title: CSI2_60.vHC.Control.Homecage

city: Zürich

first: Lukas

middle: Matthias

last: von Ziegler

address: Winterthurerstrasse 190

department: D-HESZ

institute: ETH Zürich

data_processing:
Adaptor trimmed with cutadapt (v 1.15), maximum error rate of 0.05 and a minimum length of 15
Pseudoalignment using kallisto (version 0.44.0) on the GENCODE M17 transcriptome
Aggregation on the protein coding level
Genome_build: GRCm38
Supplementary_files_format_and_content: .h5 files with kallisto output (pseudoaligned read counts).

molecule: polyA RNA

source_name: ventral hippocampus

growth_protocol: Mice are all from a C57BL/6J Background and male. Age of the mice is between 2 and 3 months

extract_protocol:
Trizol
illumina TrueSeq

treatment_protocol: Chronic social instability (CSI) or Control. Homecage (no acute stress, control group) or 30min Restraint stress

tag: csi

value: Control

value: Homecage


title: CSI2_6.vHC.CSI.Homecage

status: Public on Apr 21 2021

type: SRA

country: Switzerland

library_source: transcriptomic

organism: Mus musculus

value: CSI

tag: condition


title: CSI2_56.vHC.Control.Homecage


title: CSI2_55.vHC.Control.Homecage


title: CSI2_59.vHC.Control.Restraint

value: Restraint


title: CSI2_8.vHC.CSI.Homecage


title: CSI2_58.vHC.Control.Homecage


title: CSI2_7.vHC.CSI.Homecage


title: CSI2_9.vHC.CSI.Homecage


title: CSI2_53.vHC.Control.Homecage


title: CSI2_52.vHC.Control.Homecage


title: CSI2_51.vHC.Control.Homecage


title: CSI2_49.vHC.Control.Restraint


title: CSI2_5.vHC.CSI.Homecage


title: CSI2_48.vHC.Control.Homecage


title: CSI2_54.vHC.Control.Restraint


title: CSI2_50.vHC.Control.Homecage


title: CSI2_47.vHC.Control.Homecage


title: CSI2_46.vHC.Control.Restraint


title: CSI2_44.vHC.Control.Homecage


title: CSI2_43.vHC.Control.Restraint


title: CSI2_40.vHC.Control.Homecage


title: CSI2_41.vHC.Control.Homecage


title: CSI2_45.vHC.Control.Homecage


title: CSI2_57.vHC.Control.Homecage


title: SPDC_mp_8hr

city: Pohang

first: Changhon

last: Lee

address: 77 Cheongam-Ro, Nam-Gu

country: South Korea

institute: POSTECH

data_processing:
QC/adapter sequence trimming for raw FASTQ sequences  Raw read quality evaluation by FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc ) with default options.  Adapter sequence trimming by CutAdapt (https://pypi.python.org/pypi/cutadapt)
Mapping on mouse reference genome  By TopHat2 (http://tophat.cbcb.umd.edu) and bowtie2 (http://bowtie-bio.sourceforge.net)
Expression and DEG analysis  Expression analysis by CuffLinks (http://cufflinks.cbcb.umd.edu) with default options[4].  DEG analysis by CuffDiff (http://cufflinks.cbcb.umd.edu) with significance thresholds as FDR<0.05, p<0.001, and p<0.01. Scatter plot and volcano plot by in-house R scripts. Unsupervised clustering by in-house R scripts
Genome_build: mm10

molecule: total RNA

source_name: SP-DC

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with Ribospin II RNA purification kit (GeneAll, Korea)
TruSeq Stranded mRNA Sample Preparation Protocol (Illumina)

tag: strain

tag: treatment

value: MGCP


title: SPDC_mp_4hr


title: SPDC_mp_2hr


title: CSI2_4.vHC.CSI.Restraint


title: SPDC_mock_8hr

value: mock


title: CSI2_39.vHC.Control.Homecage


title: CSI2_38.vHC.Control.Homecage


title: CSI2_37.vHC.Control.Homecage


title: SPDC_mock_2hr


title: SPDC_mock_0hr


title: CSI2_35.vHC.Control.Homecage


title: CSI2_36.vHC.Control.Homecage


title: CSI2_34.vHC.Control.Homecage


title: mock_1

first: Gi-Cheon

middle: careful

last: Kim

state: Hyoja-dong Namgu

address: POSTECH, postech biotech center Rm 430, Hyoja-dong Namgu, pohang

institute: IBS

source_name: COL-DC


title: MGCP_1


title: mock_2


title: CSI2_3.vHC.CSI.Homecage


title: CSI2_32.vHC.Control.Homecage


title: CSI2_31.vHC.Control.Homecage


title: CSI2_30.vHC.CSI.Homecage


title: CSI2_42.vHC.Control.Homecage


title: CSI2_33.vHC.Control.Restraint


title: CSI2_29.vHC.CSI.Homecage


title: CSI2_28.vHC.CSI.Homecage


title: CSI2_26.vHC.CSI.Restraint


title: CSI2_27.vHC.CSI.Restraint


title: CSI2_24.vHC.CSI.Homecage


title: CSI2_22.vHC.CSI.Homecage


title: CSI2_25.vHC.CSI.Homecage


title: CSI2_23.vHC.CSI.Homecage


title: CSI2_21.vHC.CSI.Restraint


title: MGCP_2


title: SPDC_mock_4hr


title: CSI2_20.vHC.CSI.Homecage


title: CSI2_2.vHC.CSI.Homecage


title: CSI2_19.vHC.CSI.Homecage


title: CSI2_18.vHC.CSI.Homecage


title: CSI2_17.vHC.CSI.Restraint


title: CSI2_14.vHC.CSI.Homecage


title: CSI2_13.vHC.CSI.Homecage


title: CSI2_16.vHC.CSI.Homecage


title: CSI2_12.vHC.CSI.Homecage


title: CSI2_1.vHC.CSI.Homecage


title: CSI2_10.vHC.CSI.Homecage


title: CSI2_11.vHC.CSI.Restraint


title: KCERT_1

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

country: USA

institute: University of Michigan

data_processing:
Read alignment and counting was carried out via Cell Ranger (10X Genomics), v3.0.0 For replicate group 1 (KCERT_1 and KCERT_GNAT3_KO_1) and v3.1.0 for replicate group 2 (KCERT_2 and KCERT_GNAT3_KO_2).
A custom mouse gene reference was used that included the base GRCm38/mm10 referenced and the yellow fluorescent protein (YFP) sequence.
fastq files were extracted from bam files using cellranger bamtofastq (cellranger v3.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: For each sample, barcodes (TSV), features (TSV), and counts matrix (MTX) files are included, both filtered and unfiltered (raw).

source_name: pancreas

extract_protocol:
Pancreas was collected, lymph nodes removed, digested with 1 mg/ml collagenase type V and filtered to single cells. Dead cells were excluded using MACS Dead Cell Removal Kit.
Cells were processed using the 10x Genomics Chromium Controller and the associated Chromium library and gel bead kits.

treatment_protocol: GNAT3 ablated or wild type controls harboring Ptf1aCreERT/+; KrasLSL-G12D/+; R26LSL-EYFP/+ alleles were treated with 5 mg of tamoxifen for 5 days at 8- to 10- weeks old then cerulein treated for 5 days at 250 mg/kg and harvested after 6 weeks.

tag: genotype

value: Kras LSL-G12D/+; Ptf1a CreERT/+; R26 LSL-EYFP


title: Rreb1 KO Rep 4

city: New York

first: Sophie

middle: M

last: Morgani

state: NY

address: Rockefeller Research Labs, 430 E 67th St

department: Development Program

institute: Sloan Kettering Institute, MSKCC

description: Rreb1 Mutant Rep3

data_processing:
The output data (FASTQ files) are mapped to the target genome using the rnaStar aligner [Dobin2012] that maps reads genomically and resolves reads across splice junctions. We use the 2 pass mapping method outlined in [Engström2013] in which the reads are mapped twice. The first mapping pass uses a list of known annotated junctions from Ensemble. Novel junctions found in the first pass are then added to the known junctions and a second mapping pass is done (on the second pass the RemoveNoncanoncial flag is used). After mapping we post process the output SAM files using the PICARD tools to: add read groups, AddOrReplaceReadGroups which in additional sorts the file and coverts it to the compressed BAM format.
We then compute the expression count matrix from the mapped reads using HTSeq (www-huber.embl.de/users/anders/HTSeq) and one of several possible gene model databases. The raw count matrix generated by HTSeq are then be processed using the R/Bioconductor package DESeq (www-huber.embl.de/users/anders/DESeq) which is used to both normalize the full dataset and analyze differential expression between sample groups.
The data was clustered in several ways using the normalized counts of all genes that a total of 10 counts when summed across all samples. 1. Hierarchical cluster with the correlation metric (Dij = 1 - cor(Xi,Xj)) with the Pearson correlation on the normalized log2 expression values. 2. Multidimensional scaling 3. Principal component analysis. Heatmap are generated using the heatmap.2 function from the gplots R package. For the Heatmaps the top 100 differentially expressed genes are used. The data plot was the mean centered normalized log2 expression of the top 100 significant genes. For mouse datasets we run a gene set analysis using the GSA package with gene sets from the Broads mSigDb. The sets used were: Mouse: c1, c2, c3, c4, c5
Supplementary_files_format_and_content: We provide .bam files for each sample and a differential gene expression list generated as described.

