title: P08H-3, bodywall

data_processing:
Step1: Decontamination. Genomic ONT reads were mapped onto the mitochondrial (Accession: OL802212) reference with minimap2 (v2.17) and extracted with bbmap (v38.86) filterbyname.sh.
Step2: Nuclear reads were mapped onto the reference genome (Accession: LSH3601) with mnimap2
Step3: Methylation calling with Nanopolish (v0.13.2). The raw electric signatures (or squiggles) were fetched and aligned back onto their respective mapped reads. Then, the likelihoods of each CpG-containing 6-mer given a 5-base alphabet (with A, T, G, C and M for methylated cytosines) were  calculated and CpG call groups (i.e. sequences containing one or multiple CpG motifs within 10bp of each other) were considered methylated if their log-likelihood of being methylated was twice that of being unmethylated (LLR>2).
Step4: Per-CpG normalisation: We generated a bed file of all CpGs using seqkit (v0.15.0) locate function and mapped to it the respective methylation call coverages and frequencies with bedtools (v2.29.2) map function.
Assembly: JAODUP01
Supplementary files format and content: tab-delimited text file of methylation call coverage and frequency for all CpGs. The file includes contig_id, start position (the first base on the chromosome is 0), end position (non-inclusive), methylation call coverage (number of reads for which methylation could be assessed), methylation frequency (methylated reads / total reads assessed)
Supplementary files format and content: UCSC Genome Browser bigWig format file of genome-wide CpG methylation frequency : contig_id, start coordinate, stop coordinate, and methylation level (#methylated reads/ total reads called for methylation). Minimum methylation call coverage threshold=1X (no coverage-based filtering).
Library strategy: DNA-seq

organism: Paralvinella palmiformis

source_name: body wall

extract_protocol:
Phenol-chloroform followed by ethanol precipitation
A whole-genome shotgun library was prepared by Novogene (Beijing, China) for sequencing on the Oxford Technologies Nanopore (ONT) PromethION platform

value: body wall


title: 20220628_dusp4 silencing 28062022_09 cre si_09

status: Public on Nov 06 2022

type: RNA

city: Regensburg

first: Alexander

last: Scheiter

state: Bavaria

address: Franz-Josef-Strauss Allee 11

department: Institute of Pathology

country: Germany

institute: University of Regensburg

hyb_protocol: Nanostring hybridization protocol by manufacturer

scan_protocol: nCounter digital analyzer

data_processing: nsolver advanced analysis

label: nanostring reporter and capture probes

molecule: total RNA

organism: Mus musculus

source_name: AKT/NRAS Cre DUSP4 siRNA 3

label_protocol: Nanostring label protocol by manufacturer

growth_protocol: Growth in DMEM medium in incubator

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: DUSP4 siRNA vs. SCR

tag: cell line

value: AKT/NRAS Cre

tag: cell type

value: cell line (derived from AKT/NRAS double injected hepatocellular carcinoma in a mouse by hydrodynamic injection) with Cre knockout for AKT

tag: genotype

value: AKT/NRAS Cre DUSP4 siRNA


title: Tle3 Cut&Run,  co-culure WT DN1 cells 3

type: SRA

city: Xi'an

first: Xiaoke

last: Ma

state: Shaanxi

address: No.2 South TaiBai Road

country: China

institute: Xidian University

library_source: genomic

data_processing:
Cut&Run reads were trimmed to retain 36 bp from 5'-end using Trimmomatic v0.39
Cut&Run reads were aligned to the mm9 genome using Bowtie2 version 2.4.4. Mapping reads with the quality score over 30 were retained.
To create Cut&Run binding profiles for visualization, the locations of the mapped reads were coverted to the bigWig file format using bamCoverage in deepTools(v3.5.1) with the RPKM normalization.
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: Cut&Run-sequencing

molecule: genomic DNA

source_name: OP9-DL1 co-cultured WT DN1 thymocytes

growth_protocol: LSK (Lin–ScaI+c-Kit+) bone marrow cells were sort-purified from WT C57BL/6 mice and co-cultured with OP9-DL1 stromal cells for 8 days. Then, Lin–CD25–CD44+ DN1 cells were sort-purified for downstream analyses.

extract_protocol:
DN1 thymocytes were crossed-linked with formaldehyde, and then incubated with Tle3 antibody overnight, followed by incubation with Protein A/G-MNase, calcium-mediated MNase activation. The reaction was stopped and then genomic DNA fragments were extracted.
The DNA segments from Tle3 Cut&Run were end-repaired and ligated to indexed Illumina adaptors, followed by amplification by PCR with a low number of cells (18-21 cycles). The resulting libraries were seqeunced with Illumina Hiseq-X platform.

value: OP9-DL1 co-cultured WT DN1 thymocytes

tag: chip antibody


title: 20220628_dusp4 silencing 28062022_08 cre si_08

source_name: AKT/NRAS Cre DUSP4 siRNA 2


title: a180126_Mm_FL_PD_wt_45s_P09H

city: Chicago

first: François

last: Spitz

state: IL

address: 920 E 58th St

department: Department of Human Genetics

country: USA

institute: University of Chicago

description: MARS-Seq

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, transcrit counting and aggregation were made using the MARS-Seq computational pipeline (https://github.com/tanaylab/MARS-SEQ).
Assembly: mm9
Supplementary files format and content: Tab-separated count matrix

source_name: Wild-type forelimb bud, 45s, PD photoconversion, MARS-seq

extract_protocol:
E11.5 mouse embryos were collected. Limbs were dissected and dissociated by incubation at 37˚C with 0.22 Wunsch unit/mL Liberase TM (Roche, 5401119001). The cell suspension was then stained with live (Calcein Violet, Life Technologies, C34858) and dead (Sytox Red, Thermo Fisher Scientific, S34859). Live cells were sorted into 384-well plates by FACS.
Library preparation was performed according to the MARS-Seq protocol (Jaitin et al., Science 2014). Briefly,  single cells were sorted into 384-well capture plates containing lysis solution and barcoded poly(T) RT primers (including UMIs and a well-specific barcode). After evaporation of the lysis buffer, the RT reaction was performed and unused RT primers were digested using Exonuclease I (NEB). Following pooling by half plates. second-strand cDNA synthesis was then performed and products were in vitro transcribed overnight using T7 polymerase (NEB) for linear amplification. RNA was fragmented and a partial Illumina Read1 sequencing adapter containing a plate-specific barcode was single-strand ligated using T4 RNA ligase I (NEB). Products were reverse-transcribed. Finally, the product was purified and PCR-amplified by PCR (14 cycles) with primers containing the Illumina P5-Read1 and P7-Read2 sequences. Concentration of the purified library was assessed with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument (Agilent Technologies). Libraries were pooled and paired-end sequenced using an Illumina NextSeq 500 sequencer.

tag: tissue

value: Forelimb bud

value: KikGR1 het

tag: strain

tag: Stage

tag: embryo id

tag: photoconversion pattern

value: PD

tag: half plate_barcode

value: CATG

tag: sequencing batch


title: a180126_Mm_FL_PD_wt_45s_P09A

description: MARS-Seq

value: AGTC


title: MP008 LTA

city: New York

first: Ignacio

last: Hernandez-Morato

state: NY

address: 180 Fort Washington Ave. 8th floor. Room 860

department: Otolaryngology-Head And Neck Surgery

institute: Columbia University

description:
summary.csv
est_counts_transcipts_kallisto.txt
tpm_values_transcripts_kallisto.txt

library_source: transcriptomic

data_processing:
We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
Assembly: Human: GRCh38; Mouse: GRCm38
Supplementary files format and content: tab-delimited text files include tpm values for each Sample
Supplementary files format and content: computed from tximport R package

organism: Rattus norvegicus

source_name: striated muscle

extract_protocol:
We extracted high-quality RNA from the distinctive intrinsic laryngeal muscles using a spin-column technology.
For STRPOLYA, a poly-A pull-down method is used  to enrich mRNAs from total RNA samples; library construction was proceeded using Illumina TruSeq chemistr.

value: striated muscle

value: Sprague-Dawley

tag: Sex

value: Female

value: WT

tag: anatomical position

value: Right

tag: developmental stage

tag: muscle type

value: LTA


title: Tle3 Cut&Run,  co-culure WT DN1 cells 2


title: Tle3 Cut&Run,  co-culure WT DN1 cells 1


title: MP007 PCA

value: PCA


title: 20220628_dusp4 silencing 28062022_07 cre si_07

source_name: AKT/NRAS Cre DUSP4 siRNA 1


title: Tle3 Cut&Run, Tle134 KO total thymocyes (neg. control)

source_name: Tle134 KO total thymocytes

value: Tle134 KO total thymocytes


title: 20220628_dusp4 silencing 28062022_06 akt nras scr_06

source_name: AKT/NRAS DUSP4 SCR 3

value: AKT/NRAS

value: cell line derived from AKT/NRAS double injected hepatocellular carcinoma in a mouse by hydrodynamic injection

value: AKT/NRAS DUSP4 SCR


title: MP006 MTA

value: Left

value: MTA


title: 20220628_dusp4 silencing 28062022_05 akt nras scr_05

source_name: AKT/NRAS DUSP4 SCR 2


title: MP005 LTA


title: ATAC-seq, DN1 cells, Tle134 mutant (KO3)

data_processing:
ATAC-seq reads were trimmed retain 36 bp from 5'-end using Trimmomatic v0.39
ATAC-seq reads were aligned to the mm9 genome using Bowtie2 version 2.4.4. Mapping reads with the quality score over 30 were retained.
To create ATAC-seq coverage plots, the locations of the mapped reads were coverted to the bigWig file format using bamCoverage in deepTools(v3.5.1) with the RPKM normalization.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: Thymocyte at DN1 stage

growth_protocol: WT or Tle134-deficient DN1 (Lin–TCRb–CD8a–CD25–CD44+) thymocytes were sort-purified for downstream analysis.

