the MFI values for all analytes in each sample and  replicate MFI values were averaged.
CTD Array version 2 Platform Raw MFI_02272024.xlsx: raw data
matrix_MFI.txt: Numerical values represent median fluorescent intensity (MFI).

label: R-PE conjugated goat anti-human IgG secondary antibody

source_name: Serum/Plasma

label_protocol: Decondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

extract_protocol: Blood was collected from SLE patients and healthy controls and then processed into serum or plasma which was then screened by array.

value: Prototype Autoimmune Disease Sample

tag: condition

value: Serum/Plasma


title: Serum-NegativeControl-rep16-Phase II

description: Phase II of the experimental design


title: Prototype Scl-70


title: Serum-NegativeControl-rep23-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep13-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep21-Phase II

description: Phase II of the experimental design


title: Prototype RNP


title: Prototype Mitochondrial


title: Prototype Ro/SSA


title: Serum-NegativeControl-rep18-Phase II

description: Phase II of the experimental design


title: Prototype Histone


title: Serum-NegativeControl-rep11-Phase II

description: Phase II of the experimental design


title: Prototype Centromere


title: Prototype La/SSB


title: Serum-NegativeControl-rep8-Phase II

description: Phase II of the experimental design


title: Subject 2026 D21

value: Healthy Control


title: Subject 2026 D42


title: Serum-NegativeControl-rep15-Phase II

description: Phase II of the experimental design

value: Serum


title: Serum-NegativeControl-rep9-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep6-Phase II

description: Phase II of the experimental design


title: Serum-NegativeControl-rep10-Phase II

description: Phase II of the experimental design

value: male


title: Serum-NegativeControl-rep5-Phase II

description: Phase II of the experimental design

value: NegativeControl


title: Serum-NegativeControl-rep7-Phase II

description: Phase II of the experimental design


title: Subject 2026 D0


title: Serum-NegativeControl-rep4-Phase II

description: Phase II of the experimental design


title: Subject 2025 D42


title: Serum-NegativeControl-rep14-Phase II

description: Phase II of the experimental design


title: Subject 2025 D21


title: Serum-NegativeControl-rep3-Phase II

description: Phase II of the experimental design


title: Subject 2023 D42


title: Subject 2025 D0


title: Serum-NegativeControl-rep1-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep60-Phase II

description: Phase II of the experimental design

source_name: Serum,LungCancer,Phase II

value: LungCancer


title: Serum-NegativeControl-rep2-Phase II

description: Phase II of the experimental design


title: Subject 2023 D21


title: Subject 2023 D0


title: Subject 2022 D42


title: Serum-LungCancer-rep56-Phase II

description: Phase II of the experimental design

tag: smoke

value: no

tag: surgery

value: yes


title: Serum-LungCancer-rep58-Phase II

description: Phase II of the experimental design

value: Phase II


title: Subject 2022 D21


title: Serum-LungCancer-rep57-Phase II

description: Phase II of the experimental design

value: female

value: Serum autoantibody proteins IgG


title: Subject 2021 D42


title: Serum-LungCancer-rep55-Phase II

description: Phase II of the experimental design

value: Serum autoantibody proteins IgM


title: Subject 2021 D0


title: Serum-LungCancer-rep59-Phase II

description: Phase II of the experimental design


title: Subject 2021 D21


title: Subject 2019 D42


title: Serum-NegativeControl-rep12-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep53-Phase II

description: Phase II of the experimental design


title: Subject 2019 D0


title: Serum-LungCancer-rep50-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep51-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep52-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep49-Phase II

description: Phase II of the experimental design


title: Subject 2016 D42


title: Subject 2016 D21


title: Subject 2016 D0


title: Subject 2014 D21


title: NIH3T3, H2A.Z, CFDP1 siRNA ChIP 2

city: Rochester

first: Thomas

middle: Gustav Heinrich

last: Diekwisch

state: NY

address: 601 Elmwood

department: Oral and Craniofacial Sciences

institute: Eastman Institute for Oral Health

data_processing:
ChIP-seq analysis was performed using Nextflow bioinformatics pipeline. Illumina FASTQ filews were converted to FASTA using format conversion tool and filtered with a median score threshold of 20.0 (Format ASCII-33).
Sequence reads were combined and condensed to merge overlapping reads and to extend read lengths (1 cycle).
Homer package was used to align reads with mm10 mouse genome, obtain tag directory and identify all possible peaks.
Peak sequences were used as reference to which reads from individual samples were aligned.
Peak identification was achieved by comparing the peaks coverage (RPKM) between sample and input control. Peak files (.bed) were converted to wiggle files for visualization.
Assembly: mm10
Supplementary files format and content: bigWig, bed

source_name: Embryo

growth_protocol: Complete DMEM, 10% FBS, 2mM Glutamine, 1X Pen/Strep. Cells were cultured at 37C, 5% CO2.

extract_protocol:
Control and treated cells were fixed with 1.1% Formaldehyde for 10 min at room temperature and quenched with 125mM Glycine. Extracted nuclei were sonicated using Q700 Sonicator system (Qsonica).
ChIP seq library was constructed using 5ng of ChIP DNA using KAPA HTP Library Preperation Kit (Kapa Biosystems). Library amplication was performed for 13 cycles in a thermocycler. Amplified libraries were size selected for 250-500bp range using AMPure XP beads (Beckman Coulter). Library size and distrubution was checked on Agilent Bioanalyzer.

treatment_protocol: control and CFDP1 siRNA for 72 hours.

value: Embryo

value: Embryonic fibroblasts

value: CFDP1 siRNA, 72h


title: Serum-LungCancer-rep47-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep48-Phase II

description: Phase II of the experimental design


title: Subject 2014 D0


title: Subject 2022 D0


title: NIH3T3, H2A.Z, control siRNA ChIP 2

value: Wild type

value: Control siRNA, 72h


title: NIH3T3, H2A.Z, CFDP1 siRNA ChIP 1


title: Serum-LungCancer-rep44-Phase II

description: Phase II of the experimental design


title: NIH3T3, H2A.Z, control siRNA ChIP 1


title: Serum-LungCancer-rep45-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep46-Phase II

description: Phase II of the experimental design


title: NIH3T3, H2A.Z, ChIP 2

value: CFDP1 transfection


title: Subject 2019 D21

value: Healthy Control

value: Serum/Plasma


title: NIH3T3, H2A.Z, ChIP 1


title: NIH3T3, FLAG, ChIP 1

value: anti-FLAG


title: NIH3T3, FLAG, ChIP 2


title: Subject 2010 D0


title: wt rep 4

city: Bloomington

first: Jared

middle: Michael

last: Schrader

state: IN

address: 212 S Hawthorne Dr

department: Biology

institute: Indiana University

description:
WT8
8_wt_rep4

data_processing:
library strategy: GRO-seq
GRO-Seq samples were first stripped of adapter sequences using cutadapt. 3’ end reads were then aligned to the yeast s288c genome downloaded from SGD (version R64-3-1). To determine the readthrough index, we used the 3’ end annotations from SGD for mRNAs in YPD media. For each mRNA, we filtered the mRNAs to include only mRNAs whose 3’ end are at least 500 nucleotides (nt) from the next gene on the same strand. Next, we selected mRNAs that were at least 500 nt in length or longer, and whose expression values were at least 1 read per nucleotide. We then calculated the readthrough index as the ratio of reads in a downstream window (50 to 500 nt after the 3’ end) divided by an upstream window (-500 to -50 nt in front of the 3’ end) (Baejen et al., 2017).
Assembly: R64-3-1
Supplementary files format and content: xlsx termination readthrough index

organism: Saccharomyces cerevisiae

growth_protocol: All protocols were performed exactly as described in O'Brien et al., 2023 (O'Brien, M. J., Gurdziel, K., & Ansari, A. (2023). Global Run-On sequencing to measure nascent transcription in Saccharomyces cerevisiae. Methods, 217, 18-26.). Growth and permeabilization of yeast cells 1. 3 mL of YPD liquid medium is inoculated with the yeast strain of interest and is grown overnight at 30 ◦C with shaking. 2. The next morning, 1–2 mL of overnight grown culture is diluted to 100 mL in YPD medium. Cells are allowed to grow till A600 reaches 0.8. 3. Cells are harvested by centrifugation at 1,864 g at 4 ◦C for 5 min. 4. Cell pellet is resuspended in 10 mL of ice-cold 1X TBS and centrifuged at 1,864 g at 4 ◦C for 5 min. 5. Washed cell pellet is resuspended in 1 mL of ice-cold permeabilization buffer and transferred to a chilled 1.5 mL lock top microcentrifuge tube. 6. Cells in permeabilization buffer are kept as close to 0 ◦C as possible by packing the microfuge tube in 50 mL conical tubes packed with ice. This is to prevent any ongoing transcription. 7. Cells are permeabilized by gently shaking on a Corning LSE nutating mixer or a similar instrument in the buffer at 4 ◦C for 20 min. 8. Permeabilized cells are centrifuged at 800 g for 5 min at 4 ◦C. 9. Cell pellet is resuspended in 100 μL of storage buffer, flash frozen in liquid nitrogen, and stored at 􀀀 80 ◦C. The permeabilized yeast cells in storage buffer may be kept at 􀀀 80 ◦C for several months. This may be a good step to pause the experiment. CRITICAL: It is important that cells are harvested when they are in mid-logarithmic phase. At a higher A600, the proportion of dead cells increases, and it may adversely affect the efficiency of the TRO reaction.