source_name: Embryonic day 7.5 mouse embryo

growth_protocol: E7.5 embryos were obtained from Rreb1+/- intercrosses.

extract_protocol:
Frozen tissue was homogenized in TRIzol Reagent (ThermoFisher catalog # 15596018) using the QIAGEN TissueLyser at 15 Hz for 2-3 min with a Stainless Steel Bead (QIAGEN catalog # 69989). Phase separation was induced with chloroform. RNA was precipitated with isopropanol and linear acrylamide and washed with 75% ethanol. The samples were resuspended in RNase-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 150 g of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102), with 8 cycles of PCR. Samples were barcoded and run on a HiSeq 4000 in a 50 bp/50 bp paired end run, using the HiSeq 3000/4000 SBS Kit (Illumina). An average of 47 million paired reads was generated per sample. The percent of mRNA bases averaged 67%.

treatment_protocol: Parietal endoderm was removed from embryos and used for genotyping.

tag: developmental stage

tag: tissue

value: Whole embryo


title: Rreb1 KO Rep 5

description: Rreb1 Mutant Rep4


title: LS8, SARS-CoV-2 infected Donor8_rep2

city: Jerusalem

first: Dana

last: Wolf

address: Ein Kerem

department: Dept. of clinical Microbiology & Infectious Diseases

country: Israel

institute: Hadassah University Hospital

data_processing:
Raw fastq files were generated with bcl2fastq, version 2.20.0.422.
Trimming low quality and adapter bases was done with Cutadapt, version 2.10, using parameters -q32,32 -O 1 --match-read-wildcards -m 15 and the appropriate adapter sequence (-a parameter).
Alignment was done with TopHat, version 2.1.1, using parameters -N 5 --read-gap-length 5 --read-edit-dist 10 --segment-length 19 --read-realign-edit-dist 3 --no-coverage-search --library-type fr-firststrand and the human genome together with the viral ones (both the indexed genome and the gene annotations given with -G).
Counting of reads per gene was done with htseq-count, version 0.12.4, with parameters
Normalization and differential expression were calculated with DESeq2, version 1.22.2, with default parameters, after removing genes with less than 10 counts. Samples of each tissue were analyzed separately. Genes with a significant effect, padj<0.1, were further filtered according to their baseMean and log2FoldChange values, demanding baseMean>5 and |log2FoldChang|>5/sqrt(baseMean) + 0.3.
Genome_build: GRCh38, supplemented with sequences from MN985325.1 (SARS-CoV-2) and GCA_001343785.1 (Influenza, includes accessions FJ984387.1, GQ323558.1, FJ969539.1, FJ969540.1, FJ969536.1, FJ984386.1, FJ969537.1 and FJ969538.1)
Supplementary_files_format_and_content: Excel files with all relevant data. General gene details (columns A-L), followed by raw counts in each sample, then by normalized counts in each sample, a column for the baseMean value (from DESeq2), columns for the results output from DESeq2 for each comparison, and a column with cluster assignment for K-means clustering analysis of significant genes. Each pairwise comparison has a column "best", where the value "FALSE" is for non-significant, the value "TRUE" is for padj<0.1 but without passing further filterring, and the value "THR" for padj<0.1 and passing further filtering on the log2FoldChange value. A "?" denotes missing value.

organism: Homo sapiens

source_name: Lung tissue

growth_protocol: The tissues were incubated in enriched RPMI medium with 10% fetal bovine serum, 2.5 μg glucose/ml, 2 mM glutamine, 100 IU/ml penicillin, 100 μg/ml streptomycin (Biological Industries, Beit Haemek, Israel), and 0.25 μg/ml amphotericin B at 37°C , 5% CO2.

extract_protocol:
Tissues were washed extensively, frozen and RNA was purified using M&N Nucleospin RNA purification kit according to the protocol.
RNA libraries were prepared for sequencing using the KAPA Stranded mRNA-Seq Kit according to the recommended protocol.

treatment_protocol: Tissues were placed in 48-well plates (~5 slices/well to maintain optimal viability) and were inoculated with the virus (2x10^5 tcid50/well) for 12 h to allow effective viral adsorption. Following viral adsorption, the cultures were extensively washed. RNA was extracted 24h post infection.

tag: individual

value: Donor 8

value: Lung

tag: infection

tag: time point

value: 24 hours post infection


title: LS8, SARS-CoV-2 infected Donor8_rep1


title: Rreb1 KO Rep 6

description: Rreb1 Mutant Rep5


title: Rreb1 KO Rep 3

description: Rreb1 Mutant Rep2


title: Rreb1 KO Rep 2

description: Rreb1 Mutant Rep1


title: Rreb1 WT Rep 5

description: Rreb1 Wildtype Rep4


title: Rreb1 WT Rep 6

description: Rreb1 Wildtype Rep5


title: LS6, SARS-CoV-2 infected Donor6_rep1

value: Donor 6


title: LS7, SARS-CoV-2 infected Donor7_rep1

value: Donor 7


title: Rreb1 WT Rep 4

description: Rreb1 Wildtype Rep3


title: Rreb1 WT Rep 3

description: Rreb1 Wildtype Rep2


title: LS5, SARS-CoV-2 infected Donor5_rep2

value: Donor 5


title: CSI2_15.vHC.CSI.Homecage


title: LS4, SARS-CoV-2 infected Donor4_rep2

value: Donor 4


title: LS5, SARS-CoV-2 infected Donor5_rep1


title: TNFα_mouse_rep6 [mR14_TNF]

city: Los Angeles

first: Jiwen

last: Li

address: 635 Charles E. Young Dr. S.

institute: UCLA

data_processing:
FASTQ files were mapped using STAR, then use the output BAM files do HTSEQ or Rsubread to generate count files. We calculated RPKM by running EdgeR-Limma-Voom in R.
Genome_build: GRCm38 and GRCh38
Supplementary_files_format_and_content: excel spreadsheet includes RPKM values for each sample.

growth_protocol: Except that serum selected astrocyte samples were cultured in serum medium, other cultured samples were cultured in defined serum-free medium.

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, 217004) under the protocols of the manufacturer
We used the Ovation RNA-seq system V2 (Nugen 7102) to perform first and second-strand cDNA synthesis. We then used the Next Ultra RNA-seq library prep kit for Illumina (NEB E7530) and NEBNext® multiplex oligos for Illumina (NEB E7710 E7500 E7730) to perform end repair, adaptor ligation, and 9-10 cycles of PCR enrichment according to manufacturer’s instructions.

treatment_protocol: All treatments were proceeded on 3DIV in serum-free medium. Astrocytes were treated by TNFα for 48hr, by Poly I:C for 72hr, or by hypoxia for 72hr.

value: brain; cortex

tag: cell type

value: Astrocytes

value: TNFα


title: TNFα_mouse_rep4 [mR10_TNF]


title: TNFα_mouse_rep5 [mR13_TNF]


title: LS4, SARS-CoV-2 infected Donor4_rep1


title: Rreb1 WT Rep 2

description: Rreb1 Wildtype Rep1


title: LH8, Influenza A infected Donor8_rep1

value: Influenza A


title: LS7, SARS-CoV-2 infected Donor7_rep2


title: TNFα_mouse_rep2 [mR6_TNF]


title: TNFα_mouse_rep1 [mR4_TNF]


title: LH7, Influenza A infected Donor7_rep2


title: LH7, Influenza A infected Donor7_rep1


title: KCERT_GNAT3_KO_1

value: Kras LSL-G12D/+; Ptf1a CreERT/+; R26 LSL-EYFP; Gnat3 -/-


title: LH6, Influenza A infected Donor6_rep2


title: LS6, SARS-CoV-2 infected Donor6_rep2


title: LH6, Influenza A infected Donor6_rep1


title: TNFα_control_mouse_rep5 [mR13_Ctrl]


title: TNFα_control_mouse_rep6 [mR14_Ctrl]


title: TNFα_mouse_rep3 [mR9_TNF]


title: LH5, Influenza A infected Donor5_rep2


title: TNFα_control_mouse_rep4 [mR10_Ctrl]


title: TNFα_control_mouse_rep3 [mR9_Ctrl]


title: LH4, Influenza A infected Donor4_rep2


title: TNFα_control_mouse_rep1 [mR4_Ctrl]


title: TNFα_control_mouse_rep2 [mR6_Ctrl]


title: LM8, Mock infected Donor8_rep2

value: Uninfected


title: LH8, Influenza A infected Donor8_rep2


title: LH4, Influenza A infected Donor4_rep1


title: LM8, Mock infected Donor8_rep1


title: PolyI:C_mouse_rep3 [BC10_polyIC_mouse]


title: LM7, Mock infected Donor7_rep2


title: LM7, Mock infected Donor7_rep1


title: PolyI:C_mouse_rep4 [BC14_polyIC_mouse]


title: PolyI:C_control_mouse_rep3 [BC9_polyIC_Ctrl_mouse]


title: PolyI:C_mouse_rep2 [BC6_polyIC_mouse]