extract_protocol:
DN1 thymocytes were treated with TN5 transposase to generate tagged DNA fragments.
TN5-tagged DNA fragements were purified, PCR amplified to build ATAC-seq libraries

value: Thymocyte at DN1 stage


title: MP004 PCA


title: a180126_Mm_FL_AER_wt_45s_P08A

description: MARS-Seq

source_name: Wild-type forelimb bud, 45s, AER photoconversion, MARS-seq

value: Forelimb bud

value: KikGR1 het

value: AER

value: TCCG


title: 20220628_dusp4 silencing 28062022_04 akt nras scr_04

source_name: AKT/NRAS DUSP4 SCR 1


title: MP003 MTA

value: striated muscle

value: Sprague-Dawley


title: 20220628_dusp4 silencing 28062022_02 akt nras si_02

source_name: AKT/NRAS DUSP4 siRNA 2

value: AKT/NRAS DUSP4 siRNA


title: ATAC-seq, DN1 cells, Tle134 mutant (KO1)


title: a180126_Mm_FL_AER_wt_45s_P06H

description: MARS-Seq

value: GCGC


title: ATAC-seq, DN1 cells, WT3

value: WT


title: ATAC-seq, DN1 cells, WT2


title: MP001 PCA

value: Female

value: Right

value: PCA


title: scRNA-seq_191641B_SA05jiaT_1_1

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

description:
The neurons were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 3000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell with a paired-end 150 bp (PE150) reading strategy.
SA05jiaT_cellranger_outputs.tar

data_processing:
For the bulk RNA-seq, RNA-seq reads were aligned to the human reference GRCh38 genome and transcriptome using HISAT2 (v.2.1.0) . RNA differential expression analysis was performed using the DESeq2 package (v.1.30.0) . The cutoff criterion was set as adjusted P value < 0.05, and absolute log2(fold change) ≥ 1
For the scRNA-seq, raw sequencing data was processed with Cell Ranger software version 3.1 (10X Genomics) for FASTQ generation and GRCh38 human reference genome was used for alignments. For filtering and unsupervised clustering, the gene expression matrixs from Cell Ranger results were used for downstream analysis, using R 4.1.1.
Assembly: hg38
Supplementary files format and content: raw counts of bulk RNA-seq and outputs of cellranger software, which include barcodes, gene features and expression matrix for each sample

organism: Homo sapiens

source_name: hiPSC-derived GABAergic neurons

extract_protocol:
For the bulk RNA-seq, total RNA was extracted using the Trizol reagent kit (Life Technology Inc) and mRNA was enriched by Oligo (dT) beads and then transcripted into cDNA. For the scRNA-seq,  adherent GABAergic neurons were dissociated by 1 ml of trypLE (Life Technology Inc) for 30 min in the condition of 37°C and 5% CO2 into single cell when differentiated in vitro for 35 days. The cell debris and other aggregates were removed by additional low-speed centrifugation. Droplet-based single-cell RNA sequencing was performed using the 10X Genomics Chromium Single Cell platform, version 3. Approximately 5,000 cells were captured for each sample onto a Chromium Single Cell 3’ Chip (10X Genomics, PN-120236), and the released RNA in each cell was barcoded through reverse transcription in individual gel beads in emulsions (GEMs).
For the bulk RNA-seq, library construction and RNA sequencing was completed using the Illumina HiSeqTM 4000 platform. For the scRNA-seq, S1000TM Touch Thermal Cycler (Bio Rad) was used for reverse transcription at 53°C  for 45 min, followed by 85°C for 5 min and final hold at 4°C. The quality of cDNA was accessed on Agilent 4200 (Agilent Technologies). Libraries of scRNA-seq were established by the Chromium Single Cell 3’ Library & Gel Bead Kit V3 (10X Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell.

tag: culture time

value: 40 days in vitro

value: brain

value: hiPSC-derived GABAergic neurons

tag: disease state

value: sMDD


title: 20220628_dusp4 silencing 28062022_01 akt nras si_01

source_name: AKT/NRAS DUSP4 siRNA 1

tag: cell line

value: AKT/NRAS

value: cell line derived from AKT/NRAS double injected hepatocellular carcinoma in a mouse by hydrodynamic injection


title: a180126_Mm_FL_AER_wt_45s_P05H

description: MARS-Seq

value: Forelimb bud

value: KikGR1 het

value: CGCC


title: a180126_Mm_FL_AER_wt_45s_P08H

description: MARS-Seq

value: AER

value: AGGG


title: a180126_Mm_FL_AER_wt_45s_P05A

description: MARS-Seq

value: ACTT


title: ATAC-seq, DN1 cells, WT1

tag: cell type

value: Thymocyte at DN1 stage


title: AP2-Sp_cismut_clone2_RNA-seq

status: Public on Nov 05 2022

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

description: transcriptome of salivary gland sporozoites

data_processing:
Reads were mapped on the P. berghei genome by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” set to 1000. Mapping data were analyzed by Feature counts software.
Assembly: PlasmoDB, version 3
Supplementary files format and content: read counts

organism: Plasmodium berghei

source_name: oocysts/oocyst sporozoites

growth_protocol: Balb/c mice were infected with wild-type parasitesi or mutant parasites with binding sites of AP2-Sp muteted in the upstream of the AP2-Sp gene (AP2-Sp_cicmut). Infected mice were subjected to mosquito bites. Fully engorged mosquitoes were maintainedat 20 ℃. Midguts were disected 14 days after infective blood meal (oocysts/oosyst sporozoites). Salivary glands were disected 24 days after infective blood meal (salivary gland sporozoites).

extract_protocol:
Dissected midguts were soaked in RNA Later solution until finishing the dissection. RNA extraction was performed using Isogen 2 (Nippon gene) according to the manufacturer’s protocol. Dissected midguts were lysed in lysis solution in the kit using Tissuelyser system (Quiagen). Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s protocols.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

value: oocysts/oocyst sporozoites

value: ANKA

tag: genotype


title: AP2-Sp_cismut_clone1_RNA-seq


title: a180126_Mm_FL_AER_wt_45s_P07H

description: MARS-Seq

value: GGTA


title: scRNA-seq_191641B_NC3_1_1_1

description:
The neurons were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 3000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell with a paired-end 150 bp (PE150) reading strategy.
NC3-1_cellranger_output.tar

value: healthy


title: ATAC-seq, DN1 cells, Tle134 mutant (KO2)


title: 20220628_dusp4 silencing 28062022_03 akt nras si_03

source_name: AKT/NRAS DUSP4 siRNA 3

value: AKT/NRAS DUSP4 siRNA


title: a180126_Mm_FL_AER_wt_45s_P07A

description: MARS-Seq

value: TTTC


title: a180126_Mm_FL_AER_wt_45s_P06A

description: MARS-Seq

value: AAAC


title: Ex Vivoheterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, rep3

city: Wuhan

first: Zheng

last: Wang

state: China

address: Zhongnan Hospital, Wuhan University

institute: Zhongnan Hospital, Wuhan University

description:
Gene expression in heterotopic ossification tissue
HO3
heterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, replicate 3

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least half of samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

organism: Mus

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. Then, the enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted from the tissues using TRIzol reagent (Invitrogen Life Technologies, CA, USA).. The concentrations of the RNA samples were determined by OD260 using a NanoDrop ND-1000 instrument. The integrity of RNA were assessed by electrophoresis on a denaturing agarose gel.

treatment_protocol: Achilles tendon and heterotopic ossification tissues were preserved in liquid nitrogen

tag: gender

value: male

tag: age

value: heterotopic ossification tissue


title: Ex Vivoheterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, rep4

description:
Gene expression in heterotopic ossification tissue
HO4
heterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, replicate 4

tag: tissue


title: Ex Vivoheterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, rep2

description:
Gene expression in heterotopic ossification tissue
HO2
heterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, replicate 2


title: Ex Vivo Achilles tendon, 9wk, rep4

description:
Gene expression in Achilles tendon
Control4
Achilles tendon, 9wk, replicate 4

source_name: Achilles tendon, 9wk

value: Achilles tendon


title: JGES-reprogramming-day6_scRNA-seq

city: Guangzhou

first: Jing

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

data_processing:
The fastq files of each sample were mapped to mm10 genome using cellranger v2.1.1.
The MEF contamination in ESC dataset  were excluded by clustering combined expression profile of MEF and ESC.
Genome_build: mm10
Supplementary_files_format_and_content: CellRanger sparse matrix format of raw UMI counts.

source_name: reprogramming cells

growth_protocol: MEFs were infected with 4  (Jdp2, Esrrb, Glis1 and Sall4) retrovirus every 24 hours for twice.  Then change the medium to iCD3 plus Rock inhibitor and induction with indicated days.

extract_protocol: For Single cell RNA-seq, we prepared the libraries following the Chromium Single Cell 3’ Reagent Kits Guide. The single cell libraries were quantified by Quant-iT dsDNA Assay kit, high sensitivity (Thermo Fisher) on Qubit 2.0, and the sequenced on HiSeqX10.

treatment_protocol: For single cell preparation, the reprogramming cells (day0-day7) were digested by 0.25% trypsin for two minutes and collected into a 1.5ml tube and centrifuged at 250g for 5 minutes. The cells were washed twice with PBS plus 0.04% BSA, and then the single cells were obtained by filtering with a 70µm cell strainer. Before loading to single cell sorting Chip, cells were diluted to 0.5-1.0 million per ml according the results of cell counting.

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 144 hours before digested for sequencing.

tag: day of reprogramming

tag: strain

value: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x 57BL/6J) to 129S4/SvJaeJ female mice.


title: Ex Vivo Achilles tendon, 9wk, rep3

description:
Gene expression in Achilles tendon
Control3
Achilles tendon, 9wk, replicate 3


title: scRNA-seq_190722D_SAO5_1_1

description:
The neurons were dissociated by trypLE (Life technology) into single cells. The cell debris and other aggregates were removed by an additional low-speed centrifugation. About 3000 cells were captured and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a S1000TM Touch Thermal Cycler (Bio Rad) at 53 degrees Celsius for 45 min, followed by 85 degrees Celsius for 5 min and final hold at 4 degrees Celsius. cDNA was generated and then amplified, and quality was assessed using an Agilent 4200. scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit V3 (10x Genomics, 1000075) and then sequenced on an Illumina NovaSeq6000 with a sequencing depth of at least 750000 reads per cell with a paired-end 150 bp (PE150) reading strategy.
SA05_cellranger_outputs.tar

value: 40 days in vitro

value: brain

value: hiPSC-derived GABAergic neurons

value: sMDD


title: JGES-reprogramming-day5_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 120 hours before digested for sequencing.


title: Ex Vivo Achilles tendon, 9wk, rep1

description:
Gene expression in Achilles tendon
Control1
Achilles tendon, 9wk, replicate 1


title: JGES-reprogramming-day2_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 48 hours before digested for sequencing.


title: JGES-reprogramming-day4_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 96 hours before digested for sequencing.


title: JGES-reprogramming-day3_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 72 hours before digested for sequencing.


title: JGES-reprogramming-day1_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 24 hours before digested for sequencing.


title: Ex Vivo Achilles tendon, 9wk, rep2

description:
Gene expression in Achilles tendon
Control2
Achilles tendon, 9wk, replicate 2


title: mouse liver leukocyte, dasatinib treatment, scRNAseq

city: Sydney

first: Moumita

last: Paul

state: New South Wales

address: Level 5 East 59, Charles Perkins Centre D17, The University of Sydney

country: Australia

institute: The University of Sydney

data_processing:
Sample demultiplexing, cell label and UMI processing, gene counting and aggregation was performed with the BD Rhapsody™ WTA Analysis Pipeline (Revision 7) available at Seven Bridges Genomics (https://www.sevenbridges.com). Sample Tag demultiplexing parameters are as follows: "SampleTag07_mm" for dasatinib untreated CD44+, "SampleTag08_mm" for dasatinib untreated CD44+PD1-, "SampleTag09_mm" for dasatinib untreated CD44+PD1high, "SampleTag10_mm" for dasatinib treated CD44-, "SampleTag11_mm" for dasatinib treated CD44+PD1-, and "SampleTag12_mm" for dasatinib treated CD44+PD1high populations.
Assembly: mm10
Supplementary files format and content: Rhapsody WTA Pipeline output: DasTest_RSEC_MolsPerCell_Unfiltered.csv.gz containing raw count matrix, DasTest_Sample_Tag_Calls.csv containing sample demultiplexing matrix

molecule: polyA RNA

source_name: liver leukocyte

extract_protocol:
Murine liver was dissected following a 20ml PBS flush, and mechanically processed through a 100micron stainless steel sieve with ice-cold RPMI 1640 (with L-glutamine, supplemented with 2% FCS). The tissue slurry was washed, and debris removed through centrifugation with isotonic Percoll. The cell pellet was washed once more and then resuspended in red cell lysis buffer. After another wash, the isolated liver leukocytes are subjected to dasatinib treatment (if applicable), and stained with an antibody cocktail and subsequent viability dye. The treated and untreated samples were sorted on a BD Influx for CD8+ populations of interest (CD44- naive, CD44+PD1-, and CD44+ PD1high) and then washed for Rhapsody antibody-surface sample tag staining and capture following the manufacturer's protocol ("Single Cell Labelling with the BD Single-Cell Multiplexing Kit and BD AbSeq Ab-Oligos" Doc ID: 214419 Rev. 2.0, "Single Cell Capture and cDNA Synthesis with the BD Rhapsody Single-Cell Analysis System" Doc ID: 210966 Rev. 1.0).
Library preparation was performed following the protocol "mRNA Whole Transcriptome Analysis (WTA) and Sample Tag Library Preparation Protocol" Doc ID: 23-21712-00 from BD.