extract_protocol:
Isolation of total RNA 1. Spin down cells from the transcription run-on reaction at 1,100 g for 5 min at 4 ◦C in a tabletop centrifuge. 2. Quickly resuspend the cell pellet in 500 μL phenol (pH 7.4). 3. Add an equal volume of AES buffer and incubate at 65 ◦C for 5 min. Mix contents on a vortexer for 10 s, once every minute. 4. Incubate on ice for 5 min. 5. Add 200 μL of chloroform, mix contents on a vortexer at maximum speed for 30 s and incubate at room temperature for 2 min. CRITICAL: Chloroform step must be performed in fume hood. 6. Centrifuge at 14,220 g for 5 min at 4 ◦C. 7. Transfer the upper aqueous phase to a new tube. 8. Ethanol precipitate by adding 2 μL GlycoBlue, sodium acetate (final concentration 300 mM), 2.5X volume of 100 % room temperature ethanol, mixing on a vortexer, incubating contents at room temperature for 10 min followed by centrifugation at 14,220 g for 20 min at 4 ◦C. 9. The precipitated RNA forms a gel-like, blue pellet on the side and bottom of the tube. 10. Remove supernatant carefully and rinse the pellet with 750 μL of ice-cold 75 % ethanol. 11. Centrifuge at 14,220 g for 5 min at 4 ◦C. 12. Remove the supernatant carefully and air dry the pellet for 5–10 min. CRITICAL: It is important not to let the RNA pellet dry completely as this will greatly decrease its solubility in the next step. 13. Resuspend the RNA pellet in 100 μL DEPC-H2O and proceed to purification on QIAGEN RNeasy kit as described below (the QIAGEN RNeasy kit serves to exchange the buffer and remove any unincorporated BrUTPs, as these may inhibit binding of labeled RNA during affinity purification). Purification of RNA on the QIAGEN kit The method for purification of RNA on the QIAGEN kit is adapted from the standard protocol described in the QIAGEN handbook. The detailed protocol is as follows: 1. The RNA sample is adjusted to a total volume of 100 μL with DEPC-H2O. 2. Add 350 μL of RLT buffer and mix thoroughly by pipetting up and down. 3. Add 250 μL of 100 % ethanol and mix thoroughly. 4. Transfer the entire sample, approximately 700 μL, to a RNeasy Mini spin column placed in a 2 mL collection tube. 5. Centrifuge at 1,727 g for 30 s at room temperature and discard the flow-through (this step allows binding of RNA to the column). 6. Add 500 μL of RPE buffer to the spin column, centrifuge at 1,727 g for 1 min at room temperature and discard the flow-through. Repeat this step once more (this is the washing step that removes contaminants from the column). 7. Spin at 1,727 g again for 2 min at room temperature to remove any trace of RPE buffer. 8. Remove the spin column from the collection tube. Place into a fresh 1.5 mL microcentrifuge tube and perform elution. 9. Elution is performed in two steps: Step I: Add 50 μL of DEPC-H2O directly onto the matrix of the spin column, rest for 5 min at room temperature, and centrifuge at 160 g for 1 min at room temperature. It is possible that there will be no eluent or very little eluent after the spin. Transfer the eluent, if any, to a new microfuge tube and keep on ice. Step II: Add 50 μL of DEPC-H2O directly onto the matrix of the column, rest for 5 min at room temperature, and centrifuge at 14,220 g for 2 min at room temperature. 10. Combine eluents from steps 9. The total volume of eluent is 100 μL. 11. Measure RNA concentration using the Nanodrop. RNA concentration at this stage is in the range of 100–500 μg. Measuring RNA at this point is to ensure that RNA is not lost during purification on the kit. PAUSE POINT: RNA at this stage can be stored at 􀀀 80 ◦C for several months. 2.2.4. Affinity purification of nascent RNA 1. Transfer 50 μL of Protein G Dynabeads slurry to a 1.5 mL microcentrifuge tube. 2. Allow magnetic beads to settle by incubating the tube containing beads on magnetic rack for 1 min. 3. Discard the bead storage buffer. 4. Wash beads by resuspending in 0.5 mL TBST, gently shaking on a nutator at 4 ◦C for 3 min, allowing beads to settle on magnetic rack, and then carefully removing the supernatant. 5. Repeat the washing step once more. 6. Resuspend washed beads in 50 μL TBST. 7. Add 2 μg of anti-BrdU monoclonal antibodies to washed beads and gently shake on a nutator for 10 min at room temperature. 8. Add 150 μL of blocking buffer and incubate for 30 min with gentle shaking at room temperature. 9. Capture antibody-bound blocked beads using the magnetic rack and discard the buffer. 10. Wash beads twice with 300 μL of TBSTR as described above in step 4. 11. Resuspend beads in 100 μL TBSTR. 12. Incubate bromo-UMP labelled RNA from section 2.2.3 above at 65 ◦C for 5 min in a water bath (this step is to denature any RNA secondary structure that may reduce the efficiency of RNA binding to the antibody). 13. Keep RNA on ice for 2 min. 14. Mix RNA with affinity beads from step 11 and incubate on a nutator with gentle shaking for 30 min at room temperature. 15. After a brief spin, capture beads on the magnetic rack. 16. Discard the supernatant. 17. Wash beads three times as described above in step 4 with TBSTR on magnetic rack. 18. Resuspend beads with bound RNA in 0.5 mL of TRIzol reagent. 19. Incubate for 5 min at room temperature. 20. Add 100 μL of chloroform to the tube in fume hood. 21. Shake vigorously on a vortexer and incubate the sample at room temperature for 10 min. 22. Centrifuge at 14,220 g for 10 min at 4 ◦C. 23. The upper aqueous phase containing RNA is carefully transferred to a 1.5 mL microcentrifuge tube. CRITICAL: It is important not to take even a trace of the lower, red, organic phase while transferring RNA as it may contain contents that may affect the quality of the GRO-seq library. 24. Ethanol precipitate RNA by adding 2 μL GlycoBlue, sodium acetate (final concentration 300 mM), 2.5X volume of 100 % room temperature ethanol, mixing on a vortexer, and incubating contents at room temperature for 10 min followed by centrifugation at 14,220 g for 20 min at 4 ◦C. CRITICAL: The amount of affinity purified labelled RNA at this stage is very small. Addition of GlycoBlue, which acts as an inert carrier that helps to precipitate small amounts of RNA, maximizes RNA yield, and ensures that RNA pellet is visible after precipitation. 25. The RNA forms a blue pellet. Carefully remove and discard the supernatant. CRITICAL: The RNA pellet is flimsy and easily detaches from the wall of the microcentrifuge tube. Take extreme caution while removing supernatant as it is easy to lose the RNA pellet at this step. 26. Rinse pellet with 1 mL of ice-cold 75 % ethanol. 27. Centrifuge at 14,220 g for 5 min at 4 ◦C. 28. Carefully remove the supernatant. 29. Air-dry the pellet for 5–10 min. 30. Resuspend pellet in 22 μL of DEPC-H2O. CRITICAL: The RNA at this point is extremely low in concentration. Use only 1 μL of the sample to measure concentration by Nanodrop. PAUSE POINT: Affinity purified, nascent RNA at this stage can be stored at 􀀀 80 ◦C for several months. CRITICAL: Before proceeding with library preparation, it is important to check if there is DNA contamination in the sample by RT-PCR analysis with and without reverse transcriptase. If performing RTPCR, RNA concentration as low as 100 ng per reaction can be used.
