title: 873_WT_K4_R1

data_processing:
Raw peaks were aligned to the mm10 mouse genome using the NGS Data Charmer pipeline with default settings (HISAT v.0.1.6b)
Peak calling was performed using macs2 (v.2.1.1) on individual files with default settings
Differential peaks using Diffbind package (v3.8.4)
Assembly: mm10
Supplementary files format and content: macs2 narrowPeak .xls file
Supplementary files format and content: bigWig file

source_name: placenta

extract_protocol:
Chromatin from hemisected placental tissues were fixed with 1% formaldehyde rotated for 12 minutes at room temperature and was subsequently quenched using a final concentration of 125mM glycine. Samples were thoroughly homogenized and washed with ice cold PBS. Fixed chromatin was sonicated using a Covaris E220 for 30-60 minutes at 4°C with the following conditions: peak incident power, 140; duty factor, 10%; Cycles/burst, 200; Water level, 0. Equal amounts of chromatin per sample were rotated with select antibodies (2.5 μg antibody/sample of either H3K4me3Q5ser (MilliporeSigma ABE2580) or H3K4me3 (Active Motif 39159)) bound to M-280 Dynabeads at 4°C overnight. The next morning, samples were washed, eluted, and reverse-crosslinked at 65°C. Samples underwent RNA and protein digestion, and DNA was purified using QIAQuick MinElute Spin columns (Qiagen 28140). 1% inputs were removed prior to antibody incubation and purified in parallel with corresponding immunoprecipitates.
TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012)

value: placenta

value: WT


title: 873_WT_Input_R1

status: Public on Jan 23 2024

type: SRA

city: New York

first: Jennifer

middle: C

last: Chan

state: New York

address: 1470 Madison Ave 9-201

department: Neuroscience

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Embryonic placenta collections at designated time points

tag: tissue

tag: developmental stage

tag: Sex

tag: genotype

tag: chip antibody

value: Input


title: N-12

city: Shenbei

first: Weidong

last: Zhao

state: Liaoning

address: 77 Puhe Road, Shenbei New District

department: Department of Developmental Cell Biology

country: China

institute: China Medical University

library_source: transcriptomic

data_processing:
FASTP v 0.18.0
Alignment with rRNA: Bowtie2(version 2.2.8) was used for mapping reads to rRNA database. The rRNA mapped reads then will be removed.
Alignment with Reference Genome: Paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 with “-rna-strandness RF” and other parameters set as a default.
Quantification of Gene Abundance:The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM value was calculated to quantify its expression abundance and variations, using StringTie software.
Differentially expressed genes (DEGs): RNAs differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: Ensembl release 98 GRCh38.p13
Supplementary files format and content: processed data.txt file includes count and FPKM values of each sample

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: The blood samples from the recruited subjects were collected in anticoagulant tubes.

extract_protocol:
RNA was harvested using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA). 1.0 μg of tatal RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s protocol.

treatment_protocol: The erythrocytes were lysed by Red Blood Cell Lysis Solution and the leukocytes were isolated by density gradient centrifugation.  CD14+ monocytes were separately isolated from the leukocytes using magnet‐mediated separation with the specific magnetic beads (Miltenyi Biotech.), respectively.

value: blood

tag: cell type

value: Primary monocyte

tag: disease state

value: control


title: GW4064_4

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

description:
donor1
G4.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt

data_processing:
The ONT Guppy workflow (version 2.1.0) was used for basecalling the DRS data with the parameters "--flowcell FLO-MIN106 --kit SQK-RNA002 -x cuda:all --records_per_fastq 0" being employed
The FASTQ files were aligned to the GRCh38 human genome reference and GRCm38 mouse genome reference respectively using minimap2/2.17, with the parameters "-ax splice -uf -k14" being employed.
The FLAIR pipeline (https://github.com/BrooksLabUCSC/flair) with some modifications was employed to identify the isoform from the aligned reads.
The nanopore reads were quantified to DRS annotation using FLAIR quantify by default parameters. Only alignments with quality scores of 1 or greater were counted.
Assembly: GRCh38 and mm10
Supplementary files format and content: tab-delimited text files include TPM (Transcripts Per Million) for each sample; isoform structure BED files

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Liver

extract_protocol:
The 75 ug of fresh Trizol isolated RNAs were adjusted to a volume of 100 μL with nuclease-free water. The polyadenylated RNAs were selected using the Dynabeads™ mRNA Purification Kit (Invitrogen, Cat. 61006) following the manufacturer's instructions.
The 500 ng of fresh isolated polyadenylated RNAs were used for nanopore direct RNA sequencing (DRS) generally following the Oxford Nanopore Technologies (ONT) SQK-RNA002 kit protocol, including the optional reverse transcription step recommended by ONT. Libraries were loaded onto ONT R9.4 flow cells (Oxford Nanopore Technologies) and were sequenced using the GridION platform, with the standard MinKNOW/19.12.5 protocol script being used.

tag: strain

value: TKNOG

tag: host organism

value: TKNOG Mus musculus

tag: xenograft organism

value: Homo sapiens

tag: treatment

value: Liver


title: N-13


title: N-17


title: lung adenocarcinoma tissue 1, prior to osimertinib

city: Shanghai

first: Jiaqi

last: Liang

state: Shanghai

address: 180 Fenglin Road

institute: Zhongshan Hospital Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCh38.p13
Supplementary files format and content: FPKM

source_name: lung adenocarcinoma

extract_protocol:
RNA was harvested using TRIZOL
RNA libararies for RNA-seq were prepared using SMARTER mRNA-seq Library Kit

value: lung adenocarcinoma


title: 873_WT_Dual_R1


title: N-11


title: GW4064_2

description:
donor1
G2.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: N-15


title: GW4064_3

description:
donor1
G3.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: N-10


title: H1975OR ZNF2632

source_name: Tumor

growth_protocol: Cells were maintained in DMEM

treatment_protocol: Stepwise osimertinib

value: Tumor

tag: cell line

value: NSCLC cell

value: ZNF263 overexpressed


title: GW4064_1

description:
donor1
G1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: H1975OR ZNF2631


title: Rosiglitazone_4

description:
donor1
R4.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt

value: Rosiglitazone


title: 868_WT_Input_R1


title: 868_WT_Dual_R1


title: H1975OR NC2


title: Rosiglitazone_3

description:
donor1
R3.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: lung adenocarcinoma tissue 2, prior to osimertinib


title: 867_WT_K4_R1


title: Rosiglitazone_2

description:
donor1
R2.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: HCC827OR ZNF2632


title: Control_S2_S7_GPR101_TSS

city: Pieve Emanuele

first: Giampaolo

last: Trivellin

state: Lombardy

address: Via Rita Levi Montalcini 4

country: Italy

institute: Humanitas University

description: wild-type control. GPR101 viewpoint

data_processing:
Sequencing data were demultiplexed and mapped to human reference genome (GRCh37/hg19). Reads located in restriction fragments flanked by restriction recognition sites of the same enzyme, in fragments smaller than 40 bp or within a window of 10 kb around the viewpoint were filtered out. Mapped reads were then converted to read counts per restriction fragment of first restriction enzyme.
For visualization, all samples were normalized for million mapped reads (reads per million, RPM) for a given genomic region (chrX:135,000,000-137,000,000, hg19) and smoothened using a 10-fragment running window algorithm.
Assembly: human genome GRCh37/hg19
Supplementary files format and content: Normalized 4C-seq profiles
Library strategy: 4C-seq

source_name: Blood

extract_protocol:
4C-seq libraries were prepared following the published protocol (van de Werken et al., 2012). For the GPR101 viewpoint, Csp6 and DpnII were used for the first and second digestion, repsectively. For RBMX and VGLL1 viewpoints, DpnII and Csp6 were used for the first and second digestion, repsectively. Parallel PCR reactions were performed to amplify from a total of 1 µg template per 4C library and viewpoint. PCR reactions were pooled and purified using 1.8x volume of AMPure XP beads (Agencourt, A63881).
Samples were indexed and sequenced with Ilumina Hi-Seq technology according to standard procedures.

treatment_protocol: Approximately, 1 × 10E6 to 2.5 × 10E6 cells from nucleated cell isolates from peripheral blood samples were used as input material for 3C library preparation. Trypsinized or disaggregated cells were filtered through 40 µm cell strainer and pelleted by centrifugation at 500x g. Cells were fixed in 5 ml of 2 % formaldehyde in 10 % FCS/ PBS and incubated for 10 minutes at room temperatures to cross-link chromatin. The reaction was quenched with glycine at a final concentration of 0.125 M and incubation at room temperature for 5 minutes. Cells were pelleted by centrifugation for 5 minutes at 500x g at 4ºC and washed on ice twice with 1x PBS. Cell pellets were either snap frozen in liquid nitrogen or processed for nuclei extraction. For nuclei extraction, fixed cells were resuspended in 2 ml freshly prepared lysis buffer (50 mM Tris pH7.5; 150 mM NaCl; 5 mM EDTA; 0.5 % NP-40; 1.15 % Triton X-100; 1x Roche Complete protease inhibitors) and incubated for 10 minutes on ice. Nuclei were pelleted by centrifugation for 5 minutes, 800x g at 4ºC and washed with 1x PBS.

value: wild-type control

value: Blood

value: PBMCs


title: H1975OR NC1


title: Control_S2_S7_RBMX_TSS

description: wild-type control. RBMX viewpoint


title: Control_S2_S7_VGLL1_TSS

description: wild-type control. VGLL1 viewpoint


title: Rosiglitazone_1

description:
donor1
R1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: S17_GPR101_TSS

description: X-linked acrogigantism patient. GPR101 viewpoint

value: X-linked acrogigantism


title: Fenofibrate_4

description:
donor1
F4.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt

value: Fenofibrate


title: HCC827OR ZNF2631


title: 868_WT_K4_R1

value: placenta

value: WT


title: 867_WT_Dual_R1


title: Fenofibrate_3

description:
donor1
F3.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: 749_Oct3 KO_K4_R1

value: Oct3 KO


title: N-1

value: blood

value: Primary monocyte

value: control


title: HCC827OR NC1


title: S17_RBMX_TSS

description: X-linked acrogigantism patient. RBMX viewpoint


title: S17_VGLL1_TSS

description: X-linked acrogigantism patient. VGLL1 viewpoint


title: PC9OR ZNF2632


title: Fenofibrate_2

description:
donor1
F2.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt

value: TKNOG

value: TKNOG Mus musculus

value: Homo sapiens

value: Liver


title: 749_Oct3 KO_Dual_R1


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 2, replicate III

city: Münster

first: Ileana

last: Salto

state: Nordrhein-Westfalen

address: Von-Esmarch-Str. 56

country: Germany

institute: Institute für Infektiologie. ZMBE. Münster

description:
rnc_T2_37_minusCa_III
III_T0_25_vs_rnc_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv

data_processing:
Downstream analysis, included assessment of the general quality of sequencing output FastQC (Babraham Bioinformatics)) and mapping to the reference genomes (YPIII chromosome and virulence plasmid pYV) (NC_010465.1 and NC_006153.2) (Bowtie2 with default parameters (Langmead and Salzberg, 2012)). Uniquely mapped reads were obtained using SAMtools (Li et al., 2009)
Assembly: YPIII chromosome (NC_010465.1 ) and virulence plasmid pYV (NC_006153.2)
Supplementary files format and content: csv files containing reports obtained by DESeq2 R-package.

