title: Subject D, Post-exercise, First session D_T1_2

description: Subject D, Post-exercise, First session

value: D


title: E571K1_Pro_B

status: Public on Sep 01 2021

type: SRA

city: New York

first: Omar

last: Abdel-Wahab

state: NY

address: 1275 York Ave

department: HOPP

country: USA

institute: MSKCC

description:
E571K1_Pro_B
murine_annotated_combined.counts

library_source: transcriptomic

data_processing:
Gene expression analysis was performed using the gene expression estimates computed by RSEM in units of transcripts per million (TPM). Those estimates were then further normalized using the TMM method (8), with a reference set of all protein-coding genes. Differentially expressed genes were defined as those with an associated Bayes factor ≥ 100 (computed using Wagenmakers’s Bayesian framework (9)) and an associated fold-change ≥ 1.5.
Genome_build: GRCh37

molecule: total RNA

organism: Mus musculus

source_name: XPO1-E571K mutant Pro_B cell

growth_protocol: Xpo1E571K/WT mice on a pure C57BL/6 background were crossed to B lineage CD19-cre mice (1), tamoxifen-inducible CAG-CreERT mice (2), and/or E-Myc (3) transgenic mice, each of which were also maintained on a pure C57BL/6 background.   Eight-week-old female CD45.1 C57BL/6J mice (The Jackson Laboratory) were used as recipients for bone marrow transplantation assays and eight-week-old female NSG mice (The Jackson Laboratory) were used for cell line xenografting. Blood was collected by submandibular bleeding using heparinized microhematocrit capillary tubes (Thermo Fisher Scientific). For assessment of germinal center formation, age- and sex-matched C57BL/6J mice were immunized intraperitoneally at 8 to 12 weeks of age with 0.5 ml of a 2% sheep red blood cell (SRBC) suspension in PBS (Cocalico Biologicals) or PBS as control. Automated peripheral blood counts were obtained using a ProCyte Dx Hematology Analyzer (IDEXX). Primary patient samples  Studies were approved by the Institutional Review Board of Memorial Sloan Kettering Cancer Center and conducted in accordance to the Declaration of Helsinki protocol. Patients provided samples after their informed consent and primary human de-identified CLL samples derived from whole peripheral blood or BM mononuclear cells were utilized.

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns.
Poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300 bp DNA fragments were isolated and sequenced on the Illumina HiSeq 2000 (100M 101 bp reads per sample)

treatment_protocol: Cells were incubated with antibodies in PBS/2% BSA (without Ca2+ and Mg2+) for 30 minutes on ice. For hematopoietic stem and progenitor cell analysis from adult mouse bone marrow, cells were stained with a lineage cocktail of monoclonal antibodies including B220 (RA3-6B2), CD19 (1D3), CD3 (17A2), CD4 (GK1.5), CD8a (53-6.7), CD11b (M1/70), Gr-1 (RB6-8C5), NK1.1 (PK136) and Ter119, allowing for mature lineage exclusion from the analysis. The composition of mature hematopoietic cell lineages in the bone marrow, spleen, thymus and peripheral blood was assessed using a combination of antibodies against B220, CD19, CD3, CD4, CD8a, CD11b, CD25 (PC61.5), CD44 (IM7), Gr-1, IgM (Il/41), CD43 (S11). All FACS sorting was performed on FACS Aria, and analysis was performed on an LSR Fortessa (BD Biosciences). Data analysis was performed using the FlowJo software.

tag: cell type

value: Pro B cell

tag: tissue

value: bone marrow

tag: genotype/variation

value: XPO1-E571K mutant


title: E571K1_mature_B

description:
E571K1_mature_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant mature_B cell

value: mature B cell


title: E571K2_mature_B

description:
E571K2_mature_B
murine_annotated_combined.counts


title: Subject C, Pre-exercise, First session C_T1_1

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Subject C, Pre-exercise, First session

data_processing:
The expression levels of each sample were normalized as Transcripts Per Kilobase Per Million (TPKM) by dividing the read count of each transcript model with its length and scaling the total per sample to one million using Kalisto V0.4.4. Quality control of raw and mapped reads was done using FastQC version 0.11.8.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample
Supplementary_files_format_and_content: Matrix table with logCPM for every gene and every sample

molecule: polyA RNA

organism: Homo sapiens

source_name: Human skeletal muscle, Vastus lateralis

extract_protocol:
RNA was isolated from cleaned muscle specimens using Trizol and subsequent cleaning using RNAeasy columns. Libraries were prepared using standard Illumina TrueSeq prep-kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Vastus lateralis

tag: Sex

value: Male

tag: subject

value: C

tag: time

value: First session

tag: exercise

value: Pre


title: E571K1_Pre_B

description:
E571K1_Pre_B
murine_annotated_combined.counts

source_name: XPO1-E571K mutant Pre_B

value: Pre B


title: Subject B, Post-exercise, Ninth/Last session B_T9_2

value: B

value: Ninth/Last session

value: Post


title: Subject C, Post-exercise, Ninth/Last session C_T9_2


title: PCLS_Media_UV-RV1B_72h_donor6_rep1

type: RNA

city: Stevenage

first: Ken

middle: A

last: Saunders

state: Hertfordshire

address: Gunnels Wood Road

country: United Kingdom

institute: GSK

description: Gene expression data precision cut lung slice

hyb_protocol: Labelled cDNA was hybridized onto human HG‐U133_Plus_2.0 microarrays (Affymetrix).

scan_protocol: Standard Affymentrix protocols

data_processing: Data was GCRMA normalized and quality control checked in Omicsoft Array Studio

label: Biotin

source_name: Precision cut lung slices treated with Media and UV-RV1B, for 72hr

label_protocol: FL-Ovation cDNA Biotin Module V2 kit (NuGen).

growth_protocol: Human lung lobes were obtained from male and female patients undergoing surgery. The average age of patients was 63 ± 8 years. Precision cut lung slices of approximately 300um each containing only small airways were obtained and cultured in DMEM

extract_protocol: PCLS were flash frozen after collection and total RNA was isolated from frozen samples

treatment_protocol: PCLS in 500 µl DMEM per well were infected with 1 x 10^6/ mL RV1b by inoculation for 2 h at 33 °C. As controls, PCLS were treated with UV-inactivated virus of the same batch or medium only. Supernatant was subsequently replaced by fresh medium and samples were post-incubated with infection medium until 1 day or 3 days post infection, in the presence or absence of 100nM rupintrivir or pleconaril.

tag: treatment

value: Media

tag: challenge

tag: replicate

tag: individual

value: donor_ID 6

tag: date

value: Precision cut lung slices


title: PCLS_Media_Control_72h_donor6_rep2

source_name: Precision cut lung slices treated with Media only, for 72hr

value: Control


title: PCLS_Pleconaril_RV1B_72h_donor6_rep1

source_name: Precision cut lung slices treated with Pleconaril and RV1B, for 72hr

value: Pleconaril


title: 5_RNA-seq

city: Ann Arbor

first: Fengbiao

last: Mao

state: Michigan

address: 1301 Catherine St

department: Department of Pathology

institute: University of Michigan

data_processing:
Basecalls performed using CASAVA version 1.8
Sequencing adapters and low quality sequencing reads were excluded using the Trim Galore program (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).
TopHat2(Kim et al., 2013) was used to align the reads to the University of California Santa Cruz (UCSC) mouse mm10 reference genome, allowing up to two mismatches and a Phred-scaled mapping quality ≥ 4.
The bioconductor package edgeR(Robinson et al., 2010) was used to identify genes that were differentially expressed between CON and GCS groups based on the number of mapped paired-end reads for each gene counted by the Python package HTSeq (http://www.htseq.org/).The genes for which p values and false discovery rate (FDR) values were below 0.05 were considered differentially expressed between CON and GCS groups.
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files include RNA information for each Sample.The genes for which p values and false discovery rate (FDR) values were below 0.05 were considered differentially expressed between CON and GCS groups.

extract_protocol:
Total RNA was extracted from the hippocampi of F1m-GCS and F1m-CON mice, and CON-/SUP-treated cells using the RNeasy Mini Kit (QIAGEN, Germany).The RNA quality was assessed using the Bioanalyser 2100 RNA 6000 Nano Kit (Agilent Technologies, USA).
mRNA-Seq libraries were generated from total RNA with polyA+ selection of mRNA using the TruSeq RNA Sample Prep Kit v2 (Illumina, USA), and transcriptomes were sequenced using the Hiseq 2000 Sequencing System (Illumina) in paired-end mode.

treatment_protocol: From embryonic day 9 (E9) to the day of birth, half of the pregnant dams received a choline-supplemented diet (5 g/kg choline chloride; F0f-GCS), while the remaining dams received a normal diet (1.1 g/kg choline chloride; F0f-CON). Offspring derived from F0f-GCS (namely F1GCS) and F0f-CON mice (namely F1CON) were fed with a basal diet after birth and subjected to mood-related behavioral tests at 2 month old.Hippocampal HT22 cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, and were treated with 5µM choline chloride (CON) and 70 µM (SUP) choline chloride for 48 h.

value: hippocampal neuron cell

value: Brain/Hippocampus


title: 5022-SUP_RRBS

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8
After removal of the adaptor sequences and trimming of low quality sequences by using cutadapt, the reads from each of the biological replicates were aligned to mouse mm10 reference genome as well as the size-selected MspI fragments generated by our in silico simulation.
Because of the strand specificity of DNA methylation, two rounds of alignments were carried out, i.e. the bisulfite converted reads were aligned to the genome sequences termed the “T genome” with each cytosine converted to thymine and in the meanwhile the reads were also aligned to the genome sequences termed the “A genome” with each guanine converted to adenosine.
The alignments were carried out with BGI SOAPaligner verison2.21(Li et al., 2009) with default parameters, allowing up to five mismatches for successful mapping. Both replicates showed near complete (> 99%) bisulfite conversion of non-CpG cytosine.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: Tab-delimited text files include Methylc information for each Sample.The DNA methylation levels in Nr3c1 and Crebbp promoters in the hippocampi of F1m-GCS and F1m-CON mice were examined by DNA bisulfate conversion and PCR amplification and Sequencing using the EZ DNA Methylation-GoldTM Kit (Zymo Research, USA) following the manufacturer’s standard protocol.

molecule: genomic DNA

extract_protocol:
The DNA methylation levels in Nr3c1 and Crebbp promoters in the hippocampi of F1m-GCS and F1m-CON mice were examined by DNA bisulfate conversion and PCR amplification and Sequencing using the EZ DNA Methylation-GoldTM Kit (Zymo Research, USA) following the manufacturer’s standard protocol.
RRBS libraries for the hippocampi of F1m-GCS and F1m-CON were constructed as previously described(Cai et al., 2015; Gu et al., 2011). Briefly, 500 ng of genomic DNA was digested with 20 units of MspI (NEB, USA) in a 20 μl reaction for 20 h at 37 °C. After purification, the digested products were blunt-ended, and then dA was added, followed by methylated-adapter (Illumina, USA) ligation. To obtain DNA fractions in 40-120 bp and 120-220 bp range of MspI-digested products, two ranges (160-240 bp and 240-340 bp) of adapter-ligated fractions were excised from 2% agarose gel. The size-selected DNA was bisulfite-treated for two rounds using EpiTect Bisulfite Kit (Qiagen, German) following the manufacturer’s standard protocol. The final libraries were generated by amplification with HiFi HotStart Uracil + ReadyMix PCR kit (KAPA, USA). The quality and quantity were analyzed by an Agilent 2100 Bioanalyzer (Agilent Technologies, USA) and qPCR, respectively. Illumina HiSeq 2000 was used to sequence the libraries according to the manufacturer’s protocol.