Preparation of cDNA library. Begin first strand synthesis of RNA-seq library preparation with total volume from step 5 of “rRNA depletion” following the protocol described in NEBNext Ultra II Directional RNA Library Prep Kit for Illumina Instruction section 2.6 First Strand cDNA Synthesis, and described below (https://www.neb. com//media/nebus/files/manuals/manuale7760_e7765.pdf). First strand cDNA synthesis 1. Assemble the first strand synthesis reaction on ice by adding the following components in a total volume of 20 μL: 10 μL of rRNA depleted RNA from the step above, 8 μL of NEBNext Strand Specificity Reagent, 2 μL of NEBNext First Strand Synthesis Enzyme Mix. 2. Mix contents thoroughly by pipetting up and down. 3. Perform first strand cDNA synthesis by incubating the reaction mixture in a thermocycler with the following settings: 10 min at 25 ◦C, 15 min at 42 ◦C, 15 min at 70 ◦C, hold at 4 ◦C. Second strand cDNA synthesis 1. Assemble the second strand synthesis reaction on ice by adding the following components to the first strand synthesis reaction from the step above in a total volume of 80 μL: 8 μL of NEBNext Second Strand Synthesis Reaction Buffer with dUTP Mix, 4 μL of NEBNext Second Strand Synthesis Enzyme Mix, 48 μL of nuclease-free water. 2. Keep the tube on ice and thoroughly mix by pipetting. 3. Incubate for 1 h at 16 ◦C in a thermocycler for second strand cDNA synthesis. Purification of double-stranded cDNA using NEBNext Sample Purification Beads 1. Resuspend the NEBNext sample purification beads by agitating on a vortex. 2. To the previously prepared 80 μL second strand cDNA synthesis mix from the step above, add 144 μL of the resuspended beads and mix thoroughly. 3. Incubate at room temperature for 5 min followed by a brief spin to collect contents at the bottom of the tube. 4. Place the tube on a magnetic rack to separate the beads and discard the supernatant. 5. To the magnetic beads, now add 200 μL of 80 % ethanol. 6. Incubate at room temperature for 30 s and discard the supernatant. 7. Repeat steps 5 and 6 once more. 8. Air dry the beads for up to 5 min. CRITICAL: Do not air-dry for longer than 5 min as the DNA recovery is compromised. 9. The tube is removed from the magnetic rack and DNA is eluted from the beads by adding 53 μL of 0.1X TE buffer, thoroughly vortexing, briefly spinning, and incubating at room temperature for 2 min. 10. Place samples on the magnetic rack and transfer 50 μL of the supernatant containing eluted DNA to a PCR tube. PAUSE POINT: The samples may be stored at 􀀀 20 ◦C at this point. cDNA library end prep 1. To the 50 μL of eluted DNA from the step above, add 7 μL of NEBNext Ultra II End Prep Reaction Buffer and 3 μL of NEBNext Ultra II Enzyme Mix in a total volume of 60 μL. 2. Mix the contents thoroughly by pipetting. 3. Incubate in a thermocycler with the following settings: 20 ◦C for 30 min, 65 ◦C for 30 min, hold at 4 ◦C. Adaptor ligation 1. Dilute the NEBNext Adaptor in ice-cold Adaptor Dilution Buffer on ice. Dilution depends on the amount of RNA input used for rRNA depletion: 5-fold for 1,000 ng-101 ng RNA input, 25-fold dilution for 100 ng-10 ng RNA input, and 200-fold for 5 ng RNA input. 2. Prepare the ligation reaction by adding the following to the end prep reaction from the step above: 2.5 μL of Diluted Adaptor, 1 μL of NEBNext Ligation Enhancer, and 30 μL of NEBNext Ultra II Ligation Master Mix in a total volume of 93.5 μL. 3. Pipette the mix thoroughly followed by a brief spin to collect residual liquid at the bottom. 4. Incubate the mix at 20 ◦C for 15 min in a thermocycler. 5. To the mix, add 3 μL of USER Enzyme, mix thoroughly by pipetting, and incubate at 37 ◦C for 15 min in a thermocycler. Purification of ligation reaction 1. To the ligation reaction mix, add 87 μL of NEBNext Sample Purification Beads and thoroughly mix by vortexing. 2. Incubate the mix at room temperature for 10 min followed by a brief spin. 3. Place the tube on a magnetic rack and discard the supernatant. 4. Add 200 μL of 80 % ethanol, incubate at room temperature for 30 s, then discard the supernatant. 5. Repeat steps 3 and 4 once more. 6. Briefly spin and place tube back on the magnetic rack, carefully removing the residual ethanol. 7. Air dry the magnetic beads for a maximum of 5 min. CRITICAL: Do not air-dry for longer than 5 min as the DNA recovery is compromised. 8. Remove the tube from the magnetic rack and elute the DNA by addition of 17 μL of 0.1X TE. Mix thoroughly by vortexing followed by a brief spin and incubation at room temperature for 2 min. 9. Place the tube on the magnetic rack and transfer 15 μL of the supernatant to a PCR tube. PAUSE POINT: The samples may be stored at 􀀀 20 ◦C at this point. PCR enrichment of adaptor ligated DNA 1. The PCR amplification of ligated DNA is performed in a volume of 50 μL. The PCR reaction mix contains 15 μL of adaptor ligated DNA, 25 μL of NEBNext Ultra II Q5 Master Mix, and 10 μL of Index Primer Mix. 2. Thoroughly mix by pipetting followed by a brief spin. 3. Incubate in a thermocycler with the following reaction conditions: 1 cycle of initial denaturation for 30 s at 98 ◦C, 7–16 cycles (adjusted for based upon RNA input) of denaturation and annealing/extension at 98 ◦C for 10 s and 65 ◦C for 75 s, respectively, a final extension for 5 min at 65 ◦C, and hold at 4 ◦C. Recommended PCR cycles are as follows, based on amount of RNA input: 7–8 cycles for 1,000 ng, 11–12 cycles for 100 ng, 14–15 cycles for 10 ng, and 15–16 cycles for 5 ng. Purification of PCR reaction 1. Vortex NEBNext Sample Purification Beads and add 45 μL of resuspended beads to the 50 μL PCR reaction from the step above. 2. Mix thoroughly by vortexing and incubate at room temperature for 5 min. 3. Spin briefly and place the tube on a magnetic rack. Discard the supernatant. 4. Add 200 μL of 80 % ethanol to the tube, incubate at room temperature for 30 s, and discard the supernatant. 5. Repeat steps 3 and 4 once more. 6. Air dry the beads for a maximum of 5 min. CRITICAL: Do not air-dry for longer than 5 min as the DNA recovery is compromised. 7. Remove the tube from the magnetic rack and elute DNA by adding 23 μL of 0.1X TE, mix thoroughly by vortexing, briefly spin, and incubate at room temperature for 2 min. 8. Place the tube on the magnetic rack and transfer 20 μL of supernatant to a new PCR tube. This is the cDNA library/GRO-seq library. PAUSE POINT: The samples may be stored at 􀀀 20 ◦C at this point. cDNA library assessment cDNA library quality was assessed to verify the library size (200–700 bp peak), purity and quantity using Agilent Tape Station 2200 gDNA-QG protocol following the manufacturer’s protocol in the link below and described briefly here: (https://www.agilent.com/cs/library/user manuals/Public/ScreenTape_gDNA_QG.pdf). 1. Prepare sample by mixing 1 μL cDNA library (10–100 ng/μL) from the step above with 10 μL Genomic DNA Sample Buffer. 2. Prepare ladder by mixing 1 μL Genomic DNA Ladder with 10 μL Genomic DNA Sample Buffer. 3. Vortex using IKA vortexer and adaptor at 2000 rpm for 1 min. 4. Briefly spin down to collect samples in the bottom of the tube. 5. Launch the 2200 TapeStation Controller Software and load Genomic DNA ScreenTape device and loading tips into the 2200 TapeStation instrument. 6. Load cDNA library samples and ladders from steps a and b above into the 2200 TapeStation instrument. 7. Select the required samples on the 2200 TapeStation Controller Software. 8. Click Start and specify a file name with which to save your results. CRITICAL: It is important to thaw all samples, bring them to room temperature and mix contents before use. Quantification of cDNA library Quantify libraries using the Qubit assay following Qubit_dsDNA_HS_ Assay_UG protocol following manufacturer’s protocol in the link below and described briefly here: (https://tools.thermofisher. com/content/sfs/manuals/Qubit_dsDNA_HS_Assay_UG.pdf). 1. Prepare 200 μL of working solution for each standard and cDNA library sample by diluting the Qubit_dsDNA HS Reagent 1:200 in Qubit_dsDNA HS Buffer, in 0.5 mL plastic PCR tubes. CRITICAL: Do not use glass tubes. 2. To quantify the standard solutions, transfer 190 μL working solution and 10 μL of each standard solution #1 and #2 into a new Qubit 0.5 mL tube. 3. To quantify the libraries, transfer 198 μL of working solution and 2 μL of cDNA library sample into a new Qubit 0.5 mL tube. 4. Mix well, gently, while avoiding bubbling. 5. Briefly spin to get the contents at the bottom of the tube and incubate for 2 min at room temperature. 6. Read sample concentration by selecting dsDNA High Sensitivity as the assay type on the Qubit instrument. CRITICAL: The fluorescence signal is stable for up to 3 h at room temperature and is sensitive to temperature.
rRNA removal by QIAseq FastSelect–rRNA Yeast Kit followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina

treatment_protocol: Transcription run-on reaction 1. Prepare TRO master mix in a 1.5 mL microcentrifuge tube as described above. 2. To 28 μL TRO mix, add 2 μL of BrUTP (100 mM) along with 2 μL each of 100 mM ATP, CTP, and GTP. 3. Add 49 μL of DEPC-H2O to the mix. 4. Add 5 μL (100 units) of RNase inhibitor (SUPERase) to the mix and pipette gently several times to mix reagents. 5. Add 10 μL of 10 % Sarkosyl and mix by pipetting. The solution may become more viscous, whitish, and opaque. 6. Preheat the resultant TRO reaction mixture to 30 ◦C. 7. Thaw permeabilized yeast cells in storage buffer (from step 9 of 2.2.1). Add 100 μL of permeabilized cells to 100 μL of preheated TRO reaction mixture. Mix by gently pipetting the contents up and down 15 times, and place in a water bath at 30 ◦C. 8. Perform transcription run-on reaction at 30 ◦C for 5 min. During the run-on reaction, gently agitate the tube by tapping with finger after every minute to facilitate mixing of cells with TRO reaction mixture to allow more reproducible results.

value: S. cerevisiae cells

value: wt


title: Serum-LungCancer-rep42-Phase II

description: Phase II of the experimental design

value: male

value: Serum

value: LungCancer

value: no


title: Serum-LungCancer-rep41-Phase II

description: Phase II of the experimental design

value: yes

value: Phase II

value: Serum autoantibody proteins IgG


title: Subject 2008 D42


title: Serum-LungCancer-rep40-Phase II

description: Phase II of the experimental design

value: female

value: Serum autoantibody proteins IgM


title: wt rep 3

description:
WT7
7_wt_rep3


title: Serum-LungCancer-rep39-Phase II

description: Phase II of the experimental design


title: wt rep 1

description:
WT5
5_wt_rep1


title: Subject 2008 D21


title: sua7-1 rep4

description:
Mut4
4_sua7-1_rep4


title: Subject 2010 D42


title: sua7-1 rep3

description:
Mut3
3_sua7-1_rep3


title: Serum-LungCancer-rep38-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep43-Phase II

description: Phase II of the experimental design


title: Subject 2008 D0


title: Serum-LungCancer-rep54-Phase II

description: Phase II of the experimental design


title: Subject 2010 D21


title: RNA-seq_SIMA929

data_processing:
Basecalls performed using CASAVA
raw paired-end reads were mapped by STAR_2.5.3a(parameters "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10 --alignIntronMax 500000 --chimSegmentMin 20 --chimJunctionOverhangMin 20")
gene level quantification and differential gene expression analysis were done by St Jude Cloud RNAseq pipeline (WARDEN, https://platform.stjude.cloud/workflows/warden)
Genome_build: hg19(GRCh37)
Supplementary_files_format_and_content: gene-based raw counts txt file

growth_protocol: BE2C, KELLY, SIMA, SKNAS, SKNSH and SKNFI cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2. For xenograft model, SIMA 5x106cells were mixed with matrigel and injected in to CB17SCID mice through subcutaneous method.

extract_protocol:
100 to 200 x 10e3 cells were seeded in a 6-well plate. Next day, cells were treated with DMSO and 100 nM of QC6352 for 48 hours. Total RNA from cells and tumor tissues were performed using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: Cells were treated with 0.1% DMSO or QC6352 100nM for 48h. For SIMA xenografts, tumor were treated either QC6352 50mg/kg body weight once per day or vehicle for 6 day and harvested for RNA extraction.

value: SIMA xenograft

value: QC6352 treatment


title: Serum-LungCancer-rep37-Phase II

description: Phase II of the experimental design


title: RNA-seq_SIMA928


title: RNA-seq_SIMA926


title: Serum-LungCancer-rep36-Phase II

description: Phase II of the experimental design


title: Subject 2006 D21


title: Subject 2006 D42


title: RNA-seq_SIMA924


title: RNA-seq_SIMA921


title: Subject 2006 D0


title: Serum-LungCancer-rep35-Phase II

description: Phase II of the experimental design


title: RNA-seq_SIMA925

value: Vehicle treatment


title: RNA-seq_SIMA930


title: Subject 2005 D42

value: Healthy Control


title: wt rep 2

description:
WT6
6_wt_rep2


title: Serum-LungCancer-rep34-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep33-Phase II

description: Phase II of the experimental design


title: RNA-seq_SIMA922


title: RNA-seq_SKNFI_QC_002

value: SKNFI

value: QC6352 200nM treatment


title: sua7-1 rep2

description:
Mut2
2_sua7-1_rep2

value: S. cerevisiae cells


title: Subject 2005 D21

value: Serum/Plasma


title: Subject 2005 D0


title: Serum-LungCancer-rep32-Phase II

description: Phase II of the experimental design

value: male


title: RNA-seq_SKNFI_QC_001


title: RNA-seq_SKNFI_DMSO_002

value: DMSO 0.1% treatment


title: Subject 2002 D42


title: RNA-seq_SKNSH_QC_002

value: SKNSH


title: Serum-LungCancer-rep31-Phase II

description: Phase II of the experimental design

value: Serum

value: LungCancer

value: no


title: Subject 2002 D21


title: Serum-LungCancer-rep30-Phase II

description: Phase II of the experimental design

value: yes

value: Phase II

value: Serum autoantibody proteins IgG


title: RNA-seq_SKNSH_DMSO_002


title: RNA-seq_SKNSH_QC_001


title: RNA-seq_SKNSH_DMSO_001


title: RNA-seq_SKNAS_QC_002

value: SKNAS


title: Subject 2002 D0


title: RNA-seq_SIMA923

value: SIMA xenograft


title: Serum-LungCancer-rep28-Phase II

description: Phase II of the experimental design

value: Serum autoantibody proteins IgM


title: Subject 46 D42

value: SLE Patient


title: RNA-seq_SKNAS_DMSO_002


title: RNA-seq_SKNAS_DMSO_001


title: Serum-LungCancer-rep27-Phase II

description: Phase II of the experimental design


title: Subject 46 D23/24


title: RNA-seq_Kelly_QC_002

value: KELLY


title: Serum-LungCancer-rep29-Phase II

description: Phase II of the experimental design

value: female


title: Serum-LungCancer-rep26-Phase II

description: Phase II of the experimental design


title: RNA-seq_Kelly_QC_001

value: QC6352 200nM treatment


title: RNA-seq_SKNFI_DMSO_001

value: SKNFI


title: RNA-seq_Kelly_DMSO_002


title: Subject 44 D42

value: Serum/Plasma


title: RNA-seq_Kelly_DMSO_001

value: DMSO 0.1% treatment


title: RNA-seq_SIMA_QC_002

value: SIMA


title: Serum-LungCancer-rep25-Phase II

description: Phase II of the experimental design

value: male

value: Serum


title: RNA-seq_SIMA_QC_001


title: Subject 44 D23/24


title: RNA-seq_SIMA_DMSO_002


title: Serum-LungCancer-rep24-Phase II

description: Phase II of the experimental design

value: LungCancer

value: no


title: RNA-seq_SIMA_DMSO_001


title: Subject 44 D0


title: Serum-LungCancer-rep23-Phase II

description: Phase II of the experimental design

value: yes

value: Phase II


title: RNA-seq_SKNAS_QC_001

value: SKNAS


title: RNA-seq_BE2C_QC_001


title: RNA-seq_BE2C_DMSO_002


title: Prototype PAP

data_processing:
Barebeed MFI values were subtracted from the MFI values for all analytes in each sample and  replicate MFI values were averaged.
ACA Array version 2 Platform Raw MFI_02272024.xlsx:  raw data
matrix_MFI.txt: Numerical values represent median fluorescent intensity (MFI).