organism: Yersinia pseudotuberculosis

growth_protocol: Y. pseudotuberculosis YPIII and the isogenic Δrnc mutant YP356 were grown in LB medium to exponential phase (OD600 0.5)

extract_protocol:
Pellet from 2ml bacteria culture were snap frozen in liquid nitrogen and resuspended, lysed and later incubated with Roti® Aqua Phenol. Aqueous layer was washed with chloroform/isoamyl-alocohol (24:1) and RNA precipitated adding 1/10 volume of 3M NaOAc (pH 4.5) and 3 volumes of 95% EtOH.  RNA pellet was washed with 70% EtOH and resupsended in RNase free water.
RNAseq libraries were prepared using a NEBNext Ultra II Directional RNA Library Prep Kit - Bacteria, according to the manufacturer’s instructions.

treatment_protocol: The cultures were split and grown at 25°C (time 0), 37°C, or 37°C in the presence of 20 mM Na2C2O4 and 20 mM MgCl2  (Ca2+ depletion) in triplicates. After 1 h (time 1) and 4 h ( time 2).

value: delta_rnc (RNase III-deficient mutant)

value: 37 degrees C growth in LB 20 mM Na2C2O4 and 20 mM MgCl2


title: Fenofibrate_1

description:
donor1
F1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 2, replicate II

description:
rnc_T2_37_minusCa_II
III_T0_25_vs_rnc_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: 718_Sert KO_K4_R1

value: Sert KO


title: DMSO_4

description:
donor1
D4.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt

value: DMSO


title: 867_WT_Input_R1

value: Input


title: PC9OR NC2

value: Tumor

value: NSCLC cell


title: 718_Sert KO_Input_R1

value: placenta


title: PC9OR NC1


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 2, replicate I

description:
rnc_T2_37_minusCa_I
III_T0_25_vs_rnc_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: DMSO_3

description:
donor1
D3.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: DMSO_2

description:
donor1
D2.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: HCC827OR NC2


title: 718_Sert KO_Dual_R1


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 2, replicate III

description:
III_T2_37_minusCa_III
III_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv

source_name: YPIII

value: YPIII

value: wt


title: 717_Sert KO_K4_R1


title: 749_Oct3 KO_Input_R1

value: Oct3 KO


title: 717_Sert KO_Dual_R1


title: 717_Sert KO_Input_R1


title: DMSO_1

description:
donor1
D1.fastq
nanopore_human_transcripts_tpm_donor1.txt
nanopore_mouse_transcripts_tpm_donor1.txt


title: liver, feeding 28days, rep2

city: Changsha City

first: min

last: xie

address: No. 728 Shuanghe road

institute: Hunan Fisheries Science Institute

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. After removing adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcript by using Trinity (vesion: 2.4) in paired-end method. The longest transcript was choose as a unigene based the similarity and length of a sequence for subsequent analysis.
The function of the unigenes was annotated by alignment of the unigenes with the NCBI nonredundant (NR), SwissProt, and Clusters of orthologous groups for eukaryotic complete genomes (KOG) databases using Blastx with a threshold E-value of 10−5 . The proteins with the highest hits to the unigenes were used to assign functional annotations thereto. Base on the SwissProt annotation，Gene ontology (GO) classification was performed by the mapping relation between SwissProt and GO term. The unigenes were mapped to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database to annotate their potential metabolic pathways.
FPKM and read counts value of each unigene was calculated using bowtie2 and eXpress . DEGs were identified using the DESe (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If results of different databases conflicted with each other, a priority order of NR, SwissProt, KOG were followed when deciding CDS of Unigenes. When a Unigene appeared unaligned to any of the above databases, ESTScan software was applied to decide its CDS. MISA was used for SSR prediction and Primer3 for primer design.
Assembly: assembly
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Elopichthys bambusa

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis. The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or Illumina HiSeq X Ten) and 125bp/150bp paired-end reads were generated.

value: feeding


title: liver, feeding 28days, rep3


title: HEK293T, baseline,rep3

city: San Francisco

first: Xiaokun

last: Shu

state: CA

address: 555 Mission Bay Boulevard South, CVRI,RM484

institute: University of California, San Francisco

data_processing:
Raw FASTQ files were quality checked using FASTQC . Then fastp was used to quality trim FASTQ files using default setting.
Clean reads were processed to pseudo-align to human genome (hg38) using star.
HT-seq was used for gene counts quantification
Differential expressed genes were defined by edgeR with |log2FC| > 0.58,  p-value < 0.01, FDR < 0.05. DEGs based hypergeometric test and gene set enrichment analysis were produced by clusterProfiler.C56
Assembly: human genome (hg38)
Supplementary files format and content: csv files include raw counts

extract_protocol:
Total RNA was extracted by Quick-RNA Microprep Kit (Zymo Reserch, R1051).
Library was prepapred by Novogen

value: Mock


title: Y. pseudotuberculosis YP356 , 37°C, time 2, replicate II

description:
rnc_T2_37_plusCa_II
III_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv

value: 37 degrees C growth in LB


title: liver, feeding 28days, rep1


title: HEK293T, baseline,rep1


title: 700_Oct3 KO_K4_R1


title: liver, fasting 28days, rep3

value: fasting


title: 700_Oct3 KO_Input_R1


title: YAP-MAML2_control,DMSO,rep3

description: YAP-MAML2_SPARK_off_control_rapamycin_G15

value: DMSO 5hrs


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 2, replicate I

description:
III_T2_37_minusCa_I
III_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: Y. pseudotuberculosis YPIII, 37°C, time 2, replicate III

description:
III_T2_37_plusCa_III
III_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 2, replicate II

description:
III_T2_37_minusCa_II
III_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: liver, fasting 28days, rep2

value: Liver


title: 700_Oct3 KO_Dual_R1


title: YAP-MAML2_control,DMSO,rep2

description: YAP-MAML2_SPARK_off_control_rapamycin_G14


title: 697_Oct3 KO_K4_R1


title: Y. pseudotuberculosis YPIII, 37°C, time 2, replicate II

description:
III_T2_37_plusCa_II
III_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_control,DMSO,rep1

description: YAP-MAML2_SPARK_off_control_rapamycin_G13


title: Y. pseudotuberculosis YP356 , 37°C, time 2, replicate III

description:
rnc_T2_37_plusCa_III
III_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv

value: delta_rnc (RNase III-deficient mutant)


title: liver, fasting 28days, rep1


title: HEK293T, baseline,rep2


title: liver, feeding 8days, rep3


title: 697_Oct3 KO_Input_R1


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 1, replicate III

description:
rnc_T1_37_minusCa_III
III_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv

value: 37 degrees C growth in LB 20 mM Na2C2O4 and 20 mM MgCl2


title: 697_Oct3 KO_Dual_R1


title: Y. pseudotuberculosis YPIII, 37°C, time 2, replicate I

description:
III_T2_37_plusCa_I
III_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_III_T2_37_minusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_control,rapamycin,rep3

description: YAP-MAML2_SPARK_off_control_rapamycin_G12

value: rapamycin 5hrs


title: Y. pseudotuberculosis YP356 , 37°C, time 2, replicate I

description:
rnc_T2_37_plusCa_I
III_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T2_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T2_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T2_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_control,rapamycin,rep2

description: YAP-MAML2_SPARK_off_control_rapamycin_G11


title: liver, feeding 8days, rep2


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 1, replicate II

description:
rnc_T1_37_minusCa_II
III_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: Y. pseudotuberculosis YP356, 37°C minus Ca2+, time 1, replicate I

description:
rnc_T1_37_minusCa_I
III_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_minusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_control,rapamycin,rep1

description: YAP-MAML2_SPARK_off_control_rapamycin_G10


title: liver, fasting 8days, rep3


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 1, replicate III

description:
III_T1_37_minusCa_III
III_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_SPARK-OFF,DMSO,rep3


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 1, replicate II

description:
III_T1_37_minusCa_II
III_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: 689_Sert KO_Dual_R1

value: Sert KO


title: 689_Sert KO_Input_R1

value: Input


title: YAP-MAML2_SPARK-OFF,DMSO,rep2


title: 684_Tph1 KO_K4_R1

value: Tph1 KO


title: liver, fasting 8days, rep2


title: Y. pseudotuberculosis YPIII , 37°C minus Ca2+, time 1, replicate I

description:
III_T1_37_minusCa_I
III_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_minusCa_vs_III_T2_37_plusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_minusCa_vs_III_T2_37_minusCa.csv
III_T1_37_minusCa_vs_rnc_T2_37_minusCa.csv


title: YAP-MAML2_SPARK-OFF,DMSO,rep1


title: liver, fasting 8days, rep1


title: YAP-MAML2_SPARK-OFF,rapamycin,rep3


title: Y. pseudotuberculosis YP356, 37°C, time 1, replicate III

description:
rnc_T1_37_plusCa_III
III_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: 684_Tph1 KO_Input_R1


title: YAP-MAML2_SPARK-OFF,rapamycin,rep2


title: 684_Tph1 KO_Dual_R1


title: 14 day mock stroma enriched submandibular salivary gland replicate 2

city: Albany

first: Melinda

last: Larsen

state: NY

address: 1400 Washington Ave., LSRB 10

department: Dept. of Biological Science

institute: University at Albany, SUNY

description:
Mock_stroma_2
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v7.0.1 at the University at Albany Center for Functional Genomics.
Assembly: mm10
Supplementary files format and content: Cellranger filtered_feature_bc_matrix (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Submandibular Salivary Gland