treatment_protocol: Isolated liver leukocytes were either untreated or treated with 50nM dasatinib for 30 minutes at room temperature prior to surface antibody and viability staining for cell sorting

value: liver leukocyte

value: 12 weeks

tag: in vivo_treatment

value: Primed with 178.3 (H-2Kb) skin graft, inoculated with AAV-Kb

tag: in vitro_treatment

value: incubation with or without dasatinib


title: R07B-5, vestimentum_nanopore

city: Montreal

first: Maeva

last: Perez

state: Qc

address: 1375 Avenue Thérèse-Lavoie-Roux

country: Canada

institute: Université de Montréal

data_processing:
Step1: Decontamination. Genomic ONT reads were mapped onto the mitochondrial (Accession: KJ872501) and symbiont (Accession: LDXT01) references with minimap2 (v2.17) and extracted with bbmap (v38.86) filterbyname.sh.
Step2: Nuclear reads were mapped onto the reference genome (Accession: NP49301) with minimap2
Step3: Methylation calling with Nanopolish (v0.13.2). The raw electric signatures (or squiggles) were fetched and aligned back onto their respective mapped reads. Then, the likelihoods of each CpG-containing 6-mer given a 5-base alphabet (with A, T, G, C and M for methylated cytosines) were  calculated and CpG call groups (i.e. sequences containing one or multiple CpG motifs within 10bp of each other) were considered methylated if their log-likelihood of being methylated was twice that of being unmethylated (LLR>2).
Step4: Per-CpG normalisation: We generated a bed file of all CpGs using seqkit (v0.15.0) locate function and mapped to it the respective methylation call coverages and frequencies with bedtools (v2.29.2) map function.
Assembly: JAODUO01
Supplementary files format and content: tab-delimited text file of methylation call coverage and frequency for all CpGs. The file includes contig_id, start position (the first base on the chromosome is 0), end position (non-inclusive), methylation call coverage (number of reads for which methylation could be assessed), methylation frequency (methylated reads / total reads assessed)
Supplementary files format and content: UCSC Genome Browser bigWig format file of genome-wide CpG methylation frequency : contig_id, start coordinate, stop coordinate, and methylation level (#methylated reads/ total reads called for methylation). Minimum methylation call coverage threshold=10X.
Library strategy: DNA-seq

organism: Ridgeia piscesae

source_name: vestimentum

value: vestimentum


title: JGES-reprogramming-day0_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 0 hours before digested for sequencing.


title: EA3_Alectinib_7D

city: Aurora

first: Emily

last: Kleczko

state: Colorado

department: Medicine

institute: University of Colorado Anschutz Medical Campus

description: 2x151 bp reads

data_processing:
Reads were quality checked using FastQC
Illumina adapters were trimmed with bbduk
STAR aligner was used to align reads to the Mus musculus mm10 reference genome.
Counts were generated by STAR’s internal counter and reads were normalized to counts per million (CPM) using the edgeR R package
Assembly: Mus musculus mm10
Supplementary files format and content: text files include counts per million (CPM) values for each sample
Supplementary files format and content: matix table text file (.txt) includes CPM for each sample

growth_protocol: EML4-ALK-positive cell lines were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% streptomycin/penicillen in a humidied incubator at 5% CO2 at 37C.

extract_protocol:
RNA was isolated using Zymo quickRNA Miniprep Kit (cat #11-328)
Libraries were constructed using an Illumina TruSEQ stranded mRNA Sample Prep Kit (Cat# RS-122-2101). Total RNA was combined with RNA purification beads to bind PolyA RNA to oligodT magnetic beads. mRNA was eluted and converted to double stranded DNA. A-tailing, adapter ligation, and PCR amplification using 15 cycles was performed to complete the library construction. 2x151 bp reads were generated

treatment_protocol: Cells were treated with 0.1% DMSO (control) or 100nM of Alectinib for 1, 3, 5, 7 days.

tag: treatment

value: 100nM Alectinib

tag: time

value: 7 day


title: EA3_DMSO_7D

description: 2x151 bp reads

value: DMSO-control


title: EA3_Alectinib_5D

description: 2x151 bp reads

value: 5 day


title: EA3_DMSO_5D

description: 2x151 bp reads


title: MISC25

city: Cambridge

first: Thomas

middle: James

last: LaSalle

state: MA

address: 415 Main Street

institute: Broad Institute

description:
Pedi_COVID_MISC_Counts.txt.gz
Pedi_COVID_MISC_TPM.txt.gz

data_processing:
A custom FASTA was generated from the Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs according to documentation in the Broad Institute GTEx-TOPMed RNA-seq pipeline (https://github.com/broadinstitute/gtex-pipeline/), with an appended SARS-CoV2 genome. GENCODE v35 with the appended SARS-CoV2 GTF was used for annotation. Raw FASTQ files were aligned to the custom genome FASTA in the Terra platform with the Broad Institute GTEx pipeline using STAR v2.5.3a, and expression quantification based on a collapsed annotation was performed using RSEM v1.3.0.
RNA-SeQC 2 (https://github.com/getzlab/rnaseqc) was used to calculate quality control metrics for each sample.
Assembly: Homo sapiens (human) genome assembly GRCh38 (hg38) following exclusion of ALT, HLA, and Decoy contigs with an appended SARS-CoV2 genome
Supplementary files format and content: Pedi_COVID_MISC_Counts.txt.gz: RNA-seq count matrix provided as a gzipped .txt file
Supplementary files format and content: Pedi_COVID_MISC_TPM.txt.gz: RNA-seq TPM matrix provided as a gzipped .txt file

source_name: Enriched neutrophils from whole blood

extract_protocol:
Blood samples were collected in EDTA vacutainer tubes and transported to the laboratory. Neutrophils were isolated from whole blood via negative selection using the EasySep™ Direct Human Neutrophil Isolation Kit (STEMCELL Technologies, Cat# 19666). All described procedures in this section were done at room temperature unless otherwise noted. Between 0.25-0.5 mL whole blood was lysed with ACK Lysis Buffer (ThermoFisher Scientific, Cat# A1049201) in a 15 mL conical tube and white blood cells were pelleted at 300 xg for 5 min. Following aspiration of the lysed red blood cells and resuspension of the pellet in 250 µL 1 mM EDTA in PBS, 50 µL each of the RapidSpheres and Isolation Cocktail were added to the cell suspension. Following a 5 min incubation, sample volumes were completed to 4 mL with 1 mM EDTA in PBS, mixed gently, and placed on an EasyEights™ EasySep™ Magnet (STEMCELL Technologies, Cat# 18103) for 5 min. Next, supernatants were transferred to new 15 mL conical tubes, 25 µL RapidSpheres were added, and the samples were gently mixed and incubated for 5 min. Samples were then placed on the magnet, and after 5 min incubation supernatants were transferred to new tubes, and were placed immediately on the magnet for a second incubation before the supernatants containing the enriched neutrophil populations were collected, pelleted, and resuspended in 1 mM EDTA in PBS. Cells were counted on a TC20™ Automated Cell Counter (Bio-Rad Laboratories, Inc., Cat# 1450102) with trypan blue staining for dead cell exclusion. Neutrophils were then lysed in TCL Buffer (QIAGEN, Cat# 1031576) with 1% 2-Mercaptoethanol at a concentration of 1000 cells/µL, flash-frozen on dry ice, and then stored at -80 °C until use. cDNA was prepared from bulk populations of 2x104 neutrophils per sample via the Smart-Seq2 protocol with some modifications to the reverse transcription step. 20 µL (at a concentration of 1000 cells/µL) of neutrophil lysates were thawed on ice and plated into 96-well plates prior to centrifugation at 1500 rpm for 30 s. RNA was purified with Agencourt RNAClean XP SPRI beads (Beckman Coulter, Cat# A63987) and then the samples were resuspended in 4 µL of Mix-1 [Per 1 sample: 1 µl (10 µM) RT primer (DNA oligo) 5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3′; 1 µl (10 µM) dNTPs; 1µl (10%, 4 U/µl) recombinant RNase inhibitor; 1 µl nuclease-free water], denatured at 72 °C for 3 min and placed immediately on ice for 1 min before 7 µL of Mix-2 [Per 1 sample: 0.75 µl nuclease-free water; 2 µl 5X RT buffer (Thermo Fisher Scientific, Cat# EP0753); 2 µl (5 M) betaine; 0.9 µl (100 mM) MgCl2; 1 µl (10 µM) TSO primer (RNA oligo with LNA) 5′-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3′; 0.25 µl (40 U/µl) recombinant RNase inhibitor; 0.1 µl (200 U/µl) Maxima H Minus Reverse Transcriptase] was added. Reverse transcription reactions were performed at 50 °C for 90 min, followed by 5 min incubation at 85 °C. Then, 14 µL of Mix-3 [Per 1 sample: 1 µl nuclease-free water; 0.5 µl (10 µM) ISPCR primer (DNA oligo) 5′-AAGCAGTGGTATCAACGCAGAGT-3′; 12.5 µl 2X KAPA HiFi HotStart ReadyMix] was added to each well and the whole-transcriptome amplification step was performed at 98 °C for 3 min, followed by 16 cycles of [98 °C for 15 s, 67 °C for 20 s, and 72°C for 6 min], and final extension at 72C for 5 min. cDNA was purified using AgencourtAMPureXP SPRI beads (Beckman Coulter, Cat# A63881) as described97, to remove all primer residue. Quality control was performed on samples prior library construction and included: (1) concentration measurements via the Qubit dsDNA high sensitivity assay kit (Invitrogen, Cat# Q32854) on the Cytation 5 Microplate Reader (BioTek); (2) cDNA size distribution using the High-Sensitivity DNA Bioanalyzer Kit (Agilent, Cat# 5067-4626).
Libraries were generated using the Nextera XT Library Prep kit (Illumina, Cat# FC-131-1024) with custom indexing adapters in a 384-well PCR plate, followed by a cleanup step to remove residual primer dimers.

value: Enriched neutrophils from whole blood

value: MISC


title: MISC22


title: MISC21


title: JGES-reprogramming-day7_scRNA-seq

value: Mouse Embryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 168 hours before digested for sequencing.

value: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ x 57BL/6J) to 129S4/SvJaeJ female mice.