treatment_protocol: From embryonic day 9 (E9) to the day of birth, half of the pregnant dams received a choline-supplemented diet (5 g/kg choline chloride; F0f-GCS), while the remaining dams received a normal diet (1.1 g/kg choline chloride; F0f-CON). Offspring derived from F0f-GCS (namely F1GCS) and F0f-CON mice (namely F1CON) were fed with a basal diet after birth and subjected to mood-related behavioral tests at 2 month old.


title: PCLS_Rupintrivir_RV1B_72h_donor6_rep1

source_name: Precision cut lung slices treated with Rupintrivir and RV1B, for 72hr

value: Rupintrivir


title: sup_RNA-seq

description: Mice are given ad libitum access to standard chow and water, except during gestational stage as described below. From embryonic day 9 (E9) to the day of birth, half of the pregnant dams received a choline-supplemented diet (5 g/kg choline chloride; F0f-GCS), while the remaining dams received a normal diet (1.1 g/kg choline chloride; F0f-CON). Offspring derived from F0f-GCS (namely F1GCS) and F0f-CON mice (namely F1CON) were fed with a basal diet after birth and subjected to mood-related behavioral tests at 2 month old.

value: hippocampus


title: Subject C, Pre-exercise, Ninth/Last session C_T9_1

value: Vastus lateralis

value: Male


title: 5023-SFF_RRBS


title: Subject B, Pre-exercise, First session B_T1_1

description: Subject B, Pre-exercise, First session

value: First session


title: Subject A, Pre-exercise, Ninth/Last session A_T9_1

value: A

value: Pre


title: 70_RNA-seq


title: PCLS_Media_RV1B_72h_donor6_rep2

source_name: Precision cut lung slices treated with Media and RV1B, for 72hr


title: PCLS_Media_UV-RV1B_72h_donor5_rep2

value: donor_ID 5


title: PCLS_Media_Control_72h_donor5_rep2


title: PCLS_Media_RV1B_72h_donor6_rep1


title: Subject A, Pre-exercise, First session A_T1_1

description: Subject A, Pre-exercise, First session


title: sff_RNA-seq


title: 3031-H3K9_ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were mapped to the UCSC mouse mm10 reference genome using Bowtie (version 1.0.0) with specific settings(Langmead et al., 2009).
We used the function “callpeak” in Model-based Alignment of ChIP-Seq version 2 (MACS2) (Feng et al., 2012) to call peaks of H3K9ac occupancy with default parameters. MACS2 compares the number of H3K9ac-enriched sequence tags in a given window (200 bp) with the number of tags in surrounding windows and with the number of tags in the same region of the input DNA library.
Different peaks of H3K9ac occupancy between CON- and SUP-treated cells were called by the function “bdgdiff” in MACS2 and visualized by the Integrative Genomics Viewer(Thorvaldsdottir et al., 2013).
Genome_build: UCSC mm10
Supplementary_files_format_and_content: Tab-delimited text files include ChIP information for each Sample.Different peaks of H3K9ac occupancy between CON- and SUP-treated cells were called by the function “bdgdiff” in MACS2 and visualized by the Integrative Genomics Viewer(Thorvaldsdottir et al., 2013).

extract_protocol:
The ChIP assays on CON- and SUP-treated HT22 cells were performed with Zymo-Spin™ ChIP kit (Zymo Research, USA) following the manufacturer’s standard protocol.
Libraries of ChIP DNA were constructed using the NEXT flex™ Illumina ChIP-Seq Library Prep Kit (Bioo Scientific, USA) following the manufacturer’s instructions with modifications.

treatment_protocol: Hippocampal HT22 cells were maintained in high-glucose Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin, and were treated with 5µM choline chloride (CON) and 70 µM (SUP) choline chloride for 48 h.


title: Subject A, Post-exercise, Ninth/Last session A_T9_2

value: Ninth/Last session


title: PCLS_Media_UV-RV1B_72h_donor5_rep1


title: PCLS_Rupintrivir_RV1B_72h_donor5_rep1


title: Subject B, Post-exercise, First session B_T1_2

description: Subject B, Post-exercise, First session

value: B

value: Post


title: PCLS_Media_Control_72h_donor5_rep1

value: Media


title: FAP_Patient_42 [H_G96]

city: Houston

first: Eduardo

last: Vilar-Sanchez

state: Texas

address: 1515 Holcombe Blvd, Unit 1360

institute: UT MD Anderson Cancer Center

data_processing:
Sequencing reads quality check and low-quality reads filtering and trimming - FastQC
Alignment: Bowtie
Expression quantification: rsem-calculate-expression in RSEM v1.2.212
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited output with raw read counts

source_name: colon mucosa from patient with FAP

extract_protocol: RNA was extracted from polyps and normal colorectal mucosa stored at 80C according to internal protocols. Total RNA was extracted, and quantified using Qubit (LifeTechnologies) and RNA quality with the Agilent 2100 Bioanalyzer in order to select samples for analysis based on RNA integrity numbers for analysis. RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: subject status

value: patient with Familial Adenomatous Polyposis  (FAP)

tag: localization

value: COLON

value: POLYP

tag: type

value: TA

value: WT

tag: batch


title: FAP_Patient_40 [H_G88]


title: 3028-INPUT_ChIP-seq

value: hippocampal neuron cell

value: Brain/Hippocampus


title: FAP_Patient_39 [H_G114]

value: NORMAL

value: UM


title: Lung.Met2

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: lung cancer bone metastases

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger 2.1.0.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: count matrix in csv

source_name: bone marrow

extract_protocol:
10X Genomics Single cell 3' gene expression V2
Dissociation of tissues into single cells: All samples were collected in Media 199 supplemented with 2% (v/v) FBS. Single cell suspensions of the tumors were obtained by cutting the tumor in to small pieces (1mm3) followed by enzymatic dissociation for 45 minutes at 37°C with shaking at 120 rpm using Collagenase I, Collagenase II, Collagenase III, Collagenase IV (all at a concentration of 1 mg/ml) and Dispase (2mg/ml) in the presence of RNase inhibitors (RNasin (Promega) and RNase OUT (Invitrogen)). Erythrocytes were subsequently removed by ACK Lysing buffer (Quality Biological) and cells resuspended in Media 199 supplemented with 2% (v/v) FBS for further analysis.

value: GnRH agonist, abiraterone (9 months), docetaxel (5 cycles)


title: FAP_Patient_39 [H_G111]


title: 3030-H3K9_ChIP-seq


title: PCLS_Pleconaril_RV1B_72h_donor5_rep1

value: Pleconaril

value: Precision cut lung slices


title: CLL_XPO_104T

description:
CLL_XPO_104T
human_annotated_combined.counts

source_name: CLL XPO1 mutated samples 4

value: Peripheral Blood


title: PCLS_Media_UV-RV1B_72h_donor4_rep2

value: donor_ID 4


title: Lung.Met1

description: lung cancer bone metastases


title: shPK-1

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: siPI4KIIIβ-transfected lung cancer cells, biological replicate 1

data_processing:
FSQ files were processed with LifeScope Genomic Analysis Software version 2.5.1.
Sequenced reads in FASTQ files were mapped to hg19 whole genome using HISAT2 (Galaxy tool version2.1.0). UCSC known transcripts were supplied in GTF format file.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks (Galaxy tool version 2.2.1.0).  UCSC known transcripts were supplied in GTF format file.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

growth_protocol: Human lung cancer cells (H23) were cultured in RPMI 1640 containing 10% FBS. Cells were maintained at 37°C in an incubator with a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from cells using RNeasy Mini Kit (Qiagen, 74106) and subjected to reverse transcription using the qScript cDNA superMix (Quanta Biosciences).
RNA samples (triplicate) were subjected to RNA sequencing by the MD Anderson Cancer Center Sequencing and ncRNA Program with Illumina TrueSeq stranded Whole Transcriptome RNAseq protocol (Illumina).

treatment_protocol: Using shRNAs against human PI4KIIIβ (TRCN0000199916 and TRCN0000199262), cells were transfected with jetPRIME® Versatile DNA/siRNA transfection reagent (Polyplus).

value: H23 lung cancer cell line

tag: cell line

tag: transfection


title: PCLS_Media_Control_72h_donor4_rep2

value: Control

tag: tissue


title: shPK-3

description: siPI4KIIIβ-transfected lung cancer cells, biological replicate 3

tag: cell type


title: shCTL-3

description: shRNA control-transfected lung cancer cells, biological replicate 3

value: shRNA control


title: 3029-INPUT_ChIP-seq


title: A03- FAC replicate 03

city: Los Angeles

first: Allison

middle: L

last: Fisher

state: CA

address: 650 Charles E Young Dr South, CHS 44-100

department: Medicine

institute: UCLA Center for Iron Disorders

description:
rsem_gene_count_Ctrl_FAC.txt
TMM_normalized_reads_count_per_million_Ctrl_FAC.txt

data_processing:
The reads were mapped to the latest UCSC transcript set using Bowtie2 version 2.1.0
Gene expression level was estimated using RSEM v1.2.15
TMM (trimmed mean of M-values) was used to normalize the gene expression
Differentially expressed genes were identified using the edgeR program
Genome_build: UCSC transcript set mm10
Supplementary_files_format_and_content: rsem_gene_count_Ctrl_FAC.txt (Text file matrix table with raw gene counts for every gene and every sample)
Supplementary_files_format_and_content: TMM_normalized_reads_count_per_million_Ctrl_FAC.txt (Text file matrix table with normalized gene counts for every gene and every sample used for analysis of differentially expressed genes)

source_name: Endothelial cells

growth_protocol: HUVECs were cultured in endothelial cell growth medium (Cell Applications #211-500)

extract_protocol:
Total RNA was extracted using a RNeasy Micro kit (Qiagen #74004) following the manufacturer's instructions
Libraries for RNA-Seq were prepared with Kapa Stranded Kit. The workflow consisted of mRNA capture, cDNA generation, and end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification.

