title: SMB21_AZA_24h_C

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

data_processing:
The libraries were sequenced as paired-end 50bp reads on an Illumina NovaSeq6000 (Illumina) with a sequencing depth of approximately 25 million clusters per sample.
Raw data QC and processing was performed using megSAP (version 0.2-135-gd002274) combined with ngs-bits package (version 2019_11-42-gflb98e63).
Reads were aligned using STAR v2.7.3a
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw read counts for each replicate.

source_name: tumor, central nervous system

growth_protocol: Cells were grown Dulbecco´s Modified Eagle´s Medium/Ham´s F-12 50/50 Mix medium (DMEM/F12) (Corning) supplemented with 2% B27 and vitamin A (Thermo Fisher Scientific), 1% GlutaMax (Thermo Fisher Scientific) and 1% penicillin-streptomycin (Thermo Fisher Scientific) in ultra-low attachment plates

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
mRNA libraries were prepared using the NEB Next Ultra II Directional RNA Library Prep Kit

treatment_protocol: SMB21 cells were treated with 3µM 5-azacytidine for 2 hours, 24 hours, or corresponding concentration of DMSO solvent.

value: tumor, central nervous system

value: Sonic hedgehog medulloblastoma

value: 3 µM 5-azacytidine


title: adult male, PBMC enriched for IgD B cell, year 1 day-120, replicate 1

status: Public on Jun 13 2024

type: SRA

city: New Haven

first: Steven

last: Kleinstein

state: Ct

address: 300 George St.

department: Pathology

country: USA

institute: Yale University

library_source: transcriptomic

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.
Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).
Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.
Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: Rds: Seurat analyses saved as R objects

molecule: polyA RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS.   A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.

tag: tissue

value: PBMC

tag: Sex

value: male

tag: age

tag: isolate


title: Blood,excercised,cell14 ,78M

city: Sydney

first: Rowena

last: Bull

state: NSW

address: Wallace Wurth Building (C27)

country: Australia

institute: University of New South Wales

description: SMARTseq2 single cell RNA sequencing data from E2-specific memory B cells

library_source: transcriptomic single cell

data_processing:
The raw data was aligned with human genome to map the heavy and light chain genes which were further annotated using IgBlast software implemented in VDJPuzzle
Inhouse pipeline used to generate the matrix that was further processed using seurat and other packages for paired-end sequences
Assembly: Sequences were processed using VDJPuzzle for BCR data and inhouse pipelines for Gene expression analysis
Supplementary files format and content: barcodes.tsv
Supplementary files format and content: features.tsv
Supplementary files format and content: matrix.mtx

molecule: total RNA

source_name: Blood

extract_protocol:
Seven to ten million cryopreserved PBMCs were sorted for E2-specific B cells as described previously. S figure 4, in the article indicates the time points selected for flow analysis and transcriptomics/repertoire analysis. In brief, PBMCs were stained with an in-house developed rE2 cocktail tetramer (Gt1a [H77] and Gt3a [UKN3A13.6]) as well as anti-CD19, anti-CD20, anti-CD10, anti-CD38, anti-IgD, anti-IgG, anti-CD27,anti-CD21 and anti-CD95 antibodies, and single cell sorted using flow cytometry. Population phenotypes were analysed with FlowJo version 10 software (Tree Star Inc.) (See CTAT Table for antibody details and see S Figure 3 for gating strategy and how gates were set for CD95 positivity based on FMO).
E2+ B cells were sorted into single wells and single cell RNA sequencing was performed following the smartseq2 protocol as previously described. BCR sequences were reconstructed using VDJpuzzle 2.0. Identification of B cell clonotypes and SHM across infections was done using Immcantation framework.  Paired-end reads from Smart-seq2 were aligned with STAR (version 2.7.1a) using the GRCh38.p13 human reference genome. Transcripts per Million (TPM) were quantified using RSEM (version 1.2.28) using rsem-calculate-expression command on HPC clusters.

value: Blood

tag: cell line

value: human samples

tag: cell type

value: Memory B cells

tag: genotype


title: adult male, PBMC enriched for IgD B cell, year 2 day-0, replicate 1


title: SMB21_AZA_24h_B

country: Germany

organism: Mus musculus

tag: treatment


title: Blood,excercised,cell13 ,78M


title: PC3_cells, DDX4_NULL, replicate 4

city: Turku

first: Lin

last: Ma

address: Kiinamyllynkatu 10

country: Finland

institute: University of Turku

data_processing:
The adapter and low-quality nucleotides were cut off from raw data by Trimmomatic (v0.39).
The clean data next were mapped to the reference human genome (GRCh37) by using STAR (v2.7.10a).
Read counts were calculated by featureCounts (v2.0.3).
Assembly: GRCh37
Supplementary files format and content: comma-separated text file includes raw counts for all samples

source_name: prostate cancer cellline

extract_protocol:
Total RNA was isolated from cells and tumors using TRIsure (BIO-38033, Meridian Bioscience) according to the manufacturer’s instructions. To remove any DNA contamination, DNase I (AMPD1, Sigma-Aldrich) was used. The quality of total RNA was ensured with Advanced Analytical Fragment Analyzer. Sample concentration was measured with Qubit® Fluorometric Quantitation, Life Technologies.
Libraries were prepared using the Illumina TruSeq® Stranded mRNA kit (part#15031047).

value: prostate cancer cellline

value: PC3 cells

value: DDX4 NULL


title: Blood,excercised,cell12 ,78M


title: PC3_cells, DDX4_NULL, replicate 3


title: adult male, PBMC enriched for IgD B cell, year 1 day-0, replicate 1


title: SMB21_AZA_24h_A


title: TGFB1 stimulated A375 INPUT 6.11.18

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

library_source: genomic

data_processing:
ChIP-Seq aligned to GRCh38 with Bowtie with max mismatch 2bp
peaks were called using MACS 2.0 with the following setting: q-value 0.05
Assembly: GRCh38
Supplementary files format and content: narrowPeak Bed files from MACS 2.0 output

molecule: genomic DNA

source_name: A375 Cells

growth_protocol: A375s were grown in filter sterilized DMEM, 10% FBS, 1% PenStrep, 1% Glutamine at 37°C

extract_protocol:
A375 cells were fixed directly in 15cm plates with 11% formaldehyde and collected by scraping. Approximately 100,000,000 cells were used per condition. Cells were lysed using lysis buffers with protease inhibitors (Roche #05056489001) and sonicated such that fragmented chromatin was 200-300bp long. Optimal chromatin length was confirmed by gel electrophoresis. Prior to antibody addition, 50µL chromatin was collected for input sample. The remaining sonicated chromatin was incubated overnight at 4°C with 10µg antibody attached to Dynabeads (Invitrogen #10004D). Samples (including inputs) were washed with wash buffers and eluted for 6 hours at 70°C, treated with RNaseA (Sigma #R4642) and ProteinaseK (Life Technologies #AM2546), and purified using Zymo ChIP DNA Concentrator kit (Genesee Scientific #11-379C).
Libraries were end repaired (VWR #ER81050), polyA tailed (Invitrogen #18252-015, NEB #M0212L), adaptor ligated (NEB #E7335), size selected using Ampure XP beads (Beckman Coulter #A63881, Life Technologies #12027), and PCR amplified (NEB #M0531).

treatment_protocol: Cells were starved for 2 hours. Treated with 10ng/mL TGFB1 ligand or 4mM HCl containing 1mg/mL BSA vehicle control for 2 hours.

tag: chip antibody

value: A375 Cells


title: adult male, PBMC, year 1, day-90, replicate 2


title: PC3_cells, DDX4_NULL, replicate 2


title: SMB21_AZA_2h_C


title: Blood,excercised,cell11 ,78M


title: SMB21_AZA_2h_A


title: SMB21_AZA_2h_B


title: PC3_cells, DDX4_NULL, replicate 1


title: Blood,excercised,cell10 ,78M


title: Blood,excercised,cell9  ,78M


title: adult male, PBMC, year 1, day-60, replicate 1


title: adult male, PBMC enriched for IgD B cell, year 1 day-35, replicate 1


title: adult male, PBMC, year 1, day-90, replicate 1


title: PC3_cells, control, replicate 4

value: Control


title: SMB21_DMSO_C

value: DMSO


title: FBS-cultured ASC sheet

type: RNA

city: Taipei

first: Yueh Chen

last: Chen

address: No.7, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist.

department: Surgery

country: Taiwan

institute: National Taiwan University Hospital

description: Gene expression of ASC sheets fabricated with fetal bovine serum

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

scan_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint Microarray (Agilent Technologies, USA) at 65°C for 17 h. After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

source_name: adipose tissue, average age 45y, average body mass index 24.7

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

growth_protocol: Adipose stem cells (ASCs) were isolated from the subcutaneous fat tissue of four non-diabetic, non-smoking female donors with an average age of 45 y (32–57 y) and an average body mass index of 24.6 (21.0–26.6). ASCs were cultured  in DMEM/F12 medium supplemented with 10% fetal bovine serum and 1 ng/mL FGF2. The cells were cultured in a humidified atmosphere with 5% CO2 at 37°C, and the medium was refreshed every 2–3 days.

extract_protocol: RNA was prepared using TRIzol™ Reagent (Invitrogen, Thermo Fisher Scientific, Inc., Waltham, MA, USA ), and chloroform is used for phase separation of RNA (aqueous phase) from DNA (inter-/organic phase). Residual genomic DNA is removed by on-column digestion with DNase I. The purified RNA is eluted from the silica-based column using Nuclease-Free Water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer with a RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA).

treatment_protocol: ASCs were seeded at a density of 1x104 cells/cm2 in the culture medium consisted of DMEM-high glucose, 1% penicillin/streptomycin, 0.02% heparin, 250 μM L-ascorbate 2-phosphate, and supplemented with 10% FBS or 5% HPL for sheet fabrication.

value: adipose tissue

tag: gender

value: female


title: Blood,excercised,cell8  ,78M


title: HPL-cultured ASC sheet

description: Gene expression of ASC sheets fabricated with human platelet lysate

source_name: adipose tissue, average age 45y, average body mass index 24.6


title: adult male, PBMC, year 1, day-5, replicate 2


title: SMB21_DMSO_B


title: PC3_cells, control, replicate 3


title: adult male, PBMC, year 1, day-5, replicate 1


title: Blood,excercised,cell7  ,78M


title: PC3_cells, control, replicate 2


title: SMB21_DMSO_A


title: Blood,excercised,cell6  ,78M


title: Blood,excercised,cell5  ,78M


title: adult male, PBMC, year 1, day-28, replicate 2


title: PC3_cells, control, replicate 1


title: intestinal RetSat ko 5

city: Berlin

first: Michael

last: Schupp

address: Hessische Str. 3-4

department: Institute of Pharmacology

institute: Charite Universitätsmedizin Berlin

data_processing:
Sequence reads were trimmed with the trimmomatic tool and default parameters
Trimmed sequences were mapped to GRCm39/mm39 using the STAR method (v2.7.6)
read count extraction was performed using featureCounts v2.0.1
Assembly: mm39
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: mouse jejunum

growth_protocol: standard mouse colony

extract_protocol:
RNA was harvested using the RNeasy kit from Qiagen, following the manufacturer`s protocol
samples were further treated with the DNase I Set from Zymo Research,following the manufacturer`s protocol
Library preparation was performed using the NEBNext Ultra II RNA Library Prep Kit and Module (New England Biolabs, USA) following manufacturer`s protocol

treatment_protocol: standard i.p. tamoxifen to induce knockout, 60 kcal% high-fat diet

value: mouse jejunum

tag: strain

value: RetSat flox/flox villin-Cre-ERT2 (+)

value: tamoxifen, high-fat diet


title: intestinal RetSat ko 4


title: PC3_tumor, DDX4_NULL, replicate 4

value: PC3 xenograft tumors


title: adult male, PBMC, year 1, day-180, replicate 2

value: PBMC


title: intestinal RetSat ko 3


title: PC3_tumor, DDX4_NULL, replicate 3


title: adult male, PBMC, year 1, day-120, replicate 1

value: male


title: intestinal RetSat ko 2


title: Blood,excercised,cell4  ,78M

value: Blood


title: Blood,excercised,cell3  ,78M

value: human samples


title: intestinal RetSat ko 1


title: PC3_tumor, DDX4_NULL, replicate 2


title: PC3_tumor, DDX4_NULL, replicate 1


title: adult male, PBMC, year 1, day-12, replicate 2


title: adult male, PBMC, year 1, day-12, replicate 1


title: Blood,excercised,cell1,78M

value: Memory B cells


title: PC3_tumor, control, replicate 4

value: prostate cancer cellline


title: adult male, PBMC, year 1, day-0, replicate 2


title: Bronchiolar cells, uninfected rep3

city: Rotterdam

first: Mart

middle: Matthias

last: Lamers

address: Wytemaweg 80

department: Viroscience

country: Netherlands

institute: Erasmus MC

data_processing:
Samples were mapped using MapandGO to hg38 containing SARS-CoV-2 sequences as reference tanscriptome (https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo)
Data was generated by paired-end sequencing of CEL-seq2 libraries, that contain samble barcode and UMI in Read1, and a part of the mRNA in Read2. To simplify downstream analysis, the data was demultiplexed per sample, and the information from read1 (barcode and UMI) was moved to the header of the corresponding read 2. This means Read2 can be mapped directly as if it were single-end data. For each sample, there are four lanes (L001, L002, L003, L004)
Genome_build: Human: Hg38
Supplementary_files_format_and_content: Tsv file containing expression counts for all genes across all samples.