title: MISC20


title: EA3_Alectinib_3D

description: 2x151 bp reads

value: 3 day


title: EA3_DMSO_3D

description: 2x151 bp reads


title: MISC19


title: EA3_DMSO_2D

description: 2x151 bp reads

value: 2 day


title: MISC24


title: EA3_Alectinib_1D

description: 2x151 bp reads

value: 1 day


title: MISC18


title: MISC16


title: EA3_DMSO_1D

description: 2x151 bp reads


title: EA3_Alectinib_2D

description: 2x151 bp reads


title: MISC23


title: EA2_Alectinib_3D

description: 2x151 bp reads


title: MISC17


title: EA2_Alectinib_5D

description: 2x151 bp reads


title: MISC14


title: MISC15


title: MISC04


title: MISC13


title: MISC03


title: EA2_DMSO_3D

description: 2x151 bp reads


title: EA2_Alectinib_2D

description: 2x151 bp reads


title: EA2_DMSO_2D

description: 2x151 bp reads


title: MISC01


title: MISC02


title: HC12

value: Healthy control


title: EA2_Alectinib_1D

description: 2x151 bp reads


title: HC11


title: HC10


title: EA1_Alectinib_5D

description: 2x151 bp reads


title: EA2_DMSO_5D

description: 2x151 bp reads


title: HC09


title: EA1_DMSO_5D

description: 2x151 bp reads


title: EA1_Alectinib_3D

description: 2x151 bp reads


title: HC08


title: HC07


title: EA1_Alectinib_1D

description: 2x151 bp reads


title: EA1_Alectinib_2D

description: 2x151 bp reads


title: HC03


title: EA1_DMSO_2D

description: 2x151 bp reads


title: EA1_DMSO_1D

description: 2x151 bp reads


title: HC05


title: EA1_DMSO_3D

description: 2x151 bp reads


title: HC02


title: HC01


title: EA2_DMSO_1D

description: 2x151 bp reads


title: COVID43

value: COVID


title: COVID42


title: COVID40


title: HC06


title: HC04


title: Cep112-/- Input

city: chengdu

first: li

last: tongtong

state: sichuan

address: sichuan

institute: xinong

data_processing:
Trim Galore, and FastQC were used to trimming and quality control from the sequence data.  Clean reads were used for protein binding site analysis.
They were mapped to the reference genome of mouse (mm10) using STAR software (version 2.5.3a) with default parameters.  Through the differential analysis of IP and Input samples, the difference fold and the significant level were evaluated.  Here, we used logFC>1 and p-value<0.05 as the standard and select the gene whose IP was up-regulated relative to input as the protein-binding gene.
Peak calling was used by exomePeak (Version 3.8) software.  Peaks were annotated using BEDTools (Version 2.25.0) and ChIPseeker.  The deepTools (version 2.4.1) was used for peak distribution analysis.  The differentially binding peaks were identified by a python script, using the Fisher test.
HOMER (version 4.10) was used to search the motifs.
Difference analysis was performed on the peaks of the treatment group and control groups’ peaks, and the different peaks were annotated.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: testis

extract_protocol:
The cells were treated with cell lysis buffer.  The 10% lysis sample was stored and named “input”, and 80% was used in immunoprecipitation reactions with anti-Cep112 antibody and named “IP”, and 10%  was incubated with rabbit IgG (Cell Signaling Technology) as a negative control and named “IgG”， respectively.  The RNA of input and IP was extracted using TRIzol reagent (Invitrogen, Invitrogen, cat.  NO 15596026).
The stranded RNA sequencing library was constructed by using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO.  DR08502, Wuhan Seqhealth Co., Ltd.  China) following the manufacturer’s instructions.  The kit eliminates duplication bias in PCR and sequencing steps, by using a unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules.  The library products corresponding to 200-500 bps were enriched, quantified, and finally sequenced on the DNBSEQ-T7 sequencer (MGI Tech Co., Ltd.  China) with the PE150 model.

value: testis

tag: chip antibody

value: anti-rabbit IgG antibody


title: Cep112+/+

value: anti-Cep112 antibody


title: Cep112+/+, Input


title: Sham_Input

city: Tianjin

first: Xinyi

last: Cao

state: State...

address: Qi Xiangtai Road, HePing District, Tianjin, P.R. China

institute: Tianjin Medical University

description: Sham cell line

data_processing:
Clean reads were aligned to the mouse reference genome (mm10) by bowtie2 (v2.3.5.1)
Reads mapped only once at locus were allowed for peak calling.
Bigwig files were derived from the output of deeptools v3.4.3
Annotation of peaks was performed using HOMER.
Assembly: mm10
Supplementary files format and content: Bigwig files were generated using deepTools v3.4.3

source_name: proximal tubular cells

growth_protocol: Mice were kept under standard laboratory conditions and allowed free access to food and water except as noted.

extract_protocol:
Isolated primary proximal tubules were crosslinked with 1% formaldehyde for 15 min at room temperature (RT). Crosslinking was stopped by glycine for 5 min at RT. Cells were lysed using cell lysis buffer (140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM EDTA, 50 mM Tris-HCl pH 8.0), and then nuclei were isolated using nuclei lysis buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 0.2% SDS). Nuclei were sonicated to generate fragments in the range of 200-500 bp, which were incubated with antibody overnight at 4°C.
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (Vazyme, # ND607-02).

treatment_protocol: Kidney bilateral ischemia-reperfusion injury (bIRI) surgery was performed. Both kidney pedicles were exposed by the retroperitoneal approach and clamped with microvessel clips for 20 min to generate a mild IRI model and 30 min to generate a severe IRI model. Sham operations were performed using the same procedure but without induction of ischemia. Mice were treated Bexarotene with after kidney injury.

value: Kidney

value: primary proximal tubular cells


title: D730_H3K27ac_input

treatment_protocol: Kidney bilateral ischemia-reperfusion injury (bIRI) surgery was performed. Both kidney pedicles were exposed by the retroperitoneal approach and clamped with microvessel clips for 20 min to generate a mild IRI model (MI) and 30 min to generate a severe IRI model (SI). Sham operations were performed using the same procedure but without induction of ischemia. Mice were treated Bexarotene with after kidney injury.

value: 30 min IRI after day 7


title: Cep112-/-


title: RXRA_Sham

description: Sham cell line

value: anti-RXR[alpha] (ET7108-99, Huabio)


title: COVID37


title: COVID20


title: COVID19


title: COVID18


title: D220_H3K27ac_input

value: 20 min IRI after day 2


title: COVID16

value: Enriched neutrophils from whole blood


title: COVID17


title: D730_H3K27ac

value: Abcam, ab4729


title: COVID15


title: D720_H3K27ac

value: 20 min IRI after day 7


title: D230_H3K27ac

value: 30 min IRI after day 2


title: COVID14


title: D220_H3K27ac


title: COVID38


title: COVID13


title: AD7_2_Bex

data_processing:
Clean reads were aligned to the mouse reference genome (mm10) by bowtie2 (v2.3.5.1)
Data from two replicates were merged at each time point for subsequent analysis
Reads mapped only once at locus were allowed for peak calling.
Bigwig files were derived from the output of deeptools v3.4.3
Annotation of peaks was performed using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using deepTools v3.4.3

extract_protocol:
A total of 100,000 cells were lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 3 mM MgCl2, 0.1% (v/v) IGPAL CA-630, 10 mM NaCl) for 20 min on ice.
The nuclei were subjected to transposition with Tn5 transposase (TD501-01, Vazyme) for 30 min at 37°C. After tagmentation, DNA was purified with VAHTS DNA Clean Beads (N41101, Vazyme) for final library construction and high-throughput sequencing on the Illumina NovaSeq platform.

tag: strain background

value: Bex


title: COVID12


title: AD7_1_Bex


title: COVID11


title: COVID10


title: D720_H3K27ac_input


title: ASham_1

value: Sham


title: AD730_1

value: 30 min IRI


title: AD730_2


title: COVID09


title: ASham_2


title: AD720_2

value: 20 min IRI


title: D230_H3K27ac_input


title: COVID07

value: COVID


title: COVID08


title: P14DCs (not T,B,CD14) BRI-1095

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
P14DCs (not T,B,CD14)
Sorted DCs from PBMC

data_processing:
Raw sequencing data was analyzed using Cellranger software with GRCh38 human reference genome.
Assembly: GRCh38

extract_protocol:
A cell suspension was generated by papain digestion, neutralization, and 70um filtration of cell extract. Cells were centrifuged, resuspended in 30% Percoll, centrifuged, washed in PBS, and cell density was quantified. Cells were suspended in PBS and 16% Opti-prep.
Libraries were prepared by the Broad Institute according to 10X V3 protocol.

treatment_protocol: Following rapid autopsy, samples were immediately incubated in Hibernate (Life Technologies, #A1247601) for 8-18 hours prior to processing.

tag: Sex

value: Male


title: P12CD14 BRI-1093

description:
P12CD14
Sorted CD14+ cells from PBMC


title: AD720_1


title: P6CD8 T cells BRI-1087

description:
P6CD8 T cells
Sorted CD8 T Cells from PBMC

value: Female


title: SCV104357_2

city: Hanover

first: Susanne

last: Häußler

address: Feodor-Lynen-Str. 7

department: Molecular Bacteriology

institute: Twincore

description:
Cells were grown in LB to an OD600 =2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.
ProcessedDataMatrix_SCV.xlsx

data_processing:
Reads were trimmed for adaptor sequences and mapped to the PA14 whole genome using a Stampy pipeline with default parameters.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

organism: Pseudomonas aeruginosa

source_name: clinical isolate

growth_protocol: cell were grown in LB to an OD600 =2

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
The removal of ribosomal RNA was performed using the Ribo-Zero Bacteria Kit (Illumina) and cDNA libraries were generated with the ScriptSeq v2 Kit (Illumina).

treatment_protocol: directly after cultivation the cells were treated with one volume of RNAprotect (Qiagen), incubated for 10 minutes at room temperature, centrifuged at 10.000 rpm and cell pellets were frozen at -80°C

tag: sample type

value: clinical isolate

tag: geographical location

tag: infection side

value: respiratory tract


title: SCV104357_1


title: P14DCs (not T,B,CD14) BRI-1083


title: AD3030_2

value: Kidney

tag: cell type

value: primary proximal tubular cells


title: AD3030_1


title: P12CD14 BRI-1081

description:
P12CD14
Sorted CD14+ cells from PBMC


title: REVb_2

source_name: Revertant "b" from parental strain SCV24

value: not applicable


title: AD3020_2


title: P10CD4 T cells BRI-1077

description:
P10CD4 T cells
Sorted CD4 T Cells from PBMC


title: P6CD8 T cells BRI-1075


title: REVb_1

value: Revertant "b" from parental strain SCV24


title: P3B cells BRI-1073

description:
P3B cells
Sorted B Cells from PBMC


title: AD3020_1


title: REVa_2

source_name: Revertant "a" from parental strain SCV24


title: REVa_1

value: Revertant "a" from parental strain SCV24


title: AD230_2


title: SCV24_2


title: AD230_1


title: P3B cells BRI-1085

description:
P3B cells
Sorted B Cells from PBMC


title: AD220_2


title: AD220_1


title: SCV24_1


title: P11Tregs BRI-1079

description:
P11Tregs
Sorted Tregs from PBMC


title: MEL-290 ERIANIN-2

city: Shanghai

first: Sipeng

last: Zuo

state: Shanghai

address: No. 12, Lane 833, Zhizaoju Road, Huangpu District

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

data_processing:
Sequencing by Illumina NovaSeq 6000
Images processed by Solexa pipeline version 1.8. Sequening quality control by fastq.gzC
Sequence reads were mapped to GRCH38 genome using Hisat2.
The FPKM calculation of gene and transcripts by R application Ballgown.
Supplementary files format and content: GRCH38
Supplementary files format and content: text files include FPKM values for each Sample

extract_protocol:
RNA was harvested using Trizol. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina) following manufacturer's protocols.