title: LM6, Mock infected Donor6_rep1


title: PolyI:C_control_mouse_rep4 [BC13_polyIC_Ctrl_mouse]


title: PolyI:C_control_mouse_rep2 [BC5_polyIC_Ctrl_mouse]


title: LM5, Mock infected Donor5_rep2


title: PolyI:C_control_mouse_rep1 [BC1_polyIC_Ctrl_mouse]


title: LM5, Mock infected Donor5_rep1


title: PolyI:C_mouse_rep1 [BC2_polyIC_mouse]


title: LH5, Influenza A infected Donor5_rep1


title: LM4, Mock infected Donor4_rep2


title: Hypoxia_mouse_rep4 [BC14_Hypoxia_mouse]

value: Hypoxia


title: Hypoxia_control_mouse_rep4 [BC13_Hypoxia_Ctrl_mouse]


title: LM4, Mock infected Donor4_rep1


title: TS3, SARS-CoV-2 infected Donor3_rep2

source_name: Nasal turbinate tissue

value: Donor 3

value: Nasal turbinate


title: Hypoxia_mouse_rep3 [BC10_Hypoxia_mouse]


title: Hypoxia_control_mouse_rep3 [BC9_Hypoxia_Ctrl_mouse]


title: TS2, SARS-CoV-2 infected Donor2_rep2

value: Donor 2


title: Hypoxia_mouse_rep2 [BC6_Hypoxia_mouse]


title: TS3, SARS-CoV-2 infected Donor3_rep1


title: TS1, SARS-CoV-2 infected Donor1_rep2

value: Donor 1


title: Hypoxia_mouse_rep1 [BC2_Hypoxia_mouse]


title: TS2, SARS-CoV-2 infected Donor2_rep1


title: Hypoxia_control_mouse_rep2 [BC5_Hypoxia_Ctrl_mouse]


title: LM6, Mock infected Donor6_rep2

value: Lung


title: Hypoxia_control_mouse_rep1 [BC1_Hypoxia_Ctrl_mouse]


title: TS1, SARS-CoV-2 infected Donor1_rep1

value: 24 hours post infection


title: shPAF_2_RNA-seq

city: Houston

first: Jae-Il

last: Park

state: Texas

address: 6565 MD Anderson Blvd

department: Experimental Radiation Oncology

institute: MD Anderson Cancer Center

data_processing:
Sequenced reads were mapped to mm9 whole genome using Tophat2
The abundance of transcript reflects gene expression level were measered using FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)
Genome_build: mm9
Supplementary_files_format_and_content: txt file including FPKM values for each sample

source_name: shPAF stably transfected mouse lung cancer cell

growth_protocol: Mouse lung cancer cell (KP cell) lines were maintained in DMEM medium with 10% FBS and 1% penicillin/streptomycin (10,000U/ml)

extract_protocol:
mRNA extract from Control versus PAF knockdowned mouse lung cancer cells using Qiagen RNeasy mini kit
Libraries were prepared for sequencing using standard Illumina protocols

tag: genotype/variation

value: PAF depleted KP cell (shPAF)

tag: cell line

value: KP

value: mouse lung tumor cell line


title: TH3, Influenza A infected Donor3_rep2


title: TH3, Influenza A infected Donor3_rep1


title: shPAF_1_RNA-seq


title: TH2, Influenza A infected Donor2_rep2


title: shCtrl_1_RNA-seq

source_name: shGFP stably transfected mouse lung cancer cell

value: control KP cell (shCtrl)


title: TH2, Influenza A infected Donor2_rep1


title: TH1, Influenza A infected Donor1_rep2


title: TH1, Influenza A infected Donor1_rep1


title: CT1

city: Cincinnati

first: Xiaoting

last: Zhang

state: OH

address: 3125 Eden Ave

department: Cancer Biology

institute: university of Cincinnati

data_processing:
mouse genome (mm10) using TopHat v.2.1.0 (1). Transcript quantification and differential expression analysis were performed by Cufflinks v2.2.1 and Cuffdiff 2, respectively (1, 2).
For differentially expression analysis, the fold-change cutoff was set at 1.5 or higher.
Benjamini–Hochberg false discovery rate adjusted P value less than 0.05 was considered statistically significant.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: MMTV-HER2 control_mammary tumor

extract_protocol:
Tumors were collected and total RNA was prepared using RNA easy mini kit. RNA sequencing libraries were generated by using TruSeq stranded mRNA library prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: FVB

value: mammary tumor

value: 2 months post palpation of the primary tumor


title: CT2


title: TM3, Mock infected Donor3_rep2


title: MH2

source_name: MMTV-HER2/MMTV-MED1_mammary tumor


title: MH1


title: TM3, Mock infected Donor3_rep1


title: TM2, Mock infected Donor2_rep2


title: UC2_20% O2_TNF/IL17

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

data_processing:
The sequencing (75 cycles single end reads) was performed on an Illumina HiSeq4000 instrument, in accordance with the manufacturer’s instructions (Illumina).
FASTQ files were created with bcl2fastq 2.18 (RRID:SCR_015058, Illumina).
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files with TPM normalised transcript abundance.

source_name: Colon organoids

growth_protocol: Single cells were seeded at 500,000 cells.mL-1 concenrtation of matrigel. Colonoids were grown at 20% oxygen in 500 µl growth media containing 50% Wnt-3A conditioned medium, 30% Advanced DMEM/F12, and 20% R-spondin conditioned medium with 10% BSA, containing factors critical for stem cell   growth (Jung et al., 2011), including Recombinant Human Noggin (0.1 µg.mL-1), Nicotinamide (1221.2 µg.mL-1), N-Acetyl-L-cysteine (163.2 µg.mL-1), Inhibitor of TGFβ type 1 activating receptor-like kinase (ALK5) A-83-01 (0.211 µg.mL-1), MAPK inhibitor SB202190 (3.31µg.mL-1), Human EGF (0.05 µg.mL-1) and Gastrin (0.02 µg.mL-1). Selective ROCK-inhibitor Y-27632 (3.203 µg.mL-1) was included in the first three days of culture in growth media and media was refreshed every other day. On day 10, organoids were switched to differentiation media where the amount of Wnt-3A conditioned medium was educed to 5% of the volume and Nicotinamide and SB202190 removed, while the pan NOTCH inhibitor DAPT (4.3 µg.mL-1) was added. Organoids were differentiated for 6 days and media was refreshed every other day.

extract_protocol:
Colonoids were collected with cell recovery solution, washed with PBS/0.1% BSA twice, snap frozen in liquid nitrogen, and stored at -80 ᵒC. Rneasy kit was used as per manufacturer's instructions.
RNA sequencing libraries were generated using SENSE FFPE total RNA-Seq library prep kit   (with RiboCop rRNA depletion) according to manufacturer’s instructions (Lexogen GmbH,   Vienna, Austria). Libraries were normalized and pooled to 2.4 nM and subject to clustering   by a cBot Cluster Generation System on HiSeq4000 flowcells (Illumina Inc., San Diego,   CA) as per manufacturer's instructions.

treatment_protocol: Fourteen days after seeding, A-83-01 was removed from differentiation media. Half of the plates with colon organoids in each donor were placed in 2% Oxygen while other half were maintained in 20% Oxygen.

tag: disease status

value: Ulcerative colitis

value: Colon

value: Differentiated colonic epithelial cells

tag: treatment 1

tag: treatment 2


title: UC1_20% O2_TNF/IL17


title: UC1_20% O2_TNF

value: TNF


title: TM1, Mock infected Donor1_rep2

value: Uninfected


title: UC1_20% O2_Untreated

value: Untreated


title: TM2, Mock infected Donor2_rep1

value: Donor 2

value: Nasal turbinate


title: shCtrl_2_RNA-seq


title: UC2_20% O2_TNF


title: TM1, Mock infected Donor1_rep1

value: Donor 1


title: UC2_20% O2_Untreated


title: 2 MJ_H2_G6

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: exome seq

library_source: genomic

data_processing:
RNA-Seq: Illumina Casava1.7 software used for basecalling.
RNA-Seq: Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
RNA-Seq: Datasets were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic. PDX RNA-seq samples were filtered to remove contamination (mouse contamination). Reads uniquely mapped only to the hg19 genome were kept, along with uniquely mapped reads that had significantly better alignment scores in the h19 genome compared to the mm10 genome.
RNA-Seq: The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the hg19 refGene annotation file available at the UCSC Genome Browser.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.

molecule: genomic DNA

growth_protocol: PDX1 and PDX2 cells were injected into mammary fat pads of NOG mice

extract_protocol:
RNA and DNA was extracted using Quiagen Blood and Tissue kits
RNAseq libraries were constructed with Illumina kit; for exome seq libraries were perpared with Agillent SureSelect Human All Exome kit V6

treatment_protocol: mice were randomized when tumors reached 5mm diameter and treated for 3 weeks; paclitaxel weekly 6.5mg/kg, lapatinib 6x/week 30mg/kg, T-DM1 weekly 3.6mg/kg, trastuzumab weekly 6mg/kg, pertuzumab weekly 20mg/kg

value: pertuzumab

tag: animal id

value: mouse 2


title: UC1_2% O2_TNF

value: 2% O2 - 48 hours


title: UC1_2% O2_TNF/IL17


title: UC1_2% O2_Untreated


title: E58-D

type: RNA

city: Newcastle

first: Simon

last: Cockell

address: Framlington Place

country: United Kingdom

institute: Newcastle University

hyb_protocol: 50 ng of the obtained biotinylated cRNA samples was hybridized onto the Illumina HumanWG-8 DASL v3 as per manufacturer's instructions.