label_protocol: Secondary antibody conjugated to a fluorophore was added to a PBS solution containing conjugated beads bound to antibodies from samples.

value: Prototype Autoimmune Disease Sample


title: Serum-LungCancer-rep22-Phase II

description: Phase II of the experimental design

value: Serum autoantibody proteins IgG

value: Serum autoantibody proteins IgM


title: RNA-seq_BE2C_QC_002


title: Subject 41 Day 42

value: SLE Patient


title: Serum-LungCancer-rep21-Phase II

description: Phase II of the experimental design

value: female


title: Subject 41 Day 23/24


title: RNA-seq_BE2C_DMSO_001


title: Prototype APS-1 (3)


title: Subject 41 Day 0


title: Prototype APS-1 (1)


title: Serum-LungCancer-rep20-Phase II

description: Phase II of the experimental design


title: Subject 46 D0


title: Prototype AMI (3)


title: Serum-LungCancer-rep19-Phase II

description: Phase II of the experimental design


title: Subject 40 D42


title: Prototype AMI (2)


title: Prototype AMI (1)


title: Subject 40 D23/24


title: Subject 2026 D42

value: Healthy Control


title: Serum-LungCancer-rep18-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep17-Phase II

description: Phase II of the experimental design


title: Subject 2026 D0


title: Subject 2026 D21


title: Serum-LungCancer-rep16-Phase II

description: Phase II of the experimental design


title: Subject 2025 D42


title: Subject 2025 D21


title: Subject 38 Day 23/24


title: Serum-LungCancer-rep15-Phase II

description: Phase II of the experimental design


title: Prototype APS-1 (2)


title: Subject 2023 D21


title: Subject 2022 D42


title: Subject 2023 D42


title: Subject 38 Day 0


title: Serum-LungCancer-rep14-Phase II

description: Phase II of the experimental design


title: Subject 2023 D0


title: Subject 2022 D21


title: Subject 35 D23/24


title: Serum-LungCancer-rep12-Phase II

description: Phase II of the experimental design


title: Subject 2022 D0


title: Subject 35 D42


title: Serum-LungCancer-rep13-Phase II

description: Phase II of the experimental design


title: Subject 2021 D42


title: Subject 2021 D0


title: Subject 40 D0


title: Serum-LungCancer-rep11-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep10-Phase II

description: Phase II of the experimental design


title: Subject 34 D42


title: Subject 38 Day 42


title: Subject 2019 D0


title: Subject 2019 D21


title: Serum-LungCancer-rep9-Phase II

description: Phase II of the experimental design


title: Subject 34 D23/24


title: Subject 2025 D0


title: Subject 2016 D42


title: Serum-LungCancer-rep8-Phase II

description: Phase II of the experimental design


title: Subject 34 D0


title: Subject 2016 D21


title: Subject 2016 D0


title: Subject 2014 D21


title: Serum-LungCancer-rep7-Phase II

description: Phase II of the experimental design


title: Subject 2014 D0


title: Subject 32 Day 42


title: Subject 35 D0


title: Subject 2010 D42


title: Subject 2010 D0


title: Subject 2021 D21


title: Subject 2010 D21


title: Serum-LungCancer-rep6-Phase II

description: Phase II of the experimental design


title: Subject 32 Day 23/24


title: Subject 32 Day 0


title: Subject 2019 D42


title: Subject 2008 D42


title: Subject 2008 D21


title: Subject 2008 D0


title: Subject 31 D42


title: Subject 31 D23/24


title: Subject 2006 D0


title: Subject 31 D0


title: Serum-LungCancer-rep5-Phase II

description: Phase II of the experimental design


title: Subject 2006 D21


title: Subject 2005 D42


title: Subject 2005 D21


title: Serum-LungCancer-rep2-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep3-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep1-Phase II

description: Phase II of the experimental design


title: Subject 29 D42


title: Subject 2004 D42


title: Subject 2005 D0


title: Serum-DiseaseControl-rep60-Phase II

description: Phase II of the experimental design

source_name: Serum,DiseaseControl,Phase II

value: DiseaseControl


title: Subject 2004 D21

value: Serum/Plasma


title: Serum-LungCancer-rep4-Phase II

description: Phase II of the experimental design


title: Subject 29 D0


title: Serum-DiseaseControl-rep58-Phase II

description: Phase II of the experimental design


title: Subject 2003 D21


title: Subject 2003 D0


title: Subject 2003 D42


title: Subject 2004 D0


title: Serum-DiseaseControl-rep59-Phase II

description: Phase II of the experimental design


title: Subject 29 D23/24


title: Subject 2006 D42


title: Serum-DiseaseControl-rep57-Phase II

description: Phase II of the experimental design


title: Subject 28 Day 23/24


title: Subject 28 Day 42


title: Subject 2002 D42


title: Subject 2002 D21


title: Serum-DiseaseControl-rep56-Phase II

description: Phase II of the experimental design


title: Subject 47 D42


title: Subject 2002 D0


title: Subject 28 Day 0


title: Subject 47 D23/24


title: Subject 21 D42


title: Subject 47 D0


title: Serum-DiseaseControl-rep55-Phase II

description: Phase II of the experimental design


title: Subject 21 D23/24


title: Subject 46 Day 0


title: Subject 46 Day 23/24


title: Subject 21 D0


title: Serum-DiseaseControl-rep54-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep53-Phase II

description: Phase II of the experimental design


title: Subject 18 Day 42


title: Subject 44 D23/24


title: Subject 41 Day 23/24


title: Subject 44 D0


title: Subject 44 D42


title: Subject 41 Day 42


title: Serum-DiseaseControl-rep52-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep51-Phase II

description: Phase II of the experimental design


title: Subject 18 Day 23/24


title: Serum-DiseaseControl-rep50-Phase II

description: Phase II of the experimental design


title: Subject 18 Day 0


title: Subject 40 Day 42


title: Subject 17 Day 42


title: Serum-DiseaseControl-rep49-Phase II

description: Phase II of the experimental design


title: Subject 40 Day 23/24


title: Subject 40 Day 0


title: Subject 4 D42


title: Subject 17 Day 23/24


title: Subject 46 Day 42


title: Serum-DiseaseControl-rep48-Phase II

description: Phase II of the experimental design


title: Subject 4 D23/24


title: Subject 38 D42


title: Subject 17 Day 0


title: Serum-DiseaseControl-rep47-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep46-Phase II

description: Phase II of the experimental design


title: Subject 38 D0


title: Subject 15 D23/24


title: Subject 41 Day 0


title: Subject 35 Day 42


title: Subject 14 Day 42


title: Subject 34 D42


title: Subject 34 D23/24


title: Subject 34 D0


title: Subject 14 Day 23/24


title: Serum-DiseaseControl-rep44-Phase II

description: Phase II of the experimental design


title: Subject 32 Day 42


title: Subject 35 Day 0


title: Serum-DiseaseControl-rep43-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep45-Phase II