tag: cell line

value: Human uveal melanoma

tag: genotype

value: WT

value: 100nM erianin treatment


title: RXRA_D7_Bex [ChIP-seq]

data_processing:
Clean reads were aligned to the mouse reference genome (mm10) by bowtie2 (v2.3.5.1)
Reads mapped only once at locus were allowed for peak calling.
Bigwig files were derived from the output of deeptools v3.4.3
Annotation of peaks was performed using HOMER.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using deepTools v3.4.3

value: Bexarotene treatment

value: anti-RXR[alpha] (ET7108-99, Huabio)


title: MP002 LTA

description:
summary.csv
est_counts_transcipts_kallisto.txt
tpm_values_transcripts_kallisto.txt

data_processing:
We multiplex samples in each lane, which yields targeted number of paired-end 100bp reads for each sample.
We use RTA (Illumina) for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming.
Assembly: Human: GRCh38; Mouse: GRCm38
Supplementary files format and content: tab-delimited text files include tpm values for each Sample
Supplementary files format and content: computed from tximport R package

source_name: striated muscle

value: striated muscle

value: Sprague-Dawley

tag: anatomical position

value: Right

tag: developmental stage

tag: muscle type

value: LTA


title: RXRA_D730_Ctrl [ChIP-seq]

tag: tissue

value: 30 min IRI


title: MEL-290 CONTROL-2


title: RXRA_D720_Ctrl [ChIP-seq]

value: 20 min IRI


title: MEL-290 CONTROL-1


title: 48_E2_Mock_F3

city: Baltimore

first: Anne

middle: E.

last: Jedlicka

state: MD

address: 615 N. Wolfe street

department: Molecular Microbiology and Immunology

institute: Johns Hopkins University, School of Public Health

description: gene expression data

hyb_protocol: Hybridization to Affymetrix Human Gene ST 2.0 arrays was performed at 45oC for 16 hours at 60 rpm in the Affymetrix rotisserie hybridization oven.  The signal amplification protocol for washing and staining of eukaryotic targets was performed in an automated fluidics station (Affymetrix FS450) using Affymetrix protocol FS450_0002.

scan_protocol: The arrays were scanned in the GCS3000 laser scanner with autoloader and 3G upgrade (Affymetrix). Quality assessment of hybridizations and scans was performed with Expression Console software (Affymetrix).

data_processing: The data were analyzed with Partek Genomics Suite version 6.6 using Affymetrix default analysis settings and virus infected samples were normalized to matched mock samples. Quantile Normalization using RMA Background correction, with  Log Base 2, and   Median Polish probeset summarization in Partek Genomics Suite 6.6.

label: biotin

source_name: non-diseased human nasal epithelial tissue

label_protocol: Biotinylated ss-cDNA were prepared according to the Affymetrix GeneChip WT PLUS Reagent Kit according to the manufacturerâ€™s recommended protocol from 100 nanograms of total RNA.

growth_protocol: Primary human nasal epithelial cells were obtained from non-diseased human donor tissue during endoscopic sinus surgery. The cells were differentiated at an air-liquid interface (ALI) in 24-well Falcon filter inserts (0.4-Î¼M pore; 0.33cm2) coated with human type IV placental collagen.

extract_protocol: Trizol Reagent and the PureLink RNA Mini kit (Ambion/Life Technologies) were used for extraction and purification of RNA. Cells were processed according to the manufacturerâ€™s protocol including the on-column DNAse treatment. Following elution of purified RNA from the PureLink columns with Nuclease-free water, quantitation was performed using a NanoDrop spectrophotometer and quality assessment determined by RNA Nano LabChip analysis on an Agilent BioAnalyzer 2100 or RNA Screen Tape on an Agilent TapeStation 2200.

treatment_protocol: Once fully differentiated, hNECs from females were exposed to E2 (10nM) or vehicle for 24h. Just prior to infection, the apical surface of hNEC cultures was washed with Dulbecco's phosphate-buffered saline with calcium and magnesium. The cultures were infected via the apical chamber with a multiplicity of infection (MOI) of 0.1 TCID50/cell or mock infected at 32Â°C in 200 ul of infection media.  After 2 hours, the inoculums were aspirated and the apical surfaces washed twice with DPBS before returning the cells to incubate at 32Â°C.

value: primary nasal epithelial cells

tag: infection status

value: uninfected Mock

tag: time/hours

value: female


title: 48_DMSO_Mock_F4

description: gene expression data

tag: treatment

value: Vehicle


title: D7_Bex_Input

value: Kidney

value: primary proximal tubular cells


title: 48_E2_Mock_F1

description: gene expression data


title: A375 ERIANIN-2

value: Human cutanoeous melanoma


title: 48_DMSO_Mock_F3

description: gene expression data


title: Ex Vivoheterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, rep1

description:
Gene expression in heterotopic ossification tissue
HO1
heterotopic ossification tissue, 9wk, Achilles tenotomy, burn injury, replicate 1

tag: gender

value: male

tag: age

value: heterotopic ossification tissue


title: 48_E2_Mock_F2

description: gene expression data


title: 48_E2_Mock_F5

description: gene expression data


title: 48_DMSO_Mock_F2

description: gene expression data


title: 48_E2_Mock_F4

description: gene expression data


title: 24_E2_Mock_F5

description: gene expression data


title: 24_E2_Mock_F4

description: gene expression data


title: MEL-290 ERIANIN-1

value: Human uveal melanoma

value: WT

value: 100nM erianin treatment


title: 24_E2_Mock_F2

description: gene expression data


title: 48_DMSO_Mock_F1

description: gene expression data


title: A375 ERIANIN-1


title: 24_E2_Mock_F3

description: gene expression data


title: 48_DMSO_Mock_F5

description: gene expression data


title: D720_Input

tag: strain background

tag: chip antibody


title: 24_DMSO_Mock_F5

description: gene expression data

tag: Sex


title: A375 CONTROL-2


title: Sham3_822

data_processing:
Low quality reads was filtered using internal software Trim Galore
Clean reads were mapped to reference using HISAT2. Only unique mapped reads were used in further analysis.
DEGs (differential expressed genes) between samples were generated by DESeq2
Bigwig files were derived from the output of deeptools v3.4.3
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated using deepTools v3.4.3

extract_protocol:
Total RNA isolation was performed using TRIzol (Invitrogen). Total RNAs from cultured cells were subjected to Oligo dT selection and adaptor ligation.
Construction of RNA-seq library was completed by BGI company (Shenzhen,China).

treatment_protocol: Kidney bilateral ischemia-reperfusion injury (bIRI) surgery was performed. Both kidney pedicles were exposed by the retroperitoneal approach and clamped with microvessel clips for 20 min to generate a mild IRI model and 30 min to generate a severe IRI model. Sham operations were performed using the same procedure but without induction of ischemia. Mice were treated bexarotene with after kidney injury.

value: Sham


title: D730_Input


title: A375 CONTROL-1


title: SCV24_passage7_2

description: Cells were passaged in LB medium for 7 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

data_processing:
mRNA reads were trimmed using the tool ‘cutadapt’ (version 3.5) with customized settings and mapped to the NC_008463.1 (PA14) reference genome from NCBI using ‘bowtie2’ (version 2.3.5.1) with the settings “--very-sensitive-local; --no-mixed; --fr; --no-unal”.
Genome_build: NC_008463.1 (PA14)
Supplementary_files_format_and_content: Processed data file is a data matrix that contains raw unique gene reads.

source_name: SCV24 passage7 2

extract_protocol:
The RNeasy Mini Kit (Qiagen) in combination with Qiashredder columns (Qiagen) was used according to the manufacturer’s instruction
Total RNA was fragmented (150-350 bp) in Fast AP-Buffer (Thermo Scientific), DNA was digested by TURBO™ DNase (Invitrogen), and RNA fragments were phosphorylated by FastAP alkaline phosphatase (Thermo Scientific). Custom-made barcodes were ligated to the RNA using the T4 ligase (New England Biolabs) and fragments were subsequently purified and concentrated using the RNA Clean & Concentrator™-25 Kit (Zymo Research) following the manufacturer’s instructions. Ribosomal RNA was removed by using the RiboZero Bacteria kit (Illumina). cDNA libraries were synthesized using the SMARTScribe Reverse Transcriptase (Takara) followed by a PCR enrichment using the AccuPrime HiFi Taq polymerase (Invitrogen). Enzymatic reactions were carried out in the presence of SUPERase·In™ RNase Inhibitor (Invitrogen); RNACleanXP beads (Agencourt) were used for all RNA purification steps. Quality checks were performed before, during and after cDNA library preparation with the RNA Nano Kit and an Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: sample type

value: clinical isolate

tag: geographical location

value: respiratory tract


title: SCV24_passage7_1

source_name: SCV24 passage7 1

tag: infection side


title: 24_DMSO_Mock_F2

description: gene expression data


title: 24_DMSO_Mock_F4

description: gene expression data


title: 24_E2_Mock_F1

description: gene expression data


title: SCV24_passage6_2

description: Cells were passaged in LB medium for 6 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage6 2


title: 24_DMSO_Mock_F1

description: gene expression data


title: SCV24_passage6_1

source_name: SCV24 passage6 1


title: 24_DMSO_Mock_F3

description: gene expression data


title: Sham2_918

tag: cell type


title: siRBM39_NT_C

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Reads were mapped to the human GRCh38 transcriptome (Ensembl cDNA release 90) and quantified using Salmon v0.8.2
Genome_build: GRch38
Supplementary_files_format_and_content: Salmon quant.sf output files with estimated read count per transcript

growth_protocol: MCF7 cells were grown in DMEM plus 10% FBS.

extract_protocol:
Total RNA was isolated with a Roche High pure RNA purification kit and stored at -80°C.
Illumina TruSeq stranded mRNA

treatment_protocol: Cells were transfected with control siRNA or siRNA targeting c-Jun or RBM39 with lipofectamine RNAiMAX reagent (Invitrogen). Twenty four hours after transfection, the media was removed and replaced by fresh media containing or not Cisplatin at a concentration of 50 µM. The cells were allowed to grow for an additional 24 h before total RNA was isolated. Three independent transfections, treatments and isolation were effectuated.

tag: sirna


title: Sham1_714


title: D730_2_828

value: 30 min IRI


title: SCV24_passage4_2

description: Cells were passaged in LB medium for 4 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage4 2


title: SCV24_passage4_1

source_name: SCV24 passage4 1


title: SCV24_passage5_1

description: Cells were passaged in LB medium for 5 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage5 1


title: SCV24_passage3_1

description: Cells were passaged in LB medium for 3 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage3 1


title: siRBM39_NT_A


title: SCV24_passage3_2

source_name: SCV24 passage3 2


title: siRBM39_NT_B


title: AP2-Sp ChIP-seq experiment-1 INPUT

data_processing:
Reads were mapped on the P. berghei genome with allowing one mismatch within 75 bp sequence using Bowtie 2.0. Bedgraph files were ceated from the mapping data (IP).
The mapping data were analyzed with the MACS2 peak-calling algorithm using approximately 3.33 × 106 in the experiment-1 and 4.54 × 106 in the experiment-2, respectively.). Numbers of INPUT reads used for normalization were 41.87 × 106 in the experiment-1 and 6.07 × 106 in the experiment-2, respectively. Conditions for peak calling included an FDR < 0.01 in both experiments.
Genome_build: PlasmoDB, version 3
Supplementary_files_format_and_content: Mapping data, bedgraph; Peak-calling, text.

source_name: INPUT

growth_protocol: Balb/c mice were infected with P. berghei expressing GFP-fused AP2-Sp. Infected mice were subjected to mosquito bites. Fully engorged mosquitoes were maintained for 14 days at 20 ℃.

extract_protocol:
Mosquito midgut was dissected and fixed immediately in 1% paraformaldehyde solution and kept in it until dissection of all mosquitoes were completed.They were sonicated with Bioruptor in the following condition: total of 20 times at 30 s in middle power in the cell lysis solution containing 1% sodium dodecyl sulfate. The supernatant was subjected to immunoprecipitation with anti-GFP antibodies using Dynabeads protein A.
Libraries were constructed using library preparation kit for SOLiD 5500 system in experiment 1 and KAPA Hyperprep kit (KAPA Biosystems) in experiment 2, respectively

treatment_protocol: Mosquito midguts were dissected and fixed immediately in 1% paraformaldehyde solution and kept in it until dissection of all mosquitoes were completed.