scan_protocol: The samples were scanned using the Illumina iScan array scanner. There were no deviations from the Illumina protocol.

data_processing: Data were processed using R/Bioconductor (the lumi package), Raw data were transformed using a Variance Stabilizing Transformation, and normalized with quantile normalization. algorithm. Probes were selected which fulfilled the criteria of Illumina probe detection p-value of <0.01.

label: biotin

source_name: Donor skin biopsy

label_protocol: The Illumina TotalPrep-96 RNA Amplification Kit was used to generate Biotin labeled (biotin-16-UTP), amplified cRNA starting from 200ng total RNA.

extract_protocol: RNA was extracted using a Picopure TM RNA Isolation kit (Arcturus Biosciences, USA) using the manufacturers standard protocol, and stored at -80 C.

treatment_protocol: Six-millimetre punch biopsies were taken from psoriatic plaques or adjacent non-lesional skin before and at 6h or 18h after irradiation with 311nm or 290nm UVB. A maximum of 4 biopsies were taken per patient. Biopsies were snap frozen.

tag: patient

tag: timepoint

tag: tisuue type

value: Lesional

tag: batch

value: skin


title: E57-D

tag: treatment


title: E58-C

tag: tissue


title: E57-B


title: E56-D


title: 2 MJ_H2_G5

description: exome seq

value: trastuzumab


title: E57-A


title: E58-B


title: E58-A


title: 2 MJ_H2_G4

description: exome seq


title: HC3_2% O2_TNF/IL17

value: Healthy control


title: E57-C


title: E55-D


title: E56-B

value: Non-lesional


title: HC3_2% O2_TNF


title: E55-C


title: E55-B


title: E56-C


title: E56-A


title: 2 MJ_H2_G3

description: exome seq

value: lapatinib


title: HC3_2% O2_Untreated

value: Colon


title: E54-D


title: 2 MJ_H2_G2

description: exome seq

value: paclitaxel


title: 2 MJ_H2_G1

description: exome seq

value: untreated


title: HC3_20% O2_TNF/IL17

value: Differentiated colonic epithelial cells


title: HC3_20% O2_TNF

value: TNF


title: HC3_20% O2_Untreated

value: Untreated


title: 2 MJ_H1_G6

description: exome seq


title: A63-D


title: HC1_2% O2_TNF/IL17


title: HC1_2% O2_TNF


title: E54-A


title: 2 MJ_H1_G3

description: exome seq


title: HC1_2% O2_Untreated


title: A63-A


title: A63-C


title: 2 MJ_H1_G2

description: exome seq


title: 36d


title: E55-A


title: 2 MJ_H1_G5

description: exome seq


title: A63-B


title: 2 MJ_H1_G1

description: exome seq


title: 34d


title: 2 MJ_H1_G4

description: exome seq


title: 1 MJ_H2_G6

description: exome seq

value: mouse 1


title: 25d


title: HC1_20% O2_TNF


title: HC1_20% O2_Untreated


title: 20a


title: 21a


title: 1 MJ_H2_G5

description: exome seq


title: 20d


title: 19c


title: 25a


title: HC1_20% O2_TNF/IL17


title: 17a


title: E54-B


title: 16d


title: 18a


title: 15d


title: HC2_2% O2_TNF/IL17


title: 1 MJ_H2_G3

description: exome seq


title: HC2_2% O2_TNF


title: 42a


title: HC2_2% O2_Untreated


title: 18d


title: HC2_20% O2_TNF/IL17


title: 15a


title: 1 MJ_H2_G1

description: exome seq


title: 15b


title: 16a


title: 1 MJ_H2_G2

description: exome seq


title: HC2_20% O2_TNF


title: 13a


title: 1 MJ_H2_G4

description: exome seq


title: HC2_20% O2_Untreated


title: 1 MJ_H1_G6

description: exome seq


title: 12a


title: o/e control_1

city: Chicago

first: zhike

last: lu

state: IL

address: 5801 South Ellis Avenue

department: department of chemistry

institute: University of Chicago

description: All small RNA from 15 to 50 nt

data_processing:
The adapters were removed by using cutadapt
the reads were aligned to the human(hg38) genome
The tRNA annotations is download from GtRNAdb2.0(ref here)
Reads mapped to tRNA and were counted.
Genome_build: hg38
Supplementary_files_format_and_content: tRNA reads count

source_name: HeLa cells

growth_protocol: Human cancer cells HeLa  were purchased from American Type Culture Collection (ATCC, Manassas, VA) and maintained in our lab with Dulbecco’s modified Eagle medium (DMEM, GIBCO, Carlsbad, CA, USA) with 10 % fetal bovine serum, and 1 % penicillin/streptomycin (Invitrogen).

extract_protocol:
Total RNA (100 μg) were denatured at 70 °C for 5 min and separated by a 15% TBE-Urea gel with 20/100 or 10/60 oligo length standard ladder (Integrated DNA Technologies, Coralville, IA). After visualized by SYBR Gold (Ref. S11494 from Life Technologies), tRFs (15~50nt) in gels were cut according to sizes and recovered by small RNA PAGE recovery kit (Zymo Research, Irvine, CA, USA).
The recovered tRFs was used to establish the library by NEB small RNA library preparation kit (E7330S).

treatment_protocol: For cell lines stably overexpressed ALKBH3: HeLa  cells transfected with double-tagged ALKBH3 (N terminal Flag and HA in tandem) in pPB-CAG vector were selected by 2 μg/ml puromycin for two weeks. Control cell lines were created similarly with vector only expressing N-terminal Flag and HA in tandem. The ALKBH3 stable overexpression and control cells were cultured in medium supplemented with 2 μg/ml puromycin. Cells were incubated with medium without puromycin for four days before experiments.

value: HeLa

tag: passages

tag: genotype

value: control


title: o/e ALKBH3_1

description: All small RNA from 15 to 50 nt

value: ALKBH3 overexpression


title: o/e ALKBH3_2

description: All small RNA from 15 to 50 nt


title: 11b


title: o/e control_2

description: All small RNA from 15 to 50 nt


title: 11a


title: UC3_2% O2_TNF/IL17

value: Ulcerative colitis

value: 2% O2 - 48 hours


title: 13c

value: Lesional

value: skin


title: 15c


title: 1 MJ_H1_G3

description: exome seq


title: RNA pull-down using Oligo Pool B2

city: Marseille

first: Anne-Marie

last: François-Bellan

address: 27 Bd Jean Moulin

department: Facute de Medecine

country: France

institute: CNRS-AMU

description:
Cell crosslinked using psoralen
RNA pull-down using Oligo Pool B (Files B)

data_processing:
Library strategy: RNA pulldown
STAR
FeatureCount
Genome_build: Rnor6.0
Supplementary_files_format_and_content: abundance measurement (counts)

organism: Rattus norvegicus

source_name: GH4C1 cell line

growth_protocol: GH4C1 somatolactotroph pituitary cells (ATCC_ CCL-82.2™, Molsheim, France) were grown in HamF10 medium supplemented with 15% horse serum and 2% fetal calf serum

extract_protocol:
RNA was isolated using NucleoSpin®RNA (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols; RNA-Seq 2 x 150 bp Strand-specific

treatment_protocol: Cells were crosslinked with psoralen

value: wild type

value: Psoralen


title: UC3_2% O2_TNF


title: RNA pull-down using Oligo Pool B1


title: RNA pull-down using Oligo Pool B3


title: RNA pull-down using Oligo Pool A3

description:
Cell crosslinked using psoralen
RNA pull-down using Oligo Pool A (Files A)


title: UC3_2% O2_Untreated


title: RNA pull-down using Oligo Pool A1


title: 1 MJ_H1_G2

description: exome seq

value: lapatinib


title: 1 MJ_H1_G5

description: exome seq

value: trastuzumab


title: 1 MJ_H1_G1

description: exome seq


title: MJH2_G6M3

description:
bulk RNA-seq from PDX
HERT2combined-gene-level-counts.csv

value: pertuzumab

value: mouse 3


title: MJH2_G6M2

value: mouse 2


title: 1 MJ_H1_G4

description: exome seq


title: UC3_20% O2_TNF/IL17

value: Colon

value: Differentiated colonic epithelial cells


title: UC3_20% O2_TNF

value: TNF


title: MJH2_G6M1

value: mouse 1


title: TRAP mRNAs ZT57 recovery 3 h  R rep 2

city: Riverside

first: Dawn

last: Nagel

state: CA

address: 900 University Avenue

institute: UC Riverside Department of Botany and Plant Sciences

description:
TRAP mRNAs (translatome)
R_TR.T9.H2

data_processing:
RNA-Seq data analysis was performed on the UCR IIGB high performance bioinformatics cluster (https://hpcc.ucr.edu/).
Trimming of indexed adapter primers was performed on raw reads using cutadapt and quality reports of raw reads were generated with the FastQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
All other steps were conducting by following the SystemPipeR workflow (Backman et al., 2016)
Trimmed reads were mapped to the TAIR10 Arabidopsis genome using the alignment program HISAT2 v2.2.0
Read counting was realized with the summarizeOverlaps function from the GenomicRanges package and using the Araport11 gff (201606).
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for every gene and every sample

