title: third_experiment_D21_HTO

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

data_processing:
For single cell analysis we used cellranger (v3.0.2) from 10X Genomics for single-cell UMI quantification and TCR clonotype assembly. Hashtags oligos (HTOs) UMI counts were processed using CITE-Seq-Count (v1.4.0). We used Seurat (v3.1.2) [1-2], an R package to analyze single cell RNA-seq data, to identify differentially expressed genes. Genes expressed in at least 10 percent of all cells belonging to clones exhibiting expansion or contraction, with the adjusted p-value by Bonferroni correction less than 0.05 and with |average logeFC| > loge(1.1) were selected as statistical significant differentially expressed genes.
For bulk RNASeq we used kallisto (v.0.46) to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 99). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis. Differentially expressed genes were defined by having adjusted p-value < 0.05 and | logFC| > log2(1.5).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with abundance and differential expressiong
Supplementary_files_format_and_content: HTML Report 10x Single Cell

source_name: T Follicular Helper (Tfh) Cells

growth_protocol: Single-cell suspensions were prepared from the spleens and lymph nodes of donor mice. CD4+ T cells were enriched using immunomagnetic negative selection (StemCell Technologies). For adoptive transfer experiments 0.5-1x106 CD4+ T cells were injected into recipient mice by intravenous injection. Resting B cell suspensions were cells were enriched using immunomagnetic positive selection using CD43 (StemCell Technologies).. ∼5 × 106 B1-8hi B cells (5 × 105 Igλ+, NP-specific B cells) composed of the indicated populations were injected into recipient mice by intravenous injection.

extract_protocol:
For bulk RNA sequencing experiments congenic OTII Tfh cells (CD4+, CD62low, CXCR5hi, PD-1hi) or positively selected B cells (500 cells) were purified by flow cytometry 18 hours after pre-immunized host mice were injected with aDEC-205 chimeric antibodies. 1ng of total RNA was used to generate full length cDNA using Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit
The cDNA was used to prepare libraries using Illumina Nextera XT DNA sample preparation kit (Cat # FC-131-1024).   Libraries with unique barcodes were pooled at equal molar ratios and sequenced on an Illumina NextSeq 500 sequencer to produce 75bp reads, following manufactures protocol (Cat# 15048776). For single cell RNA sequencing, single cell spleen suspensions were prepared from half-spleens of NP-OVA immunized SellCreERT2 ROSAtdT mice on day 7 and 21 after immunization. Samples were indexed with TotalSeqC (BioLegend) cell surface antibodies and CD4+, CD62low, CD44hi, PD1hi, CXCR5high, tdTomato+ T cells were purified by flow cytometry, pooled and loaded on to a Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the mid-Output Kit (150 paired end) for V-D-J analysis or NOVAseq for single cell gene expression. Hashtag indexing was used to demultiplex the sequencing data and generate gene-barcode matrices, respectively.

tag: genotype/variation

value: D011.10 and OTII

value: spleen

tag: molecule target

value: Antibody-bound oligos


title: X51378P3

status: Public on Mar 19 2020

type: SRA

city: Cambridge

first: Richard

last: Gilbertson

address: Robinson way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

library_source: transcriptomic

data_processing:
SE 50bp end reads aligned to GRCm38 with HISAT2 (default parameters)
Reads counted on annotated features with sub-reads featureCounts
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Mus musculus

source_name: primary cerebella

extract_protocol:
Cerebella and Tumor samples were removed  flash frozen on dry ice. RNA was extraceted using Trizol reagent. Qiagen RNeasy Plus universal kit (Cat. # 73404) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sampletype

tag: genotype

value: BD-FLY

tag: tissue

value: Cerebellum

tag: age

tag: replicate

tag: model


title: third_experiment_D21_VDJ

state: New York

country: USA

institute: The Rockefeller University

data_processing:
Library strategy: CITE-Seq
For single cell analysis we used cellranger (v3.0.2) from 10X Genomics for single-cell UMI quantification and TCR clonotype assembly. Hashtags oligos (HTOs) UMI counts were processed using CITE-Seq-Count (v1.4.0). We used Seurat (v3.1.2) [1-2], an R package to analyze single cell RNA-seq data, to identify differentially expressed genes. Genes expressed in at least 10 percent of all cells belonging to clones exhibiting expansion or contraction, with the adjusted p-value by Bonferroni correction less than 0.05 and with |average logeFC| > loge(1.1) were selected as statistical significant differentially expressed genes.
For bulk RNASeq we used kallisto (v.0.46) to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 99). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis. Differentially expressed genes were defined by having adjusted p-value < 0.05 and | logFC| > log2(1.5).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with abundance and differential expressiong
Supplementary_files_format_and_content: HTML Report 10x Single Cell

tag: strain

value: VDJ RNA


title: third_experiment_D7_HTO


title: second_experiment_D21_HTO


title: X48277P4

value: BD-FL-FL


title: X48277P2


title: X47126P1

value: BCP

value: Wnt


title: X47129P8


title: X47124

value: BDCP-FLPlus


title: X47172


title: X48275P3

value: WT


title: second_experiment_D7_VDJ


title: second_experiment_D21_VDJ


title: T9: Tcell_NO_TOTAL_OTII_TFH

value: OTII-Fucci


title: X39590

value: BDCP-FLY


title: T8: Tcell_NO_TOTAL_OTII_TFH


title: X48277P5


title: T7: Tcell_NO_TOTAL_OTII_TFH


title: X47123


title: X36279


title: second_experiment_D7_HTO


title: T5: Tcell_aDEC_LOW_TOTAL_OTII_TFH


title: T6: Tcell_aDEC_LOW_TOTAL_OTII_TFH


title: X35942


title: X48277P1


title: X35778


title: T4: Tcell_aDEC_LOW_TOTAL_OTII_TFH


title: X35940


title: X33063


title: third_experiment_D7_VDJ


title: T3: Tcell_aDEC_WT_TOTAL_OTII_TFH


title: T2: Tcell_aDEC_WT_TOTAL_OTII_TFH


title: X32707


title: T1: Tcell_aDEC_WT_TOTAL_OTII_TFH


title: X312P6


title: B6: Bcell_aDEC_LOW_LZ_GC_FUCCI

source_name: Light Zone Germinal Center B cells

value: Fucci


title: B9: Bcell_aDEC_NO_LZ_GC_FUCCI


title: X312P3

value: BDCP-FLFL


title: X312P4


title: B7: Bcell_aDEC_NO_LZ_GC_FUCCI


title: X29142


title: B8: Bcell_aDEC_NO_LZ_GC_FUCCI


title: X28050


title: B5: Bcell_aDEC_LOW_LZ_GC_FUCCI


title: X28048


title: X27717


title: B2: Bcell_aDEC_WT_LZ_GC_FUCCI


title: B3: Bcell_aDEC_WT_LZ_GC_FUCCI


title: B4: Bcell_aDEC_LOW_LZ_GC_FUCCI


title: B1: Bcell_aDEC_WT_LZ_GC_FUCCI


title: X27711


title: X28046


title: 12week_APC_rep2_RNAseq

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

institute: University of Pittsburgh

data_processing:
Paired-end reads were aligned to mm10 (mouse models) using RSEM (Li and Dewey, 2011).
We assessed the transcripts per million (TPM) changed and visualized the gene expression changes in the wild-type and ApcMin/+ mice. RSEM output files were used for downstream analysis using HOMER (Heinz et al., 2010).
DESeq2 (Love et al., 2014) was used to identify the differentially expressed genes based on significance.
To sort the data, K-means clustering was performed using Cluster 3.0 (de Hoon et al., 2004) and heatmaps were generated using Java TreeView (Saldanha, 2004).
Gene Ontology (GO) term enrichment was performed to identify gene classes that are mis-regulated using Metascape software (Tripathi et al., 2015).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: villi cells from mouse intestine

growth_protocol: 12-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and pelleted.

extract_protocol:
RNA was extracted from intestinal cells using TRIzol followed by column purification (Zymo RNA clean and concentrator column) following the manufacturers’ instructions. Total RNA was depleted of rRNA using a Ribo-Zero Gold kit and first strand cDNA was synthesized. Subsequently, second strand cDNA was synthesized, purified, and fragmented.
Following purification over a Zymo RNA clean and concentrator column, first strand cDNA was synthesized. Subsequently, second strand cDNA was synthesized, purified, and fragmented. RNA-seq libraries were prepared using Illumina technology. Briefly, end repair, A-tailing, and barcoded adapter ligation followed by PCR amplification and size selection. The integrity of the libraries was confirmed by quBit quantification, fragment analyzer size distribution assessment, and Sanger sequencing of ~10 fragments from each library. Libraries were sequenced using paired-end Illumina sequencing.

value: ApcMin/+

value: intestine

tag: cell type

value: villi cells


title: X26862


title: 12week_WT_RNAseq

value: wild-type


title: X26863


title: X25417


title: X24992


title: 12week_WT_H3K4me3

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

molecule: genomic DNA

growth_protocol: 12-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and nuclei were extracted using a hypotonic buffer.

extract_protocol:
Unfixed nuclei were bound to Concanavalin A beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by calcium chloride addition and stopped by EDTA. Fragments were released and deep sequencing libraries were prepared.
CUT&RUN

treatment_protocol: Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

tag: primary antibody, vendor, catalog number and batch

value: anti-H3K4me3, Millipore, Cat# 05-745R , Lot 2918042, used at 1:100, final

tag: secondary antibody

value: proteinA-MNase, used at 1:200


title: 12week_WT_H3K9me3_rep2

value: anti-H3K9me3, abcam Cat #ab8898, Lot #GR3217595-1, used at 1:100, final


title: X26855

value: Cerebellum


title: X23601

value: BD-FLPlus


title: 12week_WT_noab

value: no antibody added


title: X23241

value: BD-FLY


title: X23600


title: 12week_WT_H3_rep2

value: anti-Total H3, abcam Cat #ab1791, Lot #GR3198215-1, used at 1:100, final


title: 12week_APC_noab


title: 12week_WT_H3K9me3_rep1


title: X23154


title: 12week_APC_H3K9me3_rep2


title: 12week_WT_H3_rep1


title: X23149

value: BD-FL-FL


title: X23150


title: 12week_APC_rep1_RNAseq


title: 12week_APC_H3K9me3_rep1


title: X22816

value: BCP

value: Wnt


title: X22313


title: X21766


title: 12week_APC_H3_rep2


title: 12week_APC_H3_rep1


title: X20521

value: WT


title: 12week_APC_H3K4me3


title: X19113

value: BDCP-FLFL


title: X19117


title: X17956


title: X27715

value: BDCP-FLPlus


title: X10459


title: X23151


title: X17955


title: X10463


title: X12564P6


title: mIslets_III_GABA

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: Mouse pancreatic islet cells, treated with GABA(100muM) for 72hr, replicate: 3

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 2.1.0).
Sequencing data were aligned to the reference genome with Cell Ranger count and merged with Cell Ranger aggr.
Genome_build: Human: GRCh38/h38, Mouse: mm10
Supplementary_files_format_and_content: Matrices: corrected transcript per million (TPM) matrices. Data in mtx format, row names (genes), and column names (barcodes)
Supplementary_files_format_and_content: CellAnnotation_final.tsv; Annotation of cell types to barcodes

source_name: Pancreatic Islet cells

growth_protocol: Human islets were extracted cadaveric donors and shipped using the Islet Integrated Distribution Program (IIDP) Mouse islets were extracted and shipped from the Collombat laboratory. Both human and mouse islets were cultured in CMRL media supplemented with 10% FBS and 1X Glutamax, and mantained in culture at 37 C in a 5% CO2 humidified atmosphere.

extract_protocol:
Islet dissociation was performed by incubating the islets in accutase for 20 min at room temperature. Reaction was stopped by adding CMRL media with 10% FBS. The dissociated islets were filtered through a 40 µm filter to obtain a single-cell suspension.
Single-cell RNA-seq was performed using the Single Cell 3’ Library & Gel Bead Kit v2 (10x Genomics) according to the manufacturer’s protocol.