source_name: Bronchiolar epithelial cells

growth_protocol: AT2 cells were grown in 3D in alveolar medium. Bronchiolar 3D organoids were grown in AO medium, seeded on collagen-coaed transwell inserts and differentiated in pneumacult medium at air-liquid interface.

extract_protocol:
Extractions were performed using the trizol RNA extraction protocol.
mRNA, amplification and sequencing libraries were performed as described in {Junker et al., 2014}. Briefly, RNA samples were treated according to the CEL-seq protocol {Hashimshony, 2012 #36}. Illumina sequencing libraries were prepared with the TruSeq small RNA sample prep kit
Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing.

treatment_protocol: AT2 cells were grown in 3D in alveolar medium, mechanically disrupted, infected with Bavpat-1 or B.1.1.7 in suspension at a multiplicity of infection of 0.1,  plated in 3D and grown for 72 hours in expansion medium. An uninfected control was included and treated equally, apart from the addition of virus. Bronciolar 2D organoids were grown in pneumacult and left untreated. Cells were harvested by lysis in trizol.

value: Bronchiolar cells

value: Lung

value: Not infected


title: control 5

value: RetSat flox/flox villin-Cre-ERT2 (-)


title: control 4


title: PC3_tumor, control, replicate 3

value: Control


title: adult male, PBMC, year 1, day-28, replicate 1


title: adult male, PBMC, year 1, day-0, replicate 1


title: control 3


title: Bronchiolar cells, uninfected rep2


title: adult male, PBMC, enriched for IgD B cells, year 2, day-90, replicate 1


title: Blood,excercised,cell2,78M


title: adult male, PBMC, enriched for IgD B cells, year 1, day-90, replicate 1


title: control 2


title: PC3_tumor, control, replicate 2


title: METTL14-n2-IP

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
*library strategy: eCLIP
The 5’ UMI were trimmed by using umi_tools and the 3’ adapter were trimmed by using cutadapt.
Reads were filtered to remove repetitive elements and then aligned to human genome (hg38) by using STAR.
PCR duplicates were removed by using umi_tools.
BigWig files were generated by using deeptools.
To generate BED files, peak calling were done by using piranha.
Supplementary files format and content: bigWig
Supplementary files format and content: bed

extract_protocol:
UV-cross-linked cells were lysed in lysis buffer with protease Inhibitors. METTL14-bound RNA were isolated by antibody (A305-847A, Bethyl Laboratories) coupled magnetic beads and further purified as previously described (https://link.springer.com/protocol/10.1007/978-1-4939-7204-3_14).
RNA-seq libraries were prepared by using Illumina TruSeq HT Sample Prep Kit.

value: beta cell

value: IP


title: Alveolar type 2 cells, uninfected rep3

source_name: Alveolar type 2 cells

value: AT2 cells


title: adult male, PBMC, enriched for IgD B cells, year 2, day-60, replicate 1


title: Alveolar type 2 cells, uninfected rep2


title: METTL14-n2-input

value: Input


title: adult male, PBMC, enriched for IgD B cells, year 1, day-60, replicate 1


title: Alveolar type 2 cells, uninfected rep1


title: Alveolar type 2 cells infected with B.1.1.7 rep3

value: Infection with SARS-CoV-2 B.1.1.7


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep4

first: April

last: Craft

address: 300 Longwood Ave

data_processing:
Novogene
Assembly: mm10
Supplementary files format and content: gene counts in xls file

source_name: 3xR mESC

extract_protocol:
Trizol
Novogene

value: 3xR mESC

tag: time

value: day 14

value: Fsk


title: METTL14-n1-IP


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep1


title: adult male, PBMC, enriched for IgD B cells, year 2, day-6, replicate 1

value: PBMC

value: male


title: METTL14-n1-input


title: adult male, PBMC, enriched for IgD B cells, year 1, day-5, replicate 1


title: Alveolar type 2 cells infected with B.1.1.7 rep2


title: adult male, PBMC, enriched for IgD B cells, year 2, day-28, replicate 1


title: Bronchiolar cells, uninfected rep1


title: HCT116 cells,curcumin3

city: Xi'an

first: Weilongli

last: Li

address: No.1 Changle East Road

country: China

institute: Air Force Engineering University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: cancer cell

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using chloroform, isopropanol and washed with ethanol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: HCT116 cells were treated with 30μm curcumin for 24 hours,then collected cells and dissolved in trizol

value: cancer cell

value: colon cancer cell

value: WT

value: curcumin


title: HCT116 cells,curcumin2


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep3

value: DMSO


title: control 1

value: mouse jejunum

value: RetSat flox/flox villin-Cre-ERT2 (-)

value: tamoxifen, high-fat diet


title: adult male, PBMC, enriched for IgD B cells, year 1, day-28, replicate 1


title: Prg4-tdTomato+ cells isolated from Fsk-treated condition Rep5


title: Alveolar type 2 cells infected with Bavpat-1 rep3

value: Lung

value: Infection with SARS-CoV-2 Bavpat-1


title: adult male, PBMC, enriched for IgD B cells, year 1, day-180, replicate 1


title: HCT116 cells,curcumin1


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep1


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep5


title: HCT116 cells, Control3


title: adult male, PBMC, enriched for IgD B cells, year 2, day-13, replicate 1


title: Alveolar type 2 cells infected with Bavpat-1 rep2

value: AT2 cells


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep4


title: Prg4-tdTomato+ cells isolated from DMSO-treated condition Rep5


title: HCT116 cells, Control2


title: adult male, PBMC, enriched for IgD B cells, year 1, day-120, replicate 1


title: n5-pH6_6-IL2

city: Lausanne

first: Isaac

last: Crespo

state: Vaud

address: Bugnon 25A

department: Oncology

country: Switzerland

institute: Ludwig Cancer Research,UNIL

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.9.3).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus build GRCm38 genome using STAR (v. 2.5.2b, Dobin et al. 2013). The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1, Anders et al. 2014) using Ensembl 86 gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts per sample

source_name: CD8+ T cell

growth_protocol: DMEM low glucose, glutamax, pyruvate supplemented with 10% FBS, 1% NEAA, 1% P/S, 50uM b-mercaptoethanol - Cultured at 37°C/5% CO2

extract_protocol:
Ficoll to remove dead cells, washes twice with PBS, then RNA extraction using Qiagen RNeasy extraction kit
Illumina Truseq stranded mRNA

value: CD8+ T cell

value: 24 hours culture at pH6.6 in the presence of IL-2 200IU/mL


title: adult male, PBMC, enriched for IgD B cells, year 1, day-12, replicate 1


title: n5-pH7-IL2

value: 24 hours culture at pH7 in the presence of IL-2 200IU/mL


title: PC3_tumor, control, replicate 1

value: prostate cancer cellline

value: PC3 xenograft tumors

value: Control


title: Alveolar type 2 cells infected with B.1.1.7 rep1

value: Infection with SARS-CoV-2 B.1.1.7


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep3

value: 3xR mESC

value: day 14


title: HCT116 cells, Control1

value: cancer cell

value: colon cancer cell

value: WT


title: Col2a1-eGFP+ cells isolated from DMSO-treated condition Rep1

value: DMSO


title: adult male, PBMC, enriched for IgD B cells, year 2, day-0, replicate 1

value: PBMC

value: male


title: n5-pH7_4-IL2

value: 24 hours culture at pH7.4 in the presence of IL-2 200IU/mL


title: C643 cells, kinome shRNA library, docetaxel, replicate 2

city: Aurora

first: Nikita

last: Pozdeyev

state: CO

address: 1890 N. Revere Court | Mailstop F600

department: Biomedical Informatics

institute: University of Colorado

library_source: other

data_processing:
Raw sequencing data was analyzed as published previously (Dai Z, Sheridan JM, Gearing LJ, Moore DL, Su S, Wormald S, et al. edgeR: a versatile tool for the analysis of shRNA-seq and CRISPR-Cas9 genetic screens. F1000Research 2014;3:95 doi 10.12688/f1000research.3928.2.) using a bioinformatics pipeline based on the edgeR package in R
Supplementary files format and content: C643_Docetaxel_all_shRNAs.csv; comma separated file containing shRNA sequences, targeted kinases, shRNA sequence counts for each sample and statistical analysis

molecule: other

growth_protocol: C643 anaplastic thyroid cancer cells were maintained in RPMI-1650 media supplemented with 5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol: hairpin DNA was amplified, barcoded, and sequenced (Illumina HiSeq 2500)

treatment_protocol: C643 cells were treated for 14 days with 0.35 nM of docetaxel (Selleckchem, Cat #S1148) or vehicle (DMSO)

value: anaplastic thyroid cancer

tag: transduction

value: kinome shRNA library transduced

value: Docetaxel


title: n5-pH6_6

value: CD8+ T cell

value: 24 hours culture at pH6.6


title: adult male, PBMC, enriched for IgD B cells, year 1, day-0, replicate 1


title: het mouse, scRNAseq, multiplexed

city: Cincinnati

first: Timothy

last: Chlon

state: Ohio

address: 3333 BURNET AVENUE

department: Pediatrics

institute: Cincinnaty Childrens Hospital Medical Center

description: 10X Genomics Multiplexing Capture

data_processing:
Data demultiplexed using cellranger multi, version 7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Filtered count matrices in HDF5 format (output from cellranger multi)

source_name: bone marrow

growth_protocol: BoyJ mice were transplanted with 1M bone marrow mononuclear cells from Rosa-CreERT2 mice with a heterozygous floxed Ddx41 allele or wild-type. Mice were inected with 1mg tamoxifen in 50ul corn oil for two rounds of five consecutive days separated by 2 days.

extract_protocol:
CD45.2+ Lin-Kit+ cells were sorted by 3-color staining on a FACS Aria sorter (BD). Samples were hashed using TotalSeqB Cell Hashing Kit and then were pooled with 3 replicates in one smaple. Approximately 15,000 pooled cells were loaded onto the 10X for each condition (control vs. heterozygous)
The scRNA-Seq assay was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein, 10x Genomics). Briefly, Total-Seq B antibody-labeled cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate a gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every GEM was reverse transcribed into cDNA, adding an Illumina TruSeq R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The DNA conjugated to the Total-Seq B antibodies (Feature Barcodes aka FBs) was also barcoded by adding an Illumina Nextera R1, UMI, and the 10x Barcode. The cell barcoded molecules were then cleaned up with Silane DynaBeads and amplified using 14 PCR cycles. Size selection using SPRIselect reagent was performed post amplification to separate full-length cDNA from FBs. Next, full-length, barcoded cDNA was then enzymatically fragmented, sized-selected, adapter-ligated, and amplified for library construction. During the library construction, P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 were added. Separately, FBs were prepared into library constructs by incorporating P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 via PCR. Samples were pooled and run on the NovaSeq 6000 sequencer with a S4 flow cell using the following sequencing parameters: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.

treatment_protocol: Mice were sacrificed 8 weeks after the transplant and bone marrow was harvested by crushing the leg bones.