extract_protocol:
Submandibular and sublingual glands were harvested, and excess fat and interstitial tissue was removed. The glands were then transferred to a dish containing 1X PBS, liberase TL Research Grade low Thermolysin (Roche), DNase I, and dispase and microdissected for 7-9 minutes. The sample was then incubated in a 37°C incubator for 15 minutes and triturated. After trituration, the sample was incubated for an additional 5 minutes in a 37°C incubator and triturated once more. A 15 mL conical tube was placed on ice and the entire sample was transferred to the conical tube and incubated for 10 minutes. The supernatant was isolated and transferred to a fresh conical tube and was centrifuged for 5 minutes at 450xg. The supernatant was removed and discarded, and the cell pellet was resuspended in isolation buffer composed of sterile-filtered Ca2+- and Mg2+-free 1X PBS, 0.1% bovine serum albumin, and 2mM ethylenediaminetetraacetic acid. 5 mg of EpCAM-A647 (catalog: 118212, BioLegend) and Ter119 (catalog: 50-133-27, eBioscience/ThermoFisher) was added to the cell suspension and incubated at 4°C for 10 minutes for depletion of epithelial and red blood cells, respectively. The cell suspension was washed using isolation buffer and centrifuged at 450xg for 5 minutes. The supernatant was discarded, and the cell pellet was resuspended in 1 mL of isolation buffer and 25 uL of sheep anti-rat Dynabeads, which bind to the EpCAM and Ter119 labeled cells, (catalog: 11035, Invitrogen) before incubating on ice for 20 minutes on a rocker. The sample was placed on a microcentrifuge magnet for 2 minutes, and the supernatant was transferred to a fresh microcentrifuge tube to remove labeled epithelial and red blood cells. An additional epithelial and red blood cell depletion was performed. The sample was then depleted of dead cells using a dead cell removal kit (catalog: 130-090-101, Miltenyi Biotec) following manufacturer’s instructions. Cells were counted and resuspended to a concentration of 1000 cells/mL. Following the manufacturer’s protocol for the Chromium Next GEM Single Cell 3’ Reagent kits v3.1, scRNAseq libraries were generated.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

treatment_protocol: Mice underwent either a 14 day ligation surgery, where a metal clip was applied to the main ducts of the submandibular and sublingual glands and remained in place for 14 days or mock surgery where the ducts were located without applying a clip.

value: Female

value: Submandibular Salivary Gland

value: Stromal Enriched

value: 14 day mock surgery


title: 14 day mock stroma enriched submandibular salivary gland replicate 3

description:
Mock_stroma_3
10X Genomics


title: Y. pseudotuberculosis YP356, 37°C, time 1, replicate II

description:
rnc_T1_37_plusCa_II
III_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: 676_Tph1 KO_K4_R1

value: placenta


title: liver, feeding 8days, rep1

value: feeding


title: YAP-MAML2_SPARK-OFF,rapamycin,rep1


title: 14 day mock stroma enriched submandibular salivary gland replicate 1

description:
Mock_stroma_1
10X Genomics


title: 676_Tph1 KO_Input_R1


title: Y. pseudotuberculosis YPIII , 37°C, time 1, replicate III

description:
III_T1_37_plusCa_III
III_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv

value: YPIII

value: wt


title: 676_Tph1 KO_Dual_R1


title: Colletotrichum camelliae △CcCp1 treated rep 3

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

description:
CPmZC3
2-year-old tea plant
Colletotrichum camelliae △CcCp1 treated sample 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Camellia sinensis var. sinensis GWHACFB00000000 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps. Prior to assembly, the low quality reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed. software CutAdapter, parameters -o 5 -p 100.
Read alignment software, software HISAT, version 2.0, parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9.
Perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie, version 1.3.0, parameters -b dta -q phred33-quals.
Assembly: Camellia sinensis var. sinensis GWHACFB00000000 (NGDC).
Supplementary files format and content: 4_genes_fpkm_expression.xlsx: Excel file includes counts and FPKM values for each Sample.

organism: Camellia sinensis

source_name: leaf

growth_protocol: The tea plant Zhongcha 108 were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark. The plants were watered once a week and kept growing for about 2 years.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. 10ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: The Colletotrichum camelliae CCA and △CcCp1 were grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the plant leaves were spray infected with 1*10^6 spores mL-1. The buffer without any spores were sprayed as untreated control (CKZC). All leaves were harvested at 24 hours and frozen at -80℃ for RNA sequencing.

value: leaf

tag: age

value: 2 years

tag: cultivar

value: Zhongcha 108

value: Colletotrichum camelliae <delta>CcCp1 infected


title: 674_Tph1 KO_K4_R1


title: Colletotrichum camelliae △CcCp1 treated rep 2

description:
CPmZC2
2-year-old tea plant
Colletotrichum camelliae △CcCp1 treated sample 2


title: Y. pseudotuberculosis YPIII , 37°C, time 1, replicate II

description:
III_T1_37_plusCa_II
III_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv

value: 37 degrees C growth in LB


title: TSBE3 EK +sgRNA 2

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

data_processing:
All the downstream analysis was based on clean data. Reads were aligned to the human hg38 reference genome using STAR (v.2.7.10b)83. Aligned BAMs were tag added and sorted with SAMtools (v.1.18). Duplication was removed using the Picard MarkDuplicates module (v.3.11) (https://github.com/broadinstitute/picard) and unmapped reads were filtered using SAMtools. BAMs were converted to mpileup format with SAM- tools, which records integrated mutation information. The significant mutation information was extracted based on mpileup files. The sites with coverage higher than 25, a mutation count of at least 6 and mutation ratios over 5% were subsequently collected as filtered sites.
Assembly: human hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HeLa

extract_protocol:
Trizal extract RNA
TruSeq PE Cluster Kit v3-cBot-HS (Illumina)

value: HeLa

value: TSBE3 EK +sgRNA


title: 674_Tph1 KO_Input_R1

value: Input


title: Y. pseudotuberculosis YPIII , 37°C, time 1, replicate I

description:
III_T1_37_plusCa_I
III_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_III_T1_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
III_T1_37_plusCa_vs_III_T2_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
III_T1_37_plusCa_vs_III_T2_37_minusCa.csv
III_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv


title: TSBE3 EK +sgRNA 1


title: 674_Tph1 KO_Dual_R1

value: Tph1 KO


title: Colletotrichum camelliae CCA treated rep 3

description:
CCZC3
2-year-old tea plant
Colletotrichum camelliae CCA treated sample 3

value: Colletotrichum camelliae CCA infected


title: TSBE3 EK +sgRNA 3


title: Y. pseudotuberculosis YP356, 37°C, time 1, replicate I

description:
rnc_T1_37_plusCa_I
III_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
III_T1_37_plusCa_vs_rnc_T1_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T1_37_minusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_plusCa.csv
rnc_T1_37_plusCa_vs_III_T2_37_minusCa.csv
rnc_T1_37_plusCa_vs_rnc_T2_37_minusCa.csv

value: delta_rnc (RNase III-deficient mutant)


title: CGBE-CDG +sgRNA 2

value: CGBE-CDG +sgRNA


title: Y. pseudotuberculosis YP356, 25°C, time 0, replicate III

description:
rnc_T0_25_III
III_T0_25_vs_rnc_T0_25.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv

value: 25 degrees C growth in LB


title: CGBE-CDG +sgRNA 1


title: Y. pseudotuberculosis YP356, 25°C, time 0, replicate I

description:
rnc_T0_25_I
III_T0_25_vs_rnc_T0_25.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv


title: Y. pseudotuberculosis YP356, 25°C, time 0, replicate II

description:
rnc_T0_25_II
III_T0_25_vs_rnc_T0_25.csv
rnc_T0_25_vs_III_T1_37_plusCa.csv
rnc_T0_25_vs_rnc_T1_37_plusCa.csv
rnc_T0_25_vs_III_T1_37_minusCa.csv
rnc_T0_25_vs_rnc_T1_37_minusCa.csv
rnc_T0_25_vs_III_T2_37_plusCa.csv
rnc_T0_25_vs_rnc_T2_37_plusCa.csv
rnc_T0_25_vs_III_T2_37_minusCa.csv
rnc_T0_25_vs_rnc_T2_37_minusCa.csv


title: Day 07

city: Omaha

first: Sankarasubramanian

last: Jagadesan

state: NE

address: 42end and Emile st

department: Department of Genetics, Cell Biology & Anatomy

institute: University of Nebraska Medical Center

description: 10X Genomics

data_processing:
Cell Ranger software v3.0.0 was used for basecalling, demultiplexing and initial analyses to create the single cell count matrix. cellranger mkfastq and cellranger count were used for this purpose with default parameters.
Assembly: mm10
Supplementary files format and content: Tab separated files and matrix files were created using cellrager count analysis

molecule: cytoplasmic RNA

source_name: infected joint tissue

growth_protocol: To model infectious complications following prosthetic joint surgery, a mouse model of S. aureus PJI was used. Mice were anesthetized using ketamine/xylazine prior to an initial incision made through the quadriceps. A secondary incision was then created to laterally displace the patellar tendon prior to generating a burr hole in the distal end of the femur using a 26-gauge needle. An orthopedic-grade nickel-titanium Kirschner wire (0.6 mm diameter; Custom Wire Technologies) was inserted through the burr hole into the medullary canal, whereupon 10^3 colony-forming units (CFUs) of S. aureus were inoculated at the tip of the wire. Slow-release Buprenex was administered subcutaneously following surgery to provide analgesia for 72 h. Mice were monitored daily to ensure normal ambulatory function and the lack of discernable pain behaviors.

extract_protocol: To recover CD45+ cells from the soft tissue surrounding the infected joint by FACS, tissue homogenates were filtered, and red blood cells (RBCs) were eliminated by rapid lysis in H2O, with isotonic conditions returned with the addition of 10X PBS. Next, cells were incubated with TruStain FcX (BioLegend) prior to staining with CD45-APC (RRID: AB_312977), Ly6G-PE (RRID: AB_1186099), CD11b-FITC (RRID: AB_312789), F4/80-PE-Cy7 (RRID: AB_893490), and Ly6C-PerCP-Cy 5.5 (Cat. #560525; BD). Dead cells were excluded from analysis using a Zombie UV fixable Live/Dead stain (Cat. #423108; BioLegend).