treatment_protocol: Islets were treated with 10muM Artemether, 100 muM GABA, 10 muM FoxO inhibitor and DMSO as control for 36 and 72 hours.

value: Pancreatic Islet cells

tag: treatment

tag: treatment time


title: mIslets_III_FoxO

description: Mouse pancreatic islet cells, treated with FOXO inhibitor for 72hr, replicate: 3

value: FOXO inhibitor


title: mIslets_III_DMSO

description: Mouse pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 3

value: DMSO (Control)


title: mIslets_III_A10

description: Mouse pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 3

value: Artemether (10muM)


title: mIslets_II_A10

description: Mouse pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 2


title: mIslets_I_DMSO

description: Mouse pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 1


title: mIslets_II_FoxO

description: Mouse pancreatic islet cells, treated with FOXO inhibitor(10muM) for 72hr, replicate: 2

value: FOXO inhibitor(10muM)


title: mIslets_I_FoxO

description: Mouse pancreatic islet cells, treated with FOXO inhibitor(10muM) for 72hr, replicate: 1


title: mIslets_II_DMSO

description: Mouse pancreatic islet cells, treated with DMSO (Control) for 72hr, replicate: 2


title: mIslets_I_GABA

description: Mouse pancreatic islet cells, treated with GABA(100muM) for 72hr, replicate: 1


title: mIslets_I_A1

description: Mouse pancreatic islet cells, treated with Artemether (10muM) for 72hr, replicate: 1


title: X17957


title: mIslets_II_GABA

description: Mouse pancreatic islet cells, treated with GABA(100muM) for 72hr, replicate: 2


title: Sample_257_Incisional biopsy

city: Bergen

first: Stian

last: Knappskog

department: Department of Clinical Sciences

country: Norway

institute: University of Bergen

data_processing:
De-multiplexing was performed using the Illumina CASAVA software
FastQC was run on all samples with the main purpose to assess sequence qualit
The raw sequencing files (fastq) were processed using the novel miRNA prediction algorithm mirdeep v2.0.0.5
Potential novel miRNAs were identified using the human reference genome and already identified miRNAs from humans and other hominids from miRbase 20
Genome_build: hg19
Supplementary_files_format_and_content: novel miRNAs

organism: Homo sapiens

extract_protocol:
Incisional biopsies were collected before chemotherapy from 223 patients with locally advanced breast cancer in a prospective study designed to identify the response to epirubicin (n = 109) and paclitaxel (n = 114) monotherapy. Primary response to therapy as well as long-term follow up (>10 years or death) was recorded for all patients.
Tissue samples were snap-frozen in liquid nitrogen in the operating theatre and stored in liquid nitrogen until further processing. Total RNA was extracted from the biopsies using miRvanaTM kit (ThermoFisher), according to the manufacturer’s instructions
single sequencing were performed on Illumina HiSeq 2500 to obtain 50bp reads

tag: gender

value: female

value: locally advanced breast cancer

value: epirubicin monotherapy

tag: estrogen receptor (er) status

value: positive

tag: molecule subtype

value: small RNA


title: X17954

value: Cerebellum


title: Sample_240_Incisional biopsy


title: Sample_248_Incisional biopsy

value: paclitaxel monotherapy

value: negative


title: Sample_247_Incisional biopsy


title: Sample_235_Incisional biopsy


title: Sample_236_Incisional biopsy


title: Sample_259_Incisional biopsy


title: mIslets_III_A1


title: Sample_219_Incisional biopsy


title: Sample_207_Incisional biopsy


title: Sample_203_Incisional biopsy


title: Sample_220_Incisional biopsy


title: mIslets_II_A1


title: Sample_199_Incisional biopsy


title: mIslets_I_A10


title: Sample_192_Incisional biopsy


title: APC_H3K4me3_rep2

data_processing:
library strategy: CUT&RUN
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

source_name: APC_H3K4me3_villi cells from mouse intestine

extract_protocol:
5-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and nuclei were extracted using a hypotonic buffer.
Unfixed nuclei were bound to ConcanavalinA beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase.
Cleavage of Mnase was initiated by Ca** addition and stopped by chelation. Fragments were released and deep sequencing libraries were prepared.

tag: strain background

tag: genotype/variation

value: ApcMin/+

value: small intestine

tag: primary antibody

value: anti-H3K4me3, Millipore, Cat# 05-745R , Lot 2918042, used at 1:100, final

value: proteinA-MNase, used at 1:200


title: APCrep2_RNAseq

description:
5-week wild-type mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and pelleted
RNA was extracted from intestinal cells using TRIzol followed by column purification (Zymo RNA clean and concentrator column) following the manufacturers’ instructions. Total RNA was depleted of rRNA using a Ribo-Zero Gold kit and first strand cDNA was synthesized. Subsequently, second strand cDNA was synthesized, purified, and fragmented.

growth_protocol: 5-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and pelleted.


title: WT_RNAseq


title: Sample_186_Incisional biopsy


title: WT_H3K4me3_rep2

source_name: WT_H3K4me3_villi cells from mouse intestine

value: wild type


title: WT_H3K4me3_rep1


title: Sample_172_Incisional biopsy


title: Bcells_TENT5C_wt_3

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

data_processing:
Illumina bcl2fastq 2.20 software used for basecalling.
Sequence reads were mapped to the mm10 mouse genome build using STAR v. 2.6.1a
Counts for each transcript were collected using featureCounts from Subread package (v. 1.6.3),  with options -Q 10 -p -B -C -s 2 -g gene_id -t exon and Gencode vM19 annotation.
Differential expression analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include DESeq2 normalized counts for each sample.

source_name: primary B cells activated in vitro

growth_protocol: Mice were bred in conventional conditions at the Animal House at the Faculty of Biology, University of Warsaw under 12h light/dark cycle at an ambient temperature of 22°C. Health monitoring was performed regularly at the IDEXX laboratory. Experimental mice originated from heterozygotic matings and as a result were cohoused littermates. All procedures were approved by the I Local Ethical Committee in Warsaw, Poland. All mice were sacrificed by cervical dislocation and spleen was isolated immediately. Naïve B-cells were isolated from spleen using immunomagnetic negative selection with EasySep Mouse B Cell Isolation Kit  (Stemcell; 19854) according to the manufacturer’s instructions. Primary cells were cultured in RPMI 1640 ATCC’s modified (Invitrogen) supplemented with 15% FBS (Invitrogen), 100 nM 2-mercaptoethanol (Sigma), penicillin/streptomycin (Sigma) and activators or mitogens.

extract_protocol:
RNA isolation was performed with Trizol reagent (Invitrogen, 15596) according to the manufacturer’s instructions and followed by ribodepletion using a Ribo-Zero Kit (Epicentre, RZG1224), according to the manufacturer's recommendations  and spike-in with external RNA (ERCC RNA Spike-In Mix, 4456740).
Strand-specific libraries were prepared using a dUTP protocol (KAPA Stranded RNA-Seq Library Preparation Kit), according to the manufacturer. Library quality was assessed using chip electrophoresis performed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: 20 ng/ml IL-4 (Peprotech),  20 ug/ml LPS (Santa Cruz) for 7 days

value: mixed C57BL/6J X CBA

tag: genotype

tag: batch


title: Sample_154_Incisional biopsy

tag: tissue


title: Sample_153_Incisional biopsy


title: Bcells_TENT5C_wt_2


title: Sample_146_Incisional biopsy


title: Sample_140_Incisional biopsy


title: Sample_142_Incisional biopsy


title: Sample_138_Incisional biopsy


title: Bcells_TENT5C_wt_1


title: APCrep1_RNAseq


title: Sample_132_Incisional biopsy


title: Bcells_TENT5C_KO_3

value: TENT5C KO


title: WT_H3K9m3_rep2

description:
5-week wild-type mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and nuclei were extracted using a hypotonic buffer.
Unfixed nuclei were bound to Concanavalin A beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by calcium chloride addition and stopped by EDTA. Fragments were released and deep sequencing libraries were prepared.

data_processing:
Barcode adapter sequences removed
Reads mapped to mm10 genome using Bowtie2, and allowing 1 mismatch
Picard used to remove duplicates
Low quality reads were removed (MAPQ <10)
Reads divded into size classes: 1-120 or 150-500
Aligned reads were processed in HOMER by using the “annotatePeaks” command to make 20 bp bins over regions of interest and sum the reads within each window.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

growth_protocol: 5-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and nuclei were extracted using a hypotonic buffer.

extract_protocol: CUT&RUN

value: anti-H3K9me3, Abcam, Cat# ab8898 , Lot GR3217595-1, used at 1:100, final

value: proteinA-MNase generated by Fazzio lab, used at 1:200


title: APC_H3K9m3_rep2

description:
5-week ApcMin/+  mice were sacrificed, and their small intestine were removed and washed with PBS. After scraping villi cells from mouse intestine, cells were pelleted, washed with cold PBS, and nuclei were extracted using a hypotonic buffer.
Unfixed nuclei were bound to Concanavalin A beads, washed, followed by successive addition of primary antibodie followed by proteinA-Mnase. Cleavage of Mnase was initiated by calcium chloride addition and stopped by EDTA. Fragments were released and deep sequencing libraries were prepared.


title: APC_H3K9m3_rep1


title: APC_H3K4me3_rep1

tag: age


title: WT_H3K9m3_rep1


title: APC_H3_rep2

value: anti-H3, Abcam, Cat# ab1791 , Lot GR3198215-1, used at 1:100, final


title: Sample_127_Incisional biopsy

value: female

value: locally advanced breast cancer


title: Sample_114_Incisional biopsy


title: Sample_107_Incisional biopsy

value: positive


title: Sample_102_Incisional biopsy

value: small RNA


title: Sample_108_Incisional biopsy


title: APC_H3_rep1


title: Sample_101_Incisional biopsy

value: epirubicin monotherapy


title: WT_H3_rep2


title: APC_NoAb_rep2


title: Sample_087_Incisional biopsy


title: Bcells_TENT5C_KO_1


title: APC_NoAb_rep1


title: Sample_086_Incisional biopsy

value: paclitaxel monotherapy


title: WT_NoAb_rep1


title: Sample_080_Incisional biopsy

value: negative


title: Sample_130_Incisional biopsy


title: Sample_071_Incisional biopsy


title: Sample_129_Incisional biopsy


title: MCS_TiB2

city: Houston

first: Fatima

middle: A

last: Merchant

state: TX

address: Technology Building, Room 304 4300 Calhoun Road

department: Engineering Technology

institute: University of Houston

description: Interrogated Sample TiB2

data_processing:
RNA-seq files were processed with CLC Genomics Workbench v12 (Qiagen); reads were mapped to hg38 human reference genome from which count data were derived
DESeq2 was used to correct for multiple hypothesis testing and determine significantly modified transcripts
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files including per sample: gene name, chromosome region, ENSEMBL identifier, total counts, RPKM, TPM, CPM

source_name: MCS cells grown on a micropatterned TiB2 surface

growth_protocol: HUVEC cells were cultured in Medium 199 supplemented with 20% FBS, 1% fungizone, 1% penicillin/streptomycin, 1% heparin, 1% HEPES and 1% endothelial cell growth factor (Sigma-Aldrich). MCS cells were cultured in DMEM supplemented with 10% FBS (Sigma-Aldrich)

extract_protocol:
Total RNA was extracted and prepared using MiRNeasy Mini Kit following manufacturer's instructions (Qiagen)
RNA libraries were prepared with QIAseq Stranded Total RNA library kit using 100ng input RNA (Qiagen)

treatment_protocol: Cells from passages 1-9 were seeded at 600/mm2 cell density onto patterned substrates, which were cleaned and sterilized in a standard process using acetone, methanol, IPA, DI water and 70% ethanol. There was no biochemical or chemical functionalization of the substrates prior to cell culture.