treatment_protocol: HUVECs were treated with solvent or 100 uM ferric ammonium citrate for 30h

value: Umbilical vein

value: HUVECs

tag: vendor

value: American Type Culture Collection

tag: catalog #

value: FAC


title: CLL_XPO_105T

description:
CLL_XPO_105T
human_annotated_combined.counts

source_name: CLL XPO1 mutated samples 5

tag: genotype/variation


title: CLL_XPO_102T

description:
CLL_XPO_102T
human_annotated_combined.counts

source_name: CLL XPO1 mutated samples 2


title: PCLS_Media_RV1B_72h_donor5_rep2

value: Media

tag: time

value: donor_ID 5


title: shCTL-1

description: shRNA control-transfected lung cancer cells, biological replicate 1


title: PCLS_Media_UV-RV1B_72h_donor4_rep1

tag: treatment


title: shPK-2

description: siPI4KIIIβ-transfected lung cancer cells, biological replicate 2


title: PCLS_Media_Control_72h_donor4_rep1

tag: challenge


title: PCLS_Pleconaril_RV1B_72h_donor5_rep2

tag: replicate


title: CLL_XPO_103T

description:
CLL_XPO_103T
human_annotated_combined.counts

source_name: CLL XPO1 mutated samples 3


title: A02- FAC replicate 02


title: PCLS_Rupintrivir_RV1B_72h_donor4_rep1

value: Rupintrivir

tag: individual


title: Melanoma.Met1

description: Melanoma bone metastases


title: PCLS_Rupintrivir_RV1B_72h_donor5_rep2

tag: date


title: shCTL-2

description: shRNA control-transfected lung cancer cells, biological replicate 2


title: PCLS_Media_RV1B_72h_donor5_rep1


title: Subject A, Post-exercise, First session A_T1_2

description: Subject A, Post-exercise, First session

value: Vastus lateralis

tag: Sex

value: Male

tag: subject

value: A

value: First session

tag: exercise

value: Post


title: PCLS_Pleconaril_RV1B_72h_donor4_rep1

value: Pleconaril

value: Precision cut lung slices


title: iopromide 2

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (NC_00) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3  NC_002947.4
Supplementary_files_format_and_content: Excel files include FPKM values for each sample

organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

source_name: E. coli bacteria + P. putida bacteria + IncPα plasmid

growth_protocol: liquid LB culture at 30 °C

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in 10 mL 0.5 mg/L ibuprofen, 0.5 mg/L naproxen, 0.5 mg/L gemfibrozil, 0.5 mg/L diclofenac, 0.5 mg/L propanolol, and 1.0 mg/L  iopromide , at 25 °C, without shaking

value: mixed culture

tag: strain #1

value: E. coli K-12 LE392

tag: strain #2

value: P. putida KT2440

tag: strain #3

value: IncP{alpha} RP4 plasmid


title: 424_NonTreated_TCRseq

city: Chapel Hill

first: William

last: Kim

state: NC

address: 450 West Dr

department: Lineberger Comprehensive Cancer Center

institute: UNC Chapel Hill

data_processing:
RNAseq:
75b paired-end reads were sequenced on a NextSeq 500 Desktop Sequencer using a high output flow cell kit (Illumina), yielding an average of over 28M reads per sample.
QC-passed reads were aligned to the mouse reference genome using STAR
Transcript abundance estimates for each sample were performed using SALMON
Raw SALMON read counts for all RNAseq samples were normalized by DESeq2
TCRseq:
Illumina MiSeq for TCRseq base calling
TCRseq reads were mapped and quantified using MiXCR
raw MiXCR outputs for all samples were analysis by tcR
Supplementary_files_format_and_content:
RNA-seq: Normalized count values for each sample
TCRseq: TRQ morisita index for all samples
Genome_build: mm10

source_name: C57BL/6_bladder tumor_Vehicle

extract_protocol:
RNA was extracted with Qiagen RNeasy Plus Mini kit
Libraries were prepared using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
TCR libraries were prepared using SMARTer Mouse TCR a/b Profiling Kit (TaKaRa)

tag: host strain

tag: cell line source

tag: tissue

value: bladder tumor

value: Vehicle

tag: molecule type

value: amplicon


title: Control treated TCR

city: Durham

first: Erika

last: Crosby

address: 203 Research Dr. MSRBI Room 407

institute: DUKE UNIVERSITY MEDICAL CENTER

description: TCR library

data_processing:
Fastq files for paired-end reads and the index file for each samples was processed using 10X cellranger v 2.1.0 count program to generate an expression count matrix for TCR library for each sample.
Fastq files for paired-end reads and the index file for each samples was processed using Partek® Genomics Suite® software (version 9.0.20, Copyright ©; 2018 Partek Inc)
GEX files had tags trimmed and sequences were aligned to the mm10 reference genome (STAR aligner 2.6.1) and UMI counts were deduplicated and filtered to include only barcodes that corresponded to a cell.
Transcripts were quantified and single cell counts were filtered to include cells with total reads between 655-20,000; expressed genes 60-3,500; and a maximum of 10% mitochondrial reads.
Counts were normalized to counts per million and log(2) transformed. TCR genes were removed prior to performing PCA and graph-based clusters were assigned using the top 15 principle components.
Genome_build: mm10
Supplementary_files_format_and_content: 4T1_GroupA_S1.txt or 4T1_GroupC_S8.txt contains the following in columns: cellular barcode, gene expression, graph based cluster ID, cell classification ID, corresponding TCR (if applicable), treatment group
Supplementary_files_format_and_content: Meta-data-onlyTCR+_CD3_cells.txt contains the following in columns: cellular barcode, graph based cluster ID, cell classification ID, corresponding TCR, cel cycle info, treatment group, clonal expansion, exhaustion, activation, and CXCR3 signature scores

source_name: Tumor

growth_protocol: HER2 expression was induced in mammary tissues of one month old mice, spontaneous breast tumor growth were monitored weekly

extract_protocol:
Breast tumors were removed and processed into single cell suspensions as described in manuscript, and live single CD45+ cells were sorted.
10X Genomics gene expression and TCR libraries were generated using Chromium Single Cell 5’ Library Construction Kit (V1.1). A targeted cell recovery of 10,000 cells were used for each sample.
scRNA seq (10X Genomics), Single Cell 5' Gene Expression and TCR Libraries, 26x8x98 single i7 index. GEX sequenced on NovaSeq 6000 (500M PE-reads/sample) and TCR sequenced on MiSeq (1.5M PE-reads/sample)

treatment_protocol: Control or IL12 plasmid injected intratumorally followed by electroporation

tag: cell type

value: Control plasmid


title: propanolol 2


title: PCLS_Media_RV1B_72h_donor4_rep1

value: Media

tag: time

value: donor_ID 4


title: MeT-5A_A2780 Exos

city: Hangzhou

first: Conghui

last: Wang

state: China

address: No.1 Xueshi Road

country: China

institute: Zhejiang University

description: lncRNA

data_processing:
Raw fastq sequences were treated with Trimmomatictools(v 0.36) using the following options: TRAILING:  20, MINLEN:235 and CROP:235, to remove trailing sequences below a phred quality score of 20 and to  achieve uniform sequence lengths for downstream clustering processes.
Sequencing read quality was inspected using the FastQC software. Adapter removal and read trimming  were performed using Trimmomatic. Sequencing reads were trimmed from the end (base quality less than  Q20) and filtered by length (less than 25).
Paired-end reads were aligned to the mouse reference genome mm10 with HISAT2. HTSeq v0. 6.0 was used  to count the reads numbers mapped to each gene.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: MeT-5A cells

growth_protocol: MeT-5A cells were seed on 6-well plates with M199 medium supplemented with 10% exosome-depleted FBS.

extract_protocol:
Total RNA of MeT-5A cells was extracted by TRIzol Reagent.
Fragmented RNA (the average length was approximately 200 bp) were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA). The libraries were paired-end sequenced  (PE150, Sequencing reads were 150 bp) using IlluminaHiSeq 3000 platform.
lncRNA sequencing

treatment_protocol: Exosomes from two cancer cells (SKOV3 cells and A2780 cells) were co-cultured with MeT-5A cells for 48h, PBS treatment acted as the control group.

value: human mesothelial cells

tag: treatment

value: treated with A2780 exosomes


title: A01- FAC replicate 01

value: Umbilical vein

value: HUVECs

tag: vendor

value: American Type Culture Collection

tag: catalog #

value: FAC


title: A01 - Ctrl solvent replicate 01

value: control


title: iopromide 3

value: mixed culture


title: IL12 treated TCR

description: TCR library

value: IL-12 plasmid


title: A03 - Ctrl solvent replicate 03


title: PCLS_Pleconaril_RV1B_72h_donor4_rep2

value: Pleconaril

tag: challenge

tag: replicate

tag: individual

value: Precision cut lung slices


title: 423_Treated_TCRseq

source_name: C57BL/6_bladder tumor_Entinostat

value: bladder tumor

value: Entinostat


title: MeT-5A_SKOV3 Exos

description: lncRNA

value: treated with SKOV3 exosomes


title: 421_Treated_TCRseq

value: amplicon


title: A02 - Ctrl solvent replicate 02


title: PCLS_Rupintrivir_RV1B_72h_donor4_rep2

value: Rupintrivir

tag: date


title: PCLS_Media_Control_24h_donor4_rep2

source_name: Precision cut lung slices treated with Media only, for 24hr

value: Media

value: Control

value: donor_ID 4


title: iopromide 1

value: E. coli K-12 LE392

value: P. putida KT2440

value: IncP{alpha} RP4 plasmid


title: 419_Baseline_TCRseq

source_name: C57BL/6_bladder tumor_Baseline

value: Baseline


title: 418_Treated_TCRseq


title: propanolol 3


title: diclofenac 3


title: PCLS_Media_RV1B_72h_donor4_rep2


title: propanolol 1


title: MeT-5A_PBS

description: lncRNA

value: human mesothelial cells

value: treated with PBS


title: PCLS_Media_UV-RV1B_24h_donor4_rep1

source_name: Precision cut lung slices treated with Media and UV-RV1B, for 24hr


title: diclofenac 2

value: mixed culture


title: 426_Baseline_TCRseq


title: gemfibrozil 3


title: PCLS_Media_Control_24h_donor4_rep1


title: PCLS_Rupintrivir_RV1B_24h_donor4_rep2

source_name: Precision cut lung slices treated with Rupintrivir and RV1B, for 24hr


title: diclofenac 1


title: 416_Baseline_TCRseq


title: WT-T-H3K36me3-rep3

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (mm10) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

source_name: Setd2 wild type liver tumor

growth_protocol: Normal tissues were from 8-month male mice without DEN treatment of Setd2 KO or WT mice. Liver tumors were from 8-month mice with DEN treatment of Setd2 KO and WT mice.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).

treatment_protocol: For DEN-induced HCC，the 2-week-old male mice were administered with one dose of DEN at 25 mg/kg by intraperitoneal injection. Then the mice were fed normally for 8 months until being sacrificed.