value: infected joint tissue

value: CD45+ cells


title: Day 14

description: 10X Genomics


title: 14 day ligated stroma enriched submandibular salivary gland

description:
Ligated_stroma_1
10X Genomics

value: Female

value: Submandibular Salivary Gland

value: Stromal Enriched

value: 14 day ligation surgery


title: Day 03

description: 10X Genomics


title: negative control 2

value: negative control


title: Colletotrichum camelliae △CcCp1 treated rep 1

description:
CPmZC1
2-year-old tea plant
Colletotrichum camelliae △CcCp1 treated sample 1

value: leaf

value: 2 years

value: Zhongcha 108

value: Colletotrichum camelliae <delta>CcCp1 infected


title: F333 uterus

city: Charleston

first: Joe

middle: R

last: Delaney

state: SC

address: 173 Ashley Avenue

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

data_processing:
RNA STAR
featureCounts
Assembly: mm10 (GRCm38.86)
Supplementary files format and content: transcript counts from featureCounts

source_name: F333 uterus

growth_protocol: Standard RPMI 1640, actively dividing cells

extract_protocol:
Qiagen RNeasy kit
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina with NEBNext Poly(A) mRNA Magnetic Isolation Module

value: F333 uterus

value: ovarian cancer


title: CK rep 2

description:
CKZC2
2-year-old tea plant
Uninfected control sample replicate 2

value: Uninfected (control)


title: CGBE-CDG +sgRNA 3

value: HeLa


title: Y. pseudotuberculosis YPIII , 25°C, time 0, replicate III

description:
III_T0_25_III
III_T0_25_vs_rnc_T0_25.csv
III_T0_25_vs_III_T1_37_plusCa.csv
III_T0_25_vs_rnc_T1_37_plusCa.csv
III_T0_25_vs_III_T1_37_minusCa.csv
III_T0_25_vs_rnc_T1_37_minusCa.csv
III_T0_25_vs_III_T2_37_plusCa.csv
III_T0_25_vs_rnc_T2_37_plusCa.csv
III_T0_25_vs_III_T2_37_minusCa.csv
III_T0_25_vs_rnc_T2_37_minusCa.csv

value: YPIII

value: wt


title: Y. pseudotuberculosis YPIII , 25°C, time 0, replicate I

description:
III_T0_25_I
III_T0_25_vs_rnc_T0_25.csv
III_T0_25_vs_III_T1_37_plusCa.csv
III_T0_25_vs_rnc_T1_37_plusCa.csv
III_T0_25_vs_III_T1_37_minusCa.csv
III_T0_25_vs_rnc_T1_37_minusCa.csv
III_T0_25_vs_III_T2_37_plusCa.csv
III_T0_25_vs_rnc_T2_37_plusCa.csv
III_T0_25_vs_III_T2_37_minusCa.csv
III_T0_25_vs_rnc_T2_37_minusCa.csv

value: 25 degrees C growth in LB


title: negative control 3


title: negative control 1


title: BG.LPS_KO-3

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence by SOAPnuke (BGI, Hongkong).
Reads were mapped and aligned with Hisat2 and counted using the R package Rsubread, featureCounts.
Then, differential expressed genes (DEGs) were compared and analyzed using the R package DESeq2.
Assembly: Mus musculus reference genome GRCm39.
Supplementary files format and content: normalized_counts_*.txt: Tab-delimited text files include normalized counts data for WT and MGMT KO (Rep.1-3) in the same condition.
Supplementary files format and content: *_DESeq.csv: Comma-separated text files include DESeq2 results.

source_name: Macrophages

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen).
RNA libraries for RNA-seq were prepared using DNBSEQ Eukaryotic Strand-specific mRNA library (BGI).

treatment_protocol: BMM were induced to be trained macrophages by priming with Pachyman B-glucan (Megazyme, USA) for 24 h. After resting for 48 h, BMMs were stimulated with E.coli LPS for 6 h.

value: Macrophages

value: MGMT KO


title: Colletotrichum camelliae CCA treated rep 1

description:
CCZC1
2-year-old tea plant
Colletotrichum camelliae CCA treated sample 1

value: Colletotrichum camelliae CCA infected


title: CK rep 1

description:
CKZC1
2-year-old tea plant
Uninfected control sample replicate 1


title: Colletotrichum camelliae CCA treated rep 2

description:
CCZC2
2-year-old tea plant
Colletotrichum camelliae CCA treated sample 2


title: F318 LOV

source_name: F318 LOV

value: F318 LOV


title: BG.LPS_KO-2


title: WM989 dabrafenib and trametinib then dabrafenib and trametinib treated, scRNA-seq

city: Philadelphia

first: Dylan

middle: L

last: Schaff

state: PA

address: 421 Curie Blvd, BRB II/II rm 445

department: Bioengineering

institute: University of Pennsylvania

description: 10X Genomics

data_processing:
Data was processed using CellRanger software 5.0.1 and reads were aligned to the hg38 assembly.
When count matrices were generated, sequencing reads from our custom clone barcodes were also linked with 10X cell barcodes.
Outputs from the filtered feature-barcode matrix were uploaded.
Assembly: hg38
Supplementary files format and content: *.matrix.mtx: Sparse count matrix
Supplementary files format and content: *.features.tsv: Tab-separated list of features (genes or clone) and identifiers for type of feature.
Supplementary files format and content: *.barcodes.tsv: 10X cell barcodes

source_name: Melanoma

extract_protocol:
Resistant cells were trypsinized and washed with PBS before following the 10X Genomics 3' v3.1 protocol to generate single cell emulsions with beads. We loaded cells with a goal of acquiring 10,000 cells per condition.
Library construction was performed following the 10X Genomics 3' v3.1 protocol. In brief, single cells were encapsulated into gel bead-in-emulsions (GEMs) using a chromium controller. PolyA RNA from each cell was reverse transcribed into cDNA. cDNA from all cells were pooled and cleaned up using Dynabeads before being PCR amplified and size selected using AMPure XP beads. Full-length cDNA was then fragmented before adding sequencing primers and indices and doing a final amplication. The final product was again cleaned using AMPure XP beads and sequenced.

value: Melanoma

value: BRAF V600E


title: Subject AA6, 2 weeks tofacitinib

city: Aurora

first: Matthew

middle: D

last: Galbraith

state: CO

department: Department of Pharmacology; Linda Crnic Institute for Down Syndrome

data_processing:
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
FASTQ files from two sequencing runs were merged to obtain ≥40x10^6 raw reads.
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (FPKM).

source_name: whole blood

extract_protocol:
Whole blood samples were collected into PAXgene Blood RNA Tubes (PreAnalytiX/Qiagen) and RNA purified using a PAXgene Blood RNA Kit (Qiagen). RNA quality was assessed using an Agilent 2200 TapeStation and quantified by Qubit (Life Technologies).
Globin RNA depletion, poly-A(+) RNA enrichment, and strand-specific library preparation were carried out using a Tecan Universal Plus mRNA-Seq with NuQuant, Hu Globin AnyDeplete kit (Cat #0521B-A0). Paired-end 150 bp sequencing was carried out on an Illumina NovaSeq 6000 instrument by the Genomics Shared Resource at the University of Colorado Anschutz Medical Campus.

treatment_protocol: Baseline followed by 5 mg of tofacitinib twice daily for 16 weeks.

value: whole blood

value: Trisomy 21

value: Male

tag: subject id

tag: qualifying condition

value: alopecia areata

value: 2 weeks tofacitinib


title: BG.LPS_KO-1


title: F318 ROV

source_name: F318 ROV

value: F318 ROV

value: ovarian cancer


title: WM989 dabrafenib and trametinib then CoCl2 treated, scRNA-seq

description: 10X Genomics

value: dabrafenib and trametinib then CoCl2


title: WM989 dabrafenib and trametinib then cisplatin treated, scRNA-seq

description: 10X Genomics


title: CK rep 3

description:
CKZC3
2-year-old tea plant
Uninfected control sample replicate 3

value: leaf

value: 2 years

value: Zhongcha 108

value: Uninfected (control)


title: F319 uterus

source_name: F319 uterus

value: F319 uterus


title: Subject AA6, 8 weeks tofacitinib

institute: University of Colorado Anschutz Medical Campus

value: 8 weeks tofacitinib


title: Subject AA6, 16 weeks tofacitinib

value: 16 weeks tofacitinib


title: Y. pseudotuberculosis YPIII , 25°C, time 0, replicate II

description:
III_T0_25_II
III_T0_25_vs_rnc_T0_25.csv
III_T0_25_vs_III_T1_37_plusCa.csv
III_T0_25_vs_rnc_T1_37_plusCa.csv
III_T0_25_vs_III_T1_37_minusCa.csv
III_T0_25_vs_rnc_T1_37_minusCa.csv
III_T0_25_vs_III_T2_37_plusCa.csv
III_T0_25_vs_rnc_T2_37_plusCa.csv
III_T0_25_vs_III_T2_37_minusCa.csv
III_T0_25_vs_rnc_T2_37_minusCa.csv

value: YPIII

value: wt

value: 25 degrees C growth in LB


title: Subject AA6, Baseline

value: whole blood

value: Trisomy 21

value: Baseline


title: BG.LPS_WT-3

value: Macrophages

value: WT


title: F339 ROV

source_name: F339 ROV

value: F339 ROV

value: ovarian cancer


title: F319 ROV

source_name: F319 ROV

value: F319 ROV


title: BG.LPS_WT-2


title: WM989 CoCl2 then dabrafenib and trametinib treated, scRNA-seq

description: 10X Genomics

value: Melanoma

value: BRAF V600E

value: CoCl2 then dabrafenib and trametinib


title: Subject AA5, 16 weeks tofacitinib

value: Female

value: alopecia areata


title: F361 peritoneal tumor

source_name: F361 peritoneal tumor

value: F361 peritoneal tumor


title: Subject AA5, 8 weeks tofacitinib

value: 8 weeks tofacitinib


title: WM989 CoCl2 then CoCl2 treated, scRNA-seq

description: 10X Genomics

value: CoCl2 then CoCl2


title: BG24_KO-3

value: MGMT KO


title: F326 ROV

source_name: F326 ROV

value: F326 ROV


title: WM989 CoCl2 then cisplatin treated, scRNA-seq

description: 10X Genomics

value: CoCl2 then cisplatin


title: Subject AA5, 2 weeks tofacitinib

value: whole blood

value: Trisomy 21

value: 2 weeks tofacitinib


title: F326 splenic tumor

source_name: F326 splenic tumor

value: F326 splenic tumor


title: BG24_KO-2

value: Macrophages


title: Subject AA5, Baseline

value: Baseline


title: WM989 cisplatin then dabrafenib and trametinib treated, scRNA-seq

description: 10X Genomics

value: Melanoma


title: WM989 cisplatin then CoCl2 treated, scRNA-seq

description: 10X Genomics

value: BRAF V600E

value: cisplatin then CoCl2


title: Subject AA4, 8 weeks tofacitinib

value: Male


title: WM989 cisplatin then cisplatin treated, scRNA-seq

description: 10X Genomics

value: cisplatin then cisplatin


title: F364 ROV

source_name: F364 ROV

value: F364 ROV

value: ovarian cancer


title: BG24_KO-1


title: Subject AA4, 2 weeks tofacitinib

value: alopecia areata


title: BG24_WT-3

value: WT


title: WM989 CoCl2 treated, scRNA-seq

description: 10X Genomics


title: R6/1 striatum rep3 [hd3st]