value: mesenchymal stem cells (MCS)

tag: surface


title: Sample_064_Incisional biopsy


title: MCS_Plastic

description: Control Plastic

source_name: MCS cells grown on conventional tissue culture flasks

value: Plastic


title: HUVEC_Plastic

description: Control Plastic

source_name: HUVEC cells grown on conventional tissue culture flasks

value: human umbilical vein cells (HUVEC)


title: Sample_054_Incisional biopsy


title: WT_H3_rep1

tag: strain


title: HUVEC_TiB2

description: Interrogated Sample TiB2

source_name: HUVEC cells grown on a micropatterned TiB2 surface

tag: cell type


title: Sample_058_Incisional biopsy


title: Sample_036_Incisional biopsy


title: Bcells_TENT5C_KO_2


title: Sample_062_Incisional biopsy


title: HH039_NASH

data_processing:
Paired-end reads were aligned to hg38 using QIAGEN’s CLC Genomics workbench and were assessed as transcript per million (TPM).
To sort the data, K-means clustering was performed using Cluster 3.0 (de Hoon et al., 2004) and heatmaps were generated using Java TreeView (Saldanha, 2004).
Ingenuity pathway analysis (IPA) was used to identify differentially expressed genes, predict downstream effects, and identify targets (QIAGEN Bioinformatics; www.qiagen.com/ingenuity)
Regulatory effects analysis within IPA was used to identify the relationships between upstream regulators and biological functions.
Genome_build: hg38
Supplementary_files_format_and_content: bedGraph

source_name: Hepatocytes from NASH patient

extract_protocol:
Total RNA was depleted of rRNA using pooled antisense oligo hybridization and depletion through RNaseH digestion
Following purification over a Zymo RNA clean and concentrator column, first strand cDNA was synthesized. Subsequently, second strand cDNA was synthesized, purified, and fragmented. RNA-seq libraries were prepared using Illumina technology. Briefly, end repair, A-tailing, and barcoded adapter ligation followed by PCR amplification and size selection. The integrity of the libraries was confirmed by quBit quantification, fragment analyzer size distribution assessment, and Sanger sequencing of ~10 fragments from each library. Libraries were sequenced using paired-end Illumina sequencing.

tag: individual

value: NASH patient

value: isolated primary hepatocytes


title: HH041_AlcoholicCirrhosis

source_name: Hepatocytes from alcohol-mediated Laennec's cirrhotic patient


title: HH038_NASH


title: HH040_AlcoholicCirrhosis

value: alcohol-mediated Laennec's cirrhotic patient


title: WT_NoAb_rep2

tag: primary antibody, vendor, catalog number and batch

tag: secondary antibody


title: Sample_018_Incisional biopsy

tag: treatment


title: Sample_013_Incisional biopsy

tag: gender


title: HH027_normal

source_name: Hepatocytes from normal patient

value: normal patient


title: Sample_034_Incisional biopsy

tag: estrogen receptor (er) status


title: Sample_011_Incisional biopsy

tag: molecule subtype


title: Sample_010_Incisional biopsy


title: Sample_024_Incisional biopsy


title: HH025_normal


title: Tratamiento B2

city: Bogotá

first: LUIS

middle: ALBERTO

last: GOMEZ

state: Boogotá

address: El Dorado avenue 51-20

department: Dirección de Investigación Científica y Tecnológica

country: Colombia

institute: Instituto Nacional de Salud

data_processing:
The reads of small RNA samples aligned against the following reference databases: mature miRNA, other RNA, and genomic by using The BaseSpace® App, Small RNA v1.0.
The quality of the reads was analyzed using MultiQC and confirmed by FastQC in Galaxy platform (https://usegalaxy.org/).
The alignments executed for readings obtained between 17-35 nucleotides against the reference genome for Mus musculus and other databases, including miRBase version 21 to identify the mature miRNAs.  In each case, we assigned the name of the miRNAs when 100% identity presented between reading and the miRBase reference.
We performed the alignments, quality control, and normalization of the readings obtained by sequencing in the BaseSpace Small RNA App (Illumina).
To analyze the differentially expressed miRNAs, we used the DESeq2 library (Bioconductor) in R code and the shrinkage estimator for the variance distribution.
Genome_build: mm9
Supplementary_files_format_and_content: Comma Separated Values (CSV) files including count matrix of global and normalized; as well as three files (Deseq.res treatment A vs. Control, Deseq.res treatment B vs. Control and Deseq.res treatment B vs. treatment A) with differential expression of miRNAs obtained for DESeq2.

source_name: Melanoma cells

growth_protocol: An average of 1.5 * 105 B16F1 cells (of epithelial morphology and adherent growth from C57BL / 6J mouse skin) were seeded and cultured in DMEM advance supplemented with 10% (v/v) of fetal bovine serum at pH 7.2 to 7.4, penicillin (100 U. mL-1) and streptomycin (100 µg. mL-1). We incubated the cells at 37 ° C with 5% CO2 and 98% humidity.

extract_protocol:
We lysed B16F1 cells with TRIzol reactive (Invitrogen) and collected the lysate in 1.5 mL tubes. To solubilize the melanin, we heated for 2 min at 65°C. By successive centrifugations with chloroform, isopropanol, and 75% ethanol, the pellet was obtained and dried at room temperature for 10 minutes. The extracted RNA was re-suspended in transport buffer following the manufacturer's recommendations. For RT-qPCR, total RNA was re-suspended in H2O DEPC and quantified by spectrophotometry. To obtain enriched fractions of small RNAs (≤ 200 nucleotides) was used miRVanaTM miRNA Isolation Kit (Ambion, Austin, USA) following the manufacturer's recommendations. We evaluated the quality of RNA by RIN number (RNA integrity number).
To build the library, it was through TruSeq Small RNA Library Prep. Kit (Illumina) following the manufacturer's recommendations. For this, a fraction of total RNA was coupled to 5` and 3` adapters to perform the corresponding RT-PCR for 15 cycles. The products of the amplification were separated by 6% polyacrylamide gel electrophoresis, and the region of the amplified library containing the fraction of miRNAs (from 140-150 nucleotides), was separated, precipitated with ethanol and quantified on nanodrop. Selected libraries were pooled and run on an Illumina Hiseq 2500, single read (SR 1*50) format to generate 1.0 * 106 readings per sample.

treatment_protocol: Between 10-12 hours after seed, we changed by fresh medium and added BrdU or L-Tyr to a final concentration of 2.5 µg. mL-1 and 5.0 mM, respectively. Finally,  we incubated the cells for 72 hours without medium change.

tag: cell line

value: Melanoma cells

tag: exposition

value: exposed to BrdU


title: Tratamiento B3


title: Tratamiento B1


title: Sample_004_Incisional biopsy


title: Sample_007_Incisional biopsy


title: Sample_003_Incisional biopsy


title: Tratamiento A3

value: exposed to L-Tyr


title: Sample_051_Incisional biopsy

value: female


title: AZA rep 2

city: Stanford

first: Mark

middle: Emile

last: Pepin

state: CA

address: 870 Quarry Road

department: Cardiovascular Medicine

institute: Stanford University

data_processing:
To evaluate sequencing quality, FastQC (0.11.7) was used both before and after adapter trimming via TrimGalore (0.4.4).
The bisulfite-reduced and sequenced reads were then aligned to the CT- and GA-converted human hg38 (GRCh38.p12) genome assembly via BWA-meth to quantify relative alignment of methylated and unmethylated CpGs, respectively.
We then quantified differential DNA methylation in 500-base windows to exploit the regional CpG methylation analysis afforded by RRBS using the R package methylKit (1.8.0).
Alignments were first filtered for those with <99.9% methylated CpGs and sequencing depth > 10X to remove PCR-biased and low-coverage CpG sites, respectively.
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: Differentially-methylated regions in response to 5-AZA relative to vehicle (DMSO) in ASCs.

source_name: adipose-derived stem cell

growth_protocol: Human subcutaneous adipose tissues was collected from abdominal wall resection of healthy donors (n=2), who underwent cosmetic surgery. Adipose tissue was transferred to the laboratory and processed under sterile conditions within 24 h. Isolation of ASCs was performed as previously described [Ceccarelli S., 2018]. Briefly, tissue fragments were washed extensively with sterile phosphate-buffered saline containing 2% penicillin/streptomycin and minced. The extracellular matrix was digested with 0.075% collagenase type I for 30-60 min at 37°C and 5% CO2. The suspension was filtered to remove debris and centrifuged for 5 min at 2000 rpm. The pellets of stromal vascular fraction (SVF) containing ASCs were washed with PBS, then resuspended in the culture medium and transferred to a culture flask. ASCs were self-selected out of the SVF, since they were adherent to the plastic tissue cultureware.

extract_protocol:
Genomic DNA was isolated from ASCs, treated with or without 10 μM 5-aza, using the GeneJET Genomic DNA Purification Kit (Thermo Scientific). DNA concentration and purity were determined using Qubit 3 Fluorometer (Invitrogen) and NanoDrop 2000 (Thermo Scientific). DNA integrity was checked on 1% agarose gel.
2 μg of genomic DNA were used for each library preparation. Each DNA sample was digested by MspI restriction enzyme. The digested products were purified with the GeneJet PCR Purification Kit (Thermo Fisher Scientific) and libraries were prepared by TruSeq Library Prep Kit (Illumina,  USA). Fragments were bisulfite converted using the EZ DNA Methylation-Gold Kit (Zymo Research, USA). The converted DNA was amplified using PfuTurbo Cx Hotstart DNA Polymerase (Agilent Technologies, USA). The amplified fragments were purified by AMPure XP Beads and further quantified by the Agilent 4200 TapeStation (Agilent Technologies, USA).

treatment_protocol: The DNA methyltransferase inhibitor 5-aza was purchased from Sigma-Aldrich (Milan, Italy) and was reconstituted at 10 mM using dimethyl sulfoxide (DMSO). ASCs were seeded at a cell density of 5x103 cells/cm2. After cell attachment, the medium was changed to freshly made culture medium containing 10 μM 5-aza. After 24 h, the 5-aza containing culture medium was refreshed for another 24 h (total treatment 48 h). Control samples were treated with DMSO alone at 0.1% (v/v) concentration.

value: adipose-derived stem cell

value: AZA


title: Tratamiento A1


title: Tratamiento A2


title: Sample_002_Incisional biopsy

value: locally advanced breast cancer

value: small RNA


title: Control 3

value: not exposed


title: Control 2


title: DMSO rep 2

value: DMSO


title: HH036_normal


title: AZA rep 1


title: Control 1


title: 63

city: Basel

first: Marc

middle: Yves

last: Donath

state: Basel-Stadt

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University Hospital of Basel

description: counts.tsv

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20.0.422 was used to generate FASTQ files
Initial quality checks were performed with FastQC version 0.11.4
Quality trimming and adaptor clipping was performed using Trimmomatic version 0.36 using the options "LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15" and reads were aligned using the splice aware aligner STAR version 2.7.0.
Count-tables were produced using HTSeq version 0.6.1
Subsequent analyses were performed in R (v3.5.3, www.r-project.org) using the DESeq2 package version 1.20.0
Genome_build: GRCh38
Supplementary_files_format_and_content: processed data are available in the form of normalized count-tables as genereated by the DESeq2 package version 1.20.0.

molecule: polyA RNA

source_name: circulating blood bulk monocytes

growth_protocol: After  blood samples were taken, the cells were put on a shaker at room temperatuer until preparation for fluorescence activated cell sorting (max. 1h). After sorting, cells were immediately lysed in RNA-lysis buffer und stored at -80°C.

extract_protocol:
Nucleo Spin RNA II Kit (Machery Nagel).
TruSeq Stranded mRNA HT Sample Preparation kit (Illumina, USA)

treatment_protocol: Cells did not receive additional treatments ex-vivo.