tag: Stage

value: oocyst/oocyst sporozoite

tag: strain

value: ANKA

tag: genotype

value: GFP-fused AP2-Sp expressing


title: siJUN_CP_B

value: siJUN

value: cisplatin


title: siJUN_CP_C


title: SCV24_passage2_1

description: Cells were passaged in LB medium for 2 days and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage2 1


title: D720_3_827

source_name: proximal tubular cells

tag: tissue

value: Kidney

value: 20 min IRI


title: SCV24_passage5_2

source_name: SCV24 passage5 2


title: SCV24_passage1_2

description: Cells were passaged in LB medium for 1 day and samples for RNA sequencing were taken at OD600=2 and incubated for 10 min in RNAprotect reagent (Qiagen) at room temperature, centrifuged for 10 min at 10,000 rpm and the pellet was frozen at -80°C for bacterial RNA extraction.

source_name: SCV24 passage1 2


title: AP2-Sp ChIP-seq experiment-1 IP

description: AP2-Sp_ChIP-seq_peaks_exp1.txt, AP2-Sp_IP_1.bedgraph

source_name: IP


title: D720_2_827

value: primary proximal tubular cells


title: siJUN_NT_C


title: SCV24_passage1_1

source_name: SCV24 passage1 1


title: D730_1125_2


title: siJUN_NT_B


title: D720_1212_2


title: siJUN_NT_A


title: D3030_2_824


title: siCTRL_CP_C

value: siCTRL


title: JGES-D5_ATAC-seq

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
ATAC-seq reads were aligned to the mm10 genome assembly using bowtie2 with options --very-sensitive
Data were filterd using samtools -q  35 and awk '!x[$0]++'
peaks were called using run_dfilter15 with options -non-zero -bs=100 -ks=20 -lpval=3 -refine -std=5
Genome_build: mm10
Supplementary_files_format_and_content: bed file were generated with genomeCoverageBed and bedGraphToBigbed. Scores represent the number of fragments overlapping each genomic position.

source_name: reprogramming cells

growth_protocol: Primary mouse embryonic fibroblasts (MEFs) were isolated from E13.5 mouse embryos from crossing male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) to 129S4/SvJaeJ female mice.

extract_protocol:
For ATAC-seq, a total of 50,000 cells were washed once with cold PBS and resuspended in 50ul lysis buffer. The suspension of nuclei was then centrifuged for 10 min at 500g at 4°C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase and 22.5 μl nuclease-free H2O) of Nextera DNA library Preparation Kit (96 samples) (FC-121-1031, Illumina), and incubated at 37°C for 30min. DNA was isolated using a MinElute Kit (Qiagen).
ATAC-seq libraries were first subjected to 5 cycles of pre-amplification. To determine the suitable number of cycles required for the second round of PCR the library was assessed by quantitative PCR as described5, and the library was then PCR amplified for the appropriate number of cycles. Libraries were purified with a Qiaquick PCR (Qiagen) column. Library concentration was measured using a KAPA Library Quantification kits (KK4824) according to the manufacturers instructions. Library integrity was checked by gel electrophoresis. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturers instructions.

treatment_protocol: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 120 hours before digested for sequencing.

value: male Oct4-GFP transgenic allele-carrying mice (CBA/CaJ × C57BL/6J) crossed to 129S4/SvJaeJ female mice

tag: passages

tag: genotype/variation

tag: day of reprogramming


title: JGES-D3_ATAC-seq

treatment_protocol: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 72 hours before digested for sequencing.

value: Primary mouse embryonic fibroblasts (MEFs)


title: D3030_1_824

tag: treatment


title: JMC120-2-5 Batch3

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

institute: University of Rochester

data_processing:
Sequences aligned against the C. albicans SC5314 genome using the Splice Transcript Alignment to a Reference (STAR) algorithm counted with HTSeq, normalized for total counts (counts per million, CPM).
Non-specific filtering strategy used to remove genes with low expression values
Differential expression was assessed by DESeq2
cpm Normalization
Summerized by Htseq
Assembly: C. albicans SC5314 genome ASM18296v3
Supplementary files format and content: text file from deSeq

organism: Candida albicans

extract_protocol:
RNA was harvested using Zymo YeaSTar kit following manufacturer's protocols.
Illumina TruSeq RNA library kit following manufacturer's protocols

tag: phenotype

value: caspofungin adapted


title: siCTRL_CP_B


title: SMC60-3-4 Batch1


title: JGES-D1_ATAC-seq

treatment_protocol: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 24 hours before digested for sequencing.

tag: strain background


title: D3020_5_624


title: JMC120-2-5 Batch2


title: JMC120-2-5 Batch1


title: siJUN_CP_A


title: SMC60-3-4 Batch3


title: siCTRL_CP_A


title: JGES-D0_ATAC-seq

treatment_protocol: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 0 hours before digested for sequencing.


title: JGES-D7_ATAC-seq

treatment_protocol: Mouse Enbryonic Fibroblasts infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours and then induced in iCD3 medium for 168 hours before digested for sequencing.


title: siCTRL_NT_C


title: JMC160-3-5 Batch3


title: D3030_3_520


title: D3020_4_527


title: D3020_2_527


title: JEGS-D7-RNA-seq-rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
RNAseq reads were aligned to the mm10 genome assembly using rsem with options --bowtie2 --bowtie2-sensitivity-level very_sensitive
expected_count were extract from the sample_name.genes.results and merged together to get a big table
RNAseq data was normalized by EDAseq
Genome_build: mm10
Supplementary_files_format_and_content: tsv file was generated form normalized RNAseq data, it include all samples' RNAseq data

extract_protocol:
Total RNAs were prepared with TRIzol. VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme) was used for library constructions and sequencing done with NextSeq500 Mid output 150 cycles (FC-404-2001, Illumina) for RNA-seq.
For RNA-seq, TruSeq RNA Sample Prep Kit (RS-122-2001, Illumina) was used for library construction and the sequencing was done using a NextSeq 500 High Output Kit v2 (75 cycles) (FC-404-1005, Illumina), according to the manufacturers instructions.

value: infected with Jdp2, Sall4, Esrrb and Glis1 retrovirus for 48 hours


title: siCTRL_NT_B


title: JMC160-3-5 Batch2


title: JEGS-D5-RNA-seq-rep2


title: D230_3_823


title: JMC160-3-5 Batch1


title: JRCT1  Batch3

value: parental strain


title: D230_2_726


title: salivary gland sporozoitess_RNA-seq_experiment-3

description: transcriptome of salivary gland sporozoites

data_processing:
Reads were mapped on the P. berghei genome by HISAT2. Parameters of HISAT2 were set to default except for the option “--max-intron” set to 1000. Mapping data were analyzed by Feature counts software.
Assembly: PlasmoDB, version 3
Supplementary files format and content: read counts

source_name: salivary gland sporozoites

extract_protocol:
Dissected midguts were soaked in RNA Later solution until finishing the dissection. RNA extraction was performed using Isogen 2 (Nippon gene) according to the manufacturer’s protocol. Dissected midguts were lysed in lysis solution in the kit using Tissuelyser system (Quiagen). Total RNA was extracted using the ISOGEN II (NIPPON GENE, Japan) according to the manufacturer’s protocols.
Libraries were constructed from total RNA using KAPA mRNA Hyperprep kit (KAPA Biosystems), and sequencing was performed with Illumina NEXTseq sequence (Single read - illumina NextSeq 500),

tag: developmental stage

value: salivary gland sporozoites

value: wild type


title: JEGS-D3-RNA-seq-rep2


title: JEGS-D1-RNA-seq-rep2


title: JRCT1  Batch2


title: D230_1_726

value: 30 min IRI


title: salivary gland sporozoitess_RNA-seq_experiment-2


title: D220_3_828


title: JEGS-D0-RNA-seq-rep2


title: JRCT1  Batch1


title: D730_1125_1


title: salivary gland sporozoitess_RNA-seq_experiment-1


title: JEGS-D7-RNA-seq-rep1


title: D220_2_828


title: oocysts/oocyst sporozoites_RNA-seq_experiment-3

description: transcriptome of oocysts/oocyst sporozoites

source_name: oocysts/oocyst sporozoites

value: oocysts/oocyst sporozoites


title: SC5314 Batch3


title: D220_1114


title: oocysts/oocyst sporozoites_RNA-seq_experiment-2

value: ANKA


title: SC5314 Batch2


title: Bex_D7_3

value: Bexarotene treatment


title: SC5314 Batch1


title: siCTRL_NT_A


title: JEGS-D3-RNA-seq-rep1


title: JEGS-D5-RNA-seq-rep1


title: JEGS-D1-RNA-seq-rep1


title: Bex_D7_2


title: AP2-Sp ChIP-seq experiment-2 INPUT

value: oocyst/oocyst sporozoite

value: GFP-fused AP2-Sp expressing


title: oocysts/oocyst sporozoites_RNA-seq_experiment-1


title: Bex_D7_1

value: Kidney


title: JEGS-D0-RNA-seq-rep1


title: AP2-Sp ChIP-seq experiment-2 IP

description: AP2-Sp_ChIP-seq_peaks_exp2.txt, AP2-Sp_IP_2.bedgraph


title: Human MSD patient fibroblast line G, tazarotene treatment, 6 days, rep3

status: Public on Nov 04 2022

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
Base calling: bcl2fastq (v.2.20.0)
Read alignment: STAR (v.2.7.3a)
Read counting:  featureCounts/subread (v.2.0.0)
Differential expression: DESeq2 (v.1.22.2)
Assembly: hg38
Supplementary files format and content: All *exonCount.txt files contain read counts generated by featureCounts (subread) software. These files were used for doing differential expression analysis.

source_name: cell line G

growth_protocol: Patient skin fibroblasts were grown in DMEM supplemented with 10% fetal calf serum and 1% penicillin/streptomycin under 5% CO2 at 37C  supplemented with 10% fetal calf serum and 1% penicillin/streptomycin  Patient skin fibroblasts were grown in Dulbecco’s modified Eagle’s medium (Invitrogen, Karlsruhe, Germany) under 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Trizol/chloroform method and cleaned up using the Zymo RNA clean & concentrator-5 kit
RNA libraries for RNA-seq were prepared using TruSeq Stranded lotal RNA Library Prep following manufacturer's protocols.