tag: genotype

value: Setd2 wild type

value: liver tumor

tag: age

tag: chip antibody

value: H3K36me3(abcam, ab9050)

value: intraperitoneal injection with DEN


title: WT-T-Input-rep2

description: Input for WT-T-H3K27ac-rep2 and WT-T-H3K36me3-rep2


title: gemfibrozil 2

tag: strain #1

tag: strain #2

tag: strain #3


title: WT-T-Input-rep3

description: Input for WT-T-H3K27ac-rep3 and WT-T-H3K36me3-rep3

tag: tissue


title: 411_Treated_TCRseq

tag: host strain

tag: cell line source

value: bladder tumor

value: Entinostat

tag: molecule type


title: 414_NonTreated_TCRseq

tag: treatment

value: Vehicle

value: amplicon


title: WT-T-Input-rep1

description: Input for WT-T-H3K27ac-rep1 and WT-T-H3K36me3-rep1


title: 410_NonTreated_TCRseq


title: gemfibrozil 1


title: 415_Baseline_TCRseq


title: WT-T-H3K36me3-rep1


title: naproxen 3


title: naproxen 2


title: 408_NonTreated_TCRseq


title: PCLS_Pleconaril_RV1B_24h_donor4_rep1

source_name: Precision cut lung slices treated with Pleconaril and RV1B, for 24hr

value: Pleconaril

tag: time

value: Precision cut lung slices


title: WT-T-H3K27ac-rep3

value: H3K27ac( abcam, ab4729)


title: miRNA_HPH3

city: Kunming

first: xiqian

last: xing

state: Yunnan

address: No. 176, Qingnian Road

department: Department of Respiratory Medicine

institute: The Affiliated Hospital of Yunnan University, The Second People's Hospital of Yunnan Province

data_processing:
Illumina HiSeq sequencing platform was used
After the quality inspection results were passed, next-generation sequencing technology (Next-Generation Sequencing, NGS) was used to perform paired-end sequencing of these libraries based on the Illumina HiSeq sequencing platform
After data filtering (Cutadapt) and quality evaluation (FastQC), the RNA-Seq data was compared to the reference genome (Tophat2), and the data source for the reference genome is the Ensembl database (http://www.ensembl.org/, Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa).
Then, we use HTSeq to compare the Read Count value of each gene as the original expression of the gene, and use FPKM to normalize the expression. Matrix table with raw gene counts for every gene and every sample
Genome_build: Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa, FASTA for novel lncRNA and circRNA included on the series record.
Supplementary_files_format_and_content: raw gene counts

organism: Rattus norvegicus

source_name: Lung

extract_protocol:
Lung was removed, flash frozen on dry ice.
After extracting total RNA from three randomly selected right lung tissue samples using TRIzol (Invitrogen, CA, USA), the rRNA in the total RNA was removed by a ribosomal RNA removal kit, and the RNA was interrupted to 200-300 bp fragments by ion interruption.
The long  RNAs using Illumina, Poly-A enrichment, Illumina TrueSeq paired-end library construction, and short RNAs using Illumina, Poly-A enrichment, Illumina TrueSeq single-end library construction.
Subsequently, using RNA as a template, the first and second strands of cDNA. After the library is constructed, PCR amplification is used to enrich the library fragments, and the library size is 300-400bp.
Then, the Agilent 2100 Bioanalyzer was used for quality inspection of the library, including total concentration and effective concentration.

tag: strain

value: Sprague Dawley

value: lung

value: post natal 6-8 weeks

value: atmospheric hypoxia


title: PCLS_Pleconaril_RV1B_24h_donor4_rep2

tag: challenge

value: donor_ID 4


title: miRNA_HPH2


title: PCLS_Rupintrivir_RV1B_24h_donor4_rep1

value: Rupintrivir

tag: replicate


title: 405_NonTreated_TCRseq


title: 403_Treated_TCRseq


title: miRNA_HPH1


title: WT-T-H3K27ac-rep1

value: Setd2 wild type


title: PCLS_Media_UV-RV1B_24h_donor4_rep2

value: Media

tag: individual


title: PCLS_Media_RV1B_24h_donor4_rep2

source_name: Precision cut lung slices treated with Media and RV1B, for 24hr

tag: date


title: WT-T-H3K27ac-rep2

tag: genotype

value: liver tumor


title: 402_NonTreated_TCRseq


title: WT-T-H3K36me3-rep2

tag: age

value: H3K36me3(abcam, ab9050)

value: intraperitoneal injection with DEN


title: miRNA_Con3

value: control


title: WT-NT-Input-rep3

description: Input for WT-NT-H3K27ac-rep3 and WT-NT-H3K36me3-rep3

source_name: Setd2 wild type normal liver tissue

value: normal liver tissue

tag: chip antibody


title: naproxen 1

value: mixed culture

tag: strain #1

value: E. coli K-12 LE392

value: P. putida KT2440

value: IncP{alpha} RP4 plasmid


title: ibuprofen 3

tag: strain #2


title: 413_Treated_TCRseq

value: bladder tumor

value: Entinostat

value: amplicon


title: WT-NT-Input-rep2

description: Input for WT-NT-H3K27ac-rep2 and WT-NT-H3K36me3-rep2


title: control 2

tag: strain #3


title: ibuprofen 2

tag: tissue


title: miRNA_Con1

value: Sprague Dawley

value: lung

value: post natal 6-8 weeks


title: HPH3

value: atmospheric hypoxia


title: 422_Baseline_TCRseq

tag: host strain

value: Baseline


title: WT-NT-H3K36me3-rep2

value: Setd2 wild type


title: ibuprofen 1


title: 401_Baseline_TCRseq

tag: cell line source


title: WT-NT-Input-rep1

description: Input for WT-NT-H3K27ac-rep1 and WT-NT-H3K36me3-rep1


title: control 3


title: WT-NT-H3K36me3-rep1

value: H3K36me3(abcam, ab9050)


title: WT-NT-H3K27ac-rep3

value: H3K27ac( abcam, ab4729)


title: Con3

value: control


title: Con2


title: Foxp3YFPCre Treg (WT-5)

first: KLaus

last: Schmitz-Abe

address: 300 Longwood Avenue

department: Asthma, Allergy and Immunology

institute: Children's Hospital Boston

data_processing:
fastq files to bam files to vcf files: Rsubread (align, V2.0.1), Default parameters, output= all vcf files
vcf files to count file: Rsubread (feature Counts, V2.0.1), Default parameters, output= "SKT4-Counts.xlsx"
Count file to Gene differential expression file: edgeR (version 3.28) , Default parameters,
Count file to Gene differential expression file: DESeq2 (version 1.26.0) , Default parameters,
Count file to Gene differential expression file: Lima (version 3.42.2) , Default parameters,
Join results: Variant explorer Pipeline (V2.1), , output= "SKT4-Diff.Gene_expression.xlsx"
Genome_build: Mus musculus GRCm38/mm10 (UCSC reference)
Supplementary_files_format_and_content: vcf files and Excel file

source_name: spleen

extract_protocol:
The cells were sorted our using Foxp3YFP reporter, then they were lysed using RLT buffer. The RNA was extracted using the Qiagen miniRNasy kit as per manufacturer's protocol
RNA to cDNA was performed using the SMART-Seq v4 Ultra Low Input RNA kit using the manufacturer's protocol

tag: group

value: B

tag: cell type

value: Treg cells

value: WT

value: spleen


title: HPH2

tag: treatment


title: HPH1

tag: strain


title: control 1

value: mixed culture

value: E. coli K-12 LE392

value: P. putida KT2440

value: IncP{alpha} RP4 plasmid


title: WT-NT-H3K36me3-rep3

value: normal liver tissue


title: WT-NT-H3K27ac-rep1


title: Foxp3YFPCre Treg (WT-7)


title: AS-tetoff-MYCN_D-3

city: Birmingham

first: Han-Fei

last: Ding

state: Alabama

address: WTI 602D, 1824 6th Avenue South

department: Pathology

institute: University of Alabama at Birmingham

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were normalized, significance determined by ANOVA, and fold change calculated with the Partek Genomics Suite (Partek Inc., St. Louis, MO).

label: TdT

label_protocol: TdT-labled cRNA were prepared with an Affymetrix GeneChip WT Terminal labeling kit

growth_protocol: SK-N-AS_tetoff_MYCN cells were cultured in DMEM (HyClone SH30022, Thermo Scientific) supplemented with 10% FBS (HyClone SH30396, Thermo Scientific).

extract_protocol: Total RNA was isolated from the cell samples using Trizol (Invitrogen), and RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

treatment_protocol: SK-N-AS_tetoff_MYCN cells were treated with or without 1 µg/ml doxycycline for 6 days.

tag: cell line

value: human neuroblastoma cell line


title: miRNA_Con2

value: Sprague Dawley

value: lung

value: post natal 6-8 weeks


title: Con1


title: Foxp3YFPCre Treg (WT-4)


title: AS-tetoff-MYCN_D+3

value: 1 µg/ml doxycycline for 6 days


title: Foxp3YFPCre Treg (WT-6)


title: PCLS_Media_RV1B_24h_donor4_rep1

description: Gene expression data precision cut lung slice

value: Media

tag: challenge

tag: replicate

tag: time

value: donor_ID 4

value: Precision cut lung slices


title: Foxp3YFPCre Treg (WT-3)

value: B

tag: genotype


title: cKO-T-Input-rep3

description: Input for cKO-T-H3K27ac-rep3 and cKO-T-H3K36me3-rep3

source_name: Setd2 knockout liver tumor

value: Setd2 knockout

value: liver tumor

tag: age

value: intraperitoneal injection with DEN


title: cKO-T-Input-rep2

description: Input for cKO-T-H3K27ac-rep2 and cKO-T-H3K36me3-rep2

tag: chip antibody


title: RNA-Seq MGT_siAJSZ_s2

city: Baltimore

first: Chulan

last: Kwon

state: MD

address: 720 Rutland Ave, Ross 954

department: Medicine, Cardiology, Heart & Vascular Institute, Institute for Cell Engineering, and Cellular and Molecular Medicine

institute: Johns Hopkins University

description:
MGT_siAJSZ_s2
HDFs treated with MGT and siAJSZ

data_processing:
Trimmomatic (0.36) min quality 35, min length 36
HISAT2 (2.0.4) mapping
Subread featureCounts (1.5.2) processing
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts matrix

source_name: dermal fibroblasts

growth_protocol: HDFs were added to 384-well plates at 103 cells/well

extract_protocol:
On day 2, cells were collected and RNA was extracted using TRIzol. Cells were pooled from 16 wells per sample, and two biological replicates per condition were analyzed.
Library preparation was performed by Novogene using their in-house preparation protocol. . Briefly, mRNA was enriched using oligo (dT) beads and fragmented randomly using a fragmentation buffer. cDNA was generated from mRNA template using a random hexamer primer followed by second-strand synthesis. Terminal repair, A ligation, and sequencing adaptor ligation were then performed. The final libraries were generated through size selection and PCR enrichment
bulk RNA seq. Samples were sequenced to an approximate depth of 35–40 million reads per sample.

treatment_protocol: transfected with siRNAs (siATF7IP, siJUNB, siSP7, siZNF207 in combination) in iCRM. The next day (day 0), the cells were transduced with 1 µL/well mouse MGT retrovirus diluted in iCRM.

value: siAJSZ


title: Foxp3YFPCre Treg (WT-2)

value: Treg cells

value: WT

value: spleen


title: AS-tetoff-MYCN_D+2


title: cKO-T-Input-rep1

description: Input for cKO-T-H3K27ac-rep1 and cKO-T-H3K36me3-rep1


title: CLL_XPO_101T

first: Omar

last: Abdel-Wahab

address: 1275 York Ave

institute: MSKCC

description:
CLL_XPO_101T
human_annotated_combined.counts

data_processing:
Gene expression analysis was performed using the gene expression estimates computed by RSEM in units of transcripts per million (TPM). Those estimates were then further normalized using the TMM method (8), with a reference set of all protein-coding genes. Differentially expressed genes were defined as those with an associated Bayes factor ≥ 100 (computed using Wagenmakers’s Bayesian framework (9)) and an associated fold-change ≥ 1.5.
Genome_build: GRCh37

source_name: CLL XPO1 mutated samples 1

extract_protocol:
RNA was extracted from sorted mouse cell populations using Qiagen RNeasy columns.
Poly(A)-selected, unstranded Illumina libraries were prepared with a modified TruSeq protocol. 0.5X AMPure XP beads were added to the sample library to select for fragments <400 bp, followed by 1X beads to select for fragments >100 bp. These fragments were then amplified with PCR (15 cycles) and separated by gel electrophoresis (2% agarose). 300 bp DNA fragments were isolated and sequenced on the Illumina HiSeq 2000 (100M 101 bp reads per sample)

value: Peripheral Blood

tag: genotype/variation


title: WT-NT-H3K27ac-rep2

value: Setd2 wild type

value: normal liver tissue

value: H3K27ac( abcam, ab4729)


title: AS-tetoff-MYCN_D-1

value: human neuroblastoma cell line


title: AS-tetoff-MYCN_D-2


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-7)

value: A

value: Het


title: RNA-Seq MGT_s2

description:
MGT_s2
HDFs treated with MGT


title: RNA-Seq MGT_siAJSZ_s1

description:
MGT_siAJSZ_s1
HDFs treated with MGT and siAJSZ


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-5)


title: RNA-Seq MGT_s1

description:
MGT_s1
HDFs treated with MGT


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-4)


title: LID - cells from infected well residing on low stiffness 3 kPa gels

city: Tübingen

first: Effie

last: Bastounis

state: Baden-Württemberg

address: Auf der Morgenstelle 28/E7

department: Interfaculty Institute of Microbiology and Infection Medicine

country: Germany

institute: University of Tübingen

description: 2x10^5 cells grown on 12 mm collagen I coated low stiffness (3 kPa) polyacrylamide hydrogels for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells where trypsinized and RNA was extraceted from all cells in the infected well.