tag: patient number

tag: status pre or post meal

value: Pre

value: Jardiance [10mg]

tag: occurence of hyopglycemia

value: no

tag: patient gender

value: male

tag: deseq2 size factor

tag: lanes

tag: number of technical replicates


title: 61

description: counts.tsv

value: Kineret [100mg]


title: 64

description: counts.tsv

value: Post


title: Lmo2tg; Ldb1-KO DN4, replicate 5

city: Bethesda

first: Apratim

last: Mitra

state: MD

address: 6 Center Dr Building 6B Room 2B206

department: Division of Developmental Biology

institute: NICHD

data_processing:
The raw reads were aligned using STAR version 2.5.2a. Technical replicates for each sample were specified at the command-line as comma-separated values. Reads were then quantified using featureCounts version 1.4.6-p3.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table of raw sequencing reads for each gene per sample (24421 genes x 28 samples).

source_name: CD4 T cells

growth_protocol: C57BL/B6:CD45.1 congenic mice and Lck-Cre transgenic were from Taconic Farms. Rosa26-EYFP-Cre reporter mice were obtained from Jackson labs.  The generation of Lmo2-tg mice and Ldb1flox/flox mice was described previously.  Rag1-Cre transgenic and IL-7Ra-Cre transgenic mice were provided by Terence Rabbitts (University of Oxford) and Hans-Reimer Rodewald (German Cancer Research Center, DKFZ), respectively. Mice were bred and maintained in an NIH Research Animal Facility in accordance with ACUC specifications. Mouse procedures were approved by the NICHD ACUC committee.

extract_protocol: Library preparation for the Illumina HiSeq2500 was performed using the TruSeq RNA Sample Prep V2 kit (Illumina). Pooled barcoded libraries were sequenced to generate paired-end 101 bp reads.

tag: cell type

value: CD4 T cells

tag: cell subtype

tag: genotype

value: Lmo2tg; Ldb1-KO


title: 60

description: counts.tsv

value: Placebo

value: yes


title: Lmo2tg; Ldb1-KO DN4, replicate 2


title: Lmo2tg; Ldb1-KO DN2/3, replicate 3


title: Lmo2tg; Ldb1-KO DN4, replicate 3


title: 66

description: counts.tsv


title: 58

description: counts.tsv


title: 65

description: counts.tsv


title: Lmo2tg; Ldb1-KO DN4, replicate 4


title: 57

description: counts.tsv


title: DMSO rep 1


title: Lmo2tg; Ldb1-KO DN2/3, replicate 1


title: Lmo2tg; Ldb1-KO DN4, replicate 1


title: Lmo2tg; Ldb1-KO DN2/3, replicate 4


title: Lmo2tg; Ldb1-KO DN2/3, replicate 2


title: 55

description: counts.tsv


title: 56

description: counts.tsv


title: Lmo2tg DN4, replicate 5


title: 54

description: counts.tsv

value: female


title: Lmo2tg DN4, replicate 3


title: Lmo2tg DN4, replicate 4


title: 52

description: counts.tsv


title: Lmo2tg DN4, replicate 2


title: 53

description: counts.tsv


title: 62

description: counts.tsv


title: Lmo2tg; Ldb1-KO DN2/3, replicate 5


title: Lmo2tg DN2/3, replicate 3


title: Lmo2tg DN2/3, replicate 4


title: 51

description: counts.tsv


title: Lmo2tg DN2/3, replicate 2


title: Lmo2tg DN2/3, replicate 5


title: Wild type DN4, replicate 4

value: wild type


title: Lmo2tg DN2/3, replicate 1


title: 50

description: counts.tsv


title: Wild type DN4, replicate 3


title: Lmo2tg DN4, replicate 1


title: 49

description: counts.tsv


title: 45

description: counts.tsv


title: 48

description: counts.tsv


title: Wild type DN4, replicate 2


title: 40

description: counts.tsv


title: 43

description: counts.tsv


title: 46

description: counts.tsv


title: Wild type DN2/3, replicate 3


title: 41

description: counts.tsv


title: 38

description: counts.tsv


title: 39

description: counts.tsv


title: Wild type DN2/3, replicate 1


title: Wild type DN2/3, replicate 4


title: Wild type DN2/3, replicate 2


title: 37

description: counts.tsv


title: 36

description: counts.tsv


title: 30337: microbial 16S rRNA genes

city: New York

first: Elodie

last: Ghedin

address: 12 Waverly Place

department: Biology

institute: NYU

data_processing:
Library strategy: 16s rRNA gene amplicon sequencing
The 16S rRNA gene sequencing data was processed through the Quantitative Insights into Microbial Ecology (QIIME)  pipeline. The reads were joined and demultiplexed with join_paired_ends.py and split_library_fastq.py respectively, and the sequences were clustered into Operational Taxonomic Units (OTUs) at a 97% similarity threshold with the closed-reference OTU picking method and the greengene database (gg_13_8_otus)
Taxonomic assignment of the representative sequence from each OTU was made using the Ribosomal Database Project (RDP) classifier.

organism: human metagenome

source_name: Human nasal wash and throat sample

extract_protocol:
Genomic DNA was isolated from the respiratory samples with the PowerSoil DNA Isolation Kit
The 16S rRNA gene V4 region was amplified with methods published in Caporaso, et al. (2012). The primers included the Illumina flowcell adapter sequences and region-specific sequences, where the reverse primers included barcode sequences. The PCR reaction was carried out using Q5 Hot Start High-Fidelity DNA Polymerase and the conditions were 94 degrees C for 2 min, 33 cycles of 94 degrees C for 30s, 55 degrees C for 30s and 72 degrees C for 1 min 30s, followed by 72 degrees C for 10s and hold at 10 degrees C. The PCR reactions were purified using 0.65X volumes of Agencourt RNAClean XP beads. The library was sequenced using an Illumina PE 2x250 V2 kit on an Illumina MiSeq Sequencer .

tag: tissue

value: Human nasal wash and throat sample

tag: source

value: Human upper respiratory tract

tag: ID

tag: age

tag: Sex

value: Male

tag: strain

value: Influenza B


title: 47

description: counts.tsv

tag: treatment


title: 6955: microbial 16S rRNA genes

value: H1N1 pdm


title: 42

description: counts.tsv

tag: patient number


title: 30191: microbial 16S rRNA genes


title: Wild type DN4, replicate 1


title: 35

description: counts.tsv

tag: status pre or post meal

value: Pre


title: 34

description: counts.tsv

value: Jardiance [10mg]

tag: occurence of hyopglycemia


title: 30427: microbial 16S rRNA genes

value: Female


title: 6019: microbial 16S rRNA genes


title: 32

description: counts.tsv

tag: patient gender


title: 3522: microbial 16S rRNA genes


title: 29

description: counts.tsv

value: no

tag: deseq2 size factor


title: 33

description: counts.tsv

tag: lanes


title: 7098: microbial 16S rRNA genes


title: 30

description: counts.tsv

tag: number of technical replicates


title: 30348: microbial 16S rRNA genes


title: 26

description: counts.tsv


title: 27

description: counts.tsv

value: Kineret [100mg]


title: 30112: microbial 16S rRNA genes


title: 7047: microbial 16S rRNA genes


title: 6667: microbial 16S rRNA genes


title: SOB3-GFP Input

city: Yokohama

first: David

middle: Seth

last: Favero

state: International

address: 1-7-22 Suehirocho, Tsurumi-ku

department: CSRS

country: Japan

institute: RIKEN

description: Input control for SOB3-GFP ChIP

data_processing:
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by BaseSpace Sequence Hub (Illumina) or bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 0.12.9 with the setting "-m 1".
Peak-calling: Peaks were called using the "callpeak" command in MACS2 with the following parameters: "-g 119480000 -m 2 50 -B --SPMR -q 0.05".
Generation of bigwig files: Fold-enrichment bdg format files were generated by using the treatment pileup and control lambda output files generated from "callpeak" as inputs for the MACS2 "bdgcmp" command with the setting "-m FE". The bdg files were converted to bigwig format using the "bedGraphToBigWig" program (UCSC).
Genome_build: TAIR10
Supplementary_files_format_and_content: Fold enrichment bigwig files (ChIP vs Input); peak calls in BED format from MACS2

organism: Arabidopsis thaliana

source_name: SOB3-GFP Input

growth_protocol: 22°C constant temperature with long-day photoperiod (16h light/8h darkness) under white fluorescent light (~35-55 μmol/m2/sec) on sucrose-free 1X MS medium containing 0.8% Gelzan CM

extract_protocol:
Frozen samples were ground using mortar and pestle. Ground tissue was mixed with fixation buffer and formaldehyde added to 1% final concentration. Fixation was stopped after 10 minutes by addition of glycine. Solution was filtered twice through miracloth and then centrifuged to pellet cells.  Pellet was resuspended in extraction buffer containing 1% Triton X-100 to lyse cells and centrifuged to pellet nuclei. Pellet with nuclei was resuspended in nuclei separation buffer containing 1.7 M sucrose and centrifuged to separate nuclei from debris. Nuclei were resuspended in nuclei lysis buffer containing 1% SDS and flash frozen twice in liquid nitrogen in order to lyse nuclei.  Subsequently, chromatin was sonicated in a Bioruptor (Diagenode) to an average size of approximately 200-400 bp.
Libraries were constructed from input or ChIPed DNA using the TruSeq ChIP Library Preparation Kit (Illumina) according to manufacturer's instructions, with the exception of the "Purify Ligation Products" step, which was skipped. Library quality was validated using the Agilant 2200 TapeStation with D1000 ScreenTape & Reagents. Qubit dsDNA HS Assay Kit was used with the Qubit 2.0 Fluorometer (Invitrogen) for quantitation of DNA.

tag: ecotype

value: Columbia (Col-0)

tag: genotype/variation

value: ProSOB3::SOB3-GFP sob3-4

value: 14 days old

tag: time of harvest

value: whole plant

tag: chip antibody


title: SOB3-GFP ChIP replicate 2

description: ChIP-seq for SOB3-GFP replicate 2

source_name: SOB3-GFP ChIP

tag: tissue

value: Anti-GFP antibody - ChIP Grade (ab290, Abcam)


title: 28

description: counts.tsv

value: Post

value: yes

value: female


title: 25

description: counts.tsv

value: Placebo


title: pif4 pif5 pif7 RNA-seq replicate 3

description: RNA-seq for pif4 pif5 pif7 (triple LOF pif mutant) replicate 3

data_processing:
Generation of fastq files: Raw data files (bcl format) were converted to fastq files by bcl2fastq (Illumina).
Alignment: Reads were mapped to the Arabidopsis reference using Bowtie 1.2.1 with the following parameters: '-all -best -strata'.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab-delimited data with transcript CPM (counts per million mapped reads) values for each sample

source_name: pif4 pif5 pif7 RNA-seq

growth_protocol: 22°C constant temperature with long-day photoperiod (16h light/8h darkness) under white fluorescent light (~35-55 μmol/m2/sec) on sucrose-free 1X MS medium containing 0.6% Gelzan CM

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN) according to manufacturer's instructions, including on-column DNase digestion to eliminate genomic DNA.
Isolated RNA was subjected to library preparation using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems) with NEBNext Multiplex Oligos for Illumina (New England Biolabs) used as adapters and Agencourt AMPure XP (Beckman Coulter) beads used instead of KAPA Pure Beads.