treatment_protocol: Cells were treated at day 0 with 10 µM tazarotene, 5 µM adapalene dissolved in DMSO or DMSO as control, medium and drugs were replenished at day 3, harvesting at day 6

tag: cell line

value: cell line G

value: Human MSD patient fibroblast line

value: tazarotene


title: Human MSD patient fibroblast line G, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line G, DMSO treatment, 6 days, rep3

value: DMSO


title: Human MSD patient fibroblast line G, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line G, adapalene treatment, 6 days, rep3

value: adapalene


title: Human MSD patient fibroblast line G, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line G, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line F, tazarotene treatment, 6 days, rep3

source_name: cell line F

value: cell line F


title: Human MSD patient fibroblast line F, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line G, adapalene treatment, 6 days, rep1


title: MDA PCa 2b

city: Washington

first: Anelia

last: Horvath

state: DC

address: 2300 I street NW, Ross Hall, Suite 731

institute: George Washington University

data_processing:
Illumina’s RTA and CASAVA pipeline
Sequencing datasets were quality assessed using fastqc (v. 0.11.9).
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.38
Trimmed sequence reads were mapped to Homo_sapiens.GRCh38.cdna.all.fa Ensembl v.101
Salmon v.1.2.0
Assembly: Homo_sapiens.GRCh38.cdna.all.fa Ensembl v.101
Supplementary files format and content: .txt, raw read counts, normalized read counts (TPM)

source_name: MDA PCa 2b

growth_protocol: MDA PCa 2b cells were obtained from American Type Tissue Collection (ATCC, Manassas, VA) and maintained in Kaighn's Modification of Ham's F-12 medium supplemented with 20% FBS, 25 ng/ml cholera toxin (Sigma-Aldrich, St. Louis, MO), 10 ng/ml mouse Epidermal Growth Factor (Corning), 5 mM phosphoethanolamine (Sigma-Aldrich), 100 pg/ml hydrocortisone (Sigma-Aldrich), 45 nM sodium selenite (Sigma-Aldrich), 5 ug/ml human recombinant insulin (Life Technologies), and 1% penicillin-streptomycin. RC77 T/E cells were maintained in Keratinocyte-SFM media (Gibco) supplemented with epidermal growth factor and bovine pituitary extract. All cell lines were maintained at 37°C and 5% CO2.

extract_protocol:
RNA from MDA PCa 2b and RC77 T/E cells was isolated using TRIzol extraction (Invitrogen, Waltham, MA), isopropanol-precipitated with GlycoBlue (Fisher Scientific, Pittsburgh, PA) and quality assessed using an Agilent 2100 Bioanalyzer system where RIN scores of all isolated RNA were > 9.0.
Paired-end library of the prostate cancer cell lines was constructed using NEBNext Ultra Directional RNA kit.

value: MDA PCa 2b

value: prostate cancer cell line

value: untreated cells


title: RC77 T/E

source_name: RC77 T/E

value: RC77 T/E


title: Human MSD patient fibroblast line F, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line F, DMSO treatment, 6 days, rep3


title: Human MSD patient fibroblast line F, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line F, tazarotene treatment, 6 days, rep1


title: Human MSD patient fibroblast line F, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line F, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line F, adapalene treatment, 6 days, rep1


title: Human MSD patient fibroblast line E, tazarotene treatment, 6 days, rep3

source_name: cell line E

value: cell line E


title: Human MSD patient fibroblast line E, tazarotene treatment, 6 days, rep1


title: Human MSD patient fibroblast line E, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line E, DMSO treatment, 6 days, rep3


title: Human MSD patient fibroblast line E, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line E, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line G, tazarotene treatment, 6 days, rep1


title: Human MSD patient fibroblast line E, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line E, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line E, adapalene treatment, 6 days, rep1


title: Human MSD patient fibroblast line D, tazarotene treatment, 6 days, rep1

source_name: cell line D

value: cell line D


title: Human MSD patient fibroblast line D, DMSO treatment, 6 days, rep3


title: Human MSD patient fibroblast line D, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line D, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line D, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line C, tazarotene treatment, 6 days, rep3

source_name: cell line C

value: cell line C


title: Human MSD patient fibroblast line D, adapalene treatment, 6 days, rep1


title: Human MSD patient fibroblast line D, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line C, tazarotene treatment, 6 days, rep1


title: Human MSD patient fibroblast line C, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line C, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line C, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line B, tazarotene treatment, 6 days, rep2

source_name: cell line B

value: cell line B


title: Human MSD patient fibroblast line C, adapalene treatment, 6 days, rep1


title: Human MSD patient fibroblast line C, adapalene treatment, 6 days, rep2


title: SCV24_passage2_2

source_name: SCV24 passage2 2

tag: sample type

value: clinical isolate

value: respiratory tract


title: Human MSD patient fibroblast line C, DMSO treatment, 6 days, rep3


title: Human MSD patient fibroblast line B, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line B, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, tazarotene treatment, 6 days, rep3

source_name: cell line A

value: cell line A


title: Human MSD patient fibroblast line B, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line B, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line D, tazarotene treatment, 6 days, rep3


title: Human MSD patient fibroblast line D, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, adapalene treatment, 6 days, rep3


title: Human MSD patient fibroblast line A, tazarotene treatment, 6 days, rep1


title: Human MSD patient fibroblast line A, DMSO treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, adapalene treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, DMSO treatment, 6 days, rep3


title: Human MSD patient fibroblast line C, tazarotene treatment, 6 days, rep2


title: Human MSD patient fibroblast line A, DMSO treatment, 6 days, rep1


title: Human MSD patient fibroblast line A, adapalene treatment, 6 days, rep1


title: Human MSD patient fibroblast line B, tazarotene treatment, 6 days, rep3


title: Human MSD patient fibroblast line B, tazarotene treatment, 6 days, rep1


title: Patient_187, Serum, iMCD, Cycle4_Day1

type: protein

city: Philadelphia

first: David

last: Fajgenbaum

state: PA

address: 3535 Market St, 717

institute: University of Pennsylvania

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat
Failed QA; removed from processed data

hyb_protocol: Hybridization protocol done in accordance with SomaLogic standard operating procedures and best practices.

scan_protocol: Scan protocol done in accordance with SomaLogic standard operating procedures and best practices.

data_processing: SomaLogic SOMAscan pre-processing was performed, and 1,178 analytes passed quality control. Data were log2 transformed and capped at 2.5th and 97.5th percentiles. Batches were bridged together by the average log ratio of technical replicates for each analyte. Following quality control sample exclusion, pretreatment samples available for analysis included 88 iMCD patients, 42 healthy donors, and 20 each of RA, HL, and HHV8-MCD. Longitudinal samples available for analysis included samples from day 8 and day 64 of treatment from 73 iMCD patients.

molecule: protein

source_name: Serum

label_protocol: Label protocol done in accordance with SomaLogic standard operating procedures and best practices.

extract_protocol: Protein extracted from serum in accordance with SomaLogic standard operating procedures and best practices.

tag: patient label

tag: disease state

value: iMCD

tag: batch

tag: Sex

value: M

tag: age

value: TRUE

value: Placebo + BSC

value: FALSE


title: Patient_194, Serum, iMCD, Cycle4_Day1

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat

value: Siltuximab + BSC


title: Patient_186, Serum, iMCD, Cycle4_Day1

value: F


title: Human MSD patient fibroblast line B, adapalene treatment, 6 days, rep1

tag: cell type

value: Human MSD patient fibroblast line

value: adapalene


title: Patient_198, Serum, iMCD, Cycle1_Day8


title: Patient_75, Serum, iMCD, Cycle1_Day1


title: Patient_188, Serum, iMCD, Cycle1_Day1


title: Patient_188, Serum, iMCD, Cycle1_Day8


title: Patient_88, Serum, iMCD, Cycle1_Day1


title: Patient_75, Serum, iMCD, Cycle1_Day8


title: Patient_88, Serum, iMCD, Cycle1_Day8


title: Patient_83, Serum, iMCD, Cycle1_Day8


title: Patient_90, Serum, iMCD, Cycle1_Day8


title: Patient_90, Serum, iMCD, Cycle1_Day1


title: Patient_192, Serum, iMCD, Cycle4_Day1


title: Patient_198, Serum, iMCD, Cycle1_Day1


title: Patient_87, Serum, iMCD, Cycle1_Day1


title: Patient_92, Serum, iMCD, Cycle1_Day8


title: Patient_87, Serum, iMCD, Cycle1_Day8


title: Patient_185, Serum, iMCD, Cycle4_Day1


title: Patient_152, Serum, iMCD, Cycle1_Day1, Rep 1

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat
Technical replicate used for batch normalizing


title: Patient_197, Serum, iMCD, Cycle1_Day1


title: Patient_152, Serum, iMCD, Cycle1_Day8


title: Patient_152, Serum, iMCD, Cycle1_Day1, Rep 2

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Technical replicate used for batch normalizing


title: Patient_190, Serum, iMCD, Cycle4_Day1


title: Patient_197, Serum, iMCD, Cycle1_Day8


title: Patient_189, Serum, iMCD, Cycle4_Day1


title: SMC60-3-4 Batch2

state: NY

tag: strain

value: caspofungin adapted


title: Patient_191, Serum, iMCD, Cycle4_Day1


title: Patient_80, Serum, iMCD, Cycle1_Day8


title: Patient_80, Serum, iMCD, Cycle1_Day1


title: Patient_81, Serum, iMCD, Cycle1_Day8


title: Patient_81, Serum, iMCD, Cycle1_Day1


title: Patient_196, Serum, iMCD, Cycle1_Day8


title: Patient_195, Serum, iMCD, Cycle4_Day1


title: Patient_147, Serum, iMCD, Cycle4_Day1


title: Patient_148, Serum, iMCD, Cycle1_Day8


title: Patient_148, Serum, iMCD, Cycle1_Day1


title: Patient_92, Serum, iMCD, Cycle1_Day1


title: Patient_196, Serum, iMCD, Cycle1_Day1


title: Patient_100, Serum, iMCD, Cycle1_Day1


title: Patient_101, Serum, iMCD, Cycle1_Day8


title: Patient_103, Serum, iMCD, Cycle1_Day1


title: Patient_195, Serum, iMCD, Cycle1_Day1


title: Patient_194, Serum, iMCD, Cycle1_Day8


title: Patient_146, Serum, iMCD, Cycle1_Day1


title: Patient_101, Serum, iMCD, Cycle1_Day1


title: Patient_195, Serum, iMCD, Cycle1_Day8


title: Patient_146, Serum, iMCD, Cycle1_Day8


title: Patient_193, Serum, iMCD, Cycle4_Day1


title: Patient_193, Serum, iMCD, Cycle1_Day8


title: Patient_194, Serum, iMCD, Cycle1_Day1


title: Patient_196, Serum, iMCD, Cycle4_Day1


title: Patient_189, Serum, iMCD, Cycle1_Day8


title: Patient_197, Serum, iMCD, Cycle4_Day1


title: Patient_193, Serum, iMCD, Cycle1_Day1


title: Patient_103, Serum, iMCD, Cycle1_Day8


title: Patient_100, Serum, iMCD, Cycle1_Day8


title: Patient_191, Serum, iMCD, Cycle1_Day1


title: Patient_192, Serum, iMCD, Cycle1_Day1


title: Patient_191, Serum, iMCD, Cycle1_Day8


title: Patient_82, Serum, iMCD, Cycle1_Day8


title: Patient_190, Serum, iMCD, Cycle1_Day8


title: Patient_192, Serum, iMCD, Cycle1_Day8


title: Patient_102, Serum, iMCD, Cycle1_Day8


title: Patient_190, Serum, iMCD, Cycle1_Day1


title: Patient_99, Serum, iMCD, Cycle1_Day1


title: Patient_102, Serum, iMCD, Cycle1_Day1


title: Patient_189, Serum, iMCD, Cycle1_Day1


title: Patient_111, Serum, iMCD, Cycle4_Day1


title: Patient_187, Serum, iMCD, Cycle1_Day8


title: Patient_188, Serum, iMCD, Cycle4_Day1


title: Patient_186, Serum, iMCD, Cycle1_Day8


title: Patient_149, Serum, iMCD, Cycle4_Day1


title: Patient_151, Serum, iMCD, Cycle4_Day1


title: Patient_184, Serum, iMCD, Cycle1_Day1


title: Patient_157, Serum, iMCD, Cycle1_Day1

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat


title: Patient_142, Serum, iMCD, Cycle4_Day1


title: Patient_185, Serum, iMCD, Cycle1_Day1


title: Patient_185, Serum, iMCD, Cycle1_Day8


title: Patient_187, Serum, iMCD, Cycle1_Day1, Rep 1


title: Patient_186, Serum, iMCD, Cycle1_Day1


title: Patient_150, Serum, iMCD, Cycle4_Day1


title: Patient_183, Serum, Healthy

value: Healthy


title: Patient_158, Serum, iMCD, Cycle1_Day1


title: Patient_182, Serum, Healthy


title: Patient_82, Serum, iMCD, Cycle1_Day1


title: Patient_180, Serum, Healthy


title: Patient_178, Serum, Healthy


title: Patient_179, Serum, Healthy


title: Patient_177, Serum, Healthy


title: Patient_181, Serum, Healthy


title: Patient_187, Serum, iMCD, Cycle1_Day1, Rep 2


title: Patient_156, Serum, iMCD, Cycle1_Day1


title: Patient_166, Serum, Healthy, Rep 2

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Technical replicate; removed from processed data