value: bone marrow

value: LK


title: C643 cells, kinome shRNA library, docetaxel, replicate 1


title: n5-pH7

value: 24 hours culture at pH7


title: adult male, Lymph node, year 1, day-90, replicate 2

source_name: Lymph Node

value: Lymph Node


title: C643 cells, kinome shRNA library, vehicle, replicate 3


title: Ddx41-WT-1

first: Kwangmin

last: Choi

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

data_processing:
The quality of paired reads were checked using FASTQC (v0.11.7)
Reads were aligned against human mm10 genome using HISAT2 (v2.0.5)
Each gene-level raw counts were calculated using featureCounts (v1.5.2)
Assembly: mm10
Supplementary files format and content: Tab-delimited text file, raw gene-count matrix

extract_protocol:
RNA was isolated using the Quick-RNA Miniprep Kit (Zymo)
TruSeq Stranded mRNA library prep, follwing manufacturer protocol (Illumina)

treatment_protocol: Mice were sacrificed 8 weeks after the transplant and bone marrow was harvested by crushing the leg bones. Lin-Sca1+Kit+ cells were sorted by flow cytometry.

value: LSK


title: n5-pH7_4

value: 24 hours culture at pH7.4


title: C643 cells, kinome shRNA library, vehicle, replicate 2


title: Alveolar type 2 cells infected with Bavpat-1 rep1

value: AT2 cells

value: Lung

value: Infection with SARS-CoV-2 Bavpat-1


title: adult male, Lymph node, year 1, day-90, replicate 1


title: Ddx41-WT-2


title: n5-time0

value: No treatment/start of the experiment


title: Ddx41-WT-3


title: C643 cells, kinome shRNA library, vehicle, replicate 1

value: DMSO


title: wt mouse, scRNAseq, multiplexed

description: 10X Genomics Multiplexing Capture


title: C643 cells, kinome shRNA library, docetaxel, replicate 3


title: adult male, Lymph node, year 2, day-7, replicate 2

value: male


title: adult male, Lymph node, year 2, day-7, replicate 1


title: Ddx41-WT-4


title: MS2, IL-10 B cells

city: Philadelphia

first: Diego

middle: A

last: Espinoza

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Reads were mapped using kallisto
Genome used: GRCh38.primary_assembly.genome.fa.gz
Annotation used: gencode.v33.primary_assembly.annotation.gtf.gz
Assembly: GRCh38
Supplementary files format and content: h5, tsv, and json output for each file is included (kallisto output)

growth_protocol: B cells were maintained in X-vivo 10 Medium supplement with Glutamine and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen). 200ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: B cells were stimulated with PMA (20ng/ml) and Ionomycin (500ng/ml) for 5hrs. Cytokine defined B cell subsets were then labeled using CSA-Flow assay and sorted using FACS.

tag: individual

value: Healthy Donor 4

value: Blood

value: B cells

tag: cell subtype

tag: disease state

value: Healthy

value: PMA/Ionomycin stimulation


title: adult male, Lymph node, year 2, day-60, replicate 3


title: n4-pH7-IL2

value: CD8+ T cell

value: 24 hours culture at pH7 in the presence of IL-2 200IU/mL


title: MS2, GM-CSF B cells

value: GM-CSF-Beff


title: Ddx41-HET-7

value: bone marrow


title: n4-pH7_4-IL2

value: 24 hours culture at pH7.4 in the presence of IL-2 200IU/mL


title: Ddx41-HET-8

value: LSK


title: MS1, IL-10 B cells

value: Healthy Donor 3


title: adult male, Lymph node, year 2, day-60, replicate 2

value: Lymph Node


title: n4-pH7

value: 24 hours culture at pH7


title: Ddx41-HET;p53-HET, HETHET47

treatment_protocol: Mice were sacrificed 8 weeks after the transplant and bone marrow was harvested by crushing the leg bones. CD71+Ter119+  cells were sorted by flow cytometry.


title: MS1, GM-CSF B cells


title: Ddx41-HET;p53-HET, HETHET46


title: adult male, Lymph node, year 1, day-60, replicate 2


title: adult male, Lymph node, year 2, day-7, replicate 3


title: n4-pH7_4

value: 24 hours culture at pH7.4


title: AD, GM-CSF B cells

value: Healthy Donor 2


title: adult male, Lymph node, year 2, day-60, replicate 1

value: male


title: n4-time0

value: No treatment/start of the experiment


title: AB, IL-10 B cells

value: Healthy Donor 1

value: Blood


title: n4-pH6_6-IL2

value: 24 hours culture at pH6.6 in the presence of IL-2 200IU/mL


title: Ddx41-HET-6


title: adult male, Lymph node, year 1, day-60, replicate 1


title: Ddx41-WT;p53-HET, WTHET22


title: adult male, Lymph node, year 1, day-5, replicate 2


title: AB, GM-CSF B cells

value: B cells

value: Healthy

value: PMA/Ionomycin stimulation


title: adult male, Lymph node, year 1, day-5, replicate 1


title: Ddx41-WT;p53-HET, WTHET24


title: n3-pH7-IL2

value: CD8+ T cell

value: 24 hours culture at pH7 in the presence of IL-2 200IU/mL


title: Ddx41-WT;p53-HET, WTHET23

value: bone marrow


title: n3-pH6_6-IL2


title: n3-pH7_4-IL2

value: 24 hours culture at pH7.4 in the presence of IL-2 200IU/mL


title: n4-pH6_6

value: 24 hours culture at pH6.6


title: AD, IL-10 B cells


title: Ddx41-HET;p53-WT, HETWT32


title: Liver, all samples, Rep1-5 each

city: Osaka

first: Kota

last: Abe

address: 3-1 Yamadaoka, Suita

country: Japan

institute: RIMD, Osaka univ

description: Liver

data_processing:
Liver and Muscle samples were demultiplexed by deML(v1.1.3), and for liver (female) and muscle samples, 1M reads were randomly sampled from each fastq file obtained by using seqtk Version: 1.3.
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the N. furzeri GRZ reference genome [GRZ Assembly (05/2015); https://nfingb.leibniz-fli.de/] using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRZ Assembly (05/2015); https://nfingb.leibniz-fli.de/
Supplementary files format and content: compressed tab separated files(.tsv.gz, .txt.gz)

organism: Nothobranchius furzeri

source_name: Liver

extract_protocol:
Tissue samples were lysed in TRIzol reagent (Thermo Fisher Science) and extract RNA by using RNA Clean & Concentrator kit (Zymo Research).
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Same tissue samples were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Liver

value: mixed multiplex samples


title: adult male, Lymph node, year 1, day-28, replicate 3

value: Lymph Node


title: Muscle, all samples, Rep1-5 each

description: Muscle

source_name: Muscle

value: Muscle


title: n3-pH6_6


title: Ddx41-HET;p53-WT, HETWT34


title: n3-pH7

value: 24 hours culture at pH7


title: Ddx41-WT;p53-WT, WTWT11


title: adult male, Lymph node, year 2, day-28, replicate 2

value: male


title: adult male, Lymph node, year 1, day-28, replicate 2


title: n3-pH7_4

value: 24 hours culture at pH7.4


title: Ddx41-WT;p53-WT, WTWT12


title: PD47

city: Raebareli

first: SANJAY

last: YADAV

state: UTTAR PRADESH

address: All India Institute of Medical Sciences Dalmau Road, Munshiganj,

country: India

institute: AIIMS RAEBARLI

description:
Raw data file:
DYU39.xlxs
PD 47

data_processing:
The raw data was analyzed by ExpressionSuite software and Relative quantification of miRNAs expression was calculated by -ΔΔCt method, selecting U6 snRNA level as endogenous control. software performs all deltadeltaCt based fold-change calculations and performed student t-test to calculate p-value from the uploaded raw threshold cycle data .
Normalized values and fold-change data are available on the series record.

label: FAM-NFQ

source_name: Peripheral blood

label_protocol: A TaqMan Custom RT pool primer (Cat#A25630) of 112 miRNAs was used for cDNA synthesis by reverse transcription. Reverse transcription of mature miRNAs was carried out by using a TaqMan miRNA Reverse Transcription kit reagents (Cat# 4366597) from Thermo Fischer, USA. In short, the reaction mixture contained MultiScribe reverse transcriptase 75 units, RT buffer 1X, OpenArray Custom RT primers 1X, RNase inhibitor 2 units, 3mM MgCl2, 2.0mM deoxynucleotide triphosphates (dNTPs) and 100ng of RNA input limiting 7.5µl the final reaction volume. Thermal cycling of Reverse transcription process was repeated for additional 39 cycles of 16°C for 2 minutes, 42°C for 1 minute and 50°C for 1 second. . In Preamplification, a total 25 µl reaction volume including 2.5µl custom preamp primer pools mixed with 12.5µl of preamp master mix and 2.5µl cDNA and additional nuclease-free water add to reach the final volume. The thermal cycling condition used for preamplification were 95°C for 10 min, 55°C for 2 min, 72°C for 2 min and 12 cycles of 95°C/15 sec, 60°C/4 min. At the end of cycling, preamplification products were incubated at 99.90C for 10 min. for inactivation of enzymes. Preamplification products were diluted (1 to 40) in 0.1X Tris-EDTA buffer. The diluted preamplification products mixed with 2x TaqMan OpenArray Real-Time PCR Master Mix (Cat#4462159) and pipette on OpenArray plates by OpenArray AccuFill System from Thermo Fisher Scientific and run the preamplification product as described manufacturer on QuantStudio 12K Flex RT-PCR machine from Thermo Fisher Scientific, USA

extract_protocol: Ribopure Blood RNA Isolation Kit by Thermo Fisher was utilized to extract the RNA (including small RNAs) as suggested protocol by manufacturer protocol.

value: Male

value: Blood

value: PD


title: PD48

description:
Raw data file:
DYU39.xlxs
PD 48


title: n3-time0

value: No treatment/start of the experiment


title: adult male, Lymph node, year 2, day-28, replicate 1

first: Steven

last: Kleinstein

address: 300 George St.

data_processing:
Base calls were converted to fastq sequences and demultiplexed using the cellranger v3.1.0 mkfastq function.
Demultiplexed pair-end FASTQ reads were first preprocessed on a by-sample basis using the ‘cellranger count’ command from 10× Genomics’ Cell Ranger v.3.1.0 for alignment against the GRCh38 human reference v.3.0.0 (refdata-cellranger-GRCh38- 3.0.0). The feature biotypes were retrieved using biomaRt v.2.42.0 ([MH8] ) from Ensembl release 93 ([MH9] ).
Additional quality control was performed as follows. (1) To remove presumably lysed cells, cells with mitochondrial content greater than 15% of all transcripts were removed. (2) To remove likely doublets, cells with more than 7,000 features were removed. (3) Genes that were expressed in less than 5 cells in any sample and cells with detectable expression of fewer than 400 genes were removed.
Gene expression analysis of CellRanger output was performed using Seurat v.4.0.3.1.1
Assembly: GRCh38
Supplementary files format and content: tar.gz: compressed archive of 10X Genomics Cell Ranger output files.
Supplementary files format and content: Rds: Seurat analyses saved as R objects

extract_protocol:
PBMCs were isolated using Vacutainer CPT tubes (BD); the remaining red blood cells were lysed with ammonium chloride lysis buffer (Lonza). Cells were immediately used or cryopreserved in 10% dimethylsulfoxide (DMSO) in FBS.   A qualified physician’s assistant performed ultrasound guided fine needle aspirate (FNA) of axillary lymph nodes under the supervision of a radiologist. Lymph node dimensions and cortical thickness were measured prior to each FNA. Six passes were made using 25-gauge needles, which were flushed with 3 ml of RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin/streptomycin, followed by three 1 ml rinses. Red blood cells were lysed with ammonium chloride lysis buffer. Cells were washed twice with PBS supplemented with 2% FBS and 2 mM EDTA and immediately used or cryopreserved in 10% DMSO in FBS.
Libraries were prepared using 10x Genomics' Chromium Next GEM single cell 5' gene expression workflow.