value: Apical portions of plants (cut in hypocotyl)


title: 24

description: counts.tsv


title: 30291: microbial 16S rRNA genes

value: Human nasal wash and throat sample

tag: source

value: Human upper respiratory tract

tag: ID


title: pif4 pif5 pif7 RNA-seq replicate 2

description: RNA-seq for pif4 pif5 pif7 (triple LOF pif mutant) replicate 2

tag: age


title: 30429: microbial 16S rRNA genes

tag: Sex

tag: strain


title: pif4 pif5 pif7 RNA-seq replicate 1

description: RNA-seq for pif4 pif5 pif7 (triple LOF pif mutant) replicate 1


title: 30515: microbial 16S rRNA genes

value: Male

value: Influenza B


title: 31

description: counts.tsv

tag: patient number

value: Pre

tag: treatment


title: 8561: microbial 16S rRNA genes

value: Female


title: 22

description: counts.tsv

tag: status pre or post meal

tag: occurence of hyopglycemia


title: 23

description: counts.tsv

value: Jardiance [10mg]

value: no

tag: patient gender

tag: deseq2 size factor


title: SOB3-D RNA-seq replicate 1

description: RNA-seq for SOB3-D (AHL overexpressor) replicate 1

source_name: SOB3-D RNA-seq

value: Columbia (Col-0)


title: SOB3-D RNA-seq replicate 2

description: RNA-seq for SOB3-D (AHL overexpressor) replicate 2

value: 14 days old


title: 21

description: counts.tsv

tag: lanes

tag: number of technical replicates


title: sob3-6 RNA-seq replicate 2

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) replicate 2

source_name: sob3-6 RNA-seq

tag: ecotype

tag: genotype/variation


title: 30455: microbial 16S rRNA genes


title: sob3-6 RNA-seq replicate 3

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) replicate 3

tag: time of harvest


title: sob3-6 RNA-seq replicate 1

description: RNA-seq for sob3-6 (dominant-negative ahl mutant) replicate 1

tag: tissue


title: 20

description: counts.tsv

value: Kineret [100mg]


title: 7153: microbial 16S rRNA genes

tag: source


title: SOB3-GFP ChIP replicate 1

description: ChIP-seq for SOB3-GFP replicate 1

value: ProSOB3::SOB3-GFP sob3-4

value: whole plant

tag: chip antibody

value: Anti-GFP antibody - ChIP Grade (ab290, Abcam)


title: Col-0 RNA-seq replicate 1

description: RNA-seq for wild-type replicate 1

source_name: Col-0 RNA-seq

value: wild-type

tag: age


title: Col-0 RNA-seq replicate 2

description: RNA-seq for wild-type replicate 2


title: 19

description: counts.tsv

value: yes

value: female


title: 7965: microbial 16S rRNA genes

value: Human nasal wash and throat sample

tag: ID

tag: Sex


title: 6617: microbial 16S rRNA genes

value: Human upper respiratory tract

tag: strain


title: dgul1_rep3

city: Qingdao

first: Guodong

last: Liu

state: Shandong

address: Binhai Road 72

department: State Key Laboratory of Microbial Technology

country: China

institute: Shandong University

data_processing:
Sequenced reads with adaptor sequence at 3' end or mean quality below 20 were filtered out using Cutadapt.
Sequenced reads were aligned to the genome using HISAT2 with default parameters for paired-end reads.
Raw counts of mapped reads on gene-level were quantified using HTSeq with the union mode.
The FPKM (fragments per kilobase per million mapped fragments) value was used to show the gene expression levels. DEseq was used to compare the gene expression levels between samples and perform statistical analysis (log2FC>1 and pvalue<0.05 as DEGs).
Genome_build: Trichoderma reesei QM6a genomic sequence (NCBI assembly accession: GCF_000167675.1, v2.0)
Supplementary_files_format_and_content: One matrix table in text format including FPKM values for each gene.

organism: Trichoderma reesei

source_name: Fungal mycelia

growth_protocol: All strains were first precultured in a minimal medium with 2% glucose as carbon source for 36 h, and then inoculated to a cellulase-inducing medium with 1% cellulose as carbon source for a 48-hr cultivation at 30 degree C, 200 rpm.

extract_protocol:
Total RNA was prepared from the mycelia by grinding under liquid nitrogen with a mortar and pestle, followed by extraction using the RNAisoTM reagent (TaKaRa, Japan) according to manufacturer's protocol.
First, mRNA molecules were enriched with oligo(dT) beads and disrupted into ~300 bp fragments. Then, cDNA was synthesized using mRNA as a template. The library was prepared for sequencing by PCR and size selection.

treatment_protocol: Mycelia were filtered by filter paper.

value: gul1 deletion mutant dgul1

tag: carbon source

value: 1% (w/v) cellulose


title: 18

description: counts.tsv

tag: patient number

tag: status pre or post meal

value: Post

tag: treatment

value: Placebo

value: male


title: 6205: microbial 16S rRNA genes

value: Female

value: Influenza B


title: dgul1_rep2


title: 17

description: counts.tsv

value: Pre

tag: occurence of hyopglycemia

value: no

tag: patient gender

tag: deseq2 size factor


title: SOB3-D RNA-seq replicate 3

description: RNA-seq for SOB3-D (AHL overexpressor) replicate 3

tag: ecotype

value: Columbia (Col-0)

value: 14 days old

value: Apical portions of plants (cut in hypocotyl)


title: QPP_rep3

value: Reference strain QPP


title: 16

description: counts.tsv

value: Kineret [100mg]

tag: lanes

tag: number of technical replicates


title: QPP_rep2


title: 30304: microbial 16S rRNA genes

tag: tissue

value: Male

value: H1N1 pdm


title: QPP_rep1


title: dgul1_rep1


title: Col-0 RNA-seq replicate 3

description: RNA-seq for wild-type replicate 3

tag: genotype/variation

value: wild-type

tag: time of harvest


title: 30295: microbial 16S rRNA genes

value: Human nasal wash and throat sample

tag: source

value: Human upper respiratory tract

tag: age


title: 15

description: counts.tsv


title: 14

description: counts.tsv

value: Post

value: Jardiance [10mg]


title: 13

description: counts.tsv

value: male


title: 7637: microbial 16S rRNA genes

tag: ID

tag: Sex


title: 6777: microbial 16S rRNA genes

tag: strain


title: 12

description: counts.tsv

tag: patient number

value: female


title: 11

description: counts.tsv

tag: status pre or post meal


title: 8033: microbial 16S rRNA genes

value: Influenza B


title: 10

description: counts.tsv

tag: treatment

value: Placebo


title: 9

description: counts.tsv

value: Pre

tag: occurence of hyopglycemia

value: no


title: 30076: microbial 16S rRNA genes

value: Female


title: 6628: microbial 16S rRNA genes


title: 6929: microbial 16S rRNA genes


title: 7331: microbial 16S rRNA genes


title: BC3491 CTX 4h RP

type: RNA

city: Berlin

first: Maja

last: Milanovic

address: Augustenburgerplatz 1

department: Hematology and Oncology

country: Germany

institute: Charite University Medicine, Berlin

description: Gene expression data from primary Emu-myc lymphomas in therapy-naive state or after drug chalenge

hyb_protocol: Following fragmentation, 3 ug of cDNA were hybridized for 16 hr at 45°C on Mouse Gene ST 1.0 Arrays (Affymetrix). GeneChips were washed and stained with standard protocols in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Scanner G3000.

data_processing: Affymetrix CEL files were imported into R (version 3.5.0) and processed by the RMA workflow implemented in the oligo package (median polish probe set summarization, RMA background correction, quantile normalization). Batch Effects were reduced by Empirical Bayes methods (ComBat) in the sva package. Treatment and response were included as covariates in batch correction.

label: biotin

source_name: primary lymphoma cells, isolated from lymph nodes of Emu-myc transgenic mice with palpable lymphadenopathy

label_protocol: Biotinylated cDNA was prepared according to the standard WT Expression Kit protocol (Ambion) and GeneChip® WT Terminal Labeling and Hybridization Kit protocol (Affymetrix) using 100 ng total RNA.

growth_protocol: The lymphoma cells from lymph nodes of Emu-myc transgenic mice (explated upon spontaneous lymphoma development) were used directly for RNA extraction, without cell purification or in vitro cultivation.

extract_protocol: The total RNA from aliquots of primary lymphoma cells, explated from lymph nodes of Emu-myc transgenic mice, was prepared using an RNeasy Mini kit (QIAGEN, Valencia, California) according to the manufacturer's instructions.

treatment_protocol: Recipient mice transplanted with primary Emu-myc lymphomas were treated upon palpable lymphoma formation with a single dose Cyclophosphamide (CTX), 300mg/kg body weight, i.p.

tag: strain/background

tag: genotype

value: Emu-myc transgenic

tag: cell type

value: primary lymphoma cells from lymph node

tag: lymphoma id

value: CTX 4h

tag: response

value: Relapse Prone

tag: sample type

value: Primary diagnosis


title: ST8798 CTX 4h RP


title: 30082: microbial 16S rRNA genes

tag: tissue

value: Male


title: ST7836 CTX 4h RP


title: BC3802 CTX 4h RP


title: 6

description: counts.tsv

tag: patient gender

tag: deseq2 size factor

tag: lanes

tag: number of technical replicates


title: BC3237 CTX 4h RP


title: 8

description: counts.tsv


title: AB9842 CTX 4h RP


title: BC1590 native RP

value: native


title: BC2548 CTX 4h RP


title: ST9891 native RP


title: BC1590 CTX 4h RP


title: 6957: microbial 16S rRNA genes

value: Human nasal wash and throat sample

tag: source

value: Human upper respiratory tract

tag: ID

tag: age

tag: Sex


title: 7

description: counts.tsv

tag: patient number

tag: status pre or post meal

tag: treatment

value: Jardiance [10mg]


title: BC2548 native RP

tag: strain/background

tag: genotype


title: ST8795 CTX 4h RP

tag: cell type

tag: lymphoma id


title: ST7836 native RP

tag: response

tag: sample type


title: 6471: microbial 16S rRNA genes

tag: tissue

tag: strain

value: H1N1 pdm


title: BC3491 native RP


title: 4

description: counts.tsv

value: Post

tag: occurence of hyopglycemia

tag: patient gender

value: female

tag: deseq2 size factor

tag: lanes


title: BC3237 native RP


title: ST8798 native RP


title: BC3802 native RP


title: ST8795 native RP


title: 6271: microbial 16S rRNA genes

tag: source

tag: ID

tag: age


title: AB9842 native RP


title: 5

description: counts.tsv

tag: patient number

tag: status pre or post meal

value: Placebo

tag: number of technical replicates


title: 30515.01.TRFPB2

first: Christian

last: Forst

state: NY

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: 30515.01.TRFPB2 30515_01_trfpb2_ATGAGC

data_processing:
The sequencing reads were aligned to the human hg19 genome using star aligner (version 2.4.0g1).
featureCounts was used to quantify gene expression at the gene and exon levels based on Ensembl gene model GRCh37.70. Genes with at least 5  reads in at least 4 samples were considered expressed, otherwise absent and hence discarded.
The gene level read counts data was normalized using edgeR, multi-dimensional scaling and cluster analysis were performed to check for potential sample outliers.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited  file using log2-tranformed CPM values for each sample

source_name: PBMC_Influenza B_Final

extract_protocol:
RNA was extracted from PBMCs with  the RNeasy Mini Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols using the TruSeq RNA Library Prep Kit

tag: subject id

tag: Sex

value: Influenza B

tag: initial/final

value: Final

value: PBMC


title: ST9891 CTX 4h RP

tag: strain/background

tag: genotype

value: Emu-myc transgenic

tag: cell type

tag: lymphoma id

tag: treatment

tag: response


title: 3

description: counts.tsv

value: Pre

tag: occurence of hyopglycemia

value: no

tag: patient gender

tag: deseq2 size factor


title: BC1590 CTX 4h RES

value: primary lymphoma cells from lymph node

value: CTX 4h

value: Resistant

tag: sample type

value: 3rd relapse


title: BC3237 CTX 4h RES


title: ST8795 CTX 4h RES


title: AB9842 CTX 4h RES


title: BC3491 CTX 4h RES


title: BC3237 native RES

value: native


title: 2

description: counts.tsv

value: Kineret [100mg]

tag: lanes


title: ST9891 CTX 4h RES


title: 30515.01.TRIPB2

description: 30515.01.TRIPB2 30515_01_tripb2_CATTTT

source_name: PBMC_Influenza B_Initial

tag: age

value: Male

tag: strain

value: Initial


title: ST7836 CTX 4h RES


title: 1

description: counts.tsv

tag: patient number

tag: status pre or post meal

tag: number of technical replicates


title: 12SM_Iah1-KO_eWAT

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S Mouse Array. GeneChips were washed and stained in the Applied Biosystems Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G System.