city: Alicante

first: Luis

middle: M

last: Valor

state: Alicante

address: Av. Pintor Baeza, 12

country: Spain

institute: ISABIAL

data_processing:
Base calling using Illumina CASAVA software
Removal of adapters (Illumina TruSeq v3) using Trimmomatic
Alignment to the genome of reference (EnsDb.Mmusculus.v79) using Salmon
Removal of Ensembl ID with read counts <10 in all samples
Assembly: GRCm38 (mm10)
Supplementary files format and content: tab-delimited text file with Ensembl ID and read counts for all samples

source_name: Striatum

growth_protocol: Standard animal housing conditions

extract_protocol:
Freshly dissected striata were submerged in RNAlater until processing using TRIzol reagent and further clean-up with Rneasy Mini columns, following manufacturers’ recommendations.
Libraries were prepared using Illumina standard protocols (TruSeq Strand mRNA kit)

treatment_protocol: No treatment

tag: strain background

value: 13-15 weeks

tag: gender

value: male

value: Striatum


title: R6/1 striatum rep2 [hd2st]

tag: tissue


title: Subject AA4, Baseline

value: whole blood

value: Trisomy 21

tag: Sex


title: BG24_WT-1

tag: genotype


title: R6/1 striatum rep1 [hd1st]


title: WM989 dabrafenib and trametinib treated, scRNA-seq

description: 10X Genomics

value: dabrafenib and trametinib


title: BG24_WT-2

value: Macrophages


title: BG.LPS_WT-1


title: F364 LOV

source_name: F364 LOV

value: F364 LOV


title: Subject AA4, 16 weeks tofacitinib

value: 16 weeks tofacitinib


title: Subject AA3, 16 weeks tofacitinib


title: unstim_KO-3

value: MGMT KO

value: unstimulated


title: wt striatum rep3 [wt3st]

value: wild type


title: 689_Sert KO_K4_R1

city: New York

first: Jennifer

last: Chan

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw peaks were aligned to the mm10 mouse genome using the NGS Data Charmer pipeline with default settings (HISAT v.0.1.6b)
Peak calling was performed using macs2 (v.2.1.1) on individual files with default settings
Differential peaks using Diffbind package (v3.8.4)
Assembly: mm10
Supplementary files format and content: macs2 narrowPeak .xls file
Supplementary files format and content: bigWig file

source_name: placenta

extract_protocol:
Chromatin from hemisected placental tissues were fixed with 1% formaldehyde rotated for 12 minutes at room temperature and was subsequently quenched using a final concentration of 125mM glycine. Samples were thoroughly homogenized and washed with ice cold PBS. Fixed chromatin was sonicated using a Covaris E220 for 30-60 minutes at 4°C with the following conditions: peak incident power, 140; duty factor, 10%; Cycles/burst, 200; Water level, 0. Equal amounts of chromatin per sample were rotated with select antibodies (2.5 μg antibody/sample of either H3K4me3Q5ser (MilliporeSigma ABE2580) or H3K4me3 (Active Motif 39159)) bound to M-280 Dynabeads at 4°C overnight. The next morning, samples were washed, eluted, and reverse-crosslinked at 65°C. Samples underwent RNA and protein digestion, and DNA was purified using QIAQuick MinElute Spin columns (Qiagen 28140). 1% inputs were removed prior to antibody incubation and purified in parallel with corresponding immunoprecipitates.
TruSeq ChIP Library Preparation Kit (Illumina IP-202-1012)

value: placenta

tag: developmental stage

value: Sert KO

tag: chip antibody


title: Subject AA3, 2 weeks tofacitinib

value: Male

value: 2 weeks tofacitinib


title: WM989 cisplatin treated, scRNA-seq

description: 10X Genomics

value: Melanoma

tag: cell type

value: BRAF V600E

value: cisplatin


title: unstim_KO-2


title: Subject AA3, Baseline

value: alopecia areata

value: Baseline


title: Subject HS3, 16 weeks tofacitinib

value: whole blood

value: Trisomy 21

value: Female

value: hidradenitis suppurativa


title: wt striatum rep2 [wt2st]

value: 13-15 weeks

value: male

value: Striatum


title: unstim_KO-1

value: Macrophages

value: MGMT KO

value: unstimulated


title: unstim_WT-3

value: WT


title: wt striatum rep1 [wt1st]

value: wild type


title: Subject HS3, 8 weeks tofacitinib

value: 8 weeks tofacitinib


title: R6/1 retina rep2 [hd2ret]

source_name: Retina

value: Retina


title: unstim_WT-2


title: R6/1 retina rep3 [hd3ret]


title: R6/1 retina rep1 [hd1ret]


title: unstim_WT-1


title: Subject HS3, Baseline


title: Subject AA2, 16 weeks tofacitinib

value: Male

value: 16 weeks tofacitinib


title: E12.5_282_M_placenta_RNAseq

data_processing:
Alignment using Kallisto v.0.46.1
Reduce variation using RUV-seq (k=4) v.1.32.0
Differential expression using DESeq2 v.1.38.3
Assembly: mm10
Supplementary files format and content: csv file with normalized counts containing all samples

source_name: Placenta

extract_protocol:
Homogenization of tissue in Trizol Reagent with subsequent clean-up using Rneasy Microcolumns.
TruSeq RNA Library Prep Kit v2 (Illumina RS-122-2001)

value: Placenta

value: M


title: wt retina rep2 [wt2ret]


title: E12.5_131_M_placenta_RNAseq


title: wt retina rep3 [wt3ret]


title: Subject AA2, 8 weeks tofacitinib

value: whole blood

value: Trisomy 21

value: alopecia areata


title: wt retina rep1 [wt1ret]

value: 13-15 weeks


title: E17.5_257_F_placenta_RNAseq

value: F


title: Subject AA2, 2 weeks tofacitinib

value: 2 weeks tofacitinib


title: EC109-SI-replicate3

type: RNA

city: Nanjing

first: LiWen

last: Hu

address: 305 East Zhongshan Road

institute: Jinling Hospital, Medical School of Nanjing University

description: siRNA interfering for lncRNA MALAT1 replicate 3

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scaned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: si-MALAT1 for ESCC cell line EC109

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using Ambion® WT Expression Kit. WT Expression Kit

extract_protocol: Total RNA was isolated from cells at indicated time point with Trizol.

value: ESCC EC109

tag: transfection


title: EC109-SI-replicate2

description: siRNA interfering for lncRNA MALAT1 replicate 2


title: E17.5_55_M_placenta_RNAseq

address: 1470 Madison Ave 9-201


title: P10 Area Postrema/NTS region

first: Allison

middle: W

last: Xu

state: Caliofrnia

address: 513 Parnassus Ave., HS Building. Room S1222

department: Diabetes Center

institute: University of California San Francisco

description: 10X Genomics

data_processing:
Raw sequencing reads were processed using the 10x Genomics Cell Ranger version 2.1 pipeline and aligned with default parameters. Performed by UCSF Genomics Core
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Area Postrema/NTS (Brain)

extract_protocol:
To identify the area postrema (AP) during microdissection, 50 µl of a 1% Evans Blue solution was administered transcardially to a male P10 mouse previously anesthetized with a single i.p injection of Avertin (250 mg/kg – Sigma-Aldrich #T48402). After 5 min, the mouse was decapitated, and the brain was dissected and placed into a petri dish with ice cold sterile 1X PBS under a dissecting microscope. After visually identifying the AP (in blue), the AP-centric region was microdissected and immediately dissociated into a single cell suspension. The dissociation was carried out according to Saxena et al (40) with volumes adjusted for tissue size. Briefly, the tissue was triturated and incubated with Papain-DNase1 solution using the Worthington Papain Dissociation System (#LK003150, Worthington, NJ) for 60 minutes at 37C with constant agitation. All components of the dissociation system were equilibrated with 95% O2: 5% CO2 before use. The tissue was then further triturated by pipetting until a homogenous cell suspension was observed. The suspension was then centrifugated and resuspended in 0.04% BSA
Library preparation was performed by the UCSF Genomics Core according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: Area Postrema/NTS (Brain)

tag: strain

value: Postnatal day 10


title: Subject AA2, Baseline

value: Baseline


title: EC109-SI-replicate1

description: siRNA interfering for lncRNA MALAT1 replicate 1


title: EC109-NC-replicate3

description: Negative control replicate3

source_name: Negative control for ESCC cell line EC109

value: negative control


title: E17.5_256_M_placenta_RNAseq

value: WT


title: Subject HS2, 16 weeks tofacitinib

source_name: whole blood

value: Female

value: hidradenitis suppurativa


title: EC109-NC-replicate2

description: Negative control replicate2


title: E17.5_54_F_placenta_RNAseq


title: E17.5_251_F_placenta_RNAseq


title: A3777_52

city: Beerse

first: Nádia

last: Conceição-Neto

address: Turnhoutseweg 30

country: Belgium

institute: Janssen R&D

description: mouse liver L2-4 treated with Blank_-1 days post treatment

hyb_protocol: After fragmentation and end-labeling, the targets are hybridized to a multi-sample Clariom S plate array on a GeneTitan Multi-Channel Instrument (Thermo Fisher Scientific).

data_processing: Gene expression values were normalized by robust multiarray average normalization on the microarray probe-level data

source_name: Liver

label_protocol: Transcriptome analysis was done using the Mouse Clariom S Assay (Thermo Fisher Scientific, 902930), in combination with the GeneChip WT PLUS Reagent kit (Thermo Fisher Scientific, 902280).

extract_protocol: RNA extraction on a QiaSymphony liquid handling system using the QIAsymphony RNA extraction kit

tag: agent

value: Blank

tag: time point

value: -1 days post treatment


title: myoblast_12h-#3

city: La Jolla

first: LEI

last: SHI

address: 10010 N Torrey Pines  Rd, GEL-B

institute: Salk Institute for Biological Studies

data_processing:
Illumina  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38(https://www.gencodegenes.org/mouse/)
Fragments per kilobase of transcript per million mapped fragments (FPKM) were calculated. First step, align RNA seq reads to the genome by using  Hista2 ; and then Cufflinks will assemble transcripts and computed the FPKM vlues(http://cufflinks.cbcb.umd.edu/),following protocol from Pertea, M.et al  Nat Protoc 11, 1650-1667, (2016).
Genome_build: GRCm38(https://www.gencodegenes.org/mouse/)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample ...

source_name: myoblast C2C12

growth_protocol: Myoblasts C2C12 were purchased from ATCC (CRL 1772) and cultured in an undifferentiated state to up to approximately 50% confluency. Myoblast medium contains: DMEM supplemented with 20% heat-inactivated FBS. Cells were split after onetime PBS wash using TrypLE according to growth status.