title: adult male, Lymph node, year 1, day-28, replicate 1


title: adult male, Lymph node, year 2, day-28, replicate 3


title: adult male, Lymph node, year 1, day-180, replicate 2


title: Uninjured calvarial bone

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

institute: Johns Hopkins University

description: Uninjured bone

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Seurat V3 (https://satijalab.org/seurat/) was used for further analysis. Monocle2 (http://cole-trapnell-lab.github.io/monocle-release/) was used for pseudotime trajectory.  For regulatory network analysis, R package Epoch (https://github.com/pcahan1/epoch)  was used. Clusters with very few cells were filtered before downstream analysis. Data was scaled to mitigate the effects of the following variables number of genes detected per cell, and percent mitochondrial reads. Dimensionality reduction was performed using Seurat. Differential gene expression analysis between clusters was performed using the Seurat function FindMarkers. Violin plots, heatmap and individual UMAP plots for the given genes were generated using the Seurat toolkit ‘VlnPlot’,’ and ‘Dimplot’ functions respectively.
Assembly: NCBI GRCm38
Supplementary files format and content: Cellranger barcodes and gene count TSV matrices

source_name: Calvarial cells, un-injured

extract_protocol:
Frontal and parietal bones including defect site, coronal suture, and sigittal suture were minced and subjected to enzymatic digestions with a mixture containing collagenase type I (1 mg/ml) and collagenase type II (1 mg/ml) for 15 min * 3. Cell fractions were collected and resuspended in red blood cell lysis buffer (37°C for 5 min). Digestions were subsequently filtered through 40-μm sterile strainers. Cells were then washed in PBS and resuspended in HBSS at a concentration of ~1000 cells/μl.
Library construction was performed following 10X platform for single cell library preparation and Illumina protocols

treatment_protocol: A 1.8-mm-diameter, full-thickness, circular frontal bone defect was created in the non–suture-associated frontal bone (right side) using a microsurgical drill and a trephine drill bit. The skin was sutured, and the animals were monitored per established postoperative protocols. Mice were euthanized after 0 (Uninjured), 7 or 30 days for analysis

value: Calvarial bone

value: Calvarial cells

value: Wildtype

value: un-injured

tag: treatment time

value: 0 days


title: PD45

description:
Raw data file:
DYU39.xlxs
PD 45

tag: tissue


title: Ddx41-WT;p53-WT, WTWT10

value: bone marrow


title: adult male, Lymph node, year 1, day-180, replicate 1

institute: Yale University

tag: Sex


title: n2-pH7_4-IL2

value: CD8+ T cell

value: 24 hours culture at pH7.4 in the presence of IL-2 200IU/mL


title: PD46

description:
Raw data file:
DYU39.xlxs
PD 46


title: PD44

description:
Raw data file:
DYU39.xlxs
PD 44


title: Calvarial bone at d30 after injury

description: Injured bone 30 day

source_name: Calvarial cells, post injury d30

value: post injury

value: 30 days


title: PD43

description:
Raw data file:
DYU39.xlxs
PD 43


title: RBFOX2_STAMP_APO1_Nb_dilute_1to2000

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

data_processing:
remove adapter with Cutadapt
align to hg38 using STAR 2.4.0 (Homo sapiens) or mm10 using STAR 2.5.2 (Mus musculus)
SAILOR analysis to call C-to-U edits and keep only sites with score >0.5 and edit fraction <80%
FLARE analysis to call C-to-U edit clusters
Intersect the edit clusters from 3 replicates, which yields "*confident_peaks.bed"
Subtract STAMP confident clusters to Buffer only control, which yields "*cleaned_confident_peaks.bed"
Assembly: hg38
Assembly: mm10
Supplementary files format and content: SAILOR step yields bed file: *0.5Score0.8Fraction.fastqTr.sorted.STARUnmapped.out.sorted.STARAligned.out.sorted.bam.combined.readfiltered.formatted.varfiltered.snpfiltered.ranked.bed
Supplementary files format and content: FLARE step yields .tsv file: "*merged_sorted_peaks.fdr_0.1.d_15.scored.tsv"
Supplementary files format and content: Intersection step yields .bed file:  "*confident_peaks.bed"
Supplementary files format and content: Subtraction step yields .bed file:  "*cleaned_confident_peaks.bed"

source_name: Brain

extract_protocol:
Direct-zol RNA Miniprep Kits, Zymo Research (Cat # R2052)
Ilumina TruSeq Stranded mRNA Library Prep (Cat #  20020594)

value: Female

value: Brain

value: whole brain section

tag: replicate


title: n2-pH6_6

value: 24 hours culture at pH6.6


title: adult male, Lymph node, year 2, day-120, replicate 3

value: Lymph Node

value: male

tag: age

tag: isolate


title: RBFOX2_STAMP_APO1_Nb_dilute_1to1000

tag: cell type


title: n2-pH7

value: 24 hours culture at pH7


title: PD42

description:
Raw data file:
DYU39.xlxs
PD 42

value: Male

value: Blood

value: PD


title: n2-pH7-IL2

value: 24 hours culture at pH7 in the presence of IL-2 200IU/mL


title: adult male, Lymph node, year 2, day-120, replicate 2


title: PD40

description:
Raw data file:
DYU39.xlxs
PD 40


title: n2-pH7_4

value: 24 hours culture at pH7.4


title: n2-pH6_6-IL2

value: 24 hours culture at pH6.6 in the presence of IL-2 200IU/mL


title: adult male, Lymph node, year 2, day-120, replicate 1


title: n2-time0

value: CD8+ T cell

value: No treatment/start of the experiment


title: Calvarial bone at d7 after injury

description: Injured bone 7 day

source_name: Calvarial cells, post injury d7

value: Calvarial bone

value: Calvarial cells

tag: genotype

value: Wildtype

value: post injury

value: 7 days


title: RBFOX2_STAMP_APO1_Nb_dilute_1to500

value: Female

value: Brain

value: whole brain section


title: n1-pH6_6-IL2

tag: treatment


title: RBFOX2_STAMP_APO1_Nb_dilute_1to200


title: PD39

description:
Raw data file:
DYU39.xlxs
PD 39


title: PD38

description:
Raw data file:
DYU39.xlxs
PD 38


title: adult male, Lymph node, year 1, day-12, replicate 2

value: Lymph Node

value: male


title: adult male, Lymph node, year 2, day-120, replicate 4


title: adult male, Lymph node, year 1, day-12, replicate 3


title: n1-pH7-IL2


title: PD41

description:
Raw data file:
DYU39.xlxs
PD 41

value: Male

value: Blood


title: adult male, Lymph node, year 1, day-12, replicate 1


title: PD36

description:
Raw data file:
DYU39.xlxs
PD 36

value: PD


title: n1-pH7_4-IL2

value: 24 hours culture at pH7.4 in the presence of IL-2 200IU/mL


title: RBFOX2_STAMP_APO1_Nb_dilute_1to50


title: adult male, Lymph node, year 2, day-0, replicate 3


title: PD37

description:
Raw data file:
DYU39.xlxs
PD 37


title: Mouse_Brain_Buffer_only_replicate3


title: Mouse_Brain_Buffer_only_replicate2


title: n1-pH6_6

value: 24 hours culture at pH6.6


title: Mouse_Brain_Buffer_only_replicate1


title: n1-pH7

value: CD8+ T cell

value: 24 hours culture at pH7


title: adult male, Lymph node, year 2, day-0, replicate 2


title: adult male, Lymph node, year 1, day-0, replicate 2


title: PD35

description:
Raw data file:
DYU34.xlxs
PD 35


title: n1-pH7_4

value: 24 hours culture at pH7.4


title: RBFOX2_STAMP_APO1_Nb_dilute_1to100


title: PD33

description:
Raw data file:
DYU34.xlxs
PD 33


title: adult male, Lymph node, year 2, day-0, replicate 1


title: PD34

description:
Raw data file:
DYU34.xlxs
PD 34


title: PD32

description:
Raw data file:
DYU34.xlxs
PD 32


title: Mouse_Brain_Enzyme_only_replicate3


title: adult male, Lymph node, year 1, day-0, replicate 1


title: Mouse_Brain_Enzyme_only_replicate2


title: PD31

description:
Raw data file:
DYU34.xlxs
PD 31


title: Mouse_Brain_Enzyme_only_replicate1


title: adult male, PBMC ASC, year 2 day-7

source_name: PBMC

value: PBMC


title: Mouse_Brain_RBFOX2_replicate3


title: Larv deltaWT K27me3 Repli2

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

data_processing:
Libraries sequencing quality were analyzed using fastQC software.
Alignment of paired-end reads was done using bowtie2 to the dm6 reference genome.
Alignments with MAPQ smaller than 30 were discarded. Duplicated paired-end reads were discarded using sambamba.
For data visualization, bigWig files were produced using bamCoverage software (deeptools), ignoring duplicate reads and applying RPKM normalization.
Assembly: dm6
Supplementary files format and content: bigwigs

organism: Drosophila melanogaster

source_name: larval imaginal leg discs

growth_protocol: Drosophila Melanogaste flies grown at 20°C on standard medium

extract_protocol:
Cut&Run experiments were performed as described by Kami Ahmad in protocilas.io (https://dx.doi.org/10.17504/protocols.io.umfeu3n)
Libraries were preapred according the protocol of the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina

value: larval imaginal leg discs

value: Wild type


title: Larv gypsy3 insertion K27me3 Repli2

value: insertion gypsy


title: Larv gypsy3 insertion K27me3 Repli1


title: adult male, PBMC ASC, year 1 day-5

city: New Haven


title: Mouse_Brain_RBFOX2_replicate2

value: Female


title: Larv deltaWT K27me3 Repli1


title: PD29

description:
Raw data file:
DYU34.xlxs
PD 29


title: PD30

description:
Raw data file:
DYU34.xlxs
PD 30


title: Larv gypsy2 insertion IgG C&R Repli2

data_processing:
*library strategy: CUT&RUN
Libraries sequencing quality were analyzed using fastQC software.
Alignment of paired-end reads was done using bowtie2 to the dm6 reference genome.
Alignments with MAPQ smaller than 30 were discarded.
For data visualization, bigWig files were produced using bamCoverage software (deeptools), ignoring duplicate reads and applying RPKM normalization.
Assembly: dm6
Supplementary files format and content: bigwigs

growth_protocol: Drosophila Melanogaste flies gtown at 20°C on, standard medium


title: n1-time0

value: No treatment/start of the experiment


title: adult male, PBMC enriched for IgD B cell, year 1 day-120


title: Larv gypsy2 insertion IgG C&R Repli1


title: PD26

description:
Raw data file:
DYU34.xlxs
PD 26


title: HUVEC in SR region, rep2

city: Guangzhou

first: xihong

last: Fu

state: Guangdong Province

address: 58 Zhongshan Second Rd, Guangzhou

institute: Sun Yat-sen University

data_processing:
The acquired raw data then underwent quality control to verify suitability for subsequent analysis. After obtaining filtered reads using the filtering software SOAPnuke, we aligned and mapped the clean reads according to the reference genome using Hisat2. Then the samtools software was used to convert the file format and build the index. We used the featuresCounts software to calculate the count values of the genes.
Assembly: hg38
Supplementary files format and content: processed data.xlsx includes raw counts for each Sample

source_name: GelMA and gelatin hydrogel

growth_protocol: The human breast cancer cell line MDA-MB-231 (Chinese Academy of Sciences, Shanghai, China) was cultured in high-glucose DMEM medium (10-013-CV, Corning, USA) supplemented with 10% fetal bovine serum (FBS, 10099-141C, Gibco, USA) and 1% penicillin-streptomycin (P/S, 15140-122, Gibco, USA). Primary human mammary cancer-associated fibroblasts (HMCAFs, HUM-iCELL-f028, iCell Bioscience Inc., China) were cultured in DMEM-F12 medium (10-092-CV, Corning, USA) supplemented with 10% FBS, 1X GlutaMAX (35050-061, Gibco, USA), and 1% P/S. Human umbilical vascular endothelial cells (HUVECs, #8000, ScienCell, USA) were cultured in endothelial cell growth medium-2 (EGM-2, CC-3162, Lonza, Switzerland) supplemented with 1% P/S

extract_protocol:
We used TRIZOL to lyse cells and extract total RNA
RNA-libraries for RNA-seq were prepared using MGIEasy Fast RNA library preparation kit following manufacturor's protocol