data_processing: The data were analyzed with STT-RMA using Applied Biosysytems GeneChip Console Software ver.1.3.0

source_name: Epididymal fat

label_protocol: Biotinylated cRNA were prepared according to the standard Applied Biosystems protocol from 100 ng total RNA (Applied Biosystems GeneChip WT PLUS Reagent Kit, Applied Biosystems).

growth_protocol: Until 6 weeks of age, all male mice were fed a standard laboratory chow (CE2, Nihon CLEA). From 6 weeks of age, mice were fed a high-fat diet (pellet, 07053003 from Research Diet). Mice were kept at one animal per cage.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. After that, RNA was performed a cleanup using the QIAGEN Rneasy Mini kit.

treatment_protocol: Mice were fed a high fat diet for 12 weeks. Mice were killed by decapitation, and tissues were collected at 13:00-14:00 hours after 4-hour diet deprivation.

value: High-fat diet for 12 weeks


title: BC3802 native RES


title: 12SM_Iah1-WT_eWAT


title: 7765: microbial 16S rRNA genes

tag: tissue

value: Human nasal wash and throat sample

tag: source

value: Human upper respiratory tract

tag: ID

tag: Sex

value: Female

value: H1N1 pdm


title: RpoABC_ChIP-Seq_WT(MB1)_(AIYT-161)

city: Geneva

first: Patrick

last: Viollier

address: Rue michel Servet,1

institute: University of Geneva

description:
AIYT161-162-163 20bp.txt
AIYT161-162-163 G1 gene.txt
AIYT161-162-163 S gene.txt

data_processing:
basecalling: HiSeq Control Software HD 3.4.0.38; RTA 2.7.7; bcl2fastq2.17 v2.17.1.14
Alignement: map with BWA (Galaxy Version 0.7.17.4)
quantification: SeqMonk software 1.40.0 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus NA1000 NC_011916.1
Supplementary_files_format_and_content: txt files were generated using annotated probe report from SeqMonk. The AIYT-161-162-163 20bp was generated using 20bp probe all along the chromosome. The  AIYT-161-162-163 G1 gene and  AIYT-161-162-163 S gene represent specifically the promoter region of the G1 and S regulon of CtrA based from Fumeaux et al (PMID: 24939058) and Schrader et al (PMID: 25078267). In this case, probe of 200bp before and after the beginning of the CtrA regulated gene were created to quantify the occupancy of the polymerase on the CtrA target gene. The sheet is organized in column as follow: column 1: chromosome name; colum 2: start of the probe; column 3: end of the probe; column 4: feature; column 5: strand of the gene; column 6: reads in RPM for WT (AIYT161); column 7: reads in RPM for ∆citA (AIYT162); column 8: reads in RPM for xylX::relA' (AIYT163)

organism: Caulobacter vibrioides NA1000

source_name: bacterial culture

growth_protocol: Overnight saturated cultures of Caulobacter crescentus strains were freshly diluted in PYE media contaning 0.3% xylose and cultures were grown at 30°C to mid-log phase (OD600nm~0.5).

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of protein-G agarose (Roche, www.roche.com) and 100 μg BSA. The rest of the pre-cleared lysates was incubated overnight at 4°C with E. coli RNA polymerase antibody sampler kit (Cat 699907, Biolegend https://www.biolegend.com/fr-ch/products/e--coli-rna-polymerase-antibody-sampler-kit-15078) with the different antibodies mixed with a ratio of 1:1:1 (1:500 dilution). The immuno-complexes were captured after incubation with Protein-G agarose (pre-saturated with BSA) during a 2 h incubation at 4°C and they were washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted from the Protein-G agarose beads with two times 250 μl elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.  Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.
TruSeq ChIP Library Preparation Kit

treatment_protocol: C. crescentus wildtype and derivative cells were treated with 1% formaldehyde in 1 μM sodium phosphate buffer (pH 7.6) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.

tag: genotype

value: wild-type

tag: chip antibody

value: RNA polymerase antibody sampler kit (Cat 69907, Biolegend)


title: RpoABC_ChIP-Seq_∆citA(MB2529)_(AIYT-162)

value: {delta}citA


title: RpoABC_ChIP-Seq_xylX::relA'-FLAG(MB3282)_(AIYT-163)


title: BC2548 CTX 4h RES

tag: strain/background

value: Emu-myc transgenic

tag: cell type

tag: lymphoma id

tag: treatment

tag: response


title: 30455.01.TRFPB2

description: 30455.01.TRFPB2 30455_01_TRFPB2_CTTGTA

tag: subject id

tag: initial/final

value: Final

value: PBMC


title: BC3802 CTX 4h RES

value: primary lymphoma cells from lymph node

value: CTX 4h

value: Resistant

tag: sample type


title: BC1590 native RES

value: native

value: 3rd relapse


title: 30455.01.TRIPB2

description: 30455.01.TRIPB2 30455_01_TRIPB2_ATGTCA

tag: age

tag: strain

value: Initial


title: ST8795 native RES


title: BC2548 native RES


title: ST8798 CTX 4h RES


title: 30429.01.TRFPB2

description: 30429.01.TRFPB2 30429_01_TRFPB2_GTTTCG


title: 30429.01.TRIPB2

description: 30429.01.TRIPB2 30429_01_TRIPB2_TCGGCA


title: 3522: microbial genes

data_processing:
Contaminating human, ribosomal RNA, and adaptor sequences were removed from each dataset using DeconSeq, SortMeRNA and Trimmomatic, respectively
The filtered reads were assigned to the orthologous gene families using the FMAP bioinformatics tool (FMAP: Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies) and with the default KEGG-filtered Uniref90 reference cluster
The filtered reads were aligned to megares(antibiotic resistance database) by using BWA. The alignments were filtered that the genes need to be hit by at least two regions and at least 10 reads need to be assigned to the gene.
Supplementary_files_format_and_content: tab-delimited file with RPKM values for each gene feature and read counts for genes confer resistance to antibiotics

extract_protocol:
Total RNA was isolated from the human respiratory sample with the QIAGEN RNeasy Micro Kit
Double-stranded cDNA was synthesized and amplified from 200-500 picograms of input RNA with the NuGEN Ovation RNA-seq V2 kit and purified using the QIAquick PCR Purification Kit. cDNA was sheared to 250 bp using the S220 Focused-ultrasonicator and purified using Agencourt RNAClean XP beads. Sequencing libraries were prepared from 100 ng of purified, sheared cDNA with the NuGen Ovation Ultralow System V2 1-16. The libraries were sequenced on the Illumina HiSeq 2500 instrument with TruSeq SBS V3 chemistry according to the manufacturer’s instructions.

value: Male


title: 30191: microbial genes

value: Human nasal wash and throat sample


title: ST9891 native RES


title: 30427.01.TRFPB2

description: 30427.01.TRFPB2 30427_01_TRFPB2_CATGGC


title: 7098: microbial genes

value: Human upper respiratory tract

value: Influenza B


title: BC3491 native RES


title: 30427: microbial genes

value: Female


title: ST8798 native RES


title: 30348.01.TRIPB2


title: AB9842 native RES


title: 30337.01.TRFPB2

description: 30337.01.TRFPB2 30337_01_trfPB2_ACAGTG


title: BC1954 CTX 4h NR

value: Never Relapsed

value: Primary diagnosis


title: BC1782 CTX 4h NR


title: ST7836 native RES


title: 30427.01.TRIPB1

description: 30427.01.TRIPB1 30427_01_TRIPB1_TACAGC


title: AB7133 CTX 4h NR


title: BC1960 CTX 4h NR


title: 30348.01.TRFPB2


title: 30337.01.TRIPB2

description: 30337.01.TRIPB2 30337_01_TRIPB2_CAAAAG


title: 30304.01.TRFPB2

description: 30304.01.TRFPB2 30304_01_trfPB2_GTGAAA

source_name: PBMC_H1N1 pdm_Final

value: H1N1 pdm


title: AB9159 CTX 4h NR

value: Emu-myc transgenic


title: BC1778 CTX 4h NR


title: ST9218 CTX 4h NR


title: ST8789 CTX 4h NR


title: ST8799 CTX 4h NR


title: 6019: microbial genes


title: 30348: microbial genes


title: 7047: microbial genes


title: ST9218 native NR


title: 6667: microbial genes


title: 30291: microbial genes


title: 30429: microbial genes


title: 30112: microbial genes


title: 30292.01.TRFPB1

description: 30292.01.TRFPB1 30292_01_TRFPB1_CGATGT

value: Final


title: BC1332 native NR


title: 30304.01.TRIPB2

description: 30304.01.TRIPB2 30304_01_TRIPB2_TCCCGA

source_name: PBMC_H1N1 pdm_Initial

value: PBMC


title: 30291.01.TRIPB2

description: 30291.01.TRIPB2 30291_01_TRIPB2_GGTAGC


title: 30292: microbial genes


title: BC1332 CTX 4h NR

value: primary lymphoma cells from lymph node


title: AB9159 native NR


title: BC1954 native NR


title: BC1778 native NR


title: 30301.01.TRFPB2

description: 30301.01.TRFPB2 30301_01_trfPB2_AGTTCC


title: AB5325 CTX 4h RES

value: CTX 4h


title: AB7067 CTX 4h RES

value: Resistant


title: 7965: microbial genes


title: BC1960 native NR

value: native


title: 30301: microbial genes


title: AB7069 CTX 4h RES

value: 3rd relapse


title: ST8789 native NR


title: AB7067 native RES


title: AB6165 native RES


title: AB6397 native RES


title: AB7069 native RES


title: 30455: microbial genes


title: 30301.01.TRIPB3

description: 30301.01.TRIPB3 30301_01_TRIPB3_CAACTA

value: Initial


title: 30515: microbial genes

value: Male


title: AB7133 native NR


title: 30112.01.TRFPB2

description: 30112.01.TRFPB2 30112_01_trfPB2_CTCAGA


title: 8561: microbial genes

value: Human nasal wash and throat sample


title: BC1782 native NR


title: 30112.02.TRIPB2

description: 30112.02.TRIPB2 30112_02_tripb2_AGTCAA


title: ST8799 native NR


title: 30076.01.TRFPB2

description: 30076.01.TRFPB2 30076_01_TRFPB2_CATTTT


title: 8033: microbial genes

value: Human upper respiratory tract


title: 30304: microbial genes


title: AB6397 CTX 4h RES


title: 30292.01.TRIPB2

description: 30292.01.TRIPB2 30292_01_TRIPB2_CACGAT


title: AB6614 CTX 4h RES


title: 7153: microbial genes


title: 30082.01.TRFPB2

description: 30082.01.TRFPB2 30082_01_TRFPB2_ATGAGC


title: 30191.01.TRIPB2

description: 30191.01.TRIPB2 30191_01_triPB2_CTATAC


title: 619: microbial genes


title: AB6158 CTX 4h NR


title: 8561.01.TRIPB2

description: 8561.01.TRIPB2 8561_01_TRIPB2_CGGAAT


title: 6777: microbial genes


title: third_experiment_D21_RNA

city: NEW YORK

first: Thiago

last: Oliveira

address: 1230 YORK AVE

institute: The Rockefeller University

data_processing:
For single cell analysis we used cellranger (v3.0.2) from 10X Genomics for single-cell UMI quantification and TCR clonotype assembly. Hashtags oligos (HTOs) UMI counts were processed using CITE-Seq-Count (v1.4.0). We used Seurat (v3.1.2) [1-2], an R package to analyze single cell RNA-seq data, to identify differentially expressed genes. Genes expressed in at least 10 percent of all cells belonging to clones exhibiting expansion or contraction, with the adjusted p-value by Bonferroni correction less than 0.05 and with |average logeFC| > loge(1.1) were selected as statistical significant differentially expressed genes.
For bulk RNASeq we used kallisto (v.0.46) to map sequence reads to Mus musculus transcriptome (GRCm38/ Ensembl release 99). Kallisto TPM values were converted to absolute counts using tximport (v1.12.3) R package and DESeq2 (v.1.24.0) [3] was utilized for differential expression analysis. Differentially expressed genes were defined by having adjusted p-value < 0.05 and | logFC| > log2(1.5).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with abundance and differential expressiong
Supplementary_files_format_and_content: HTML Report 10x Single Cell

source_name: T Follicular Helper (Tfh) Cells

growth_protocol: Single-cell suspensions were prepared from the spleens and lymph nodes of donor mice. CD4+ T cells were enriched using immunomagnetic negative selection (StemCell Technologies). For adoptive transfer experiments 0.5-1x106 CD4+ T cells were injected into recipient mice by intravenous injection. Resting B cell suspensions were cells were enriched using immunomagnetic positive selection using CD43 (StemCell Technologies).. ∼5 × 106 B1-8hi B cells (5 × 105 Igλ+, NP-specific B cells) composed of the indicated populations were injected into recipient mice by intravenous injection.