data_processing:
Raw sequencing data generated from Illumina NovaSeq 6000 that pass the Illumina chastity filter are used for following analysis. Trimmed reads (trimmed 5’, 3’-adaptor bases) are aligned to reference genome. Based on alignment statistical analysis (mapping ratio, rRNA/mtRNA content, fragment sequence bias), we determine whether the results can be used for subsequent data analysis. After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤ 20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software.
The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM (fragments per kilobase of transcript per million mapped reads) in group ≥ 0.5. FPKM is equal to the number of fragments that map a certain gene or transcipt times a million divided by the length of the gene in Kb and the fragmnets number that map to all genes/transcripts.
Differentially expressed gene and transcript analyses were performed with R package ballgown. Fold change (cutoff 1.5), p-value (≤ 0.05) and FPKM (≥ 0.5 mean in one group) were used for filtering differentially expressed genes and transcripts.
Genome_build: CanFam3
Supplementary_files_format_and_content: Expression_Gene.xlsx file contains in column A the Track_id which is the database name in gene level, in column B the name of the gene, in column C its locus, in column D the strand of the gene, in column E the gene type and in colunms F through U the FPKM of each gene for each one of the samples. Likewise, Expression_Transcript.xlsx file contains in column A the Track_id which is the database name in transcript level, in column B the name of the transcript, in column C the ENSEMBL gene id of the transcript, in column D the name of the gene, in column E the locus, in column F the strand, in column F the biological type of the transcript and in colunms H through W the FPKM of trasncript in samples. Differentially_Expressed_Genes.xlsx and Differentially_Expressed_Transcripts.xlsx show differentially expressed genes or transcripts when comparisons between different groups os samples are performed. Different groups compared are shown in different sheets within the xlsx file.

organism: Canis lupus familiaris

source_name: kidney tubule

growth_protocol: G-MDCK cells were cultured in high glucose DMEM medium (Thermofisher; 11965092) containing 4500 mg/L glucose and supplemented with 10% FBS (GemBio; 900-108) as previously suggested. To generate confluent cell monolayers, 24-well plates glass-bottom for microscopy were coated with 50 µg/ml rat-tail collagen-I (diluted in 0.2 N acetic acid) for 1 h at 37°C, air-dried for 15 min, and UV-sterilized for 30 min in a tissue culture hood. Alternatively cells were seeded in collagen I coated polyacrylamide hydrogels of high stiffness (70 kPa, "H") or low stiffness (3 kPa, "L"). Hydrogels were prepared as previously described (https://www.nature.com/articles/s41598-019-54336-2). Specifically, 3 kPa hydrogels contained 5% acrylamide and 0.1% bis-acrylamide and 70-kPa hydrogels contained 10% acrylamide and 0.6% bis-acrylamide. MDCK cells were seeded at a density of 2 × 10^5 cells/well for 24 h.

extract_protocol:
Cells were harvested and lyzed using the QIAshredder Kit (Qiagen; 79656). mRNA was harvested using the RNeasy Plus Micro Kit (Qiagen; 74004) and eluted in 30 μL RNAase free water. RNA concentrations were measured using the nanodrop machine and were comparable between conditions. RNA quality and quantity were confirmed via bioanalyzer analysis performed by Arraystar Inc.
The total RNA was depleted of rRNAs by Arraystar rRNA Removal Kit. We used Illumina kits for the RNA-seq library preparation, which included procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Finally, the prepared RNA-seq libraries were qualified using Agilent 2100 Bioanalyzer and quantified by qPCR absolute quantification method
TThe DNA fragments in well mixed libraries were denatured with 0.1M NaOH to generate single-stranded DNA molecules, loaded onto channels of the flow cell at 8 pM concentration, and amplified in situ using NovaSeq 6000 S4 Reagent Kit (300 cycles). Sequencing was carried out using the Illumina NovaSeq 6000 according to the manufacturer’s instructions. Sequencing was carried out by running 150 cycles.

treatment_protocol: 24 h post-seeding MDCK cells were exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria three times with PBS, media containing 20 μg/mL gentamycin was added to cells to kill extracellular bacteria. 24 h post-infection cells were trypsinized and either left in tubes or sorted to infected and uninfected populations. All tubes containing cells in solution were treated in parallel so to lyze the cells and extract their RNA.

tag: growth

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

tag: nature

value: immortalized

tag: vendor/source

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: cKO-T-H3K36me3-rep2

value: Setd2 knockout

tag: tissue

value: liver tumor

value: H3K36me3(abcam, ab9050)


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-3)

value: Treg cells


title: cKO-T-H3K27ac-rep3

value: intraperitoneal injection with DEN


title: cKO-T-H3K27ac-rep2


title: cKO-T-H3K36me3-rep1


title: AS-tetoff-MYCN_D+1

value: 1 µg/ml doxycycline for 6 days


title: ChIP-Seq Input_1i

data_processing:
Bowtie2 (2.3.5) for mapping
MACS2 (2.1.1) for calling peaks
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files containing peaks

growth_protocol: ChIP-seq experiments were performed with 100.10^6 HDFs per replicate

extract_protocol:
SimpleChip Plus sonication chromatin IP kit (Cell Signaling Technology, 56383) according to the manufacturer directions. In brief, HDFs were grown to 80% confluency (107/sample) and then crosslinked with 1% formaldehyde (Sigma, F8775) in PBS at room temperature for 20 min with occasionally stirring. The crosslinking reaction was quenched by addition of 0.125 M glycine for 10 min, and chromatin was fragmented for 25 min using a Bioruptor Pico sonicator (Diagenode) to an average DNA fragment length of 200–500 bp.
DNA was quantified with Qubit (Invitrogen, Q32854). Samples equivalent to 100 µg of DNA were incubated overnight at 4°C with 4 µg of rabbit polyclonal anti-ATF7IP (Invitrogen, PA5-54811), rabbit monoclonal anti-JUNB (C37F9) (Cell Signaling Technology, 3753S), rabbit anti-SP7/OSTERIX (Abcam, Ab22552), or rabbit polyclonal anti-ZNF207 (Bethyl laboratories, A305-814AM). Rabbit IgG (Cell Signaling Technology, 2729) was used as a negative control. Immunocomplexes were captured by rotation with protein G-coupled magnetic beads (Cell Signaling Technologies, 9006) for 2 h at 4°C, and immunoprecipitated genomic DNA was collected by incubation with 50 μL elution buffer.  Library preparation and sequencing of immunoprecipitated and input DNA was performed by UCSD IGM core facility.

tag: sample type

value: input


title: exp_1_scrambled transfection

city: Tel Aviv

first: Carmit

last: Levy

address: Ramat Aviv

department: Human Genetics and Biochemistry

country: Israel

institute: Tel Aviv University

description: RNA expression value derived from Affymetrix Launcher software

hyb_protocol: Samples were hybridized with: miRNA-4_0 or HuGene-1_1-st-v1, as indicated (Affymetrix) and scanned at the HUJI Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed in R for background correction and RMA normalization. Normalized expression data were log-transformed.

label: biotin

source_name: WM1716 melanoma line

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Exp.1-  WM1716  melanoma cells were grown in 10% serum DMEM. Exp.2- WM3682  melanoma cells were grown in adipocytes medium.

extract_protocol: RNA was isolated from WM1716 and WM3682 cells using Trizol (Qiagen), according to the manufacturer’s instructions. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA.

treatment_protocol: Exp.1 - WM1716 melnaoma cells were stably trasfected with scrambled control or miR-211. Exp.2 - WM3682 melnaoma cells were co-cultured with adipocytes or mono-cultured. RNA was extracted at day 5.

tag: transfection

value: scrambled control


title: HSC_10%FBS-1

city: Taoyuan City

first: TSAI

middle: CHI

last: LIU

address: No. 300, Zhongda Rd., Zhongli District,

department: Department of Biomedical Sciences and Engineering

country: Taiwan

institute: National Central University

description: Gene expression data after 7 days expanded human hematopoietic stem cells with serum culture

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array. The hybridized arrays were washed and stained in the Affymetrix Fluidics Station for GeneChip450.

scan_protocol: GeneChips were scanned with the Scanner GCS3000 (Affymetrix).

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: serum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from approximately 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD34+ cells were isolated from newborn umbilical cord blood. After 7 days of ex vivo expansion in different culture systems, cells were collected.

extract_protocol: Total RNA was extracted using the miRNeasy Mini Kit (Qiagen). All the procedures were performed according to the manufacturers’ instructions.

treatment_protocol: Pellet the appropriate number of cells by centrifuging for 5 min at 300 x g in a centrifuge tube. Carefully remove all cell-culture medium by aspiration. Pellet were washed with PBS two times and then placed on ice.

value: newborn

tag: type

value: blood cell

tag: expanded stage

value: 7 days


title: HSC_SF-1

description: Gene expression data after 7 days expanded human hematopoietic stem cells with serum-free culture

source_name: serum-free


title: exp_1_miR-211 transfection


title: LD - cells from uninfected well residing on low stiffness 3 kPa gels

description: 2x10^5 cells grown on 12 mm collagen I coated low stiffness (3 kPa) polyacrylamide hydrogels for 48 h


title: LIB - cells from infected well residing on low stiffness 3 kPa gels


title: LIC - cells from infected well residing on low stiffness 3 kPa gels


title: Foxp3YFPCre Treg (WT-1)

tag: group

value: B

tag: cell type

value: WT

value: spleen


title: HSC_10%FBS


title: ChIP-Seq Input_2


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-2)

value: A

value: Het


title: ChIP-Seq ZNF207_2

description:
ZNF207_2
ChIP-seq in HDFs for Znf207

tag: input for macs2


title: HSC_SF


title: cKO-NT-Input-rep2

description: Input for cKO-NT-H3K27ac-rep2 and cKO-NT-H3K36me3-rep2

source_name: Setd2 knockout normal liver tissue

value: normal liver tissue

tag: treatment


title: cKO-T-H3K27ac-rep1

value: Setd2 knockout

value: H3K27ac( abcam, ab4729)


title: LA - cells from uninfected well residing on low stiffness 3 kPa gels

tag: cell line

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

value: immortalized

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: cKO-T-H3K36me3-rep3

tag: genotype

value: liver tumor

value: H3K36me3(abcam, ab9050)

value: intraperitoneal injection with DEN


title: LIA - cells from infected well residing on low stiffness 3 kPa gels


title: Tn cells TC rep1

city: Gainesville

first: Minghao

last: Gong

state: Florida

address: 1395 Center Drive, D6-18c

institute: University of Florida

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
Alignment of RNA-seq reads were mapped to the Mus musculus genome mm10 using STAR aligner (v2.7)
Significantly altered genes (FDR P < 0.05) were identified by DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Combined Matrix table with raw gene counts for every gene and every sample

source_name: Splenic follicular helper T cells

extract_protocol:
Total RNA was extracted from Tfh and Tn cells isolated from the spleen of each individual mouse from WT and KO using RNeasy Kit.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded RNA Sample Preparation Kit (Illumina) according to the manufacturer’s protocol.