value: GelMA and gelatin hydrogel

tag: cell line

value: HUVEC

value: human umbilical vein endothelial cells

value: WT

value: 3D printing in SR region


title: adult male, PBMC enriched for IgD B cell, year 1 day-12

value: male


title: PD25

description:
Raw data file:
DYU34.xlxs
PD 25

tag: gender

value: Male

value: Blood

value: PD


title: HUVEC in unpatterned region, rep2

value: 3D co-culture in unpatterned region (MDA-MB-231, HMCAF, HUVEC)


title: adult male, PBMC enriched for IgD B cell, year 2 day-0


title: Larv gypsy1 insertion IgG C&R Repli2


title: PD24

description:
Raw data file:
DYU34.xlxs
PD 24


title: Larv gypsy1 insertion IgG C&R Repli1


title: HUVEC in unpatterned region


title: HUVEC in CCR region,rep2

value: 3D printing in CCR region


title: adult male, PBMC enriched for IgD B cell, year 2 day-90

value: PBMC


title: adult male, PBMC enriched for IgD B cell, year 1 day-0


title: adult male, PBMC enriched for IgD B cell, year 2 day-14


title: Mouse_Brain_RBFOX2_replicate1

value: Brain

value: whole brain section


title: Larv WT IgG C&R Repli1

value: larval imaginal leg discs

value: insertion gypsy


title: PD23

description:
Raw data file:
DYU32.xlxs
PD 23


title: Larv WT IgG C&R Repli2


title: adult male, Lymph node, year 2 day-90, replicate 2

value: Lymph Node


title: adult male, Lymph node, year 2 day-90, replicate 1


title: HUVEC in CCR region

value: GelMA and gelatin hydrogel


title: PD27

description:
Raw data file:
DYU34.xlxs
PD 27


title: Larv gypsy2 insertion K27me3 C&R Repli2


title: HUVEC in SR region

value: HUVEC


title: PD21

description:
Raw data file:
DYU32.xlxs
PD 21


title: HMCAF in SR region, rep2

value: HMCAF

value: human mammary cancer-associated fibroblasts


title: PD22

description:
Raw data file:
DYU32.xlxs
PD 22


title: HMCAF in SR region

value: WT

value: 3D printing in SR region


title: adult male, Lymph node, year 2 day-60, replicate 2

value: male


title: PD20

description:
Raw data file:
DYU32.xlxs
PD 20

value: Male

value: Blood


title: HMCAF in unpatterned region, rep2

value: 3D co-culture in unpatterned region (MDA-MB-231, HMCAF, HUVEC)


title: PD28

description:
Raw data file:
DYU34.xlxs
PD 28

value: PD


title: adult male, Lymph node, year 2 day-60, replicate 1


title: PD19

description:
Raw data file:
DYU32.xlxs
PD 19


title: Larv gypsy1 insertion K27me3 C&R Repli2


title: adult male, Lymph node, year 1 day-5, replicate 2


title: PD18

description:
Raw data file:
DYU32.xlxs
PD 18


title: HMCAF in unpatterned region


title: Larv gypsy1 insertion K27me3 C&R Repli1


title: adult male, Lymph node, year 1 day-5, replicate 1


title: Larv WT K27me3 C&R Repli1

value: Wild type


title: Larv WT K27me3 C&R Repli2


title: HMCAF in CCR region, rep2

value: 3D printing in CCR region


title: HMCAF in CCR region


title: Larv gypsy2 insertion K27me3 C&R Repli1


title: PD17

description:
Raw data file:
DYU32.xlxs
PD 17


title: adult male, Lymph node, year 2 day-14, replicate 2


title: PD16

description:
Raw data file:
DYU32.xlxs
PD 16


title: MDA-MB-231 in SR region (Cell migration from CCR region), rep2

value: cancer cell

value: Cell migration from CCR region


title: Larv RE deletion K27me3 C&R Repli1

value: larval imaginal leg discs

value: deletion ring enhancer


title: adult male, Lymph node, year 1 day-120, replicate 2

value: Lymph Node


title: adult male, Lymph node, year 2 day-14, replicate 1


title: adult male, Lymph node, year 1 day-120, replicate 1


title: Larv RE deletion K27me3 C&R Repli2


title: MDA-MB-231 in SR region (Cell migration from CCR region)

value: GelMA and gelatin hydrogel


title: PD15

description:
Raw data file:
DYU32.xlxs
PD 15


title: PD14

description:
Raw data file:
DYU32.xlxs
PD 14


title: PD13

description:
Raw data file:
DYU32.xlxs
PD 13


title: MDA-MB-231 in unpatterned region, rep2


title: Larv WT-RE K27me3 C&R Repli2


title: Larv WT-RE K27me3 C&R Repli1


title: adult male, Lymph node, year 1 day-12, replicate 2


title: PD12

description:
Raw data file:
DYU26.xlxs
PD 12


title: adult male, Lymph node, year 1 day-12, replicate 1


title: MDA-MB-231 in unpatterned region


title: MDA-MB-231 in CCR region, rep2


title: Embryo gypsy1 insert 4C-seq Rep3

data_processing:
*library strategy: 4C-seq
4C sequencing were split by viewpoint by mapping the reads to the 4C primer sequences using a custom python script adapted from Grob et al. Genome Biology, 2012
4C primer sequences and genomic sequences until the next restriction site were trimmed from the reads using a custom python script adapted from Grob et al. Genome Biology, 2012
Split libraries were aligned to DM6 genome using bowtie alignment software
The aligned reads were mapped to restriction fragments and genomic bins of 1kb size using HiCdat  to obtain tabular files describing the number of reads (i.e. contact frequencies) for a given fragment or genomic bin, respectively
All subsequent analysis steps have been conducted using R.
Assembly: dm6

source_name: embryos

extract_protocol:
4C-seq was performed according to Denaud et al (see Material and Methods)
Libraries were preapred according the protocol the illumina kit (illumina 20015964)

value: embryos

value: insertion gypsy


title: adult male, Lymph node, year 2 day-0, replicate 2


title: Embryo gypsy1 insert 4C-seq Rep2


title: PD11

description:
Raw data file:
DYU26.xlxs
PD 11


title: MDA-MB-231 in CCR region

value: WT


title: adult male, Lymph node, year 1 day-0, replicate 2


title: Embryo gypsy1 insert 4C-seq Rep1


title: Embryo gypsy2 insert 4C-seq Rep6


title: PD9

description:
Raw data file:
DYU26.xlxs
PD 9


title: adult male, Lymph node, year 2 day-0, replicate 1


title: Embryo gypsy2 insert 4C-seq Rep4


title: ZH11-WT_NC_input_ChIPseq

city: Wuhan

first: Yu

last: Chang

state: Hubei

address: No.1, Shizishan Street, Hongshan District

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

description:
ZH11-WT_NC_input
ZH11-WT_rep1_IP_vs_input.bw

data_processing:
Sequencing reads were mapped to rice reference genome (MSU7) using Bowtie2. ChIP-seq peaks and the signal tracks were generated by MACS2.
Assembly: MSU7
Supplementary files format and content: ChIP-seq signal tracks in bigWig format.

organism: Oryza sativa Japonica Group

source_name: 4-leaf stage seedling

growth_protocol: The rice seeds were sprouted on half-strength MS medium in the dark for 2-3 days at 28°C, and then 4-5 days in the greenhouse. The seedlings were then moved to pots with sand/paddy (1:3) soil under natural conditions at Wuhan, China.

extract_protocol:
The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by anti-FLAG antibody (SIGMA, F3165). The ChIP DNA was eluted, purified, and dissolved in ddH2O.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.

value: 4-leaf stage seedling

value: Normal

tag: antibody


title: PD7

description:
Raw data file:
DYU26.xlxs
PD 7

value: Male


title: Embryo gypsy2 insert 4C-seq Rep5


title: PD5

description:
Raw data file:
DYU26.xlxs
PD 5

value: Blood


title: Embryo WT 4C-seq Rep6


title: adult male, lymph node, year 1 day-0, replicate 1

value: male


title: ONAC023-FLAG_OE_5_NC_input_ChIPseq

description:
ONAC023-FLAG_OE_5_NC_input
ONAC023-FLAG_OE_5_NC_rep1_IP_vs_input.bw


title: Embryo WT 4C-seq Rep5


title: PD8

description:
Raw data file:
DYU26.xlxs
PD 8

value: PD


title: ZH11-WT_NC_IP_rep2_ChIPseq

description:
ZH11-WT_NC_IP_rep2
ZH11-WT_rep2_IP_vs_input.bw

value: anti-FLAG (SIGMA, F3165)


title: PD6

description:
Raw data file:
DYU26.xlxs
PD 6


title: PD4

description:
Raw data file:
DYU26.xlxs
PD 4


title: PD3

description:
Raw data file:
DYU26.xlxs
PD 3


title: ZH11-WT_NC_IP_rep1_ChIPseq

description:
ZH11-WT_NC_IP_rep1
ZH11-WT_rep1_IP_vs_input.bw


title: Embryo WT 4C-seq Rep3

value: Wild type


title: Embryo WT 4C-seq Rep4


title: PD10

description:
Raw data file:
DYU26.xlxs
PD 10


title: PD2

description:
Raw data file:
DYU26.xlxs
PD 2


title: ONAC023-FLAG_OE_5_NC_IP_rep1_ChIPseq

description:
ONAC023-FLAG_OE_5_NC_IP_rep1
ONAC023-FLAG_OE_5_NC_rep1_IP_vs_input.bw


title: Embryo WT 4C-seq Rep2


title: PD1

description:
Raw data file:
DYU26.xlxs
PD 1


title: DJ_Seedling_NC_rep3_RNAseq

description:
DJ_Seedling_NC_rep3
GRN_count.txt

data_processing:
Sequencing reads were mapped to rice reference genome (MSU7) using Hisat2. Transcripts were assembled and count by StringTie and the differential expression was determined by R package DESeq2.
Assembly: MSU7
Supplementary files format and content: GRN_count.txt: Sequencing read counts in tab-delimited table.

extract_protocol:
The total RNAs were extracted from the seedlings using TRIzol reagent (Invitrogen™) according to the manufacturer’s instructions.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Drought treatment was carried out by stopping water supply for 7 days until the relative solid water content was below 10%. Heat treatment was performed by placing the seedlings in a growth chamber with the air temperature of 45˚C and relative humidity of 70% for 6 hours.

value: DJ


title: Embryo WT 4C-seq Rep1


title: ONAC023-FLAG_OE_5_NC_IP_rep2_ChIPseq

description:
ONAC023-FLAG_OE_5_NC_IP_rep2
ONAC023-FLAG_OE_5_NC_rep2_IP_vs_input.bw


title: C48

description:
Raw data file:
DYU39.xlxs
Control 48

value: healthy


title: DJ_Seedling_NC_rep2_RNAseq

description:
DJ_Seedling_NC_rep2
GRN_count.txt


title: Larvae gypsy2 insert 4C-seq Rep2

description: Larvae gypsy_enh_2

value: larval imaginal leg discs


title: C46

description:
Raw data file:
DYU39.xlxs
Control 46


title: DJ_Seedling_NC_rep1_RNAseq

description:
DJ_Seedling_NC_rep1
GRN_count.txt


title: Larvae gypsy2 insert 4C-seq Rep3

description: Larvae gypsy_enh_3


title: Larvae gypsy2 insert 4C-seq Rep1

description: Larvae gypsy_enh_1


title: DJ_Seedling_DS_rep3_RNAseq

description:
DJ_Seedling_DS_rep3
GRN_count.txt

value: Drought


title: C45

description:
Raw data file:
DYU39.xlxs
Control 45


title: DJ_Seedling_DS_rep2_RNAseq

description:
DJ_Seedling_DS_rep2
GRN_count.txt


title: SCBC43

first: Woonyoung

address: 1550 Orleans Street

department: Urology

description: BatchC

data_processing:
R package sva to correct batch effects (PMID: 33015620); DESeq2 to normalize sequencing data.
Assembly: hg19_ampliseq_transcriptome_ercc_v1
Supplementary files format and content: tab-delimited text file including batch-effects-corrected and normalized data for each sample

source_name: SCBC

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) samples were deparaffinized with xylene and digested with proteinase K. After centrifugation, the supernatant was used for RNA isolation.
RNA libraries were prepared using Ion Ampliseq transcriptome human gene expression kit.