extract_protocol:
For bulk RNA sequencing experiments congenic OTII Tfh cells (CD4+, CD62low, CXCR5hi, PD-1hi) or positively selected B cells (500 cells) were purified by flow cytometry 18 hours after pre-immunized host mice were injected with aDEC-205 chimeric antibodies. 1ng of total RNA was used to generate full length cDNA using Clontech’s SMART-Seq v4 Ultra Low Input RNA Kit
The cDNA was used to prepare libraries using Illumina Nextera XT DNA sample preparation kit (Cat # FC-131-1024).   Libraries with unique barcodes were pooled at equal molar ratios and sequenced on an Illumina NextSeq 500 sequencer to produce 75bp reads, following manufactures protocol (Cat# 15048776). For single cell RNA sequencing, single cell spleen suspensions were prepared from half-spleens of NP-OVA immunized SellCreERT2 ROSAtdT mice on day 7 and 21 after immunization. Samples were indexed with TotalSeqC (BioLegend) cell surface antibodies and CD4+, CD62low, CD44hi, PD1hi, CXCR5high, tdTomato+ T cells were purified by flow cytometry, pooled and loaded on to a Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5′ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol. Libraries were loaded onto an Illumina NextSeq with the mid-Output Kit (150 paired end) for V-D-J analysis or NOVAseq for single cell gene expression. Hashtag indexing was used to demultiplex the sequencing data and generate gene-barcode matrices, respectively.

tag: genotype/variation

value: D011.10 and OTII

value: spleen

tag: molecule target

value: poly A RNA


title: AB7310 CTX 4h RP

value: Relapse Prone

value: Primary diagnosis


title: AB6614 native RES

value: Emu-myc transgenic


title: 7965.01.TRFPB2

description: 7965.01.TRFPB2 7965_01_TRFPB2_TAATCG

value: Female

value: Final


title: AB6836 CTX 4h NR

value: primary lymphoma cells from lymph node

value: Never Relapsed


title: AB5325 native RES

value: Resistant


title: 6617: microbial genes

tag: tissue

tag: source


title: 7965.01.TRIPB2

description: 7965.01.TRIPB2 7965_01_TRIPB2_CAGATC

tag: Sex

value: PBMC


title: 6205: microbial genes

tag: ID

value: Influenza B


title: second_experiment_D21_RNA


title: 7765.01.TRFPB2

description: 7765.01.TRFPB2 7765_01_TRFPB2_GTGGCC

value: H1N1 pdm


title: AB7018 CTX 4h NR

tag: genotype

value: CTX 4h


title: AB7055 CTX 4h NR

tag: strain/background


title: second_experiment_D7_RNA


title: 30082: microbial genes

value: Human nasal wash and throat sample

value: Male


title: 30076.01.TRIPB2

description: 30076.01.TRIPB2 30076_01_tripb2_GTCCGC

value: Initial

tag: cell type


title: 30076: microbial genes

value: Human upper respiratory tract


title: AB7069 CTX 4h RP

tag: lymphoma id


title: 30295: microbial genes


title: AB6397 CTX 4h RP

tag: treatment


title: AB6054 CTX 4h NR

tag: response


title: AB3988 CTX 4h RP


title: BDCP Black 3 Tumor

city: Cambridge

first: Richard

last: Gilbertson

address: Robinson way

institute: University of Cambridge

data_processing:
Library strategy: DNA-seq
Raw DNA seq reads aligned to mm10 assembly
read-mapping carried out using Burrows-Wheeler aligner
Genome_build: mm10
Supplementary_files_format_and_content: copy number

source_name: cerebellum

extract_protocol:
Tumor samples were extracted from formalin fixed  paraffin tissue sections using the truXTRAC FFPE total NA Plus Kit (Covaris  520255) followed by magnetic bead-based DNA purification.
DNA libraries were prepared using Nextera Flex pre-enrichment kit (Illumina).

tag: primary tissue

value: cerebellum

tag: aberrant signalling

value: Wnt

tag: time point


title: 7637.01.TRIPB1

description: 7637.01.TRIPB1 7637_01_TRIPB1_GGCTAC

tag: subject id

tag: age

tag: initial/final


title: 8561.01.TRFPB2

description: 8561.01.TRFPB2 8561_01_trfpb2_GGCTAC

tag: strain


title: AB5766 CTX 4h NR

tag: sample type

value: Primary diagnosis


title: AB5325 CTX 4h RP

value: Emu-myc transgenic

value: Relapse Prone


title: AB7822 CTX 4h RP


title: 7637: microbial genes

source_name: Human nasal wash and throat sample

tag: tissue

tag: source


title: AB6619 CTX 4h NR


title: AB8645 native NR

value: native


title: AB7018 native NR

value: primary lymphoma cells from lymph node


title: AB6614 CTX 4h RP


title: AB5529 CTX 4h NR

value: Never Relapsed


title: AB7091 native NR


title: BCP 47177 Normal


title: 7153.01.TRFPB1

description: 7153.01.TRFPB1 7153_01_TRFPB1_ATTCCT

tag: Sex

value: Final


title: BPtchD 1382 CB Tumor

value: Shh


title: 6271: microbial genes

tag: ID

value: Female


title: BCP 2086 Tumor


title: third_experiment_D7_RNA

tag: genotype/variation

value: D011.10 and OTII

value: spleen

tag: molecule target

value: poly A RNA


title: 6957: microbial genes

value: Human nasal wash and throat sample


title: 8033.01.TRFPB2

description: 8033.01.TRFPB2 8033_01_trfPB2_TATAAT

value: Male

value: Influenza B

tag: cell type

value: PBMC


title: BPtchD 18576 CB Tumor

value: cerebellum


title: 6929: microbial genes

value: Human upper respiratory tract


title: HX58_MB3

city: Changsha

first: Xin

last: He

state: Hunan

address: No. 1 Nongda Road, Furong district, Changsha, China

institute: Hunan Agricultural University

description:
Rapeseed variety HX58
HX58 control B replicate 3.
processed data file: gene.description_fin.txt

data_processing:
Raw data (raw reads) of fastq format were first processed through in-house perl scripts. In this step, clean data/reads were obtained by removing reads containing adapter or reads containing poly-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content for the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website (http://www.genoscope.cns.fr/brassicanapus/data/) directly. Index of the reference genome was built using Hisat2 v2.0.4 and paired end reads were aligned to the reference genome using Hisat2 v2.0.4. Hisat2 was selected as the mapping tool because it can generate a database of splice junctions based on the gene model annotation file, thus providing better mapping result than other non-splice mapping tools.
HTSeq v0.9.1 was used to count the reads mapped to each gene. FPKM of each gene was calculated based on the length of the gene and read counts mapped to the gene. FPKM considers the combined effects of sequencing depth and gene length for the read counts, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Brassica napus “Aarmor-bzh”; Genoscope Brassica_napus_v4.1.chromosomes.fa, Brassica_napus.annotation_v5.gff3, Brassica_napus.annotation_v5.cds.fa, Brassica_napus.annotation_v5.pep.fa files.
Supplementary_files_format_and_content: gene.description_fin.txt: Tab-delimited text file includes read counts and FPKM values for all samples.

organism: Brassica napus

source_name: leaves

extract_protocol:
Samples were collected and flash frozen in liquid nitrogen, and total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cold shock at chilling (4°C) and freezing (−4°C) temperatures, as well as chilling and freezing stress following cold acclimation or control conditions.

tag: variety

value: leaves

tag: treatment

value: Control


title: 7637.01.TRFPB2

description: 7637.01.TRFPB2 7637_01_trfpb2_TCATTC


title: BDCP TQ 16 Tumor

tag: primary tissue

value: Wnt


title: 7047.01.TRFPB2

description: 7047.01.TRFPB2 7047_01_TRFPB2_CCGTCC


title: HX58_MB2

description:
Rapeseed variety HX58
HX58 control B replicate 2.
processed data file: gene.description_fin.txt


title: 6628: microbial genes


title: BCP 47177 Tumor

tag: aberrant signalling


title: 7765.01.TRIPB2

description: 7765.01.TRIPB2 7765_01_TRIPB2_ACTGAT

value: H1N1 pdm

value: Initial


title: BPtchD 35314 PN Tumor

tag: time point


title: AB7067 CTX 4h RP

tag: strain/background

tag: genotype

value: Emu-myc transgenic

value: primary lymphoma cells from lymph node

tag: lymphoma id

value: CTX 4h

tag: response

value: Relapse Prone

value: Primary diagnosis


title: AB7310 native RP

value: native

tag: sample type


title: AB7822 native RP


title: AB6165 CTX 4h RP


title: 6957.01.TRIPB2

description: 6957.01.TRIPB2 6957_01_triPB2_GAGTGG

tag: subject id

tag: age

value: Female

tag: strain

tag: initial/final


title: AB8645 CTX 4h NR

value: Never Relapsed


title: AB5325 native RP


title: 7331: microbial genes

tag: tissue

value: Human nasal wash and throat sample

tag: source

tag: ID

tag: Sex

value: Male


title: 6471: microbial genes


title: AB5766 native NR

tag: cell type

tag: treatment


title: 7331.01.TRIPB2

description: 7331.01.TRIPB2 7331_01_TRIPB2_TGACCA

value: PBMC


title: 7765: microbial genes

value: Human upper respiratory tract


title: HX58_FB2

description:
Rapeseed variety HX58
HX58 treated with -4℃ replicate 2.
processed data file: gene.description_fin.txt

tag: variety

value: leaves

value: -4 degree Celsius


title: 6777.01.TRFPB4

description: 6777.01.TRFPB4 6777_01_TRFPB4_CACCGG

value: Final


title: BPtchD 1382 Normal

tag: primary tissue

value: cerebellum

tag: aberrant signalling

value: Shh

tag: time point


title: AB7055 native NR

tag: strain/background

tag: genotype

value: Emu-myc transgenic

tag: lymphoma id


title: AB6158 native NR

value: primary lymphoma cells from lymph node

tag: response

tag: sample type


title: 6777.01.TRIPB2

description: 6777.01.TRIPB2 6777_01_TRIPB2_GTTTCG

tag: subject id

tag: age

tag: strain

value: Initial


title: 7331.01.TRFPB2

description: 7331.01.TRFPB2 7331_01_TRFPB2_CATGGC

value: H1N1 pdm

tag: initial/final


title: 6667.02.TRFPB2

description: 6667.02.TRFPB2 6667_02_trfPB2_GTAGAG


title: 7153.01.TRIPB1

description: 7153.01.TRIPB1 7153_01_TRIPB1_GATCAG


title: HX58_MB1

description:
Rapeseed variety HX58
HX58 control B replicate 1.
processed data file: gene.description_fin.txt

tag: tissue

value: Control


title: 7098.01.TRFPB2

description: 7098.01.TRFPB2 7098_01_TRFPB2_GTCCGC

tag: Sex

value: Influenza B


title: BPtchD 1382 PN Tumor


title: BDCP 3 Tumor

value: Wnt


title: 11X-Rituximab-Day8_rep2

city: San Diego

first: Nathan

middle: E.