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Seeds were surface sterilized and were stratified at 4°C for three days in the dark. Seedlings were grown in square petri dishes on filter paper placed on Murashige and Skoog (MS) medium supplemented with 1.5 % (w/v) sucrose. Plates were randomly arranged in the growth chamber and seedlings were grown for 10 days in 12 h light (~130 μEm-2s-1) and 12 h dark (LD) cycles at constant 22°C temperature. On day 11, plants were transferred to constant light and light intensity was reduced to 80-100 μEm-2s-1 to limit oxidative stress.

extract_protocol:
To extract mRNAs associated with ribosomes, Translating Ribosome Affinity Purification (TRAP) was performed as previously described (Reynoso et al., 2015). Total and TRAP mRNAs were isolated using biotinylated oligo(dT) and streptavidin magnetic beads (New England Biolabs) as previously described (Townsley et al., 2015)
Libraries were prepared as previously described (Townsley et al., 2015) with the modifications previously detailed (Blair et al., 2019). In the final enrichment step, indexed adapter enrichment primers were used (Townsley et al., 2015) and 12 cycles were performed to amplify the libraries.

treatment_protocol: Time of day is referred to as Zeitgeber Time (ZT), i.e. ZT48 and ZT60 corresponding to the beginning of the light and subjective night periods on day 13, respectively. On day 13, a 1 h heat stress (37°C) was applied to the seedlings (i.e. ZT47 to ZT48), every three hours (ZT48 - ZT69) on a 24 h time course, on different sets of plants (Fig. 1A). Control plants were maintained at 22°C (ZT48 - ZT72). To analyze the plant recovery, a 1 h heat stress was applied from ZT53 to ZT54. Stressed plants were transferred back to 22°C for recovery and control plants were maintained at 22°C. Seedlings were collected at ZT54, ZT55, ZT57 and ZT60, which correspond to 0 h, 1 h, 3 h and 6 h or recovery, respectively.

value: Seedlings

tag: age

value: Day 13 after sowing

value: Recovery 3 h post heat stress


title: UC3_20% O2_Untreated

value: Ulcerative colitis

tag: cell type

value: Untreated


title: TRAP mRNAs ZT57 control 3 h rep 2

description:
TRAP mRNAs (translatome)
R_TR.T9.C2

value: Control 3 h (22°C)


title: TRAP mRNAs ZT57 recovery 3 h  R rep 3

description:
TRAP mRNAs (translatome)
R_TR.T9.H3


title: TRAP mRNAs ZT57 control 3 h rep 3

description:
TRAP mRNAs (translatome)
R_TR.T9.C3


title: TRAP mRNAs ZT57 recovery 3 h  R rep 1

description:
TRAP mRNAs (translatome)
R_TR.T9.H1


title: UC2_2% O2_TNF

value: 2% O2 - 48 hours


title: UC2_2% O2_TNF/IL17


title: TRAP mRNAs ZT57 control 3 h rep 1

description:
TRAP mRNAs (translatome)
R_TR.T9.C1


title: MJH2_G5M3


title: UC2_2% O2_Untreated


title: MJH2_G5M2


title: TRAP mRNAs ZT55 recovery 1 h  R rep 3

description:
TRAP mRNAs (translatome)
R_TR.T7.H3

value: Recovery 1 h post heat stress


title: RNA pull-down using Oligo Pool A2

value: wild type

value: Psoralen


title: TRAP mRNAs ZT55 control 1 h rep 3

description:
TRAP mRNAs (translatome)
R_TR.T7.C3

value: Control 1 h (22°C)


title: MJH2_G5M1

value: trastuzumab


title: TRAP mRNAs ZT55 control 1 h rep 2

description:
TRAP mRNAs (translatome)
R_TR.T7.C2


title: TRAP mRNAs ZT55 control 1 h rep 1

description:
TRAP mRNAs (translatome)
R_TR.T7.C1


title: Patient25_histologically healthy margin of liver (HM)

city: Singapore

first: Hong Kai

address: 8 Biomedical Grove

department: Singapore Immunology Network

country: Singapore

institute: Agency for Science, Technology and Research

description: batch: 'RNA0351_EN_Yang_SCA_L4_L5'

data_processing:
By using RSEM (version 1.3.0), paired-end raw reads were aligned to the human reference genome (GRCh38 version 25 release; Gencode), and the Transcript Per Million (TPM) read values were quantitated.
Genome_build: GRCh38 version 25 release, Gencode
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: Liver tissue

extract_protocol:
Intratumoral and intrahepatic lymphocytes were first stained with anti-CD45 microbeads (Miltenyi, CD45 (TIL) MicroBeads) for 30 min on ice according to manufacturer’s protocol. Fraction of CD45+ cells were magnetically enriched using MS columns (Miltenyi). CD45+ cells were incubated with dasatinib as in mass cytometry experiment and stained with 50 ul of Live/Dead-Pacific Orange (Thermo Fisher) on ice for 20 min in dark. For single fluorochrome-tag pMHC tetramers, peptide-exchange and tetramer formation were done using the same method as metal-tag pMHC tetramers but in dark. PE-SAv (eBioscience), PE-Cy5-SAv (eBioscience), BV421-SAv (BD) and APC-SAv (Biolegend) were diluted to 20 ug/ml in PBS and added into pMHC monomer loaded with different peptides in the same manner mass cytometry experiment. Cells were stained by pMHC tetramer mixtures in the same condition as mass cytometry experiment but in dark. Cells were further stained with index sorting antibody panel in FACS buffer for 30 min on ice in dark. After the staining, cells were index-sorted into 96-well plates containing 3 ul lysis buffer through a 70 um nozzle using Aria II 5 lasers system (BD) for 30 minutes at 4 degree Celsius. Cells were washed thrice with BSA (1%) in 1X PBS at 4 degree Celsius.
The Smart-seq2 protocol was applied to prepare the libraries of single-cell cDNA with additional modifications: 1mg/ml BSA lysis buffer (Thermo Fisher) and 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina).
An indexed paired-end sequencing of 2x151 cycles was performed on all samples using Illumina HiSeq 4000 system (Illumina).

treatment_protocol: Liver resections were dissociated mechanically followed by centrifuge at 500 rpm for 2 mins to remove hepatocytes. Enriched intrahepatic lymphocytes (IHL) were washed with PBS twice and then frozen in 10% DMSO (Sigma-Aldrich) in FBS (Sigma-Aldrich). When processing perfusates cells, perfusion liquid was concentrated by serial centrifugations and then resuspended in RPMI 1640 (Gibco), and cells were further isolated by Ficoll gradient-separation.

tag: subject status

value: HBV-HCC patient

tag: subject id


title: Patient05_histologically healthy margin of liver (HM)

description: batch: RNA0351_EN_Yang_SCA' OR 'RNA0351_EN_Yang_SCA_L3'

value: Intratumoral and intrahepatic lymphocytes


title: Patient10_histologically healthy margin of liver (HM)

description: batch: 'RNA0351_EN_Yang_SCA_L4_L5'


title: MJH2_G4M4

value: mouse 3


title: TRAP mRNAs ZT54 recovery 0 h  R rep 2

description:
TRAP mRNAs (translatome)
R_TR.T6.H2

value: Recovery 0 h post heat stress


title: TRAP mRNAs ZT54 recovery 0 h  R rep 1

description:
TRAP mRNAs (translatome)
R_TR.T6.H1


title: TRAP mRNAs ZT54 control 0 h rep 3

description:
TRAP mRNAs (translatome)
R_TR.T6.C3

value: Control 0 h (22°C)


title: TRAP mRNAs ZT54 control 0 h rep 2

description:
TRAP mRNAs (translatome)
R_TR.T6.C2

value: Seedlings


title: Patient05_hepatocellular carcinoma (HCC)

description: batch: RNA0351_EN_Yang_SCA' OR 'RNA0351_EN_Yang_SCA_L3' OR 'RNA0351_EN_Yang_SCA_L4_L5'

value: hepatocellular carcinoma (HCC)


title: Patient25_hepatocellular carcinoma (HCC)

description: batch: 'RNA0351_EN_Yang_SCA_L4_L5'


title: TRAP mRNAs ZT55 recovery 1 h  R rep 2

description:
TRAP mRNAs (translatome)
R_TR.T7.H2

value: Day 13 after sowing


title: MJH2_G3M3

value: lapatinib


title: TRAP mRNAs ZT60 recovery 6 h  R rep 3

description:
TRAP mRNAs (translatome)
R_TR.T12.H3

value: Recovery 6 h post heat stress


title: MJH2_G4M1

value: mouse 1


title: Patient11_hepatocellular carcinoma (HCC)

description: batch: 'RNA0351_EN_Yang_SCA_L4_L5'