title: Patient_168, Serum, Healthy, Rep 2


title: Patient_175, Serum, Healthy


title: Patient_174, Serum, Healthy, Rep 2


title: Patient_174, Serum, Healthy, Rep 1


title: Patient_159, Serum, Healthy, Rep 2


title: Patient_173, Serum, Healthy, Rep 2


title: Patient_171, Serum, Healthy


title: Patient_170, Serum, Healthy


title: Patient_172, Serum, Healthy


title: Patient_155, Serum, iMCD, Cycle4_Day1


title: Patient_168, Serum, Healthy, Rep 1


title: Patient_176, Serum, Healthy


title: Patient_169, Serum, Healthy


title: Patient_161, Serum, Healthy


title: Patient_154, Serum, RA

value: RA


title: Patient_163, Serum, Healthy


title: Patient_162, Serum, Healthy


title: Patient_166, Serum, Healthy, Rep


title: Patient_167, Serum, Healthy


title: Patient_153, Serum, RA


title: Patient_164, Serum, Healthy


title: Patient_159, Serum, Healthy, Rep 1


title: Patient_165, Serum, Healthy


title: Patient_151, Serum, iMCD, Cycle1_Day8


title: Patient_160, Serum, Healthy


title: Patient_151, Serum, iMCD, Cycle1_Day1


title: Patient_152, Serum, iMCD, Cycle4_Day1


title: Patient_150, Serum, iMCD, Cycle1_Day8


title: Patient_104, Serum, iMCD, Cycle4_Day1


title: Patient_150, Serum, iMCD, Cycle1_Day1


title: Patient_149, Serum, iMCD, Cycle1_Day1


title: Patient_173, Serum, Healthy, Rep 1


title: Patient_148, Serum, iMCD, Cycle4_Day1


title: Patient_147, Serum, iMCD, Cycle1_Day8


title: Patient_84, Serum, iMCD, Cycle1_Day8


title: Patient_85, Serum, iMCD, Cycle1_Day8


title: Patient_143, Serum, iMCD, Cycle4_Day1


title: Patient_146, Serum, iMCD, Cycle4_Day1


title: Patient_145, Serum, iMCD, Cycle1_Day8


title: Patient_144, Serum, iMCD, Cycle1_Day1


title: Patient_145, Serum, iMCD, Cycle1_Day1


title: Patient_89, Serum, iMCD, Cycle4_Day1


title: Patient_142, Serum, iMCD, Cycle1_Day8


title: Patient_145, Serum, iMCD, Cycle4_Day1


title: Patient_142, Serum, iMCD, Cycle1_Day1


title: Patient_141, Serum, RA


title: Patient_149, Serum, iMCD, Cycle1_Day8


title: Patient_108, Serum, iMCD, Cycle4_Day1


title: Patient_140, Serum, Healthy


title: Patient_107, Serum, iMCD, Cycle4_Day1


title: Patient_110, Serum, iMCD, Cycle4_Day1


title: Patient_143, Serum, iMCD, Cycle1_Day8


title: Patient_139, Serum, Healthy


title: Patient_144, Serum, iMCD, Cycle4_Day1


title: Patient_136, Serum, Healthy


title: Patient_135, Serum, iMCD, Cycle1_Day1


title: Patient_137, Serum, Healthy


title: Patient_144, Serum, iMCD, Cycle1_Day8


title: Patient_134, Serum, iMCD, Cycle1_Day1


title: Patient_89, Serum, iMCD, Cycle1_Day8


title: Patient_143, Serum, iMCD, Cycle1_Day1


title: Patient_133, Serum, iMCD, Cycle1_Day1


title: Patient_138, Serum, Healthy


title: Patient_132, Serum, Lymphoma

value: Lymphoma


title: Patient_131, Serum, Lymphoma


title: Patient_125, Serum, Lymphoma


title: Patient_130, Serum, Lymphoma


title: Patient_126, Serum, Lymphoma


title: Patient_129, Serum, Lymphoma


title: Patient_128, Serum, Lymphoma


title: Patient_123, Serum, Lymphoma


title: Patient_122, Serum, Lymphoma


title: Patient_124, Serum, Lymphoma


title: Patient_121, Serum, Lymphoma


title: Patient_119, Serum, Lymphoma


title: Patient_117, Serum, Lymphoma


title: Patient_118, Serum, Lymphoma


title: Patient_120, Serum, Lymphoma


title: Patient_116, Serum, Lymphoma


title: Patient_113, Serum, Lymphoma


title: Patient_115, Serum, Lymphoma


title: Patient_107, Serum, iMCD, Cycle1_Day8


title: Patient_99, Serum, iMCD, Cycle4_Day1


title: Patient_112, Serum, iMCD, Cycle1_Day8


title: Patient_112, Serum, iMCD, Cycle4_Day1


title: Patient_114, Serum, Lymphoma


title: Patient_127, Serum, Lymphoma


title: Patient_112, Serum, iMCD, Cycle1_Day1


title: Patient_147, Serum, iMCD, Cycle1_Day1


title: Patient_111, Serum, iMCD, Cycle1_Day1


title: Patient_95, Serum, iMCD, Cycle1_Day8, Rep 1


title: Patient_110, Serum, iMCD, Cycle1_Day1


title: Patient_95, Serum, iMCD, Cycle1_Day8, Rep 2


title: Patient_109, Serum, iMCD, Cycle4_Day1


title: Patient_111, Serum, iMCD, Cycle1_Day8


title: Patient_106, Serum, iMCD, Cycle1_Day8


title: Patient_108, Serum, iMCD, Cycle1_Day8


title: Patient_109, Serum, iMCD, Cycle1_Day8


title: Patient_107, Serum, iMCD, Cycle1_Day1


title: Patient_105, Serum, iMCD, Cycle4_Day1


title: Patient_105, Serum, iMCD, Cycle1_Day1


title: Patient_104, Serum, iMCD, Cycle1_Day8


title: Patient_103, Serum, iMCD, Cycle4_Day1


title: Patient_91, Serum, iMCD, Cycle1_Day1, Series 1


title: Patient_104, Serum, iMCD, Cycle1_Day1


title: Patient_102, Serum, iMCD, Cycle4_Day1


title: Patient_101, Serum, iMCD, Cycle4_Day1


title: Patient_99, Serum, iMCD, Cycle1_Day8


title: Patient_93, Serum, iMCD, Cycle4_Day1


title: Patient_78, Serum, iMCD, Cycle1_Day1


title: Patient_98, Serum, iMCD, Cycle1_Day8


title: Patient_97, Serum, iMCD, Cycle1_Day8


title: Patient_78, Serum, iMCD, Cycle1_Day8


title: Patient_98, Serum, iMCD, Cycle4_Day1


title: Patient_106, Serum, iMCD, Cycle1_Day1, Rep 1


title: Patient_98, Serum, iMCD, Cycle1_Day1


title: Patient_97, Serum, iMCD, Cycle1_Day1


title: Patient_105, Serum, iMCD, Cycle1_Day8


title: Patient_106, Serum, iMCD, Cycle1_Day1, Rep 2


title: Patient_96, Serum, iMCD, Cycle1_Day8


title: Patient_93, Serum, iMCD, Cycle1_Day8


title: Patient_96, Serum, iMCD, Cycle1_Day1


title: Patient_95, Serum, iMCD, Cycle4_Day1


title: YS-03

city: Galveston

first: Juquan

last: Song

state: TX

address: 301 University Blvd.

institute: University of Texas Medical Branch at Galveston

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.7.5c) using the mouse GRCm38 genome .
RNA-Seq reads were aligned to the mouse reference using the STAR software version 2.7.5c with the parameters recommended for the ENCODE consortium.
Gene read counts obtained from the STAR quantMode GeneCounts feature using the Gencode vM25 annotation file.
miRNA read 1 adapter trimming with the mapper.pl function of miRDeep2.0.0.8 using the command mapper.pl input.fastq -e -v -u -h -k AGATCGGAAGAGCACACGTCT -l 18 -m
miRNA read1 aligned to mouse reference using STAR version 2.7.5c with parameters "--runThreadN 10 --outSAMtype BAM SortedByCoordinate  --alignIntronMax 1 --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outMultimapperOrder Random"
featureCounts v2.0.1 used to count miRNA reads with the mirBase v22 annotation file and parameters "-T12 -s 1 -t miRNA_primary_transcript  -f -M --primary -g Name -a mmu.gff3"
Assembly: GRCm38
Supplementary files format and content: Tab delimited tables of raw gene read counts per sample and miRNA read counts per sample

source_name: Gastrocnemius muscle

extract_protocol:
The New England Biolabs NEBNext Small RNA library kits was used to prepare miRNA libraries from ~1.0 ug of total RNA.
Qiagen RNeasy Mini Kit following manufacturer's protocol

tag: tissue

value: Gastrocnemius muscle

value: male

value: Young

value: Sham burn


title: Patient_94, Serum, iMCD, Cycle4_Day1

value: iMCD


title: Patient_93, Serum, iMCD, Cycle1_Day1

value: M


title: Patient_94, Serum, iMCD, Cycle1_Day1

value: TRUE


title: YS-02


title: Patient_94, Serum, iMCD, Cycle1_Day8


title: Patient_96, Serum, iMCD, Cycle4_Day1


title: Patient_92, Serum, iMCD, Cycle4_Day1


title: Patient_77, Serum, iMCD, Cycle1_Day8


title: Patient_100, Serum, iMCD, Cycle4_Day1

value: Placebo + BSC


title: YS-01


title: Patient_97, Serum, iMCD, Cycle4_Day1


title: YB-03

value: Burn


title: Patient_91, Serum, iMCD, Series 5

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Single patient series of 8 samples; removed from processed data

value: FALSE


title: AS-03

value: Adult


title: YB-01


title: AS-02


title: AB-03


title: Patient_91, Serum, iMCD, Series 8


title: AS-01


title: Patient_91, Serum, iMCD, Series 7


title: YB-02


title: Patient_91, Serum, iMCD, Series 6


title: Patient_86, Serum, iMCD, Cycle4_Day1

value: F

value: Siltuximab + BSC


title: Patient_91, Serum, iMCD, Series 3


title: Patient_91, Serum, iMCD, Series 4


title: AB-02


title: SV3-YS-02-b

extract_protocol:
Poly-A plus RNA was enriched from ~0.1ug of total RNA and used to generate libraries using New England Biolabs NEBNext Ultra II Kit.
Qiagen RNeasy Mini Kit following manufacturer's protocol


title: SV3-YS-03-b


title: AB-01


title: Patient_91, Serum, iMCD, Cycle1_Day8, Series 2


title: SV3-YB-02-b


title: Patient_76, Serum, iMCD, Cycle4_Day1


title: SV3-YS-01-b


title: Patient_88, Serum, iMCD, Cycle4_Day1