last: Lewis

address: 9500 Gilman Dr.

department: Pediatrics

institute: University of California, San Diego

data_processing:
RNA-Seq quality was assessed using FastQC. Adapter sequences and low-quality bases were trimmed using Trimmomatic (Bolger et al. 2014).
Sequence alignment was accomplished using STAR (Dobin et al. 2013) against the CHO genome (GCF_000419365.1_C_griseus_v1.0) with default parameters.
HTSeq (Anders et al. 2015) was used to quantify the expression of each gene. We performed differential gene expression analysis using DESeq2 (Anders and Huber 2010).
Genome_build: C_griseus_v1.0 (GCF_000419365.1)
Supplementary_files_format_and_content: tab-delimited text file includes count values for each Sample

organism: Cricetulus griseus

source_name: Ovary

growth_protocol: Batch cultivation was performed in 250 mL shake flasks containing 60-80 mL CD-CHO medium (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 8 mM L-glutamine (Life Technologies) and 0.2% anti-clumping reagent (Life Technologies). Prior to inoculation into fed-batch bioreactors, cells were adapted from CD-CHO medium to FortiCHO (Gibco, Carlsbad, CA, USA), OptiCHO (Gibco), or ActiPro (GE Healthcare, Chicago, IL, USA) medium during three passages. All media were supplemented with 1% Anti-Anti (Life Technologies), 0.1% anti-clumping agent (Life Technologies) and 8 mM L-glutamine (Lonza, Basel, Switzerland).

extract_protocol:
Cell cultures were resuspended in RLT buffer (Qiagen) and kept at -80°C until RNA was extracted using the RNeasy kit (Qiagen) and on-column DNAse digestion. RNA was eluted in 40µl of nuclease free water (RNAse/DNAse free); concentration was measured on Qubit and the purity was checked on Fragment Analyzer. Complementary DNA synthesis was obtained from 1 μg of RNA using the High capacity cDNA RT kit (Thermo Fisher scientific) as per manufacturer’s instructions.
Samples were diluted to 60ng/µL in 50µL and library preparation was performed with Illumina’s TruSeq Stranded mRNA Library Prep Kit High Throughput (Catalog ID: 20020595), according to manufacturer’s protocol.

value: CHO-S 11xKO

value: Ovary

value: Day 8


title: 11X-Rituximab-Day6_rep2

value: Day 6


title: HX58_FB3

description:
Rapeseed variety HX58
HX58 treated with -4℃ replicate 3.
processed data file: gene.description_fin.txt


title: 6617.01.TRFPB1

description: 6617.01.TRFPB1 6617_01_TRFPB1_CTATAC

value: Female

tag: cell type

value: PBMC


title: AB6397 native RP

tag: treatment

value: native

value: Relapse Prone

value: Primary diagnosis


title: 6955.01.TRFPB2

description: 6955.01.TRFPB2 6955_01_trfPB2_ATTCCT

value: Male

value: Final


title: 6617.01.TRIPB2

description: 6617.01.TRIPB2 6617_01_TRIPB2_GAGTGG


title: AB5529 native NR

value: Emu-myc transgenic

value: primary lymphoma cells from lymph node

value: Never Relapsed


title: AB6836 native NR


title: 6471.01.TRFPB3

description: 6471.01.TRFPB3 6471_01_TRFPB3_TACAGC

value: H1N1 pdm


title: HX58_MA1

description:
Rapeseed variety HX58
HX58 control A replicate 1.
processed data file: gene.description_fin.txt

tag: variety

value: leaves

value: Control


title: HX58_FB1

description:
Rapeseed variety HX58
HX58 treated with -4℃ replicate 1.
processed data file: gene.description_fin.txt

value: -4 degree Celsius


title: BPtchD 35314 CB Tumor

tag: primary tissue

value: cerebellum

value: Shh


title: BPtchD 18576 PN Tumor

tag: aberrant signalling


title: AB6165 native RP


title: HX58_FA3

description:
Rapeseed variety HX58
HX58 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 3.
processed data file: gene.description_fin.txt

value: -4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: 6271.01.TRIPB2

description: 6271.01.TRIPB2 6271_01_TRIPB2_CAAAAG

value: Female

value: Initial


title: AB6619 native NR

value: native


title: 6271.01.TRFPB3

description: 6271.01.TRFPB3 6271_01_TRFPB3_TCGAAG

value: PBMC


title: AB7069 native RP

value: Relapse Prone

value: Primary diagnosis


title: AB6614 native RP


title: HX58_CB3

description:
Rapeseed variety HX58
HX58 treated with 4℃ replicate 3.
processed data file: gene.description_fin.txt

value: 4 degree Celsius


title: 11X-Rituximab-Day4_rep2

value: CHO-S 11xKO

value: Ovary

tag: time point

value: Day 4


title: 6X-Rituximab-Day8_rep2

value: CHO-S 6xKO

value: Day 8


title: 6205.01.TRFPB2

description: 6205.01.TRFPB2 6205_01_TRFPB2_TGACCA

value: Influenza B

value: Final


title: HX58_CB2

description:
Rapeseed variety HX58
HX58 treated with 4℃ replicate 2.
processed data file: gene.description_fin.txt

value: leaves


title: HX58_MA3

description:
Rapeseed variety HX58
HX58 control A replicate 3.
processed data file: gene.description_fin.txt

value: Control


title: HX58_CB1

description:
Rapeseed variety HX58
HX58 treated with 4℃ replicate 1.
processed data file: gene.description_fin.txt


title: HX58_FA1

description:
Rapeseed variety HX58
HX58 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 1.
processed data file: gene.description_fin.txt

value: -4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: 6X-Rituximab-Day6_rep2

value: Day 6


title: AB3988 native RP

tag: strain/background

value: Emu-myc transgenic

value: primary lymphoma cells from lymph node


title: HX58_MA2

description:
Rapeseed variety HX58
HX58 control A replicate 2.
processed data file: gene.description_fin.txt


title: 11X-Rituximab-Day8_rep1


title: 6628.01.TRFPB2

description: 6628.01.TRFPB2 6628_01_TRFPB2_ATGTCA

value: Female

value: PBMC


title: 11X-Rituximab-Day6_rep1


title: 3522.01.TRFPB2

description: 3522.01.TRFPB2 3522_01_TRFPB2_CTCAGA

value: Male


title: Root, Roma-salt3

city: Jinan

last: Sui

address: Wenhua East Road

department: College of Life Sciences

institute: Shandong normal university

data_processing:
Generally, after total RNA is extracted from the whole transcriptome, two sequencing libraries are constructed: a small RNA library smaller than 50 nt and a de-rRNA strand specific library larger than 200 nt. The first library uses the SE50 on-boarding strategy, and the second library uses the 150PE on-boarding strategy.
Small RNA libraries smaller than 50 nt were single-ended sequenced on Illumina Hiseq 2500 on LC-BIO (Hangzhou, China), and de-rRNA strand-specific libraries larger than 200 nt were paired-end sequenced on Illumina Hiseq 4000 (lc-bio, China) .
First, Cutadapt was used to remove reads containing linker contamination, low quality bases, and undetermined bases. We used Bowtie2 and Tophat2 to map the reads to the genome of sweet sorghum, and used StringTie to assemble the mapped reads for each sample. Then, merge using a perl script to build a complete transcriptome.
After the final transcriptome was generated, StringTie and Ballgown was used to estimate the expression levels of all transcripts.
Genome_build: sorghum bicolor Ensembl release58
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sorghum bicolor

source_name: Root

extract_protocol:
Sweet sorghum in the three-leaf stage was subjected to salt treatment for 24 hours, and then RNA was harvested using Trizol reagent. The TruSeq Small RNA Sample Preparation Kit (Illumina, San Diego, USA) was used with 1 ug total RNA to construct a sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Roma

value: three-leaf phase

value: root

tag: stress

value: salt


title: AB6054 native NR

tag: genotype

tag: lymphoma id

value: native

value: Never Relapsed

value: Primary diagnosis


title: Root, Roma-salt2


title: HX58_FA2

description:
Rapeseed variety HX58
HX58 treated with -4℃ 12 h following cold acclimation (14 days 4℃) replicate 2.
processed data file: gene.description_fin.txt


title: HX58_CA2

description:
Rapeseed variety HX58
HX58 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 2.
processed data file: gene.description_fin.txt

value: 4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: 3522.01.TRIPB2

description: 3522.01.TRIPB2 3522_01_TRIPB2_ATCACG

value: Initial


title: Root, Roma-salt1


title: AB7091 CTX 4h NR

description: Gene expression data from primary Emu-myc lymphomas in therapy-naive state or after drug chalenge

value: CTX 4h

tag: response

tag: sample type


title: 619.01.TRFPB2

description: 619.01.TRFPB2 619_01_trfpb2_CTAGCT

tag: subject id

tag: age

value: H1N1 pdm

value: Final


title: 11X-Rituximab-Day4_rep1

tag: strain

value: CHO-S 11xKO

value: Ovary

value: Day 4


title: AB7067 native RP

value: Emu-myc transgenic

value: primary lymphoma cells from lymph node

value: Relapse Prone


title: 6205.01.TRIPB2

description: 6205.01.TRIPB2 6205_01_TRIPB2_ACTGAT

value: Female

value: Influenza B

tag: initial/final

value: PBMC


title: HX58_CA1

description:
Rapeseed variety HX58
HX58 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 1.
processed data file: gene.description_fin.txt

tag: tissue

value: leaves


title: 6X-Rituximab-Day4_rep2

value: CHO-S 6xKO


title: 6X-Rituximab-Day8_rep1

value: Day 8


title: Root, Roma-CK3

value: Roma

value: three-leaf phase

value: root

value: control


title: 6X-Rituximab-Day6_rep1

value: Day 6


title: 6X-Rituximab-Day4_rep1


title: Root, Roma-CK1


title: Root, Roma-CK2


title: HX17_MB3

description:
Rapeseed variety HX17
HX17 control B replicate 3.
processed data file: gene.description_fin.txt

value: Control


title: WT-Rituximab-Day6_rep2

value: CHO-S

value: Ovary


title: WT-Rituximab-Day4_rep2

value: Day 4


title: HX58_CA3

description:
Rapeseed variety HX58
HX58 treated with 4℃ 12 h following cold acclimation (14 days 4℃) replicate 3.
processed data file: gene.description_fin.txt

value: 4 degree Celsius 12 h following cold acclimation (14 days 4 degree Celsius)


title: Root, M-81E-salt2

value: salt


title: HX17_FB3

description:
Rapeseed variety HX17
HX17 treated with -4℃ replicate 3.
processed data file: gene.description_fin.txt

value: -4 degree Celsius


title: HX17_MB1

description:
Rapeseed variety HX17
HX17 control B replicate 1.
processed data file: gene.description_fin.txt


title: HX17_FB2

description:
Rapeseed variety HX17
HX17 treated with -4℃ replicate 2.
processed data file: gene.description_fin.txt


title: Root, M-81E-salt1


title: Root, M-81E-CK3


title: HX17_FB1

description:
Rapeseed variety HX17
HX17 treated with -4℃ replicate 1.
processed data file: gene.description_fin.txt


title: WT-Rituximab-Day8_rep2


title: WT-Rituximab-Day4_rep1


title: HX17_CB3

description:
Rapeseed variety HX17
HX17 treated with 4℃ replicate 3.
processed data file: gene.description_fin.txt

value: 4 degree Celsius


title: HX17_MB2

description:
Rapeseed variety HX17
HX17 control B replicate 2.
processed data file: gene.description_fin.txt


title: WT-Rituximab-Day6_rep1


title: Root, M-81E-CK2