value: SCBC


title: DJ_Seedling_DS_rep1_RNAseq

description:
DJ_Seedling_DS_rep1
GRN_count.txt


title: Larvae WT 4C-seq Rep2


title: SCBC44

description: BatchC


title: C43

description:
Raw data file:
DYU39.xlxs
Control 43


title: SCBC42

description: BatchC


title: ZH11_Seedling_NC_rep3_RNAseq

description:
ZH11_Seedling_NC_rep3
GRN_count.txt


title: C44

description:
Raw data file:
DYU39.xlxs
Control 44


title: C47

description:
Raw data file:
DYU39.xlxs
Control 47


title: SMB55_DMSO_C

type: genomic

city: Tübingen

first: Daniel

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A2)

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Sesame R package (1.20.0) on R (4.3.3); beta value generation using standard openSesame pipeline, detection p value estimation using pOOBAH.

label: Cy5 and Cy3

source_name: Sonic hedgehog medulloblastoma

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Murine cell line models of Sonic hedgehog medulloblastoma (SMB21 and SMB55) were treated with 3µM 5-azacytidine for 24 hours or corresponding concentration of DMSO solvent.

value: Sonic hedgehog medulloblastoma

value: brain tumor

value: DMSO


title: C42

description:
Raw data file:
DYU39.xlxs
Control 42


title: pupe gypsy2 insert 4C-seq Rep3

source_name: pupal imaginal leg discs

value: pupal imaginal leg discs

value: insertion gypsy


title: ZH11_Seedling_NC_rep2_RNAseq

description:
ZH11_Seedling_NC_rep2
GRN_count.txt

value: 4-leaf stage seedling

value: Normal


title: SMB55_DMSO_B


title: SCBC40

description: BatchC


title: ZH11_Seedling_NC_rep1_RNAseq

description:
ZH11_Seedling_NC_rep1
GRN_count.txt


title: Larvae WT 4C-seq Rep3


title: C40

description:
Raw data file:
DYU39.xlxs
Control 40

value: Male

value: Blood


title: SMB55_AZA_B


title: pupe gypsy2 insert 4C-seq Rep2


title: SCBC39

description: BatchC


title: SMB55_AZA_A


title: SMB21_AZA_C


title: ZH11_Seedling_HS_rep3_RNAseq

description:
ZH11_Seedling_HS_rep3
GRN_count.txt

value: Heat


title: C39

description:
Raw data file:
DYU39.xlxs
Control 39


title: pupe gypsy2 insert 4C-seq Rep1


title: ZH11_Seedling_HS_rep2_RNAseq

description:
ZH11_Seedling_HS_rep2
GRN_count.txt


title: SMB55_DMSO_A


title: SMB55_AZA_C


title: C38

description:
Raw data file:
DYU39.xlxs
Control 38


title: pupe WT 4C-seq Rep3


title: SCBC38

description: BatchC


title: SMB21_AZA_A


title: ZH11_Seedling_HS_rep1_RNAseq

description:
ZH11_Seedling_HS_rep1
GRN_count.txt


title: SMB21_DMSO_C


title: pupe WT 4C-seq Rep2


title: SCBC36

description: BatchC


title: SCBC37

description: BatchC


title: C37

description:
Raw data file:
DYU39.xlxs
Control 37


title: SCBC35

description: BatchC


title: SCBC41

description: BatchC


title: C36

description:
Raw data file:
DYU39.xlxs
Control 36


title: SCBC34

description: BatchC


title: ZH11_Seedling_DS_rep1_RNAseq

description:
ZH11_Seedling_DS_rep1
GRN_count.txt


title: SMB21_DMSO_A


title: SMB21_DMSO_B


title: ZH11_Seedling_DS_rep3_RNAseq

description:
ZH11_Seedling_DS_rep3
GRN_count.txt


title: SCBC33

description: BatchC


title: SCBC32

description: BatchC


title: SMB21_AZA_B


title: C34

description:
Raw data file:
DYU34.xlxs
Control 34


title: ZH11_Panicle_NC_rep2_RNAseq

description:
ZH11_Panicle_NC_rep2
GRN_count.txt

source_name: Panicle

value: Panicle


title: ZH11_Panicle_NC_rep1_RNAseq

description:
ZH11_Panicle_NC_rep1
GRN_count.txt


title: C33

description:
Raw data file:
DYU34.xlxs
Control 33


title: SCBC31

description: BatchC


title: C35

description:
Raw data file:
DYU34.xlxs
Control 35


title: ZH11_Seedling_DS_rep2_RNAseq

description:
ZH11_Seedling_DS_rep2
GRN_count.txt


title: C32

description:
Raw data file:
DYU34.xlxs
Control 32


title: C31

description:
Raw data file:
DYU34.xlxs
Control 31


title: ZH11_Panicle_HS_rep1_RNAseq

description:
ZH11_Panicle_HS_rep1
GRN_count.txt


title: SCBC29

description: BatchB


title: onac023_input_ChIPseq

data_processing:
Sequencing reads were mapped to rice reference genome (MSU7) using Hisat2 (for RNA-seq) and Bowtie2 (for ChIP-seq)
RNA-seq transcripts were assembled and count by StringTie and the differential expression was determined by R package DESeq2
ChIP-seq peaks and the signal tracks were generated by MACS2.
Genome_build: MSU7
Supplementary_files_format_and_content: The tab-delimited text file (count.txt) includes read counts for each RNA-seq sample. The bigWig files (.bw) record ChIP-Seq tag densities.

source_name: 4-leaf seedling

growth_protocol: The onac023 mutant and DJ seeds were sprouted on half-strength MS medium in the dark for 2-3 days at 28°C, and then 4-5 days in the greenhouse. The seedlings were then moved to pots with sand/paddy (1:3) soil under natural conditions at Wuhan, China.

extract_protocol:
The total RNAs were extracted from the seedlings using TRIzol reagent (Invitrogen™) according to the manufacturer’s instructions. The ChIP assay was performed according to Chris Bowler (Bowler et al., 2004) with some modiﬁcations. Briefly, 3 g seedling tissue were cross-linked in 1% formaldehyde by vacuum for 30 minutes. The chromatin was extracted on ice as described by Bowler method and sheared to 200-500 bp fragments by sonication. Subsequently, the DNA fragments were immunoprecipitated by homemade anti-ONAC023 polyclonal antibody. The ChIP DNA was eluted, purified, and dissolved in ddH2O.
RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Drought treatment was carried out by stopping water supply for 7 days until the relative soild water content was below 10%. Heat treatment was performed by placing the seedlings in a growth chamber with the air temperature of 45˚C and relative humidity of 70% for 6 hours.

value: Drought and heat


title: C30

description:
Raw data file:
DYU34.xlxs
Control 30


title: C29

description:
Raw data file:
DYU34.xlxs
Control 29


title: SCBC28

description: BatchB


title: mutCK_ChIPseq_input


title: SCBC27

description: BatchB


title: DJ_HS_IP_rep3_ChIPseq

value: anti-ONAC023 polyclonal antibody


title: SCBC26

description: BatchB


title: C28

description:
Raw data file:
DYU34.xlxs
Control 28

value: healthy


title: SCBC25

description: BatchB


title: SCBC24

description: BatchA


title: C27

description:
Raw data file:
DYU34.xlxs
Control 27


title: C26

description:
Raw data file:
DYU34.xlxs
Control 26


title: DJ_HS_IP_rep2_ChIPseq


title: DJ_HS_IP_rep1_ChIPseq


title: onac023_HS_IP_rep3_ChIPseq


title: TIE:EGFP MCR:MCS Tumor 2 GFP+ #3

city: Boston

first: Leonard

last: Zon

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
The single cell sort-seq data are analyzed using the scruff R package (Single Cell RNA-Seq UMI Filtering Facilitator), following the pipeline in (https://github.com/campbio/scruff). The raw fastq files are first demultiplexed, and aligned to zebrafish reference genome GRCz11 using Rsubread, and UMI filtered count matrix are generated.
Assembly: GRCz11
Supplementary files format and content: Count matrix table (tsv)

organism: Danio rerio

source_name: MCR:MCS Melanoma

extract_protocol:
Tumors were excised and dissociated for 30 minutes with occasional chopping using 0.075mg/mL liberase (Sigma #5401119001) in DMEM (Gibco #11965-092) with 1% Penstrep (Corning #30-002-CI). Dissociated samples were filtered through a 40µm filter and resuspended in FACs buffer (PBS/ 10%FBS/1% Penstrep) before filtering through a FACs tube (Corning #352235). Single cells were sorted into 384-well-cell-capture plates containing barcoded primers from Single Cell Discoveries (https://www.scdiscoveries.com/) using a BD FACS ARIA II sorter. Sorted plates of GFP+ cells and GFP-;mCherry+ cells.
Library preparation and Illumina sequencing was performed by Single Cell Discoveries.
SORT-seq

treatment_protocol: Zebrafish melanomas overexpressing empty multiple-cloning site (MCS) or SATB2 vectors.

value: MCR:MCS Melanoma

value: expressing TIE:EGFP

tag: sorted cells

value: GFP+


title: SCBC23

description: BatchA

value: SCBC


title: C25

description:
Raw data file:
DYU34.xlxs
Control 25


title: ZH11_Panicle_HS_rep2_RNAseq

description:
ZH11_Panicle_HS_rep2
GRN_count.txt


title: onac023_HS_IP_rep2_ChIPseq


title: C24

description:
Raw data file:
DYU34.xlxs
Control 24


title: SCBC30

description: BatchB


title: C23

description:
Raw data file:
DYU32.xlxs
Control 23


title: SCBC22

description: BatchA


title: onac023_HS_IP_rep1_ChIPseq


title: TIE:EGFP MCR:MCS Tumor 2 GFP-/mCherry+

value: GFP-/mCherry+


title: C22

description:
Raw data file:
DYU32.xlxs
Control 22


title: TIE:EGFP MCR:MCS Tumor 2 GFP+ #2


title: DJ_DS_IP_rep2_ChIPseq

value: Drought


title: C41

description:
Raw data file:
DYU39.xlxs
Control 41


title: SCBC20

description: BatchA


title: DJ_DS_IP_rep1_ChIPseq


title: C21

description:
Raw data file:
DYU32.xlxs
Control 21


title: C20

description:
Raw data file:
DYU32.xlxs
Control 20


title: TIE:EGFP MCR:MCS Tumor 2 GFP+ #1


title: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #3

source_name: MCR:SATB2 Melanoma

value: MCR:SATB2 Melanoma


title: SCBC19

description: BatchA


title: SCBC18

description: BatchA


title: onac023_DS_IP_rep1_ChIPseq


title: SCBC17

description: BatchA


title: C19

description:
Raw data file:
DYU32.xlxs
Control 19

source_name: Peripheral blood


title: DJ_HS_rep3_RNAseq


title: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #2


title: TIE:EGFP MCR:SATB2 Tumor 1 GFP-/mCherry+


title: SCBC16

description: BatchA


title: Larvae WT 4C-seq Rep1

value: larval imaginal leg discs

value: Wild type


title: DJ_HS_rep2_RNAseq


title: C18

description:
Raw data file:
DYU32.xlxs
Control 18


title: TIE:EGFP MCR:SATB2 Tumor 1 GFP+ #1


title: C17

description:
Raw data file:
DYU32.xlxs
Control 17


title: SCBC21

description: BatchA


title: C16

description:
Raw data file:
DYU32.xlxs
Control 16


title: SCBC15

description: BatchA


title: pupe WT 4C-seq Rep1

value: pupal imaginal leg discs


title: TIE:EGFP MCR:MCS Tumor 1 GFP+ #3


title: SCBC14

description: BatchA


title: onac023_DS_IP_rep2_ChIPseq


title: C14

description:
Raw data file:
DYU32.xlxs
Control 14

value: Male


title: C15

description:
Raw data file:
DYU32.xlxs
Control 15

value: Blood


title: SCBC13

description: BatchA


title: TIE:EGFP MCR:MCS Tumor 1 mCherry+;GFP-

value: mCherry+;GFP-


title: onac023_HS_rep2_RNAseq

value: Heat


title: SCBC12

description: BatchA


title: TIE:EGFP MCR:MCS Tumor 1 GFP+ #2


title: onac023_HS_rep1_RNAseq


title: SCBC11

description: BatchA


title: TIE:EGFP MCR:MCS Tumor 1 GFP+ #1


title: C12

description:
Raw data file:
DYU26.xlxs
Control 12


title: C13

description:
Raw data file:
DYU32.xlxs
Control 13


title: DJ_DS_rep3_RNAseq


title: Day 7, Vegfc CRE

city: Dallas

first: Sneha

last: Korlakunta

state: TX

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: 10X Genomics

data_processing:
cellranger-5.0.1
Assembly: mm10-2020-A

source_name: tendon injury

extract_protocol:
Cells from the excised tissue were isolated based on previously described methods . Briefly, tissue was digested for 45 min in 0.3% Type 1 Collagenase and 0.4% Dispase II (Gibco) in Roswell Park Memorial Institute (RPMI) medium at 37 °C under constant agitation at 120 rpm. Digestions were quenched with 10% FBS RPMI and filtered through 40μm sterile strainers. Samples were run on a FACSAria II for cell sorting to separate the Prox1-expressing population for further scRNA-seq analysis.
Single Cell 3' v3