tag: strain

value: B6.NZM-Sle1NZM2410/AegSle2NZM2410/AegSle3NZM2410/Aeg/LmoJ (TC) congenic mice

value: Splenic cells

value: Naive CD4+ T cells

tag: age

value: 8 months old

tag: gender

value: female


title: cKO-NT-Input-rep1

description: Input for cKO-NT-H3K27ac-rep1 and cKO-NT-H3K36me3-rep1

tag: chip antibody


title: LC - cells from uninfected well residing on low stiffness 3 kPa gels

tag: growth

tag: nature


title: ChIP-Seq SP7_1

description:
SP7_1
ChIP-seq in HDFs for Sp7


title: ChIP-Seq Input_1

value: input


title: HIB - cells from infected well residing on high stiffness 70 kPa gels

description: 2x10^5 cells grown on 12 mm collagen I coated high stiffness (70 kPa) polyacrylamide hydrogels for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells where trypsinized and RNA was extraceted from all cells in the infected well.

tag: tissue

tag: vendor/source


title: cKO-NT-H3K36me3-rep1


title: Tn cells TC rep4


title: HIC - cells from infected well residing on high stiffness 70 kPa gels


title: LB - cells from uninfected well residing on low stiffness 3 kPa gels


title: ChIP-Seq ZNF207_1

description:
ZNF207_1
ChIP-seq in HDFs for Znf207


title: cKO-NT-Input-rep3

description: Input for cKO-NT-H3K27ac-rep3 and cKO-NT-H3K36me3-rep3


title: Tn cells TC rep2


title: ChIP-Seq SP7_2

description:
SP7_2
ChIP-seq in HDFs for Sp7


title: ChIP-Seq Input_2i

tag: sample type


title: Tn cells B6 rep3


title: ChIP-Seq JUNB_2

description:
JUNB_2
ChIP-seq in HDFs for Junb


title: HID - cells from infected well residing on high stiffness 70 kPa gels


title: Tn cells B6 rep4


title: AML14_LSC_STAT3i

city: Aurora

first: Shanshan

last: Pei

state: CO

institute: University of Colorado

description: mRNA of leukemia stem cells isolated from leukapheresis sample treated with STAT3i

data_processing:
Raw reads generated from the Illumina HiSeq2500 sequencer were demultiplexed using bcl2fastq version 2.19.0.
Quality filtering and adapter removal are performed using Trimmomatic-0.36 with the following parameters: "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35".
Processed/cleaned reads were then mapped to reference genome hg38/gencode28 with STAR-2.6.0c given the following parameters: "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical".
DESeq2-1.16.1 within R-3.4.1 was used to perform data normalization and differential expression analysis with an adjusted p-value threshold of 0.05 on each set of raw expression measures. The ‘lfcShrink’ method was applied, which moderates log2 fold-changes for lowly expressed genes.
Genome_build: hg38/gencode28
Supplementary_files_format_and_content: normalized count matrix generated by DESeq2

source_name: leukapheresis

growth_protocol: Leukemia stem cells were isolated from leukapheresis samples grown in IMDM based media

extract_protocol:
QIAGEN RNeasy Plus
Clontech SMARTer + Nextera XT (Low Input Library)

treatment_protocol: Vehicle control (DMSO) vs. STAT3i

value: leukemia stem cells

tag: aml specimen


title: cKO-NT-H3K36me3-rep2

value: Setd2 knockout normal

value: normal liver tissue


title: Tfh cells TC rep1

value: Follicular helper T cells


title: AML13_LSC_STAT3i


title: Foxp3YFPCre/+Stk3∆/∆Stk4∆/∆ Treg (Het-1)

value: A

value: Treg cells

value: Het

value: spleen


title: Tfh cells TC rep2


title: HC - cells from uninfected well residing on high stiffness 70 kPa gels

description: 2x10^5 cells grown on 12 mm collagen I coated high stiffness (70 kPa) polyacrylamide hydrogels for 48 h

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

value: immortalized

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: Tfh cells TC rep4

value: B6.NZM-Sle1NZM2410/AegSle2NZM2410/AegSle3NZM2410/Aeg/LmoJ (TC) congenic mice

value: Splenic cells


title: Tfh cells B6 rep4

value: 8 months old


title: cKO-NT-H3K27ac-rep3

value: Setd2 knockout

value: H3K27ac( abcam, ab4729)


title: cKO-NT-H3K36me3-rep3

value: H3K36me3(abcam, ab9050)


title: ChIP-Seq ATF7IP_2

description:
ATF7IP_2
ChIP-seq in HDFs for Atf7ip


title: AML11_LSC_STAT3i

value: leukemia stem cells


title: ChIP-Seq JUNB_1

description:
JUNB_1
ChIP-seq in HDFs for Junb


title: Tfh cells B6 rep3

value: female


title: HD - cells from uninfected well residing on high stiffness 70 kPa gels


title: Tn cells B6 rep2

value: Naive CD4+ T cells


title: Setd2-WT-T-rep1

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using Tophat  v2.1.1 with default  parameters.
The gene expression level was calculated by Cufflinks (v 2.2.1).
‘FPKM’ data produced by Cufflinks 2.2.1.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
Total RNA was extracted by using EASYspin RNA Mini Kit (Aidlab RN07).
RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111).

value: Setd2 wild type

value: liver tumor

value: intraperitoneal injection with DEN


title: cKO-NT-H3K27ac-rep2

value: normal liver tissue


title: ChIP-Seq ATF7IP_1

description:
ATF7IP_1
ChIP-seq in HDFs for Atf7ip


title: Tn cells B6 rep1


title: AML6_LSC_STAT3i


title: Tfh cells B6 rep2

value: Follicular helper T cells


title: Setd2-WT-T-rep3


title: Setd2-WT-NT-rep3


title: HA - cells from uninfected well residing on high stiffness 70 kPa gels

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule


title: HB - cells from uninfected well residing on high stiffness 70 kPa gels

value: immortalized

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: AML13_LSC_Control

description: mRNA of leukemia stem cells isolated leukapheresis sample treated with vehicle control

value: Control


title: GIC - cells from infected well residing on glass

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 24 h were then exposed to Listeria monocytogenes (MOI=200) for 30 min. After washing out the bacteria, media containing 20 μg/mL gentamycin was added to cells. 24 h post-infection cells where trypsinized and RNA was extraceted from all cells in the infected well.


title: GID - cells from infected well residing on glass


title: Setd2-WT-T-rep2


title: cKO-NT-H3K27ac-rep1


title: GIA - cells from infected well residing on glass


title: AML11_LSC_Control


title: HIA - cells from infected well residing on high stiffness 70 kPa gels


title: AML14_LSC_Control


title: Setd2-cKO-T-rep3


title: GFP_O_2

city: Shanghai

first: Li

last: Wan

state: Shanghai

address: 300 Feng Lin Road

department: CAS Center for Excellence in Molecular Plant Sciences

institute: Chinese Academy of Sciences

data_processing:
The small RNA raw data was filted and then searched against small RNA databases according to the order (miRNA > piRNA > snoRNA > rfam > other sRNA) to identify known miRNAs.
We mapped small RNA clean reads to the reference genome and other small RNA databases with AASRA software, except that Rfam database was searched with cmsearch software.
Unique Molecular Identifier (UMI) was used to quantify small RNA expression.
Genome_build: Nicotiana benthamiana draft genome sequence v1.0.1
Supplementary_files_format_and_content: Annotation and read counts for every small RNA and every sample.

organism: Nicotiana benthamiana

source_name: leaves

growth_protocol: Nicotiana benthamiana was planted in the greenhouse (16-h-light/8-h-dark photoperiod) at 26°C.

extract_protocol:
Total RNA was harvested using Trizol reagent and was cut by page electrophoresis to separate 18-30 nt small RNA.
(1) 3' end adaptor ligation: Ligate the 5-adenylated and 3-blocked adaptor to the 3' end of the small RNA fragment. (2) Add Unique molecular identifiers (UMI) labeled Primer.  (3) Unligated adaptors digestion.  (4) 5' end adaptor ligation.  (5) First strand synthesis with Unique molecular identifiers (UMI) labeled Primer.  (6) Second strand synthesis.  (7) Fragment selection. Page electrophoresis was used to separate PCR products in the range of 100-120 bp.   (8) Library quantitative and pooling cyclization.  (9) Library QC.

treatment_protocol: Nicotiana benthamiana plants were infiltrated with Agrobacterium harboring plasmid 35S-NlCSP1 and 35S-GFP control, respectively. The samples consisted of four groups. Two experimental groups include N. benthamiana leaves infiltrated with NlCSP1 (NlCSP1_Z) and the upper uninfiltrated leaves (NlCSP1_O). The two control groups also include N. benthamiana leaves infiltrated with GFP (GFP_Z) and the upper uninfiltrated leaves (GFP_O). Three repeats for each group and 12 samples in total.

value: The upper uninfiltrated leaves of GFP-infiltrated Nicotiana benthamiana


title: GIB - cells from infected well residing on glass


title: GFP_O_3


title: GC - cells from uninfected well residing on glass

description: 2x10^5 cells grown on 12 mm collagen I coated glass coverslips for 48 h


title: GFP_O_1


title: Setd2-cKO-T-rep1

value: Setd2 knockout


title: Case

city: Jinan

first: Weidong

last: Zhao

address: Shandong University, Jinan, Shandong, 250012, China.

institute: Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong

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.
Then the clean reads were mapped to reference genome using hisat2.
StringTie was used to reconstruct the transcriptome.
FPKM value of each gene was calculated using cufflinks and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq (2012) R package functions estimate Size Factors and nbinomTest.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: endometrial cancer tissue

extract_protocol:
Total RNA extraction was performed with TRIzol reagent (Life Technologies, CA, USA), NEBNext Ultra RNA Library Prep Kit of Illumina (NEB, USA)  was used with three micrograms of total RNA per sample
Standard Illumina protocols was utilized for making the sequencing libraries

value: endometrial cancer tissue


title: Setd2-cKO-NT-rep3


title: Control

source_name: normal endometrium

value: normal endometrium


title: s14

city: Bethesda

first: Martina

last: Absinta

address: 10 Center Drive MSC 1400

department: NINDS

institute: NIH

data_processing:
CellRanger software was implemented for library demultiplexing, barcode processing, fastq file generation, gene alignment to the human genome (pre-mRNA GRCh38-3.0 human genome), and unique molecular identifier (UMI) counts.
Genome_build: pre-mRNA GRCh38-3.0 human genome
Supplementary_files_format_and_content: Comma-separated values files containing read counts for each gene by nucleus in matrix format.