title: TRAP mRNAs ZT55 recovery 1 h  R rep 1

description:
TRAP mRNAs (translatome)
R_TR.T7.H1


title: TRAP mRNAs ZT60 recovery 6 h  R rep 2

description:
TRAP mRNAs (translatome)
R_TR.T12.H2


title: TRAP mRNAs ZT54 control 0 h rep 1

description:
TRAP mRNAs (translatome)
R_TR.T6.C1


title: Patient46_hepatocellular carcinoma (HCC)

description: batch: RNA0351_EN_Yang_SCA_L3' OR 'RNA0351_EN_Yang_SCA_L4_L5'


title: TRAP mRNAs ZT60 recovery 6 h  R rep 1

description:
TRAP mRNAs (translatome)
R_TR.T12.H1


title: MJH2_G3M2

value: mouse 2


title: 11c

value: Lesional

value: skin


title: TRAP mRNAs ZT60 control 6 h rep 3

description:
TRAP mRNAs (translatome)
R_TR.T12.C3

value: Control 6 h (22°C)


title: MJH2_G3M1


title: TRAP mRNAs ZT60 control 6 h rep 2

description:
TRAP mRNAs (translatome)
R_TR.T12.C2


title: TRAP mRNAs ZT54 recovery 0 h  R rep 3

description:
TRAP mRNAs (translatome)
R_TR.T6.H3


title: TRAP mRNAs ZT60 control 6 h rep 1

description:
TRAP mRNAs (translatome)
R_TR.T12.C1


title: Patient10_hepatocellular carcinoma (HCC)


title: MJH2_G4M2


title: E54-C


title: MJH2_G2M3

value: paclitaxel


title: TNFα_human_rep4_3 [hR5_TNF_3]

description:
biological replicate of TNFα_human_rep4
TNFα_human_hR5_3_BC19

value: brain; cortex

value: Astrocytes

value: TNFα


title: Total mRNAs ZT57 recovery 3 h  R rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T9.H2

value: Recovery 3 h post heat stress


title: TNFα_human_rep4_2 [hR5_TNF_2]

description:
biological replicate of TNFα_human_rep4
TNFα_human_hR5_2_BC18


title: Total mRNAs ZT57 recovery 3 h  R rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T9.H1


title: MJH2_G2M2


title: Total mRNAs ZT57 control 3 h rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T9.C2

value: Control 3 h (22°C)


title: MJH2_G2M1


title: TNFα_human_rep4_1 [hR5_TNF_1]

description:
biological replicate of TNFα_human_rep4
TNFα_human_hR5_1_BC18


title: MJH2_G1M3

value: untreated

value: mouse 3


title: TNFα_human_rep3_4 [hR4_TNF_4]

description:
biological replicate of TNFα_human_rep3
TNFα_human_hR4_4_BC15


title: MJH2_G1M2


title: Total mRNAs ZT55 recovery 1 h  R rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T7.H2

value: Seedlings

value: Recovery 1 h post heat stress


title: Total mRNAs ZT55 recovery 1 h  R rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T7.H1

value: Day 13 after sowing


title: Total mRNAs ZT55 recovery 1 h  R rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T7.H3


title: TNFα_human_rep3_3 [hR4_TNF_3]

description:
biological replicate of TNFα_human_rep3
TNFα_human_hR4_3_BC15


title: Total mRNAs ZT57 control 3 h rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T9.C1


title: Total mRNAs ZT55 control 1 h rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T7.C2

value: Control 1 h (22°C)


title: MJH2_G1M1

value: mouse 1


title: TNFα_human_rep3_2 [hR4_TNF_2]

description:
biological replicate of TNFα_human_rep3
TNFα_human_hR4_2_BC14


title: Total mRNAs ZT55 control 1 h rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T7.C1


title: Total mRNAs ZT57 recovery 3 h  R rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T9.H3


title: MJH1_G6M2

description:
bulk RNA-seq from PDX
HERT1combined-gene-level-counts.csv

value: pertuzumab

value: mouse 2


title: MJH1_G6M3


title: Total mRNAs ZT54 recovery 0 h  R rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T6.H2

value: Recovery 0 h post heat stress


title: Total mRNAs ZT57 control 3 h rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T9.C3


title: TNFα_human_rep2 [hR3_TNF]


title: Total mRNAs ZT54 control 0 h rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T6.C3

value: Control 0 h (22°C)


title: TNFα_human_rep1 [hR1_TNF]


title: Total mRNAs ZT54 control 0 h rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T6.C1


title: Total mRNAs ZT54 control 0 h rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T6.C2


title: Total mRNAs ZT60 recovery 6 h  R rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T12.H3

value: Recovery 6 h post heat stress


title: MJH1_G5M3

value: trastuzumab


title: Total mRNAs ZT60 recovery 6 h  R rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T12.H2


title: TNFα_control_human_rep4_3 [hR5_Ctrl_3]

description:
biological replicate of TNFα_control_human_rep4
TNFα_control_human_hR5_3_BC21

value: brain; cortex

value: Astrocytes


title: Total mRNAs ZT60 recovery 6 h  R rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T12.H1


title: Total mRNAs ZT60 control 6 h rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T12.C3

value: Control 6 h (22°C)


title: Total mRNAs ZT60 control 6 h rep 2

description:
Total mRNAs (transcriptome)
R_TOT.T12.C2


title: TNFα_control_human_rep4_1 [hR5_Ctrl_1]

description:
biological replicate of TNFα_control_human_rep4
TNFα_control_human_hR5_1_BC20


title: MJH1_G5M1


title: MJH1_G6M1


title: TNFα_control_human_rep4_2 [hR5_Ctrl_2]

description:
biological replicate of TNFα_control_human_rep4
TNFα_control_human_hR5_2_BC19


title: Total mRNAs ZT55 control 1 h rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T7.C3


title: MJH1_G4M4


title: TNFα_human_rep3_1 [hR4_TNF_1]

description:
biological replicate of TNFα_human_rep3
TNFα_human_hR4_1_BC14

value: TNFα


title: TNFα_control_human_rep3_4 [hR4_Ctrl_4]

description:
biological replicate of TNFα_control_human_rep3
TNFα_control_human_hR4_4_BC17


title: MJH1_G5M2


title: TRAP mRNAs ZT57 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T9.H2

value: Heat stress (1 h at 37°C)


title: Total mRNAs ZT54 recovery 0 h  R rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T6.H1


title: TRAP mRNAs ZT57 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T9.H1


title: MJH1_G4M2


title: TNFα_control_human_rep3_3 [hR4_Ctrl_3]

description:
biological replicate of TNFα_control_human_rep3
TNFα_control_human_hR4_3_BC17


title: MJH1_G4M1


title: TRAP mRNAs ZT57 control rep 3

description:
TRAP mRNAs (translatome)
TR.T9.C3

value: Control (22°C)


title: TRAP mRNAs ZT57 control rep 2

description:
TRAP mRNAs (translatome)
TR.T9.C2

value: Seedlings


title: TRAP mRNAs ZT57 control rep 1

description:
TRAP mRNAs (translatome)
TR.T9.C1


title: TNFα_control_human_rep3_1 [hR4_Ctrl_1]

description:
biological replicate of TNFα_control_human_rep3
TNFα_control_human_hR4_1_BC16


title: MJH1_G3M3

value: paclitaxel

value: mouse 3


title: TNFα_control_human_rep3_2 [hR4_Ctrl_2]

description:
biological replicate of TNFα_control_human_rep3
TNFα_control_human_hR4_2_BC16


title: MJH1_G3M2


title: TRAP mRNAs ZT54 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T6.H2

value: Day 13 after sowing


title: TRAP mRNAs ZT54 control rep 3

description:
TRAP mRNAs (translatome)
TR.T6.C3


title: TNFα_control_human_rep2 [hR3_Ctrl]


title: TRAP mRNAs ZT54 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T6.H1


title: TNFα_control_human_rep1 [hR1_Ctrl]


title: TRAP mRNAs ZT54 control rep 2

description:
TRAP mRNAs (translatome)
TR.T6.C2


title: MJH1_G2M3

value: lapatinib


title: Total mRNAs ZT54 recovery 0 h  R rep 3

description:
Total mRNAs (transcriptome)
R_TOT.T6.H3


title: Total mRNAs ZT60 control 6 h rep 1

description:
Total mRNAs (transcriptome)
R_TOT.T12.C1


title: TRAP mRNAs ZT51 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T3.H3


title: TRAP mRNAs ZT54 control rep 1

description:
TRAP mRNAs (translatome)
TR.T6.C1


title: PolyI:C_human_rep4 [BC16_polyIC_human]


title: MJH1_G2M2


title: TRAP mRNAs ZT51 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T3.H2


title: PolyI:C_control_human_rep4 [BC15_polyIC_Ctrl_human]


title: TRAP mRNAs ZT57 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T9.H3


title: TRAP mRNAs ZT51 control rep 1

description:
TRAP mRNAs (translatome)
TR.T3.C1


title: PolyI:C_human_rep3 [BC12_polyIC_human]


title: TRAP mRNAs ZT51 control rep 2

description:
TRAP mRNAs (translatome)
TR.T3.C2


title: TRAP mRNAs ZT51 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T3.H1


title: TRAP mRNAs ZT51 control rep 3

description:
TRAP mRNAs (translatome)
TR.T3.C3


title: MJH1_G2M1

value: mouse 1


title: TRAP mRNAs ZT54 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T6.H3