treatment_protocol: B/T

value: tendon injury

value: unsorted

value: B/T


title: SCBC9

description: BatchA


title: DJ_DS_rep1_RNAseq


title: SCBC10

description: BatchA


title: C11

description:
Raw data file:
DYU26.xlxs
Control 11

value: healthy


title: Day 7, Prox1 eGFP

description: 10X Genomics


title: DJ_HS_rep1_RNAseq


title: DJ_DS_rep2_RNAseq


title: C10

description:
Raw data file:
DYU26.xlxs
Control 10


title: C9

description:
Raw data file:
DYU26.xlxs
Control 9


title: SCBC8

description: BatchA


title: onac023_HS_rep3_RNAseq


title: SCBC7

description: BatchA


title: Day 0, Prox1 eGFP

description: 10X Genomics

value: No treatment


title: C8

description:
Raw data file:
DYU26.xlxs
Control 8


title: onac023_DS_rep3_RNAseq


title: onac023_DS_rep2_RNAseq


title: onac023_DS_rep1_RNAseq


title: SCBC6

description: BatchA


title: Day 21, Prox1 eGFP

description: 10X Genomics


title: C7

description:
Raw data file:
DYU26.xlxs
Control 7


title: SCBC4

description: BatchA


title: Mkx siRNA KD rep #1

data_processing:
Illumina NextSeq 500 read samples at 1 x 75
Base calling with RTA version 2.4.11
BCL files were demultiplexed and converted to compressed FASTQ with filtering to strip adapters with bcl2fastq
The data were aligned to the GRCm38 reference genome using the CLC Genomics Server 21.0.3 with: Mismatch cost =2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8
FPKM calculation with CLCGenomicsServer as above
FPKM vaues log2 converted (FPKM = 0 ignored as NULL) and quantile normalized with Partek Genomics Suite v6.7
Assembly: NCBI GRCm38.p6 Mar-22
Supplementary files format and content: Text, ~.txt, file of quantile normalized log2 FPKM including Nulls

source_name: Calvaria

growth_protocol: The cells were cultured Dulbecco's Modified Eagle Medium (DMEM) supplemented with 15% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin in a humidified incubator with 5% CO2 at 37°C.

extract_protocol:
RNA extraction was performed using TRIzol reagent according to the manufacturer’s instructions
Illumina TruSeq Stranded mRNA according to the manufacturer's instructions.

treatment_protocol: The siRNA knockdown was performed using TransIT®-LT1 Transfection Reagent according to manufacture's protocol

value: Calvaria

value: Wildtype

value: Cranial suture cells

value: Transformed with SiRNA

value: Cranial suture cells derived from WT animal treated with siRNA for 48 h


title: Mkx siRNA KD rep #2


title: Scrambled control rep #3

value: Transformed with scrambled RNA

value: Cranial suture cells derived from WT animal treated with scramble RNA for 48 h


title: C5

description:
Raw data file:
DYU26.xlxs
Control 5


title: SCBC5

description: BatchA

value: SCBC


title: C6

description:
Raw data file:
DYU26.xlxs
Control 6

value: Male


title: C4

description:
Raw data file:
DYU26.xlxs
Control 4

value: Blood


title: hSAECs, OGG1, RNA-IP, Rep-2

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description: OGG1-Ab-vs-Input-cell-hg38-enriched.bedgraph

data_processing:
reads aligned to RSV genome with bowtie2 and aligned to human reference genome using STAR 2.7.11a
Assembly: hg38
Supplementary files format and content: Forward and reverse alignment to RSV in bigwig format
Supplementary files format and content: log ratio of hg38 alignment between IP and input in bedgraph format

source_name: hSAECs

growth_protocol: Small Airway Epithelial Cell Growth Medium (Ready-to-use) - Includes Basal Medium and SupplementMix (C-21070, PromoCell, Heidelberg, Germany)

extract_protocol:
At 24 hpi, cells were fixed with 1% formaldehyde for 10 min at room temperatrue. After quenching and cell lysis by RIPA, lysates were briefly sonicated. During the preparation process, we employed the iron chelator deferoxamine mesylate (252750, Millipore-Sigma) to prevent additional oxidation. The supernatant was treated with RNase A (20 µg/mL) and RNase T1 (5U) at 37°C for 30 min to digest naked viral RNA. We then subjected the supernatant to IP with an anti-OGG1 antibody (PA5-86046, Invitrogen) for 4 hours, using head-over-tail rotation for effective mixing. We incubated the ribonucleoprotein-antibody complexes with magnetic beads for 1 hour at 4°C and subsequently washed them five times with RIPA buffer. After proteinase K digestion and reversing the crosslinks, we extracted the RNA samples using TRIzol. The libraries were processed for Illumina sequencing.
stranded RNA-seq library

treatment_protocol: 100 mm of hSAECs were infected with RSV at a multiplicity of infection (MOI) of 1. After an hour of adsorption, the unbound virus was removed by PBS, and supplemented by fresh culture medium.

value: hSAECs

value: epithelium

value: RSV, 1 MOI, 24 hpi


title: hSAECs, Input, RNA-IP, Rep-2


title: SCBC3

description: BatchA


title: Scrambled control rep #1


title: SCBC2

description: BatchA


title: hSAECs, Input, RNA-IP, Rep-1

description: FLAG-Ab-vs-Input-cell-hg38-enriched.bedgraph


title: C2

description:
Raw data file:
DYU26.xlxs
Control 2

data_processing:
The raw data was analyzed by ExpressionSuite software and Relative quantification of miRNAs expression was calculated by -ΔΔCt method, selecting U6 snRNA level as endogenous control. software performs all deltadeltaCt based fold-change calculations and performed student t-test to calculate p-value from the uploaded raw threshold cycle data .
Normalized values and fold-change data are available on the series record.


title: C3

description:
Raw data file:
DYU26.xlxs
Control 3


title: Scrambled control rep #2


title: CRC Tumor T003

status: Public on Jun 12 2024

city: Camden

first: Jean-Pierre

middle: J

last: Issa

state: NJ

address: 403 Haddon Avenue

department: Research Labs

institute: Coriell Institute for Medical Research

data_processing:
*library strategy: 16S rRNA gene sequencing
Illumina MiSeq paired-end sequencing
Raw sequencing data were converted to fastq.gz files.
The 16S rRNA sequencing data were trimmed using cutadapt
DADA2 was used to filter, trim, estimate error profiles, merge paired end reads, and construct an amplicon sequence variant (ASV) table. DADA2 was also used to remove chimeras from the denoised ASVs and assign taxonomy by fitting ASV sequences to a pre-trained naïve bayes classifier built from the Silva v138 database
Species assignments were made by exact string matching to DADA2-formatted Silva v138 reference sequences.
Assembly: Silva v138 reference sequences
Supplementary files format and content: The processed data are in tab-delimited text file. The columns of the file are amplicon sequence variants and the rows are the sample IDs.

source_name: colon

extract_protocol:
tissues were lysed in 2% SDS and 25 mM EDTA overnight. Ammonium acetate (10M) was added to make the precipitate of SDS with proteins and was removed by centrifugation at 12,000 rpm. Next, DNA was precipitated using isopropanol, washed with 70% ethanol, and dissolved in dissolved in LTET (Tris 10 mM, EDTA, 0.1 mM + Tween 20,0.1% )
The 16S rRNA gene V3-V4 hypervariable region was amplified using the selected universal primers (Forward 5’-NNNNCCTACGGGNGGCWGCAG-3′, Reverse 5′- GACTACHVGGGTATCTAATCC-3′) that contained overhang nucleotide sequences (Forward 5’ TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-[locus specific sequence]-3’, Reverse 5’- GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-[locus specific sequence]-3’) for Illumina barcode indexes.

value: colon

tag: tissue type

value: CRC tumor


title: Mkx siRNA KD rep #3


title: CRC Tumor T162

data_processing:
library strategy: 16S rRNA gene sequencing
Illumina MiSeq paired-end sequencing
Raw sequencing data were converted to fastq.gz files.
The 16S rRNA sequencing data were trimmed using cutadapt
DADA2 was used to filter, trim, estimate error profiles, merge paired end reads, and construct an amplicon sequence variant (ASV) table. DADA2 was also used to remove chimeras from the denoised ASVs and assign taxonomy by fitting ASV sequences to a pre-trained naïve bayes classifier built from the Silva v138 database
Species assignments were made by exact string matching to DADA2-formatted Silva v138 reference sequences.
Assembly: Silva v138 reference sequences
Supplementary files format and content: The processed data are in tab-delimited text file. The columns of the file are amplicon sequence variants and the rows are the sample IDs.


title: C1

description:
Raw data file:
DYU26.xlxs
Control 1

extract_protocol: Ribopure Blood RNA Isolation Kit by Thermo Fisher was utilized to extract the RNA (including small RNAs) as suggested protocol by manufacturer protocol.

value: healthy


title: CRC Tumor T161


title: CRC Tumor T159


title: CRC Tumor T157


title: hSAECs, OGG1, RNA-IP, Rep-1

value: anti-OGG1 antibody (PA5-86046, Invitrogen)