description: Phase II of the experimental design


title: Subject 14 Day 0


title: Subject 4 D0


title: Serum-DiseaseControl-rep42-Phase II

description: Phase II of the experimental design


title: Subject 32 Day 0


title: Subject 12 Day 42


title: Subject 31 Day 42


title: Subject 38 D23/24


title: Subject 31 Day 0


title: Subject 31 Day 23/24


title: Subject 15 D0


title: Serum-DiseaseControl-rep40-Phase II

description: Phase II of the experimental design


title: Subject 29 Day 23/24


title: Subject 29 Day 42


title: Serum-DiseaseControl-rep39-Phase II

description: Phase II of the experimental design


title: Subject 35 Day 23/24


title: Subject 12 Day 0


title: Subject 8 Day 42


title: Subject 28 Day 42


title: Serum-DiseaseControl-rep38-Phase II

description: Phase II of the experimental design


title: Subject 32 Day 23/24


title: Subject 29 Day 0


title: Subject 28 Day 23/24


title: Serum-DiseaseControl-rep37-Phase II

description: Phase II of the experimental design


title: Subject 8 Day 0


title: Serum-DiseaseControl-rep41-Phase II

description: Phase II of the experimental design


title: Subject 28 Day 0


title: Subject 21 D42


title: Subject 21 D23/24


title: Subject 21 D0


title: Subject 12 Day 23/24


title: Subject 1 Day 42


title: Serum-DiseaseControl-rep35-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep36-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep34-Phase II

description: Phase II of the experimental design


title: Subject 18 Day 23/24


title: Subject 18 Day 42


title: Subject 1 Day 23/24


title: Subject 17 Day 42


title: Subject 18 Day 0


title: Subject 1 Day 0


title: Serum-DiseaseControl-rep33-Phase II

description: Phase II of the experimental design


title: Subject 8 Day 23/24


title: Subject 17 Day 23/24


title: Subject 17 Day 0


title: Subject 15 D23/24


title: Serum-DiseaseControl-rep32-Phase II

description: Phase II of the experimental design


title: HepG2_R688H_Variant_2

city: Huntsville

first: Brian

middle: Scott

last: Roberts

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

data_processing:
UMIs were extracted with umi_tools.
Raw reads were trimmed using bbduk.
Reads were de-duplicated with umi_tools.
Salmon was used for quantification with the Gencode Release 43 (GRCh38.p13).
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file
Supplementary files format and content: Raw counts as a matrix with samples as columns and genes as rows.

molecule: polyA RNA

growth_protocol: HepG2 cells were gorwn according to ATCC guidelines.

extract_protocol:
RNA was extracted from 6-well plates using the Norgen Total RNA Purification Kit.
Libraries were constructed using the Lexogen QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI kit.


title: Serum-DiseaseControl-rep31-Phase II

description: Phase II of the experimental design


title: Subject 15 D0


title: Serum-DiseaseControl-rep30-Phase II

description: Phase II of the experimental design


title: HepG2_R688H_Variant_1


title: Subject 14 D42


title: HepG2_R688H_Control_3


title: Serum-DiseaseControl-rep28-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep29-Phase II

description: Phase II of the experimental design


title: Subject 14 D23/24


title: HepG2_R688H_Control_2


title: HepG2_R688H_Control_1


title: Subject 14 D0


title: Subject 12 Day 42


title: female # 5_kidney sample one week afer ischemia (WL)

type: RNA

city: San Sebastian

first: Stéphane

last: Nemours

state: Guipúzcoa

address: Paseo Dr. Begiristain, s/n

country: Spain

institute: Biogipuzcoa

hyb_protocol: Briefy, sense ssDNA suitable for labeling was generated from total RNA with the GeneChip WT Plus Reagent Kit from Afymetrix (Afymetrix, Santa Clara, CA) according to the manufacturer’s instructions. Sense ssDNA was fragmented, labeled and hybridized to the arrays with the GeneChip WT Terminal Labeling and Hybridization Kit from the same manufacturer.

scan_protocol: Array plate was scanned using the Gene Titan MultiChannel System

data_processing: Bioinformatic analysis was performed at the Statistics and Bioinformatics Unit (UEB) at VHIR. Robust Multi-array Average (RMA) algorithm was used for pre-processing microarray data. Background adjustment, normalization and summarization of raw core probe expression values were defned so that the exon level values were averaged to yield one expression value per gene. The analysis was done considering the experimental factors (time points and sex) and taking into account the pairing between samples in most of the comparisons performed. Data were subjected to non-specifc fltering to remove low signal and low variability genes. Conservative thresholds were used to reduce possible false negative results. This yields a list of 3435 genes to be analyzed. Selection of diferentially expressed genes was based on a linear model analysis with empirical Bayes modifcation for the variance estimates. This method is similar to using a ‘t-test’ with an improved estimate of the variance. To account for multiple testing, p values were adjusted to obtain stronger control over the false discovery rate (FDR), as described by the Benjamini and Hochberg method. Genes with adjusted p value below 0.05 and absolute value of log2 fold change over 1 were called differentially expressed.

label: biotin

organism: Sus scrofa

source_name: kidney biopsy

label_protocol: Microarray hybridization was carried out at High Technology Unit (UAT) at VHIR. RNA integrity was assessed by Agilent 2100 Bioanalyzer (Agilent, Palo Alto, Ca). Only samples with similar RNA integrity number were accepted for microarray analysis. Gene Titan Afymetrix microarray platform and the Genechip Porcine Gene 2.1 ST 16-Array plate were used for this experiment. Starting material was 200 ng of total RNA of each sample.

extract_protocol: RNA was extracted from the PR, PS and WL kidney biopsies from each animal. The extractions were performed starting from 50 mg of each biopsy performed with the NZyol Kit following manufacturer instructions (Nzytech genes & enzymes).

tag: Sex

tag: group

value: one week afer ischemia (WL)


title: female # 4_kidney sample one week afer ischemia (WL)


title: HepG2_R1274W_Variant_3

tag: cell line


title: HepG2_R688H_Variant_3


title: Serum-DiseaseControl-rep25-Phase II

description: Phase II of the experimental design


title: female # 2_kidney sample one week afer ischemia (WL)


title: female # 3_kidney sample one week afer ischemia (WL)


title: Subject 12 Day 23/24


title: Serum-DiseaseControl-rep27-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep26-Phase II

description: Phase II of the experimental design


title: Subject 12 Day 0


title: HepG2_R1274W_Variant_2


title: female # 1_kidney sample one week afer ischemia (WL)


title: male # 5_kidney sample one week afer ischemia (WL)


title: male # 4_kidney sample one week afer ischemia (WL)


title: male # 3_kidney sample one week afer ischemia (WL)


title: Subject 8 Day 42


title: Subject 8 Day 23/24


title: Serum-DiseaseControl-rep24-Phase II

description: Phase II of the experimental design


title: HepG2_R1274W_Control_3


title: Subject 8 Day 0


title: male # 2_kidney sample one week afer ischemia (WL)


title: Subject 1 D42


title: HepG2_R1274W_Control_1


title: HepG2_R1274W_Control_2


title: HepG2_R1274W_Variant_1


title: male # 1_kidney sample one week afer ischemia (WL)


title: Subject 1 D23/24


title: Serum-DiseaseControl-rep23-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep20-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep19-Phase II

description: Phase II of the experimental design


title: female # 5_kidney sample 5 min following 30 min of ischemia (PS)

value: 5 min following 30 min of ischemia (PS)


title: female # 4_kidney sample 5 min following 30 min of ischemia (PS)


title: female # 3_kidney sample 5 min following 30 min of ischemia (PS)


title: Subject 1 D0


title: Serum-DiseaseControl-rep18-Phase II

description: Phase II of the experimental design

value: male


title: HTO, 10X Lane2, Sequencing Run 1

city: New York

first: Julia

last: Domingo

address: 101 6th Av

institute: New York Genome Center

description:
HTO_L2_quants_mat.gz
d2n_processed_data.txt
HTO_features.txt

library_source: other

data_processing:
cellranger (cDNA -  targeted gene expression count, GDO - feature ref count) or salmon alevin (HTO - feature ref) for demultiplexing and barcode feature matrix generation
QC and filtering expression matrices using custom scripts
Expression Matrices merging and normailization using Seurat
Calculation of DE values using Seurat
Assembly: refdata-gex-GRCh38-2020
Supplementary files format and content: tab separeted file
Supplementary files format and content: Pseudo bulk differential expression values per unique gene per unique sgRNA per tunique dosage perturbation (inactivation or activation)
Library strategy: ECCITE-seq