title: TRAP mRNAs ZT69 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T21.H2


title: MJH1_G1M2

value: untreated

value: mouse 2


title: MJH1_G1M3


title: MJH1_G3M1


title: TRAP mRNAs ZT69 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T21.H1


title: TRAP mRNAs ZT69 control rep 3

description:
TRAP mRNAs (translatome)
TR.T21.C3


title: MJH1_G1M1


title: PolyI:C_control_human_rep2 [BC7_polyIC_Ctrl_human]


title: TRAP mRNAs ZT69 control rep 2

description:
TRAP mRNAs (translatome)
TR.T21.C2


title: TRAP mRNAs ZT69 control rep 1

description:
TRAP mRNAs (translatome)
TR.T21.C1


title: TRAP mRNAs ZT66 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T18.H1


title: TRAP mRNAs ZT66 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T18.H2


title: TRAP mRNAs ZT66 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T18.H3


title: TRAP mRNAs ZT66 control rep 3

description:
TRAP mRNAs (translatome)
TR.T18.C3


title: PolyI:C_control_human_rep1 [BC3_polyIC_Ctrl_human]


title: TRAP mRNAs ZT63 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T15.H3


title: TRAP mRNAs ZT66 control rep 1

description:
TRAP mRNAs (translatome)
TR.T18.C1


title: Hypoxia_control_human_rep4 [BC15_Hypoxia_Ctrl_human]


title: Hypoxia_human_rep4 [BC16_Hypoxia_human]

value: Hypoxia


title: TRAP mRNAs ZT66 control rep 2

description:
TRAP mRNAs (translatome)
TR.T18.C2


title: TRAP mRNAs ZT69 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T21.H3


title: TRAP mRNAs ZT63 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T15.H2


title: PolyI:C_control_human_rep3 [BC11_polyIC_Ctrl_human]


title: Input_DNA

city: Shanghai

first: Qiang

last: Pan

address: 320 Yue Yang Road

country: China

institute: Chinese Academy of Sciences

data_processing:
For RNA seq, paired-end reads were aligned to the mouse reference genome mm10 with HISAT2.The whole samples expression levels were presented  as RPKM. The statistically significant DE genes were obtained by an adjusted P-value <0.05 and foldchange > 1.5 using the DEGseq software.
For ChIP sequencing analysis: The 75-nt sequence reads generated by Illumina equencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, unless stated otherwise, duplicate reads (“PCR duplicates”) are removed.
For ChIP-seq determination of Fragment Density: Since the 5′-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3′-ends to a length of 150-250 bp, depending on the average fragment length in the size selectedlibrary (normally 200 bp). To identify the density of fragments (extended tags) along the genome,the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can bevisualized in genome browsers (see Section V.).
For ChIP-seq, the generic term “Interval” is used to describe genomic regions with local enrichments in tag numbers. Intervals are defined by the chromosome number and a start and end coordinate. The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009). MACS is suitable to identify the binding sites of transcription factors that bind to discrete sites (often containing a consensus DNA sequence) as well as many active histone marks and methyl-C enriched regions, while SICER is used to study proteins that bind to extended regions in the genome (such as repressive histone marks or RNA polymerase II). Both methods look for significant enrichments in the ChIP/IP data file when compared to the Input data file (~ random background).
Genome_build: mm10 for RNAseq; hg38 for ChIPseq

source_name: colorectal cancer cell line

extract_protocol:
For RNA seq, total RNA was from small intestinal crypts from 2-month-old APCmin and APCmin; ZMYND8 IEC-/- mice. RNA was libraried by NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) and  sequencing (2×150 bp) by HiSeq3000. HCT116 cells (107 cells) were harvested and followed by ChIP-seq (Active Motif, Inc.) using the antibody against ZMYND8 (Bethyl A302-090A).
Fro RNA seq, libraries were prepared according to instructions of NEBNext® Ultra™ RNA LibraryPrep Kit for Illumina (NEB, USA).

treatment_protocol: For ChIP seq, HCT116 cells were cultured with 10% FBS for 24 hours.

tag: cell line

value: colorectal cancer cells

value: 10% LPDS for 24 hours

tag: antibody


title: ZMYND8_ChIP_in_SREBP2_KO

value: ZMYND8(Bethyl A302-090A)


title: 05-Hete_rep-1

city: Isehara-shi

first: Atsushi

last: Fukuda

country: Japan

institute: Tokai University

description: Female iPS cells with heterogenous XACT deletion using the CRISPR-Cas9 knockout.

data_processing:
Basecalls performed using bcl2fastq v2.20.
Sequencing adaptors, low quality reads, and bases were trimmed with Trimmomatic-0.38 tool.
The sequence reads were aligned to the Human reference genome (hg38) using STAR 2.7.1a.
The read counts allocated for each gene and transcript (Ensembl Genes 2016.12.01) were quantified using a Trimmed Mean of M-value (TMM) method using StrandNGS 3.2 software (Agilent Technologies, Santa Clara, CA).
Genome_build: hg38
Supplementary_files_format_and_content: An excel format file (XLSX) includes TMM quantification values and Ensembl gene annotations of all samples.

source_name: Human iPS cells from HPS002

extract_protocol:
Total RNA is extracted using Rneasy plus micro kit (Qiagen) with manufacturer's instructions.
Total RNA obtained from each sample was subjected to a sequencing library construction using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, MA) with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) according to the manufacturer’s protocols.
Strand specific RNA-seq  (first strand).

value: heterogenous XACT deletion

tag: gender

value: female

value: iPS cells


title: ZMYND8_ChIP_in_SREBP2_WT

value: WT


title: Hypoxia_human_rep3 [BC12_Hypoxia_human]

value: brain; cortex

value: Astrocytes


title: PolyI:C_human_rep2 [BC8_polyIC_human]


title: 04-WT_rep-2

description: Female iPS cells.

value: control


title: TRAP mRNAs ZT63 control rep 3

description:
TRAP mRNAs (translatome)
TR.T15.C3

value: Seedlings

value: Control (22°C)


title: TRAP mRNAs ZT63 control rep 2

description:
TRAP mRNAs (translatome)
TR.T15.C2

value: Day 13 after sowing


title: Hypoxia_control_human_rep3 [BC11_Hypoxia_Ctrl_human]


title: TRAP mRNAs ZT63 control rep 1

description:
TRAP mRNAs (translatome)
TR.T15.C1


title: PolyI:C_human_rep1 [BC4_polyIC_human]


title: TRAP mRNAs ZT60 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T12.H3

value: Heat stress (1 h at 37°C)


title: 03-WT_rep-1

description: Female iPS cells.


title: TRAP mRNAs ZT60 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T12.H2


title: TRAP mRNAs ZT60 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T12.H1


title: 06-Hete_rep-2


title: Hypoxia_control_human_rep2 [BC7_Hypoxia_Ctrl_human]


title: TRAP mRNAs ZT60 control rep 3

description:
TRAP mRNAs (translatome)
TR.T12.C3


title: 02-KO_rep-2

description: Female iPS cells with null XACT deletion using the CRISPR-Cas9 knockout.

value: null XACT deletion


title: Hypoxia_human_rep1 [BC4_Hypoxia_human]


title: TRAP mRNAs ZT48 heat rep 3

description:
TRAP mRNAs (translatome)
TR.T0.H3


title: Hypoxia_control_human_rep1 [BC3_Hypoxia_Ctrl_human]


title: TRAP mRNAs ZT72 control rep 2

description:
TRAP mRNAs (translatome)
TR.T01.C2


title: 01-KO_rep-1


title: TRAP mRNAs ZT60 control rep 2

description:
TRAP mRNAs (translatome)
TR.T12.C2


title: TRAP mRNAs ZT72 control rep 3

description:
TRAP mRNAs (translatome)
TR.T01.C3


title: TRAP mRNAs ZT63 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T15.H1


title: TRAP mRNAs ZT72 control rep 1

description:
TRAP mRNAs (translatome)
TR.T01.C1


title: shPAF_2_RNA-seq

data_processing:
Sequenced reads were mapped to GRCh37(hg19) whole genome using Tophat2
The abundance of transcript reflects gene expression level were measered using FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced)
Genome_build: GRCh37(hg19)
Supplementary_files_format_and_content: txt file including FPKM values for each sample

source_name: shPAF stably transfected human lung cancer cell

growth_protocol: Human lung cancer cell line, H1792 were maintained in RPMI medium with 10% FBS and 1% penicillin/streptomycin (10,000U/ml)

extract_protocol:
mRNA extract from Control versus PAF knockdowned H1792 cells using Qiagen RNeasy mini kit
Libraries were prepared for sequencing using standard Illumina protocols

tag: lentivirus

value: shPAF

value: H1792 human lung tumor cell line


title: TRAP mRNAs ZT48 heat rep 2

description:
TRAP mRNAs (translatome)
TR.T0.H2


title: TRAP mRNAs ZT48 control rep 3

description:
TRAP mRNAs (translatome)
TR.T0.C3


title: TRAP mRNAs ZT48 heat rep 1

description:
TRAP mRNAs (translatome)
TR.T0.H1


title: shPAF_1_RNA-seq


title: TRAP mRNAs ZT48 control rep 2

description:
TRAP mRNAs (translatome)
TR.T0.C2


title: Hypoxia_human_rep2 [BC8_Hypoxia_human]

value: Hypoxia


title: TRAP mRNAs ZT48 control rep 1

description:
TRAP mRNAs (translatome)
TR.T0.C1


title: Total mRNAs ZT57 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T9.H3


title: shCtrl_2_RNA-seq

value: shCtrl


title: shCtrl_1_RNA-seq


title: shlnc-HAL 3

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

description:
2772C4
processed data file: GeneMat.results.normalized_data.matrix

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were trimmed for adapters, low complexity and low quality bases using trimmomatic ver. 0.33.
Conserved paired reads were aligned with STAR ver 2.4.2 using GRCh38 and genocode GTF ver. 24.
Transcript abundance was determined using RSEM ver. 1.2.29.
Genome_build: GRCh38
Supplementary_files_format_and_content: GeneMat.results.normalized_data.matrix: Tab-delimited text file that includes normalized count values for each sample.