source_name: Brain

extract_protocol:
Snap-frozen autopsy human brain tissue sampling used a 3mm-punch biopsy tool and a cold blade. Nuclei extraction from snap-frozen human autopsy brains was performed according to the following protocol. On wet ice, the frozen, dissected tissue was lysed using a Dounce homogenizer (10 strokes with the loose pestle followed by 20 strokes with the tight pestle) in 600-μl of freshly made cold lysis buffer (low sucrose buffer, Triton X-100 20%, Rnase inhibitor 40U/μl). Part of the homogenate (200 μl) was collected for bulk RNA extraction (Qiagen RNAeasy kit) and stored at -80°C for future applications. The remaining homogenate was filtered through a 40-μm cell strainer for nuclei extraction with 4-ml of low sucrose buffer (0.64M sucrose, HEPES pH8, CaCl2, MgAc, EDTA, DTT, nuclease-free water). Sonication of the homogenate was performed for 10 sec. To remove cellular and myelin debris, a sucrose gradient (12-ml of high sucrose buffer [2M sucrose, HEPES pH8, MgAc, DTT, nuclease-free water] underneath the low sucrose buffer) was centrifuged at 3,200 g for 30 minutes, and the supernatant was discarded. Nuclei were resuspended in 1-ml resuspension solution (PBS, 5% BSA and RNAse inhibitor 40U/μl) and centrifuged for 12-min at 3,200 g. Nuclei were again resuspended in 50-μl cold resuspension solution. Nuclei were counted using trypan blue and a haemocytometer under bright field. A yield of 700–1,200 nuclei/μl per sample was targeted.
Immediately after extraction, 5,000 nuclei/sample were loaded onto a Chromium Single Cell 3′ Chip (10X Genomics) and processed for the single-nucleus cDNA library preparation (Chromium Single Cell 3’ version 3, 10X Genomics) according to the manufacturer’s instructions without modifications.
Chromium Single Cell 3’ version 3, 10X Genomics

tag: clinical phenotype

value: progressive multiple sclerosis


title: GD - cells from uninfected well residing on glass


title: NlCSP1_O_3

value: The upper uninfiltrated leaves of NlCSP1-infiltrated Nicotiana benthamiana


title: GFP_Z_3

value: GFP infiltrated leaves


title: Setd2-WT-NT-rep1

value: Setd2 wild type


title: NlCSP1_O_2


title: NlCSP1_O_1


title: Setd2-cKO-T-rep2

value: liver tumor


title: s15


title: AML6_LSC_Control

value: leukemia stem cells


title: GFP_Z_2


title: Setd2-WT-NT-rep2

value: normal liver tissue


title: Tfh cells B6 rep1

value: Splenic cells

value: Follicular helper T cells

value: 8 months old

value: female


title: GB - cells from uninfected well residing on glass

value: Madin-Darby Canine Kidney (G-MDCK) epithelial cells

value: kidney tubule

value: immortalized

value: Obtained from the Bakardjiev lab, UCSF (previously obtained from ATCC)


title: s10


title: Setd2-cKO-NT-rep2

value: Setd2 knockout


title: 10d control #8

city: Dummerstorf

first: Alexander

last: Rebl

address: Wilhelm-Stahl-Allee 2

department: Institute of Genome Biology

institute: Research Institute for Farm Animal Biology

description: control fish (w/o stress)

hyb_protocol: The hybridization procedure was performed using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Equal amount of fragmented Cy3-labeled cRNA in hybridization buffer was hybridized to 8×60 K Whole Salmon Genome Oligo Microarrays (ID 020938, Agilent Technologies) using Agilent’s recommended hybridization chamber and oven. Following hybridization, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 at 37 °C for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using the Microarray Scanner System G2505C (Agilent Technologies).

data_processing: The Agilent Feature Extraction Software 12.1.1.1 was used to read out and process the microarray image files using default settings. FES corrected the background based on a two-sided Student t-test.

organism: Coregonus maraena

source_name: control fish (w/o stress)

label_protocol: 50 ng of RNA samples was amplified and labeled with the fluorescent dye cyanine 3 using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the Low Input Quick Amp protocol. Yields of cRNA and the dye-incorporation rate were measured.

growth_protocol: Fish were grown in water recirculation tanks of the Fisheries of the State Research Center for Agriculture and Fishery Mecklenburg-Western Pomerania (Born, Germany) and BiMES - Binnenfischerei GmbH (Friedrichsruhe, Germany). Fish were reared in fresh-water recirculation systems with a stocking density of 10 kg/m³ at 18 °C and a 12:12-h day-night cycle. Water quality was maintained by automated purification and disinfection (bio-filter and UV light).

extract_protocol: Fish was dissected and a portion of the head kidney was snap-frozen in liquid nitrogen. RNeasy Mini Kit (Qiagen, Hilden, Germany) in complement with the RNase-free DNase Set (Qiagen) allowed us to obtain high-quality RNA suitable for microarray hybridizations.

treatment_protocol: The fish (n = 48 in total) used in the experiments were juvenile with a starting size of about 20 cm. They were allowed to acclimatize to the recirculation system and the experimental tanks for at least 3 weeks. Experiments were always carried out in the morning (between 8 a.m. and 11 a.m.). To avoid tank effects, fish were placed in pairs consisting of one control fish and one test fish in identical dark-polyethene tanks (2 × 8 pairs; n = 32) during the acute stress experiments (3 h and 24 h). At the start of the experiment and before the handling procedure, one fish per pair was euthanized. This fish was designated the control fish (0 h). Following the sampling of the control fish, the stress protocol was applied for one minute to the remaining fish, designated the test fish. The stress protocol consisted of hunting and catching fish inside the water with nets, intermittently lifting the fish out of the tanks and finally transferring fish into secondary tanks, where pairs of test fish were left undisturbed for either 3 h or 24 h. After this period, test fish were euthanized and tissues were sampled as described below (see 2.3.). For the chronic handling stress experiment, control fish (n = 8) and test fish (n = 8) were kept in separate tanks for the duration of the experiment. Test fish were hunted and netted in the water for one minute once a day for ten days, while the controls were left undisturbed. The net lifting and tank-transferring steps performed in the acute-stress procedure were skipped in the chronic stress experiment to avoid skin injuries. To minimize habituation, handling was always performed at a random time within the 12 h ‘daylight’ period. Fish were euthanized 10 days after the onset of the chronic-stress procedures, 24 h after the last handling procedure.

value: head kidney

value: unknown

value: juvenile fish of ~ 20 cm


title: embryo2-head-3

first: Tengjiao

last: Zhang

address: 1239 Siping Road

department: School of life science and technology

institute: Tongji University

data_processing:
Raw reads were demultiplexed, filtered and mapped to the human reference genome (GRCh38) using Cell Ranger 3.0.2 with default settings. The filtered feature-barcode matrices generated by Cell Ranger were used for further analysis.
To exclude low-quality cells and doublets, cells with fewer than 1000 genes or over 60000 UMIs were discarded. The expression matrix was normalized into UMIs per 10000 by size factors.
Iterative clustering was performed to identify cell types. First, we partitioned cells into main clusters with Seurat (r=0.5, PCs=20) using only transcription factors in highly variable genes (HVGs). Second, for each main cluster, we performed one or two rounds of clustering with HVGs of the particular cluster.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix table with raw gene counts; csv files with gene and cell annotations.

growth_protocol: Aborted embryos from donations were washed with PBS, transferred into cold Hibernate-E medium (Gibco) and immediately transported to the laboratory. Embryos with good quality were staged based on anatomical characters.

extract_protocol:
Samples were incubated at 37°C for 10 minutes and were pipetted up and down thoroughly and gently every 3 minutes. To quench the dissociation, we added 300μl FBS into each tube and centrifuge cells at 300xg for 5 min at 4°C. Cells were then resuspended in 500μl cold PBS, filtered through a 35μm strainer. Single cells were subsequently washed twice with cold PBS, centrifuged at 300xg for 5 min at 4°C and resuspended in cold PBS.
To generate sequencing libraries, a suspension of 10,000 single cells per sample was processed following the 10x Genomics protocol using Single Cell 3’ Reagent Kits v2 (10x Genomics).

treatment_protocol: We dissected each embryo on ice into four main sections, i.e., head, trunk, viscera and limb. After the dissection, each sample was placed into separate tubes, washed twice with cold PBS, cut into pieces and suspended in 300μl Hibernate-E medium with 0.05mg/ml Liberase TM (Roche).

value: embryo head

value: Female

tag: Stage

value: Carnegie Stages 13


title: s11

value: progressive multiple sclerosis


title: NlCSP1_Z_3

value: NlCSP1 infiltrated leaves


title: GFP_Z_1

value: GFP infiltrated leaves


title: GA - cells from uninfected well residing on glass


title: NlCSP1_Z_2


title: scRNA-seq_HSD_hepatocytes

city: Dallas

first: Simeng

last: Wang

address: 5323 Harry Hines

institute: UT Southwestern Medical Center

data_processing:
Raw data was demultiplexed using cellranger (version 3.1.0) and barcode-aware wrapper (version 2.17.1.14) supported by 10X Genomics’ pipeline. Transcriptomes were aligned to Genome Reference Consortium Mouse Build 38 (mm10) using STAR
Seurat (version 3.2.0) was applied for single cell transcriptome analysis and plots on R (version 3.5.1). Low quality cells and multiplets were excluded. UMI counts were scaled and variations due to differences in UMI/cell.
Cells in each pair of mice fed a chow or high-fat-and-high-sucrose diet were integrated to better understand cell identity and function.
The highest variable genes were used for UMAP visualization and clustering. Sub-clustering hepatocytes and stellate cells were based on different resolutions.
Genome_build: Genome Reference Consortium Mouse Build 38 (mm10)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: Hepatocytes from whole liver of mouse fed a high-fat-and-high-sucrose diet

growth_protocol: Mice were housed at room temperature (23˚C) and maintained on a 12 hr light/dark cycle and provided ad libitum access to rodent chow (Harlan, Teklad Global 18% Protein Rodent Diet 2018; 18% kcal from fat, 3.1 kcal/g), high-fat-and-high-sucrose diet (17% kcal from sucrose, 45% kcal from fat, Research Diets D12451).

extract_protocol:
Hepatocytes and stellate cells were isolated using pronase/collagenase digestion. After Nycodenz gradient centrifugation, whole liver tissue is digested, and we treated, washed and collected the single cell suspension.
10X Genomics Chromium Single Cell 3’ Library and Gel Beads Kit (version 3) according to manufacturer’s protocol. Libraries were sequenced on an Illumina NextSeq 500 with high output of 400 million reads.
Single Cell RNA sequencing

treatment_protocol: Two pairs of mice were used for study. One pair were fed a high-fat-and-high-sucrose diet for 17 weeks. The other pair is age-matched control mice fed a chow diet. One mouse of each pair is perfused for hepatocytes isolation; the other one of each pair is perfused for stellate cell isolation.