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For differentiation, cultures were split into 15 cm dishes, allowed to become fully confluent, washed twice with PBS, and the above Myoblast medium was replaced by Myofiber differentiation media composed by DMEM with 0.5% heatinactivated FBS. Cell morphology was monitored using an IX51 inverted microscope (Olympus).

tag: cell line

value: myoblast cell line C2C12

tag: differentiation time point


title: myoblast_12h-#1


title: Subject HS2, 2 weeks tofacitinib

value: whole blood

tag: treatment


title: myoblast_12h-#2


title: myoblast_9h-#3


title: A3777_06

description: mouse liver L3-4 treated with Blank_-1 days post treatment

scan_protocol: on a GeneTitan Multi-Channel Instrument (Thermo Fisher Scientific).


title: Subject HS2, Baseline

value: Trisomy 21

tag: subject id


title: A3777_47

description: mouse liver L1-4 treated with Blank_-1 days post treatment


title: E17.5_250_M_placenta_RNAseq

value: Placenta

value: M


title: Subject Ps1, 16 weeks tofacitinib

value: Male

tag: qualifying condition

value: psoriasis

value: 16 weeks tofacitinib


title: myoblast_9h-#2


title: A3777_30

description: mouse liver L91-4 treated with Compound JNJ-A_28 days post treatment

value: Compound JNJ-A

value: 28 days post treatment


title: Subject HS2, 8 weeks tofacitinib

value: 8 weeks tofacitinib


title: myoblast_9h-#1


title: Subject Ps1, 8 weeks tofacitinib


title: E17.5_25_F_placenta_RNAseq

value: F


title: EC109-NC-replicate1

description: Negative control replicate1

value: ESCC EC109

value: negative control


title: A3777_75

description: mouse liver L92-4 treated with Compound JNJ-A_28 days post treatment


title: A3777_56

description: mouse liver L87-4 treated with Compound JNJ-A_24 days post treatment

value: 24 days post treatment


title: myoblast_6h-#3


title: E17.5_26_M_placenta_RNAseq

value: WT


title: E9.5_266_F_placenta_RNAseq


title: Subject Ps1, 2 weeks tofacitinib

value: 2 weeks tofacitinib


title: Subject Ps1, Baseline

value: Baseline


title: E9.5_181_F_placenta_RNAseq


title: E9.5_265_M_placenta_RNAseq


title: myoblast_6h-#1

value: myoblast cell line C2C12


title: A3777_38

description: mouse liver L85-4 treated with Compound JNJ-A_24 days post treatment


title: Subject AA1, 16 weeks tofacitinib

value: whole blood

value: Trisomy 21

value: alopecia areata


title: Subject AA1, 8 weeks tofacitinib

value: Male


title: E9.5_180_M_placenta_RNAseq

value: Placenta

value: M


title: A3777_43

description: mouse liver L86-4 treated with Compound JNJ-A_24 days post treatment

value: Compound JNJ-A


title: A3777_28

description: mouse liver L93-4 treated with Compound JNJ-A_28 days post treatment

value: 28 days post treatment


title: Subject AA1, 2 weeks tofacitinib


title: E9.5_194_M_placenta_RNAseq


title: myoblast_3h-#1


title: myoblast_3h-#2


title: E9.5_163_F_placenta_RNAseq


title: Subject AA1, Baseline


title: myoblast_6h-#2


title: Subject HS3, 2 weeks tofacitinib

value: Female

value: hidradenitis suppurativa


title: E9.5_193_F_placenta_RNAseq

value: F


title: A3777_57

description: mouse liver L81-4 treated with Compound JNJ-A_23 days post treatment

value: 23 days post treatment


title: myoblast_0h-#3


title: Subject HS1, 16 weeks tofacitinib

value: 16 weeks tofacitinib


title: A3777_31

description: mouse liver L75-4 treated with Compound JNJ-A_22 days post treatment

value: 22 days post treatment


title: myoblast_0h-#2


title: A3777_44

description: mouse liver L74-4 treated with Compound JNJ-A_22 days post treatment


title: myoblast_3h-#3


title: Subject HS1, 8 weeks tofacitinib

value: 8 weeks tofacitinib


title: E9.5_162_M_placenta_RNAseq

value: WT


title: A3777_83

description: mouse liver L80-4 treated with Compound JNJ-A_23 days post treatment


title: Subject HS1, 2 weeks tofacitinib

value: 2 weeks tofacitinib


title: A3777_29

description: mouse liver L79-4 treated with Compound JNJ-A_23 days post treatment


title: Subject HS1, Baseline

value: whole blood

value: Baseline


title: A3777_10

description: mouse liver L68-4 treated with Compound JNJ-A_21 days post treatment

value: 21 days post treatment


title: A3777_48

description: mouse liver L67-4 treated with Compound JNJ-A_21 days post treatment


title: A3777_84

description: mouse liver L63-4 treated with Compound JNJ-A_18 days post treatment

value: 18 days post treatment


title: E12.5_291_M_placenta_RNAseq

value: Placenta


title: myoblast_0h-#1

value: myoblast cell line C2C12


title: Sample 11-P

city: Shanghai

first: Qingtong

last: Zhou

address: No. 138 Yixueyuan Road

department: School of Basic Medical Sciences

institute: Fudan University

description: 10 x genomics

data_processing:
The demultiplexing ,barcoded processing, gene counting and aggregation were performed in Cellranger 6.0.2
Supplementary files format and content: Tab-separated values files and matrix files

source_name: BCLM (P),  replicate 1, scRNA-seq

extract_protocol:
Tissues were transported in MACS tissue storage solution (Miltenyi Biotec) on ice within 40 min to preserve viability. Samples were rinsed with ice-cold PBS, minced on ice to pieces of less than 1 mm3 and then enzymatically dissociated for 15 min for metastatic liver tumor samples and 10 min for control liver samples at 37°C (with manual shaking every 5 min). Dissociation was carried out in DMEM containing 2 mg/mL collagenase P (Roche) and 0.2 mg/mL DNase I (Roche) as digestion medium for the tumor tissues. Collagenase III (1 mg/mL, Sigma-Aldrich) and hyaluronidase (0.1 mg/mL, Sigma-Aldrich) were additionally introduced to the digestion medium containing metastatic cancer samples to increase cell viability. The digestion suspension was then filtered using a 40 μm nylon cell strainer (Falcon), followed by centrifugation at 300× g and 4°C for 5 min. The cell pellet was resuspended in red blood cell lysis buffer (Sigma-Aldrich) for 5 min at room temperature to remove red blood cells. Samples were centrifuged (250× g, 4°C, 5 min) and resuspended in 200-500 μL (estimated) PBS containing 0.4% BSA (Sigma-Aldrich) and filtered through 40 μm cell strainers. Finally, the concentration and viability of single-cell suspension were checked by a LUNA automated cell counter (Logos Biosystems), and the cells were diluted with PBS containing 0.04% BSA to about 700-1,200 cells/μL
The single cells were loaded (aiming at 5,000 cells/sample for each chip position) onto and barcoded with a 10× Chromium Controller (10× Genomics) followed by library construction for scRNA-seq using the Chromium Single Cell 5′ Library and Gel Bead kit (V1.1) from 10× Genomics according to the manufacturer’s instructions. The 5’ gene expression libraries were sequenced on a NovaSeq 6000 system (Illumina) until sufficient saturation was reached (77.03% on average)

value: adjacent nonmalignant tissues, breast cancer

value: T Cell

tag: age


title: E12.5_243_F_placenta_RNAseq


title: MIM-Astrocytes_rep1

source_name: MIM-Astrocytes

growth_protocol: NSCs were derived from murine embryonic cortex at 14.5 embryonic days (vaginal plug considered 0.5 days). Single cell suspension was maintained in Neurobasal medium supplemented with 1X B27 and 20ng/mL of rh-EGF and h-FGF2. Primary neurospheres appeared after 6 days of culture and were used only during the first 3 passages. Cultures for NSCs were seeded at 200,000 cell/mL and maintained on standard conditions.Astrocyte cultures. Astrocytes were derived from cortical tissues postnatal or differentiated from dissociated neurospheres after a second or third passage, as described ahead. For postnatal astrocytes, cortices were isolated from P4 mice pups to get single cells and were plated as described by Schildge et al., (2013). After getting confluence the cultures were sorted with Anti-GLAST (ACSA-1) Microbead kit according manufacturer instructions. For inducing differentiation from NSCs, single cells derived from neurospheres were exposed to astrocyte media. In both cases, cells were plated over pre-treated Poly-L-Lysine plates or Poly-D-Lysine glass-coverslips using Astrocyte Differentiation Medium composed by DMEM-F12 with 10% heat inactivated FBS, 1X B27, and 1X Glutamax. Media was replaced every other day until reach a mature astrocytic phenotype corroborated by immunocytochemistry.  Neuronal cultures. Primary neurons were obtained from the cortex of E14.5 ICR mice brains. Brain dissection was performed in a cold solution of 2% glucose in PBS. Then, tissue was trypsinized and the suspension was transferred across a 40μm cell strainer to get a single cell suspension. Cells were plated in a ratio of 800,000 cells per each 22 mm poly-D-lysine coverslip with Neuron differentiation medium containing: Neurobasal media supplemented 1X B27 and 1X Glutamax. Cultures were maintained on standard conditions. Half volume of culture media was replaced every other day. In previous studies (Suzuki et al., 2016 and 2019), we tracked the disappearance of the proliferative neuronal progenitors present in the primary culture by 10μM EdU-pulses every day after plating and we found that 5 days after culture, the percentage of EdU+ cells was reduced to basal levels. We consider neurons at this time point as post-mitotic.  Primary cell cultures of adult brain tissues. Cerebella from 18.5 months old adults were dissociated and trypsinized and the cell suspension derived was filtered across 70μm cell strainer. Cells were plated in dishes coated with poly-L-lysine using Astrocyte Differentiation Media, as described for astrocyte cultures. Cells were passaged when they reached confluence of 90-100 % in a 1:3 ratio. Cultures were used at the passage 4 to 9.  Glioblastoma culture. Tumor cells obtained from mouse glioblastoma multiforme–like tumors (mice ID 005) were kindly donated by Mark Schmitt (Marumoto et al., 2009). The cells were grown in DMEM supplemented with 1X N2, 20ng/mL rhEGF, 20ng/uL FGF2. Cultures were maintained on standard conditions.