molecule: other

growth_protocol: Twenty hours post-transduction, the cell media was replaced with fresh IMDM 10% Serum Plus II Blasticidin 5 µg/mL, and four hours later, Puromycin (Invivogen ant-pr-1) was added at a final concentration of 2 µg/mL to select for cells with sgRNA integration. The transduction batch with an infection rate of ~10% was selected, and cells were sorted to near purity using FACS to remove dead cells. Cells were maintained at >90% survival and a maximum confluency of 700,000 cells/mL. On day 8 post-transduction, the cells were collected and prepared for cell hashing

extract_protocol:
Each transduced cell line was split into four batches of 500,000 cells, resulting in a total of 8 different hashes. After incubation and washes, all 8 hashed batches were pooled together and run in two reaction lanes of the 10X Chromium Next GEM Single Cell 5’ Reagent Kit v2 (single indexing, PN-1000265 and PN-1000190). The manufacturer's protocol was followed with modifications stipulated in the ECCITE-seq protocol 11. For each GEM reaction, 42,000 cells from the hash pool were used to obtain approximately 21,000 total cells, including "multiplets" (multiple cells per droplet counts)
Gene expression (cDNA), hashtags (HTOs), and guide RNA (Guide-derived oligos, GDOs) libraries were constructed following the 10x Genomics and ECCITE-seq protocols (https://cite-seq.com/eccite-seq/) with minimal modifications. Specifically, the antibody pool protein tag library steps were ignored, and a custom-designed probe library was used to enrich the cDNA for the genes of interest in the 10X Targeted Gene Expression protocol (10X PN-1000248)


title: Serum-DiseaseControl-rep22-Phase II

description: Phase II of the experimental design

value: Serum


title: Serum-DiseaseControl-rep16-Phase II

description: Phase II of the experimental design


title: GDO, 10X Lane1, Sequencing Run 1

description:
GDO_L1_feature_bc_matrix.gz
d2n_processed_data.txt
GDO_feature_ref.csv


title: female # 1_kidney sample 5 min following 30 min of ischemia (PS)


title: male # 5_kidney sample 5 min following 30 min of ischemia (PS)


title: Serum-DiseaseControl-rep21-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep17-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep15-Phase II

description: Phase II of the experimental design


title: HTO, 10X Lane1, Sequencing Run 1

description:
HTO_L1_quants_mat.gz
d2n_processed_data.txt
HTO_features.txt


title: cDNA, 10X Lane2, Sequencing Run 2

description:
cDNA_L2_feature_bc_matrix.gz
d2n_processed_data.txt
cDNA_targeted_panel.csv

library_source: transcriptomic single cell

data_processing:
cellranger (cDNA -  targeted gene expression count, GDO - feature ref count) or salmon alevin (HTO - feature ref) for demultiplexing and barcode feature matrix generation
QC and filtering expression matrices using custom scripts
Expression Matrices merging and normailization using Seurat
Calculation of DE values using Seurat
Assembly: refdata-gex-GRCh38-2020
Supplementary files format and content: tab separeted file
Supplementary files format and content: Pseudo bulk differential expression values per unique gene per unique sgRNA per tunique dosage perturbation (inactivation or activation)


title: female # 2_kidney sample 5 min following 30 min of ischemia (PS)


title: cDNA, 10X Lane2, Sequencing Run 1


title: Serum-DiseaseControl-rep14-Phase II

description: Phase II of the experimental design


title: male # 4_kidney sample 5 min following 30 min of ischemia (PS)


title: Serum-LungCancer-rep8-Phase I

description: Phase I of the experimental design

source_name: Serum,LungCancer,Phase I

value: adenocarcinoma

value: Phase I


title: GDO, 10X Lane2, Sequencing Run 1

description:
GDO_L2_feature_bc_matrix.gz
d2n_processed_data.txt
GDO_feature_ref.csv


title: Serum-DiseaseControl-rep13-Phase II

description: Phase II of the experimental design


title: male # 3_kidney sample 5 min following 30 min of ischemia (PS)


title: Serum-DiseaseControl-rep12-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep7-Phase I

description: Phase I of the experimental design

value: no

value: yes


title: Serum-LungCancer-rep6-Phase I

description: Phase I of the experimental design


title: Serum-LungCancer-rep5-Phase I

description: Phase I of the experimental design


title: cDNA, 10X Lane1, Sequencing Run 1

description:
cDNA_L1_feature_bc_matrix.gz
d2n_processed_data.txt
cDNA_targeted_panel.csv


title: male # 2_kidney sample 5 min following 30 min of ischemia (PS)


title: male # 1_kidney sample 5 min following 30 min of ischemia (PS)


title: P5miRNA

city: Hangzhou

first: Ningning

last: Xie

address: 1 Xueshi Road

institute: Women’s Hospital, School of Medicine, Zhejiang University

data_processing:
To perform analysis on mRNAs, the initial step involved utilizing Cutadapt and Perl scripts to eliminate reads containing adaptor contamination, low-quality bases, and unclear bases. Then, FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was employed for the purpose of confirming the sequence quality. The standard-compliant reads were mapped to the human genome by Bowtie2 and Tophat2. The assembled mapped reads of each specimen were processed by deployingStringTie.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample.

source_name: placenta

extract_protocol:
Isolation of the total RNA was performed using Trizol Reagent (Invitrogen, USA).
Two libraries were constructed for the purpose of whole transcriptome sequencing. The TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA) were employed to create the small RNA library. A 1 µg of total RNA was utilized in accordance with the provided protocol. Following the completion of library preparation, the created libraries underwent sequencing by employing the Illumina Hiseq2000 platform, employing a single-end configuration with a read length of 1×50 bp. For mRNA and circRNA library, first, ribosomal RNA was depleted, and the remaining RNA was fragmented. Following the purification process, the poly(A)– or poly(A)+ RNA fractions were subjected to fragmentation by means of divalent cations at an increased temperature. Additionally, the construction of the cDNA library was carried out utilizing the mRNA-Seq sample preparation kit (Illumina, San Diego, CA, USA).Finally, the paired-end sequencing was conducted on the Illumina NovaSeq 6000 system with a 2 × 150 bp read length (LC Bio, China).

value: placenta


title: female # 5_kidney sample prior to injury (PR)

value: prior to injury (PR)


title: cDNA, 10X Lane1, Sequencing Run 2


title: Serum-DiseaseControl-rep10-Phase II

description: Phase II of the experimental design

value: Phase II

value: Serum autoantibody proteins IgG


title: P4miRNA


title: P3miRNA


title: Serum-LungCancer-rep4-Phase I

description: Phase I of the experimental design

value: Serum autoantibody proteins IgM


title: Serum-DiseaseControl-rep9-Phase II

description: Phase II of the experimental design


title: female # 3_kidney sample prior to injury (PR)

value: female


title: Serum-LungCancer-rep3-Phase I

description: Phase I of the experimental design


title: female # 4_kidney sample prior to injury (PR)


title: P1miRNA


title: Serum-DiseaseControl-rep7-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep11-Phase II

description: Phase II of the experimental design


title: Serum-LungCancer-rep2-Phase I

description: Phase I of the experimental design


title: female # 2_kidney sample prior to injury (PR)


title: P2miRNA


title: Serum-NegativeControl-rep8-Phase I

description: Phase I of the experimental design

source_name: Serum,NegativeControl,Phase I

value: normal


title: Serum-LungCancer-rep1-Phase I

description: Phase I of the experimental design


title: Serum-NegativeControl-rep7-Phase I

description: Phase I of the experimental design


title: female # 1_kidney sample prior to injury (PR)


title: male # 5_kidney sample prior to injury (PR)


title: Serum-DiseaseControl-rep5-Phase II

description: Phase II of the experimental design

value: DiseaseControl


title: Serum-DiseaseControl-rep6-Phase II

description: Phase II of the experimental design


title: C4miRNA


title: C5miRNA


title: C3miRNA


title: Serum-DiseaseControl-rep8-Phase II

description: Phase II of the experimental design


title: C1miRNA


title: C2miRNA


title: Serum-DiseaseControl-rep3-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep4-Phase II