value: Liver

tag: cell type

value: Hepacytes

tag: disease state

value: NAFLD

tag: diet

value: High-fat-and-high-sucrose diet


title: Setd2-cKO-NT-rep1

first: Qinglan

last: Li

institute: Wuhan University

value: normal liver tissue

tag: treatment


title: embryo2-head-1


title: uni-0956C: VCA0956, uninduced, replicate C

city: Kalamazoo

first: Ben

middle: James

last: Koestler

state: MI

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

institute: Western Michigan University

data_processing:
Set paired end reads (Geneious)
Raw sequences were trimmed using BBDuk (Geneious)
Reads were mapped to reference (AE014073.1, AF386526.1, AF250878, and VCA0956 from NC_002506) using Geneious mapper
Expression analysis was carried out to determine RPKM, FPKM and TPM (Geneious)
Supplementary_files_format_and_content: .xlsx file contains mapping and differential expression for each Shigella gene

organism: Shigella flexneri 2a str. 2457T

source_name: Bacteria RNA

growth_protocol: S. flexneri grown in LB + DOC (0.05% w/v), supplemented with Kanamycin (50 μg/ml) to maintain pVCA0956. Cultures incubated at 37 C, shaking at 220 rpm for 3 hours.

extract_protocol:
Purelink RNA Mini Kit (Thermo Fisher, 12183020) using the manufacturers protocol with Trizol reagent
RNA libraries were prepared for sequencing using standard protocols (Genewiz). Sequencing was performed by Genewiz.

treatment_protocol: Induction of the pTac promoter of VCA0956 using IPTG (100 μM)

tag: condition

value: -IPTG

value: LB + DOC, mid-log


title: NlCSP1_Z_1


title: s13


title: embryo2-head-4


title: s9


title: Naïve B cell-HC2_Y20

city: Guangzhou

first: Binfeng

last: Chen

address: 58 Zhongshan Second Road

institute: Department of Rheumatology, The First Affiliated Hospital, Sun Yat-sen University

data_processing:
Using FastQC (version 0.11.9) for quality assessment and HISAT2 (version 7.5.0) for alignment, with parameter -p for paried sequencing, and others are all default parameters
Using FeatureCounts (version 2.0.1) for transcripts assemble and expression levels calculation
Supplementary_files_format_and_content: raw counts

source_name: Naïve B cell

growth_protocol: Naïve human B cells were isolated from 3 donors and stimulated with anti-human IgM (5μg/ml) and anti-human CD40 (1μg/ml) antibodies

extract_protocol:
RNA purification was performed using Qiagen RNeasy Kit (Valencia, CA). 50 pg of total RNA was used as input for the SMART-seq v3 cDNA synthesis kit (Takara). 1 ng of cDNA was used as input for the NexteraXT kit (Illumina) using 9 cycles of PCR amplification. Final libraries were quantitated by qPCR and sized distribution determined by Bioanalyzer prior to pooling and sequencing on a HiSeq2500 using 50bp PE chemistry.
The RNA-seq libraries were made with Illumina HiSeq protocol.

treatment_protocol: YM-58483 or vehicle for 72h

value: peripheral blood

value: naive B cell

value: treated with 20nm YM-58484


title: scRNA-seq_Chow_hepatocytes

source_name: Hepatocytes from whole liver of mouse fed a chow

tag: strain

value: Normal

value: Chow


title: InjPBS_rep3

city: Cologne

first: Ali

middle: T

last: Abdallah

address: Joseph Stelzmann Str. 26

department: Medical Faculty

institute: University of Cologne

description:
DEA_IL36_and_IL17a_vs_PBS.tsv
DEA_IL36_vs_PBS.tsv
DEA_IL17a_vs_PBS.tsv
counts.tsv

data_processing:
The RNA-Seq data primary analysis was performed with an in-house pipeline embedded in the QuickNGS workflow management system[45]: Generation of the fastq files and adapter removal was completed using the Illumina demultiplexing and conversion software bcl2fastq [https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html]. Quality control checks of the RNA-Seq data were done with fastqc available online (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Subsequently, the reads were aligned to the mm10 reference genome sequence using STAR (v2.5.2b) with default parameters [46]. In the quantification step, reads were counted with featureCounts from the subread package v1.5.1 available online (http://subread.sourceforge.net)
Differential expression analysis was performed in R using the DESeq2 package (v1.30.0) [48]: First, the size factors of each sample were estimated using the function estimateSizeFactors with default parameters, then the dispersions of the counts were estimated by setting the minimal dispersion to 10e-6 and setting the fit type parameter to “local”. Finally, the likelihood ratio test (chi-squared test) for GLMs (negative binomial likelihood ratio test) was used to generate the differentially expressed genes (log2 fold change > 1 and corrected p-value <= 0.05).
Genome_build: mm10
Supplementary_files_format_and_content: For each two pairs of conditions we provide the results table.

source_name: Injection of PBS

extract_protocol:
The tissues of the mouse ears were mechanically disrupted and homogenized by using tissue lyzer (Qiagen). The Nucleo Spin RNA (Macherey-Nagel, Düren, Germany) kit was used for total RNA extraction, according to the manufacturer’s instructions. Residual genomic DNA was removed by rDNase (RNase-free) digestion.
The cDNA libraries were generated using a TruSeq Stranded Total RNA Sample Preparation Kit (Illumina).

treatment_protocol: The cytokines IL-36γ and IL-17A (1µg of each cytokine dissolved in PBS; volume 5µl) were injected intradermally alone or in combination into the ear pinnae of C57BL/6 mice. PBS was used as control. Ear thickness measurement was performed daily. After 4 days mice were euthanized and a gene expression profiling was conducted.

value: Skin


title: embryo2-head-2

value: embryo head

value: Female

value: Carnegie Stages 13


title: 10d stressed #4

description: 10 d of repeated handling stress

source_name: 10 d of repeated handling stress

value: head kidney

value: unknown

tag: age

value: juvenile fish of ~ 20 cm


title: InjPBS_rep2


title: scRNA-seq_HSD_stellate cells

source_name: Stellate cells from whole liver of mouse fed a high-fat-and-high-sucrose diet

value: Liver

value: Stellate cells

value: NAFLD


title: uni-0956A: VCA0956, uninduced, replicate A

value: -IPTG


title: Naïve B cell-HC3_Y0

value: treated with vehicle


title: 0956C: VCA0956, induced, replicate C

value: +IPTG

value: LB + DOC, mid-log


title: 10d control #6

description: control fish (w/o stress)

tag: gender


title: 0956B: VCA0956, induced, replicate B


title: Naïve B cell-HC3_Y20

value: peripheral blood

value: naive B cell

value: treated with 20nm YM-58485


title: triple negative breast cancer biopsy

city: Boston

first: Simona

last: Cristea

state: Massachusetts

address: 450 Brookline Ave.

department: Biostatistics and Computational Biology

institute: Dana-Farber Cancer Institute

data_processing:
Sample demultiplexing, reference mapping, barcode processing and gene counting were performed using Cell Ranger 4.0.0 (10X Genomics).
Reads were aligned to the GRCh38 human reference genome. Genes expressed in at least 10 cells (yielding 10,569 genes), as well as cells with at least 100 genes expressed and less than 20% mitochondria (587 cells) were retained.
The data was preprocessed with SCTransform as implemented in Seurat 4.0.1, and normalized data was used as input for PCA, followed by dimensionality reduction on the PCA space with Uniform Manifold Approximation and Projection (UMAP). All functions were used with default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: text files containing SCT-normalized expression values (the 'data' slot in the Seurat object) for each analyzed cell after QC.

source_name: human breast

extract_protocol:
Droplet-based single-cell RNA sequencing was performed on single-cell suspension using the Chromium Single Cell 3’ v3 Library, Gel Bead and Chip Kit (10X Genomics), according to the manufacturer’s instruction.
single cell RNA-sequencing

treatment_protocol: The single-cell suspension of the sample was cryopreserved prior to sequencing.

value: treatment-naïve


title: Naïve B cell-HC1_Y0


title: InjL17A_rep2

description:
DEA_IL17a_vs_PBS.tsv
DEA_IL36_and_IL17a_vs_IL17a.tsv
counts.tsv

source_name: Injection of IL17A

value: Skin


title: 10d control #5

description: control fish (w/o stress)


title: uni-0956B: VCA0956, uninduced, replicate B


title: CM_e2r

city: Norwich

first: Wenbo

last: Ma

address: Norwich Research Park

institute: The Sainsbury Laboratory

description:
Mac_3_S117_L006
Biological replicate 1

data_processing:
The quality of the raw sequencing data was checked with FastQC v0.11.9
Read adapters were trimmed from reads using Trimmomatic v 0.36
reads were aligned with the indexed CLas-Psy62 isolate genome assembly (NC_012985.3) and parsed to it using HISAT2 v2.1.0
The number of reads mapped to each gene was counted using the feature counts function of the Rsubread package
Read counts were normalized for each sample for differential expression analysis using DESeq2 v1.30.1
Genome_build: NC_012985.3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized read counts for every genes and every sample

organism: Citrus macrophylla

source_name: midrib

extract_protocol:
Freeze-dried HLB-infected midribs (from 15–25 leaves) were ground to a fine powder in liquid nitrogen. 1ml of TLE extraction buffer was added to 100 mg citrus powder or the pellet obtained after the above bacterial isolation. Then, 60 µL of 500 mM CaCl2 was added, mixed thoroughly, and placed on ice for 10 min. Centrifugation at 12,000 x g for 10 min at 4 °C was performed, followed by two rounds of separation with 500 µl of phenol:Chloroform:isoamyl alcohol (25:25:1) and centrifugation at 15,000 x g for 10 min at 4 °C. The supernatant was mixed with 2 M LiCl and incubated overnight at -20 °C. RNA was precipitated by centrifugation at 15,000 x g for 30 min, washed twice with ice-cold 75% ethanol, centrifuged at 15,000 x g for 15 min and re-suspended in 20 µl of RNAse-free water. 10–15 adult psyllids were ground in liquid nitrogen, immediately suspended in 50 μl TRIzol® (Invitrogen) and ground until complete homogenization. An additional 950 μl of TRIzol® was added to the homogenate, followed by separation with 200 µl of chloroform, precipitation with 500 µl of isopropanol, and two washes with 75% ethanol as indicated by the manufacturer. The pellet was resuspended in 20-30 µl of RNAse-free water.
RNA was converted into sequencing-ready libraries for Illumina sequencing using TruSeq Stranded Total RNA reagents. Poly(A) Polymerase (NEB) treatment (polyA) and Poly(dT)-depleted library construction was tested in parallel. cDNA libraries were subjected to RNASeq, using an Illumina HiSeq-4000 system with 150-bp strand-specific single-end reads with technical duplicates.

treatment_protocol: pre-enrichment (bacterial isolation) performed according to Nobori et al. 2018, 1-step post enrichment using MICROBEnrich, 2-step enrichment using MICROBEnrich followed byRiboMinus Eukaryote Kit. All samples underwent ribodepletion using Illumina Ribo-Zero Plus except a subset of 2-step enrichmed RNA samples that underwent poly(A) polymerase treatment (polyA)

value: midrib

value: 2-step enrichment ribodepletion


title: 3h stressed_#8

description: 3 h after handling stress

source_name: 3 h after handling stress

value: head kidney


title: scRNA-seq_Chow_stellate cells

source_name: Stellate cells from whole liver of mouse fed a chow

value: Normal

value: Chow


title: CM_e2a

description:
CL100125429_L2_HK500CITdpmRAABRAAPEI-506
Biological replicate 1

value: 2-step enrichment polyA


title: 24h control_#4

description: control fish (w/o stress)

value: unknown

value: juvenile fish of ~ 20 cm


title: Naïve B cell-HC2_Y0


title: 10d control #7

description: control fish (w/o stress)