treatment_protocol: Cell cultures seeded on adherent conditions were kept on their respective differentiation media until reach a mature phenotype. When cultures reached 80-90% confluence, the differentiation media was removed, cells were washed twice with PBS and the media was replaced with MIM. In all cases, from the same batch of each cell culture, a control culture was also washed with PBS but maintained with their own differentiation media along all the time of the treatment. Cells in this schema, were fed every other day. The composition of MIM includes up to 6 metabolites (details of the combinations used are specified in figure legends) including Methionine, Threonine, Glycine, Putrescine, S-adenosylmethionine and Cysteine, which are dissolved in a base medium (BM) composed by DMEM-F12 plus Neurobasal in ratio 1:1, supplemented with 1X B27, 1X N2. Due to the absence of serum, either the growth factor FGF2 (20ng/mL) or reduced concentrations of serum, were used according cell type (FGF2 was added in cultures of chondrocytes, astrocytes, neurons; while it didn’t support the viability in myoblasts, where 2% of serum was used instead. Similarly, in human fibroblasts the reduction of serum was enough without any added cytokine to keep viable cultures). Cells were daily monitored to attest the change on morphology. In all cases, cells were collected on or before the fifth day after starting the MIM treatment (indicated in each specific case in the figure legend) for further analyses. Viability of cultures before at the time of collection was measured by trypan blue, and all cases above 85% viable cells were processed.

value: cortex


title: E12.5_242_M_placenta_RNAseq

value: M


title: MIM-Astrocytes_rep2


title: E12.5_283_F_placenta_RNAseq

value: F


title: Sample 11-T

description: 10 x genomics

source_name: BCLM (T),  replicate 1, scRNA-seq

value: metastatic tumor in the liver, breast cancer

value: Female


title: A3777_18

description: mouse liver L69-4 treated with Compound JNJ-A_21 days post treatment

value: Compound JNJ-A


title: MIM-Astrocytes_rep3


title: Astrocytes_rep2

source_name: Astrocytes


title: E12.5_132_F_placenta_RNAseq


title: A3777_12

description: mouse liver L62-4 treated with Compound JNJ-A_18 days post treatment


title: Sample 10-T

description: 10 x genomics

source_name: CCLM (T),  replicate 1, scRNA-seq

value: metastatic tumor in the liver, cervical carcinoma


title: A3777_89

description: mouse liver L61-4 treated with Compound JNJ-A_18 days post treatment


title: E12.5_292_F_placenta_RNAseq

value: WT


title: PC9OR ZNF2631

first: Jiaqi

last: Liang

address: 180 Fenglin Road

institute: Zhongshan Hospital Fudan University

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCh38.p13
Supplementary files format and content: FPKM

source_name: Tumor

extract_protocol:
RNA was harvested using TRIZOL
RNA libararies for RNA-seq were prepared using SMARTER mRNA-seq Library Kit

value: Tumor

value: NSCLC cell

value: ZNF263 overexpressed


title: E17.5M_55_Dual

value: placenta


title: Astrocytes_rep3


title: Sample 9-P

description: 10 x genomics


title: NSC_rep3

source_name: Neural Stem Cell


title: NSC_rep2


title: A3777_17

description: mouse liver L56-4 treated with Compound JNJ-A_16 days post treatment

value: 16 days post treatment


title: E17.5M_26_Dual


title: Sample 8-P

description: 10 x genomics


title: A3777_23

description: mouse liver L55-4 treated with Compound JNJ-A_16 days post treatment


title: NSC_rep1


title: A3777_05

description: mouse liver L57-4 treated with Compound JNJ-A_16 days post treatment


title: Glioblastoma_rep3

source_name: Glioblastoma

value: Cerebella


title: E9.5F_163_Dual

source_name: placenta


title: Sample 10-P

description: 10 x genomics

source_name: CCLM (P),  replicate 1, scRNA-seq

value: adjacent nonmalignant tissues, cervical carcinoma


title: Sample 8-T

description: 10 x genomics


title: Glioblastoma_rep2


title: A3777_70

description: mouse liver L51-4 treated with Compound JNJ-A_14 days post treatment

value: 14 days post treatment


title: A3777_88

description: mouse liver L73-4 treated with Compound JNJ-A_22 days post treatment

value: 22 days post treatment


title: E9.5F_181_Dual


title: E9.5M_162_Dual


title: E17.5F_54_Dual


title: Sample 9-T

description: 10 x genomics

value: T Cell


title: Sample 7-T

description: 10 x genomics

source_name: NCLM (T),  replicate 1, scRNA-seq

value: metastatic tumor in the liver, nasopharyngeal carcinoma


title: Glioblastoma_rep1


title: A3777_24

description: mouse liver L50-4 treated with Compound JNJ-A_14 days post treatment


title: E9.5M_180_Dual

value: M


title: A3777_68

description: mouse liver L49-4 treated with Compound JNJ-A_14 days post treatment


title: Sample 6-P

description: 10 x genomics

value: adjacent nonmalignant tissues, breast cancer


title: Sample 7-P

description: 10 x genomics

source_name: NCLM (P),  replicate 1, scRNA-seq

value: adjacent nonmalignant tissues, nasopharyngeal carcinoma

value: Female


title: Sample 6-T

description: 10 x genomics

value: metastatic tumor in the liver, breast cancer


title: A3777_53

description: mouse liver L43-4 treated with Compound JNJ-A_13 days post treatment

value: Compound JNJ-A

value: 13 days post treatment


title: CAR_9

type: protein

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Strasse 53

department: Inner Medicine 1

description: Protein lysates with still active kinases, phosphorylation of spotted peptides on chip detected with FITC labeled anti-phospho antibody

hyb_protocol: 5 μg of protein per well was loaded onto the PamChip and the assay was run on a PamStation96 (PamGene International).

scan_protocol: The degree of phosphorylation was measured in real time via the kinetic image capture program, Evolve (PamGene International)   Following 60 min incubation, the signal intensities for each peptide were analyzed using BioNavigator Software (PamGene International).

data_processing: Only peptides that showed kinetics (increase of signal in time) on at least 25 % of the arrays were included in the analysis. Nominal coefficient of variation (CV) was calculated per peptide using a 2-component error fit model using overall mean as input and was used as a filter to remove low-intensity spots. Only peptides that showed nominal CV <0.5 were included in the analysis. For kinase interpretation, a ranked list of putative kinases responsible for differences in the peptide phosphorylation was generated by upstream kinase analysis (UKA, PamGene International).

label: PY20 FITC

molecule: protein

source_name: Microglia isolated from CD19 CAR group

label_protocol: We used the STK PamGene Array according to instructions

growth_protocol: B-NHL cells were maintained in DMEM complete media with 10% FCS and Penstrip

extract_protocol: PamGene lysates were prepared according to manufacturers instructions with M-PER Mammalian Protein Extraction Reagent (ThermoFisher) containing Halt phosphatase and Halt protease inhibitor cocktails (ThermoFisher). Total protein was quantified using the Pierce BCA Protein Assay Kit (ThermoFisher).

treatment_protocol: 100000 B-NHL (A20) cells were injected iv to sublethally irradiated mice. On day 7, 10 Million CD19 CAR T cells were injected iv and mice were sacrificed on day 10. Brain was isolated and FACS sorted for microglia (CD45lo and CD11b) cells.

value: Microglia

value: Brain


title: A3777_08

description: mouse liver L44-4 treated with Compound JNJ-A_13 days post treatment


title: E12.5M_131_Dual

value: placenta

value: WT


title: CAR_7


title: Sample 5-P

description: 10 x genomics


title: E12.5F_79_Dual

value: F


title: CAR_5


title: A3777_50

description: mouse liver L39-4 treated with Compound JNJ-A_12 days post treatment

value: 12 days post treatment


title: A3777_76

description: mouse liver L45-4 treated with Compound JNJ-A_13 days post treatment


title: A3777_82

description: mouse liver L38-4 treated with Compound JNJ-A_12 days post treatment


title: Sample 4-P

description: 10 x genomics


title: CAR_3


title: E12.5M_78_Dual


title: Sample 4-T

description: 10 x genomics


title: E17.5F_25_Dual


title: E12.5F_132_Dual


title: E17.5M_55_Input

value: Input


title: NT_8

source_name: Microglia isolated from NT group


title: E17.5F_54_Input


title: NT_6


title: Astrocytes_rep1

value: cortex


title: Sample 3-T

description: 10 x genomics

source_name: TCLM (T),  replicate 1, scRNA-seq

value: metastatic tumor in the liver, thyroid carcinoma

value: T Cell

value: Male


title: Sample 3-P

description: 10 x genomics

source_name: TCLM (P),  replicate 1, scRNA-seq

value: adjacent nonmalignant tissues, thyroid carcinoma


title: A3777_80

description: mouse liver L37-4 treated with Compound JNJ-A_12 days post treatment

source_name: Liver


title: Sample 5-T

description: 10 x genomics


title: NT_5


title: E17.5M_26_Input

value: M


title: A3777_79

description: mouse liver L33-4 treated with Compound JNJ-A_11 days post treatment

value: 11 days post treatment


title: Sample 2-P

description: 10 x genomics

value: adjacent nonmalignant tissues, nasopharyngeal carcinoma


title: A3777_34

description: mouse liver L31-4 treated with Compound JNJ-A_11 days post treatment

value: Compound JNJ-A


title: Sample 2-T

description: 10 x genomics

value: metastatic tumor in the liver, nasopharyngeal carcinoma


title: E9.5F_163_Input


title: A3777_35

description: mouse liver L27-4 treated with Compound JNJ-A_10 days post treatment

value: 10 days post treatment


title: NT_3

value: Microglia

value: Brain


title: NT_1


title: A3777_87

description: mouse liver L26-4 treated with Compound JNJ-A_10 days post treatment


title: Sample 1-P

description: 10 x genomics


title: E9.5F_181_Input

value: placenta

value: WT


title: A3777_14

description: mouse liver L32-4 treated with Compound JNJ-A_11 days post treatment


title: E9.5M_162_Input


title: Sample 1-T

description: 10 x genomics


title: A3777_22

description: mouse liver L25-4 treated with Compound JNJ-A_10 days post treatment


title: M-CSF-NaCl_3

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Base calling and de-multipexing using CASAVA version 1.8.2.
The 75 bp single-end reads were trimmed using fastp v0.20.0 and aligned to the murine reference genome mm10 vM32 from GENCODE using STAR v2.7.10b with --quantMode GeneCounts.
Aligned reads sorted by coordinates were indexed using samtools v1.16.1.
Downstream data analysis was performed in R version 4.3.1 mainly using the R package DESeq2 version 1.40.2
Assembly: mm10 vM32
Supplementary files format and content: DESeq2_normalized_annotated_expression.csv: comma-separated files holding normalized and annotated expression values
Supplementary files format and content: raw_expression.csv: comma-separated files holding unnormalized and unfiltered expression values

source_name: BMDM

growth_protocol: Bone marrow was isolated from Cx3cr1GFP mice (C57BL/6J background, Jackson #000664). 10x106 cells were cultured in VLE-RPMI 1640 medium (Art.No. F 1415, Biochrom) containing 10 % FCS (Sigma), 1% Pen/Strep (PAA), and 10 ng/ml M-CSF (Peprotech). After seven days of culturing, half of the supernatant including the floating cells was discarded and fresh medium was added.