description: Phase II of the experimental design


title: Serum-DiseaseControl-rep2-Phase II

description: Phase II of the experimental design


title: hMTH7_raw_1

status: Public on Mar 01 2024

first: xiaogu

last: zheng

state: Zhejiang

address: Xiasha University Town

institute: Zhejiang Gongshang university

description: Fermentation with 100mg/mL 5-methyltetrahydrofolate

data_processing:
Briefly, raw data FASTQ files were imported into the format which could be operated by QIIME2 system using qiime tools import program. Demultiplexed sequences from each sample were quality filtered and trimmed , de-noised, merged, and then the chimeric sequences were identified and removed using the QIIME2 dada2 plugin to obtain the feature table of amplicon sequence variant (ASV) (Callahan et al. 2016).
The QIIME2 feature-classifier plugin was then used to align ASV sequences to a pre-trained GREENGENES 13_8 99% database (trimmed to the V3V4 region bound by the 338F/806R primer pair) to generate the taxonomy table (Bokulich et al. 2018)
Any contaminating mitochondrial and chloroplast sequences were filtered using the QIIME2 feature-table plugin. Appropriate methods include ANCOM, ANOVA, Kruskal Wallis, LEfSe and DEseq2 were employed to identify the bacteria with different abundance among samples and groups (Love, Huber, and Anders 2014; Mandal et al. 2015; Segata et al. 2011).
Diversity metrics were calculated using the core-diversity plugin within QIIME2. Feature level alpha diversity indices, such as observed OTUs, Chao1 richness estimator, Shannon diversity index, and Faith’s phylogenetics diversity index were calculated to estimate the microbial diversity within an individual sample.
Supplementary files format and content: allsample.txt: ASVs IDs of sample groups  (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)
Supplementary files format and content: table.tsv: ASVs IDs of sample groups  (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)
Supplementary files format and content: AllSample_GC_Q.stat.xls: Sample group (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF) processing process files
Supplementary files format and content: alpha_diversity.xls: Sample groups (Ori, Ctrl, lFA,mFA, hFA, lMTHF,mMTHF, hMTHF)alpha diversity index
Supplementary files format and content: alpha-summary.txt: Sample group (Ori, Ctrl2, FA, MTHF) alpha diversity index
Supplementary files format and content: assemble_stat.xls.txt: Sample group (Ori, Ctrl2, FA, MTHF) processing process files
Supplementary files format and content: feature-table.tsv: ASVs IDs of sample groups (Ori, Ctrl2, FA, MTHF)

organism: human feces metagenome

source_name: fecal matter (not tissue)

extract_protocol:
Total genome DNA from samples was extracted using CTAB method. DNA concentration and purity was monitored on 1% agarose gels. According to the concentration, DNA was diluted to 1ng/µL using sterile water.
16S rRNA  genes of distinct regions(16S V3-V4 ) were amplified used specific primer( 341F(5’-CCTAYGGGRBGCASCAG-3’)和806R (5’-GGACTACNNGGGTATCTAAT-3’) )with the barcode. All PCR reactions were carried out with 15 µL of Phusion® High-Fidelity PCR Master Mix (New England Biolabs); 2 µM of forward and reverse primers, and about 10 ng template DNA. Thermal cycling consisted of initial denaturation at 98℃ for 1 min, followed by 30 cycles of denaturation at 98℃ for 10 s, annealing at 50℃ for 30 s, and elongation at 72℃ for 30 s. Finally 72℃ for 5 min
The analysis was conducted by following the "Atacama soil microbiome tutorial" of Qiime2docs along with customized program scripts (https://docs.qiime2.org/2019.1/).

value: fecal matter (not tissue)

value: 16S rRNA

tag: treatment


title: male # 3_kidney sample prior to injury (PR)


title: male # 2_kidney sample prior to injury (PR)


title: hMTH5_raw_1

value: Fermentation with 100mg/mL 5-methyltetrahydrofolate


title: hMTH6_raw_1


title: Serum-NegativeControl-rep5-Phase I

description: Phase I of the experimental design


title: Serum-DiseaseControl-rep1-Phase II

description: Phase II of the experimental design

value: male


title: male # 1_kidney sample prior to injury (PR)


title: hMTH4_raw_1


title: male # 4_kidney sample prior to injury (PR)


title: Serum-NegativeControl-rep6-Phase I

description: Phase I of the experimental design

value: Serum


title: Serum-NegativeControl-rep4-Phase I

description: Phase I of the experimental design


title: Serum-NegativeControl-rep3-Phase I

description: Phase I of the experimental design


title: hMTH2_raw_1


title: hMTH1_raw_1


title: Serum-NegativeControl-rep2-Phase I

description: Phase I of the experimental design


title: hMTH3_raw_1


title: hMTH8_raw_1


title: mMTHF8_raw_1

description: Fermentation with 10mg/mL 5-methyltetrahydrofolate


title: mMTHF5_raw_1

value: Fermentation with 10mg/mL 5-methyltetrahydrofolate


title: mMTHF4_raw_1


title: mMTHF6_raw_1


title: Serum-NegativeControl-rep1-Phase I

description: Phase I of the experimental design

value: Phase I


title: mMTHF3_raw_1


title: mMTHF2_raw_1


title: mMTHF1_raw_1


title: lMTH8_raw_1

description: Fermentation with 1mg/mL 5-methyltetrahydrofolate


title: lMTH7_raw_1

value: Fermentation with 1mg/mL 5-methyltetrahydrofolate


title: lMTH3_raw_1


title: lMTH4_raw_1


title: mMTHF7_raw_1


title: lMTH1_raw_1


title: hFA8_raw_1

description: Fermentation with 100mg/mL folic acid

value: Fermentation with 100mg/mL folic acid


title: hFA4_raw_1

description: Fermentation with 100mg/mL folic acid


title: hFA3_raw_1

description: Fermentation with 100mg/mL folic acid


title: hFA5_raw_1

description: Fermentation with 100mg/mL folic acid


title: hFA6_raw_1

description: Fermentation with 100mg/mL folic acid


title: hFA2_raw_1

description: Fermentation with 100mg/mL folic acid


title: hFA1_raw_1

description: Fermentation with 100mg/mL folic acid


title: mFA8_raw_1

description: Fermentation with 10mg/mL folic acid

value: Fermentation with 10mg/mL folic acid


title: mFA4_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA7_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA6_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA2_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA5_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA3_raw_1

description: Fermentation with 10mg/mL folic acid


title: mFA1_raw_1

description: Fermentation with 10mg/mL folic acid


title: lFA6_raw_1

description: Fermentation with 16mg/mL folic acid

value: Fermentation with 16mg/mL folic acid


title: lFA8_raw_1

description: Fermentation with 16mg/mL folic acid


title: lMTH6_raw_1


title: lFA7_raw_1

description: Fermentation with 16mg/mL folic acid


title: lFA4_raw_1

description: Fermentation with 16mg/mL folic acid


title: lMTH5_raw_1


title: lFA5_raw_1

description: Fermentation with 16mg/mL folic acid


title: hFA7_raw_1

description: Fermentation with 100mg/mL folic acid


title: Ctrl8_1

description: Fermentation of faeces

value: Fermentation of faeces


title: lFA2_raw_1

description: Fermentation with 16mg/mL folic acid


title: lFA3_raw_1

description: Fermentation with 16mg/mL folic acid


title: lFA1_raw_1

description: Fermentation with 16mg/mL folic acid


title: Ctrl6_1

description: Fermentation of faeces


title: Ctrl7_1

description: Fermentation of faeces


title: Ctrl5_1

description: Fermentation of faeces


title: Ctrl3_1

description: Fermentation of faeces


title: Ctrl2_1

description: Fermentation of faeces


title: Ctrl4_1

description: Fermentation of faeces


title: K8_raw_1

description: Raw feces

value: Raw feces


title: K7_raw_1

description: Raw feces


title: K6_raw_1

description: Raw feces


title: MTHF8_1


title: K5_raw_1

description: Raw feces


title: MTHF7_1


title: K1_raw_1

description: Raw feces


title: K3_raw_1

description: Raw feces


title: MTHF6_1


title: MTHF4_1


title: K4_raw_1

description: Raw feces


title: MTHF3_1


title: MTHF2_1


title: FA6_1

description: Fermentation with 1mg/mL folic acid

value: Fermentation with 1mg/mL folic acid


title: FA8_1

description: Fermentation with 1mg/mL folic acid


title: MTHF1_1


title: FA7_1

description: Fermentation with 1mg/mL folic acid