title: CRC Tumor T156


title: CRC Tumor T155


title: CRC Tumor T153


title: SCBC1

description: BatchA


title: CRC Tumor T151


title: CRC Tumor T150


title: CRC Tumor T152


title: CRC Tumor T147


title: CRC Tumor T145


title: CRC Tumor T142


title: CRC Tumor T148


title: CRC Tumor T143


title: CRC Tumor T144


title: CRC Tumor T140


title: CRC Tumor T160


title: CRC Tumor T139


title: CRC Tumor T138


title: CRC Tumor T137


title: CRC Tumor T136


title: CRC Tumor T135


title: CRC Tumor T132


title: CRC Tumor T133


title: CRC Tumor T158


title: CRC Tumor T154


title: CRC Tumor T130


title: CRC Tumor T129


title: CRC Tumor T128


title: CRC Tumor T127


title: CRC Tumor T126


title: CRC Tumor T149


title: CRC Tumor T146


title: CRC Tumor T124


title: CRC Tumor T125


title: CRC Tumor T141


title: CRC Tumor T123


title: CRC Tumor T121


title: CRC Tumor T122


title: CRC Tumor T120


title: CRC Tumor T114


title: CRC Tumor T119


title: CRC Tumor T116


title: CRC Tumor T117


title: CRC Tumor T112


title: CRC Tumor T113


title: CRC Tumor T131


title: CRC Tumor T111


title: CRC Tumor T107


title: CRC Tumor T106


title: CRC Tumor T110


title: CRC Tumor T105


title: CRC Tumor T108


title: CRC Tumor T109


title: CRC Tumor T103


title: CRC Tumor T104


title: CRC Tumor T102


title: CRC Tumor T099


title: CRC Tumor T100


title: CRC Tumor T101


title: CRC Tumor T097


title: CRC Tumor T098


title: CRC Tumor T092


title: CRC Tumor T093


title: CRC Tumor T095


title: CRC Tumor T118


title: CRC Tumor T091


title: CRC Tumor T094


title: CRC Tumor T096


title: CRC Tumor T085


title: CRC Tumor T083


title: CRC Tumor T081


title: CRC Tumor T079


title: CRC Tumor T077


title: CRC Tumor T089


title: CRC Tumor T087


title: CRC Tumor T075


title: CRC Tumor T073


title: CRC Tumor T063


title: CRC Tumor T061


title: CRC Tumor T059


title: CRC Tumor T057


title: CRC Tumor T055


title: CRC Tumor T069


title: CRC Tumor T067


title: CRC Tumor T051


title: CRC Tumor T049


title: CRC Tumor T065


title: CRC Tumor T043


title: CRC Tumor T045


title: CRC Tumor T047


title: CRC Tumor T039


title: CRC Tumor T035


title: CRC Tumor T037


title: CRC Tumor T041


title: CRC Tumor T033


title: CRC Tumor T021


title: CRC Tumor T027


title: CRC Tumor T019


title: CRC Tumor T031


title: CRC Tumor T017


title: CRC Tumor T029


title: CRC Tumor T071


title: CRC Tumor T015


title: CRC Tumor T023


title: CRC Tumor T013


title: CRC Tumor T011


title: CRC Tumor T009


title: CRC Tumor T005


title: CRC Adjacent normal N161

value: CRC Adjacent normal


title: CRC Tumor T007


title: CRC Adjacent normal N159


title: CRC Adjacent normal N162


title: CRC Tumor T053


title: CRC Adjacent normal N158


title: CRC Adjacent normal N160


title: CRC Adjacent normal N155


title: CRC Adjacent normal N154


title: CRC Adjacent normal N156


title: CRC Adjacent normal N151


title: CRC Adjacent normal N153


title: CRC Tumor T025


title: CRC Adjacent normal N149


title: CRC Adjacent normal N152


title: CRC Adjacent normal N148


title: CRC Adjacent normal N146


title: CRC Adjacent normal N147


title: CRC Adjacent normal N145


title: CRC Adjacent normal N144


title: CRC Adjacent normal N143


title: CRC Adjacent normal N142


title: CRC Adjacent normal N135


title: CRC Adjacent normal N136


title: CRC Adjacent normal N131


title: CRC Adjacent normal N130


title: CRC Adjacent normal N139


title: CRC Adjacent normal N137


title: CRC Adjacent normal N133


title: CRC Adjacent normal N141


title: CRC Adjacent normal N128


title: CRC Adjacent normal N129


title: CRC Adjacent normal N150


title: CRC Adjacent normal N127


title: CRC Adjacent normal N132


title: CRC Adjacent normal N126


title: CRC Adjacent normal N124


title: CRC Adjacent normal N123


title: CRC Adjacent normal N125


title: CRC Adjacent normal N140


title: CRC Adjacent normal N121


title: CRC Adjacent normal N120


title: CRC Adjacent normal N119


title: CRC Adjacent normal N118


title: CRC Adjacent normal N113


title: CRC Adjacent normal N114


title: CRC Adjacent normal N117


title: CRC Adjacent normal N138


title: CRC Adjacent normal N110


title: CRC Adjacent normal N109


title: CRC Adjacent normal N112


title: CRC Adjacent normal N111


title: UT3_rep2

city: Tartu

first: Kaspar

last: Valgepea

state: Tartumaa

address: Nooruse 1

department: Institute of Technology

country: Estonia

institute: University of Tartu

data_processing:
The quality of NextSeq raw reads was verified using MultiQC (Ewels et al., 2016) and adapter sequences were trimmed using the Cutadapt package (version 2.10; Martin 2011)
Sequencing reads were aligned and mapped to the genome of C. autoethanogenum DSM 10061 (GenBank CP012395.1) using the Rsubread package (version 2.4.2; Liao et al., 2019).
Four .bam files per sample were merged using the Samtools (version 1.10; Li et al., 2009)
Genomic features were assigned using the featureCounts functions within Rsubread
Raw library sizes were normalized and transcript abundances in reads per kilobase of transcript per million mapped reads (RPKM) were estimated from feature counts and gene lengths using edgeR (version 3.32.1; Robison et al., 2010).
Assembly: GenBank CP012395.1
Supplementary files format and content: RPKM value tab-delimited text files

organism: Clostridium autoethanogenum

source_name: bacteria cell

growth_protocol: Clostridium autoethanogenum strains were grown on CO in chemically defined medium anaerobically at 37C and a pH of 5 in chemostats at dilution rate 0.5 or 1 day-1

extract_protocol:
Frozen pellets were thawed and total RNA was extracted using cellular lysis in RNase-free acid-washed glass beads (Merck) and RNeasy mini kit (Qiagen) with off-column DNase treatment followed by enrichment and purification using RNA Clean & ConcentratorTM (Zymo Research). Next, ribosomal RNA was removed using the Ribo-Zero rRNA removal kit (Illumina).
mRNA libraries were prepared using standard TruSeq library preparation protocols (Illumina).

treatment_protocol: Culture was pelleted by rapid centrifugation (5,000 × g for 3 min at 4C) followed by resuspension in 5 mL of RNAlater (Qiagen). Samples were stored at 4C overnight, centrifuged (4000 × g for 10 min at 4C) and the pellets stored at -80C.

tag: strain

value: DMS 10061 evolved isolate UT3

tag: physiological state

value: UT3 at dilution rate 0.5 day-1_replicate 2


title: CRC Adjacent normal N106


title: UT2_D1_rep1_rep3

value: DMS 10061 evolved isolate UT2

value: UT2 non-steady-state at dilution rate 1 day-1_replicate 3


title: CRC Adjacent normal N108


title: UT2_D1_rep1_rep2

value: UT2 non-steady-state at dilution rate 1 day-1_replicate 2


title: CRC Adjacent normal N105


title: CRC Adjacent normal N107


title: UT2_D0.5_rep4

value: UT2 phenotype at dilution rate 0.5 day-1_replicate 4


title: UT2_D1_rep1_rep1

value: UT2 non-steady-state at dilution rate 1 day-1_replicate 1


title: CRC Adjacent normal N103


title: CRC Adjacent normal N104


title: CRC Adjacent normal N102


title: CRC Adjacent normal N122


title: CRC Adjacent normal N101


title: CRC Adjacent normal N116


title: UT2_D0.5_rep2

value: UT2 phenotype at dilution rate 0.5 day-1_replicate 2


title: UT2_D0.5_rep1

value: UT2 phenotype at dilution rate 0.5 day-1_replicate 1


title: CRC Adjacent normal N099


title: UT2_COtoxicity_rep2

value: UT2 "CO toxicity" phenotype at dilution rate 1 day-1_replicate 2


title: CRC Adjacent normal N097


title: UT2_COtoxicity_rep3

value: UT2 "CO toxicity" phenotype at dilution rate 1 day-1_replicate 3


title: UT3_rep1

value: UT3 at dilution rate 0.5 day-1_replicate 1


title: CRC Adjacent normal N096

value: colon


title: UT1_rep3

value: DMS 10061 evolved isolate UT1

value: UT1 at dilution rate 0.5 day-1_replicate 3


title: UT2_COtoxicity_rep1

value: UT2 "CO toxicity" phenotype at dilution rate 1 day-1_replicate 1


title: UT1_rep2

value: UT1 at dilution rate 0.5 day-1_replicate 2


title: CRC Adjacent normal N094

value: CRC Adjacent normal


title: CRC Adjacent normal N095


title: UT1_rep1

value: UT1 at dilution rate 0.5 day-1_replicate 1


title: CRC Adjacent normal N093


title: UT2_D0.5_rep3

value: DMS 10061 evolved isolate UT2

value: UT2 phenotype at dilution rate 0.5 day-1_replicate 3


title: Cork 89

city: 17003 Girona

first: Mercè

last: Figueras

state: Girona

address: C/ Mª Aurèlia Campmany, 41 (campus Montilivi)

country: Spain

institute: Universitat de Girona

data_processing:
RNA-seq data were first analysed for quality control with FastQC (Andrews, 2010)
First low-quality 12 bp removal was performed with Trimmomatic v. 0.40 (Bolger et al., 2014)
Reads were mapped with GSNAP (Wu et al., 2016) against Q. suber genome (GCF_002906115.1_CorkOak1.0_genomic.fna)
Reads from each library were assembled with Cufflinks 2.2.1 (Trapnell et al., 2010)
The consensus transcriptome for all the samples was generated assembling each library with the Cuffmerge script from Cufflinks
different isoforms were collapsed and total counts were estimated by HTSeq-count 0.11.1 (Anders et al., 2015)
The count matrix generated was used to identify differentially expressed genes (DEGs) using the DESeq2 package v.1.38.3
Read counts per locus were corrected by rlog transformation and DEGs were obtained by pairwise comparisons
Assembly: GCF_002906115.1_CorkOak1.0
Supplementary files format and content: One unique file with a matrix table with regularized and log transformed read counts for each cork oak gene (locus identifier) and sample

organism: Quercus suber

source_name: outer bark of tree trunk

extract_protocol:
Total RNA was extracted from outer barks by some modifications of the method described previously (Chang et al., 1993; Chaves et al., 2014).
cDNA libraries were obtained using the MGIEasy RNA Library Prep Kit V3.1 and 3 µg of each sample

value: outer bark of tree trunk


title: CRC Adjacent normal N089


title: CRC Adjacent normal N091


title: Cork 87


title: Cork 90


title: BCG_deltaBCG1419c_A_S28

city: Seattle

first: Eliza

last: Peterson

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Raw FASTQ read data were processed using the R package DuffyNGS.
Assembly: ASM944v1
Supplementary files format and content: tab-delimited text file includes RPKM, TPM, and read counts for each sample

organism: Mycobacterium tuberculosis variant bovis BCG

source_name: Pasteur ATCC 35734

growth_protocol: Grown in Middlebrook 7H9 media with 10% OADC, 0.2% glycerol, 0.05% Tween 80, using tissue cultured flasks with vented caps, at 100 rpm, 37ºC up to an OD600nm 0.8.

extract_protocol:
Cells in RNA later were transferred to a tube containing Lysing Matrix B and vigorously shaken at max speed for 30 s in a FastPrep 120 homogenizer  three times. Tubes were centrifuged for 1 min (max speed), then 66 μL of 3 M sodium acetate pH 5.2 added and mixed well. Acid phenol (pH 4.2) was added at 726 μL and tubes were inverted to mix well (~60 times). Samples were incubated at 65° C for 5 min, inverting tubes to mix samples every 30 s. Then, centrifuged at 14,000 rpm for 5 min and upper aqueous phase was transferred to a new tube. 3 M sodium acetate (pH 5.2) was added at 1/10th volume along with 3x volumes of 100% ethanol. Sample was mixed well and incubated at -20°C for 1 hr or overnight. Following incubation, samples were centrifuged at 14,000 rpm for 30 min at 4°C, ethanol was discarded and 500 μL of 70% ethanol was added. Samples were centrifuged again at 14000 rpm for 10 min at 4°C, supernatant discarded, and any residual ethanol removed using pipet. Pellet was allowed to air dry, resuspended in 30-40 μL of RNase free water and quantified by Nanodrop (Thermo Scientific). This was followed by in solution genomic DNA digestion using RQ1 Dnase (Promega) following manufacturer’s recommendation. RNA quality was analyzed in a 2100 Bioanalyzer system. Total RNA samples were depleted of ribosomal RNA using the Illumina Ribo-Zero Bacteria rRNA Removal Kit.
Samples were prepared with Illumina TrueSeq Stranded mRNA HT library preparation kit and sequenced on the NextSeq 2000 instrument with NextSeq P2 (200 cycles) kit.

value: Pasteur ATCC 35734

value: bacterial culture

value: BCG1419c deletion


title: CRC Adjacent normal N098


title: BCG_deltaBCG1419c_B_S29


title: CRC Adjacent normal N083


title: CRC Adjacent normal N085


title: BCG_deltaBCG1419c_C_S30


title: Cork 91


title: CRC Adjacent normal N100


title: CRC Adjacent normal N079


title: BCG_wildtype_B_S26

value: WT


title: BCG_wildtype_C_S27


title: CRC Adjacent normal N092


title: CRC Adjacent normal N077


title: CRC Adjacent normal N075


title: BCG_wildtype_A_S25


title: CRC Adjacent normal N087