extract_protocol:
RNA was isolated with Qiazol and miRNeasy micro kit (Qiagen) according to the manufacturer’s protocol.
Library construction was performed according to the manufacturer´s instructions using the Tru-Seq RNA library preparation kit v2. 100 ng of RNA was converted into cDNA libraries

treatment_protocol: The cells were treated with 62mM NaCl for 24 h. Floating cells were discarded and adherent cells were detached by application of 2 mM EDTA in PBS and used for RNA sequencing.

value: BMDM

tag: mouse

value: NaCl


title: M-CSF-NaCl_1


title: M-CSF-NaCl_2


title: E9.5M_180_Input

tag: tissue

value: Input


title: CONTROL_LPS#2

city: Ann Arbor

first: Sascha

last: Goonewardena

state: Michigan

address: 1500 E Medical Center Dr

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
RNA was sequenced using Illumina NextSeq (HO) 150 cycle Sequencing.
Trimmed using Trim_Galore (v 0.5.0)
Aligned using STAR (v 2.6.0)
UMI collapsed using Lexogen’s supplied collapse_UMI_bam binary.
Reference and Annotation: GRCh38 from ENSEMBL
Assembly: GRCh38 from ENSEMBL
Supplementary files format and content: tab delimited text file of Raw counts of each smples  Generated using Bioconductor R package Rsubread and featureCounts function
Supplementary files format and content: tab delimited text file of counts per million of each smples

source_name: Blood

extract_protocol:
Cells were lysed with RLT Plus Buffer (QIAGEN, Cat. No. 1053393)followed by RNA purifcationusing RNeasy Plus Micro Kit (QIAGEN, Cat. No. 74034) according to manufacturer’s protocol.
RNA-seq libraries were prepared using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen; Cat. No. 015) with the UMI add-on kit.

treatment_protocol: PBMC from severe COVID-19 subjects (n = 3) and age-matched controls (n = 3) and stimulated them with the TLR4 ligand LPS (1 ug /ml for 2 hours).TLR ligand (LPS) were obtained from InvivoGen

value: Blood

value: peripheral blood mononuclear cells

tag: group

tag: infection

value: control

value: TLR4 ligand LPS (1 microgram /ml for 2 hours)


title: E12.5F_132_Input

state: New York

tag: developmental stage

tag: Sex

value: F

tag: genotype


title: M-CSF-unstim_2

tag: cell type

value: unstim


title: A3777_36

description: mouse liver L21-4 treated with Compound JNJ-A_9 days post treatment

value: 9 days post treatment


title: CONTROL_NT#2

value: No treatment


title: A3777_71

description: mouse liver L15-4 treated with Compound JNJ-A_8 days post treatment

value: Compound JNJ-A

value: 8 days post treatment


title: A3777_20

description: mouse liver L19-4 treated with Compound JNJ-A_9 days post treatment


title: CONTROL_LPS#3


title: A3777_51

description: mouse liver L14-4 treated with Compound JNJ-A_8 days post treatment


title: COVID-19_LPS#1


title: E12.5F_79_Input

tag: chip antibody


title: E12.5M_78_Input

value: M


title: M-CSF-unstim_1

tag: strain


title: M-CSF-unstim_3


title: COVID-19_LPS#2


title: E12.5F_65_Input


title: E12.5M_131_Input


title: E17.5F_25_Input


title: E17.5M_44_Input


title: CONTROL_NT#3


title: E17.5M_36_Input


title: CONTROL_LPS#1


title: EC109-SI-replicate1

description: siRNA interfering for lncRNA MALAT1 replicate 1

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on GeneChip Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: si-MALAT1 for ESCC cell line EC109

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix)

extract_protocol: Extraction of cells，then total RNA was extracted using a miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: ESCC EC109

tag: transfection


title: A3777_90

description: mouse liver L90-4 treated with Vehicle_28 days post treatment

tag: agent

value: Vehicle

tag: time point

value: 28 days post treatment


title: COVID-19_NT#1

tag: treatment


title: EC109-NC-replicate2

description: Negative control replicate2

source_name: Negative control for ESCC cell line EC109

value: negative control


title: A3777_42

description: mouse liver L89-4 treated with Vehicle_28 days post treatment


title: EC109-NC-replicate3

description: Negative control replicate3


title: A3777_58

description: mouse liver L13-4 treated with Compound JNJ-A_8 days post treatment


title: EC109-SI-replicate3

description: siRNA interfering for lncRNA MALAT1 replicate 3


title: A3777_85

description: mouse liver L9-4 treated with Compound JNJ-A_7 days post treatment

value: 7 days post treatment


title: E17.5F_34_Input

value: placenta

value: WT

value: Input


title: A3777_49

description: mouse liver L88-4 treated with Vehicle_28 days post treatment


title: COVID-19_NT#2

value: Blood

value: peripheral blood mononuclear cells


title: A3777_13

description: mouse liver L8-4 treated with Compound JNJ-A_7 days post treatment


title: HUVEC_shAmotL2_rep6

city: Stockholm

first: Lars

last: Holmgren

state: Stockholm

address: Solnavägen 30

department: Oncology Pathology

country: Sweden

institute: Karolinska Institute

description:
Data S1 HUVEC_shAmotL2_vs_V_shScr_peak_compare_table.tsv
Data S2 HUVEC_shAmotL2_vs_shScr_down_peak_related_genes.txt

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ ≥ 13), non-mitochondrial chromosome, and properly paired reads (longer than 18 nt). All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel -- keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering. distribution of peak over various functional areas is analysed by ChIPseeker software.
Assembly: hg38
Supplementary files format and content: BigWig
Supplementary files format and content: *peak_compare_table (Data S1)
Supplementary files format and content: The first four columns refer to peak information
Supplementary files format and content: (1) Chromosome
Supplementary files format and content: (2) PeakStart
Supplementary files format and content: (3) PeakEnd
Supplementary files format and content: (4) oriSummitPos
Supplementary files format and content: (N) Count_*The number of reads to the peak was compared in each sample
Supplementary files format and content: (N) RPM_*   The proportion of 1M reads in each sample in peak
Supplementary files format and content: (N) FoldEnrich_*Enrichment of reads in each experimental group
Supplementary files format and content: (N) log2foldchange  log2?fold enrichment?
Supplementary files format and content: (N) In_*  Whether as the peak of this experiment
Supplementary files format and content: (N) Distance   Distance between peak and TSS
Supplementary files format and content: The five columns are information about the genes closest to TSS
Supplementary files format and content: (N) GeneStart
Supplementary files format and content: (N) GeneEnd
Supplementary files format and content: (N) ClosestTSS_ID
Supplementary files format and content: (N) Symbol
Supplementary files format and content: (N) Strand
Supplementary files format and content: Data S2 - peak related genelist

source_name: Endothelial

growth_protocol: Human umbilical vein endothelial cells (HUVEC, Promocell, Heidelberg, Germany) were cultured in Endothelial cell medium (ECM; ScienCell) supplemented with 5% foetal calf serum (FCS) (v/v), 1% endothelial cell growth supplement (ECGS) and 1% Pen/Strep antibiotic cocktail and were cultured on 0.2% gelatin (Sigma-Aldrich) (w/v in PBS)-coated plates. Human umbilical arterial endothelial cells (HUAEC, Promocell, Heidelberg, Germany)) were cultured as above in endothelial cell basal medium (ECBM) MV medium (Promocell) supplemented with 2% foetal calf serum (FCS) (v/v), 0.4% Endothelial Cell Growth Supplement, 0.1 ng/ml epidermal growth factor (recombinant human), 1 ng/ml basic fibroblast growth factor (recombinant human), 90 μg/ml heparin and 1 μg/ml hydrocortisone. Both HUVEC and HUAEC were grown to passage 4 or 5.

extract_protocol:
Using the ATAC-seq library preparation ATAC-seq library preparation kit (ActiveMotif) HUVEC and HUAEC cells were transduced with shScr and shAmotL2 for 72 h before cells were trypsinised and counted using Trypan blue. 100,000 cells were centrifuged, and nuclei was extracted using ice-cold ATAC-lysis buffer (according to the kit protocol; Active Motif) and the pellet resuspended in the Tn5 tagmentation master mix. The transposition reaction was incubated at 37°C for 30 min at 800 rpm using a thermomixer. Tagmented DNA was purified according to the protocol’s column purification step.
Tagmented DNA was purified according to the protocol’s column purification step, followed by PCR amplification of tagmented DNA for 10 cylces using Illumina’s Nextera indexed adapters.  After the PCR reaction, libraries were purified with the SPRI magnetic beads and library quality, and concentration was assessed with Qubit bioanalyzer. 4 independent experiments were prepared for ATAC-seq for both HUVEC and HUAEC, resulting in 16 libraries in total. Libraries were then sequenced with the Illumina Hiseq platform with a 150bp paired-end repeats protocol.

treatment_protocol: Lentiviral supernatants were produced in HEK293T cells following transfection using Lipofectamine 3000 (Invitrogen) transfection agent with 3rd generation packaging plasmids and either shScr (SHC332; Sigma), shAmotL2 (MXS19; Sigma), shAmotL2 #1 (GAACAAGATGGACAGTGAAAT) or shAmotL2 #2 (GAGAGATTGGAATCTGCAAAT) (VectorBuilder). HUVEC or HUAEC cells were transfected with the above lentiviral supernatants diluted (2:1) with ECMB supplemented media with polybrene (8μg/ml) (Sigma) overnight. The following day viral supernatants were removed and replaced with fresh supplemented media and cultured for 72-96h post transduction before downstream analysis.

value: Endothelial

tag: cell line

value: HUVEC

value: Lentivirus


title: COVID-19_LPS#3

value: TLR4 ligand LPS (1 microgram /ml for 2 hours)


title: EC109-SI-replicate2

description: siRNA interfering for lncRNA MALAT1 replicate 2


title: E17.5F_29_Input

value: F


title: HUVEC_shAmotL2_rep7


title: E9.5F_129_Input


title: COVID-19_NT#3

value: No treatment


title: EC109-NC-replicate1

description: Negative control replicate1


title: E9.5M_122_Input

value: M