source_name: Breast cancer cell line

growth_protocol: MCF7 cells were cultured in RPMI-1640 supplemented with 5% Fetal Bovine Serum and were stably transfected with an expression vector containing shLuc (control shRNA) and shlnc-HAL-2 (lncRNA-HAL targeting shRNA), using Xfect (Clontech) and selecting stably transfected clones with 0.7ug/mL of puromycin. The cells were analyzed for lncRNA-HAL expression 72 hours after seeding by qRTPCR and found a 0.5 decrease in lncRNA-HAL expression in MCF7 shlnc-HAL-2 cells.

extract_protocol:
RNA was isolated with Trizol.
Library was constructed using TruSeq stranded total RNA Illumina.
RNAseq 2x 76 Paired End.

value: Breast cancer cell line

value: Transfected with a vector expressing shlnc-HAL2

tag: type of transfection

value: Stable


title: shlnc-HAL 1

description:
2772C1
processed data file: GeneMat.results.normalized_data.matrix


title: shlnc-HAL 2

description:
2772C3
processed data file: GeneMat.results.normalized_data.matrix


title: shLuc 3

description:
MCF7C3
processed data file: GeneMat.results.normalized_data.matrix

value: Transfected with a vector expressing shLuc


title: shLuc 4

description:
MCF7C4
processed data file: GeneMat.results.normalized_data.matrix


title: shLuc 2

description:
MCF7C2
processed data file: GeneMat.results.normalized_data.matrix


title: Total mRNAs ZT57 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T9.H1


title: Total mRNAs ZT57 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T9.H2


title: Total mRNAs ZT57 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T9.C3


title: Total mRNAs ZT57 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T9.C2


title: Total mRNAs ZT54 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T6.H2


title: Total mRNAs ZT54 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T6.H3


title: Total mRNAs ZT54 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T6.C3


title: Total mRNAs ZT54 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T6.H1


title: Total mRNAs ZT54 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T6.C1


title: shLuc 1

description:
MCF7C1
processed data file: GeneMat.results.normalized_data.matrix


title: Total mRNAs ZT54 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T6.C2


title: fer-8-Root-Rep-2

city: Vancouver

first: Andrew

last: Wilson

state: BC

address: 2185 East Mall

department: Michael Smith Laboratories

country: Canada

institute: University of British Columbia

data_processing:
High quality reads were mapped to the Tair 10 genome using Bowtie2
transcript quantification was performed with RSEM

source_name: fer-8 is hsm13 in the manuscript

growth_protocol: Arabidopsis seeds were surface sterilized (washed in 70% ethanol for 2 min, 10% bleach for 2 min, and 3 times in sterile water), and stored at 4°C for at least 2 days before use. For assays on plates with solid media, seedlings were grown on 1/2× MS medium with 1% phytoagar and 1% sucrose. Plates were grown at 22°C under 90-100 μE light on a 12 hours light / 12 hours dark cycle.  For both the parental line (pCYP71A12:GUS) and hsm13, samples were harvested at 11 days after germination. Shoots from 2 plants or roots from 5 plants were pooled for each sample. RNA was extracted using a Qiagen RNAeasy isolation kit.

extract_protocol:
QIAGEN RNeasy Mini Kit
RNA samples with a concentration higher than 300 ng/uL and RIN number high than 8 were used for library preparation. Construction of libraries and sequencing were performed at the Michael Smith Genome Sciences Center (http://www.bcgsc.ca/). Paired end 75 bp RNA-sequencing was performed using an Illuminia Hi-seq 2500 platform. The total RNA was DNase I treated and QC'ed using Agilent RNA Nano assay for quality and concentration.   Ribosomal RNAs (rRNA) are generally removed from total RNA either by polyA+ selection.

treatment_protocol: No treatment

value: root


title: fer-8-Root-Rep-1


title: Total mRNAs ZT51 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T3.H3


title: Total mRNAs ZT51 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T3.H2


title: Total mRNAs ZT51 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T3.H1


title: Total mRNAs ZT51 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T3.C2


title: Total mRNAs ZT51 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T3.C1


title: fer-8--Leaf-Rep1

value: leaf


title: CYP-Root-Rep-1

source_name: CYP means pCYP71A12:GUS reporter line

value: WT


title: CYP-Root-Rep-2


title: Total mRNAs ZT69 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T21.H3


title: Total mRNAs ZT69 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T21.H2


title: chimera_rep3 [BC43_chimera_astro]

description:
mixture of huma and mouse astrocyte RNA
chimera_astrocyte_BC43

organism:
Homo sapiens
Mus musculus

source_name: chimera

value: brain; cortex

value: Astrocytes

value: chimera


title: fer-8--Leaf-Rep2


title: Total mRNAs ZT69 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T21.H1

value: Seedlings

value: Day 13 after sowing


title: CYP-Leaf-Rep1


title: Total mRNAs ZT69 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T21.C3

value: Control (22°C)


title: Total mRNAs ZT69 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T21.C2


title: Total mRNAs ZT69 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T21.C1


title: chimera_rep2 [BC38_chimera_astro]

description:
mixture of huma and mouse astrocyte RNA
chimera_astrocyte_BC38


title: Total mRNAs ZT51 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T3.C3


title: chimera_rep1 [BC17_chimera_astro]

description:
mixture of huma and mouse astrocyte RNA
chimera_astrocyte_BC17


title: Total mRNAs ZT66 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T18.H3

value: Heat stress (1 h at 37°C)


title: 10 min post infection, Vector 1

city: Bethesda

first: Deborah

last: Hinton

state: MD

address: 8 Center drive

institute: NIDDK

data_processing:
Read data in fastq format was demultiplexed and aligned to E. coli str. K-12 substr. MG1655 (NC_000913.3) or E. coli virus T4  (NC_000866.4) reference genome using STAR v2.5.2
Default alignment behavior was altered with the following arguments: --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --clip3pAdapterSeq AGATCGGAAGAGCGTCGTGTA --alignIntronMax 1.
RNA gene counts in both reference genomes were then quantified using the same NCBI gene definitions utilized in mapping index construction using the subread featureCounts v1.4.6-p3 package
Count data was normalized using Deseq2, which utilizes a normalization of means method for sample normalization and comparison.
Differential expression between conditions was represented as a fold change, and genes with both a fold change ≥2 or ≤ 0.5and adjusted p value ≤ 0.05 were considered significant.
Genome_build: NC_000913.3 or  NC_000866.4
Supplementary_files_format_and_content: Comma seperated value text files include: 1) the fold change of each gene in two different samples determined using subread featureCounts v1.4.6-p3 package; 2) Benjamini-Hochberg p-value.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Bacteria

growth_protocol: E. coli str. K-12 substr. MG1655 containing either pNW129 or pNW129-MotB were grown to early log phase (OD600 ~ 0.3)  then induced with 0.2% arabinose for 20 minutes. Phage T4 was added to the culture at MOI 10.

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
The cDNA library was prepared using a modified RNATagSeq workflow as previously described (Shishkin, A.A. et al. 2015 Nat Methods). Optimum fragmentation of the total RNA samples in this library was determined to be 3 min at 94C in FastAP buffer (Thermo Fischer Scientific).  The cDNA Library was run on a Bioanalyzer using the Agilent High Sensitivity DNA Kit to evaluate the quality of the library.  The concentration of the cDNA library was determined by qPCR using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA).

tag: strain

value: K-12 substr. MG1655

tag: plasmid


title: 10 min post infection, Vector 2


title: Vegetative stage replicate 3 [NovaSeq]

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

description:
V3
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv

data_processing:
Sequence reads were aligned, quantified by Cell Ranger with default setting except using normalized="none" for aggr function.
Low quality cellsor outliers were filtered out from the data by the following threshold: 200 < total Gene count < 7000, 500 <total UMI count <30000.
Normalization (SCTransform), batch correction (Harmony) and dimension reduction (PCA and UMAP) were conducted in Seurat.
raw_sc_Dicty_3_stage.tsv was generated by removing streaming stage cells from the matrix.
raw_sc_Dicty_3_stage_ds.tsv (used for pseudotime analysis) was generated by downsampling the raw_sc_Dicty_3_stage.tsv.
Genome_build: AX4
Supplementary_files_format_and_content: Matrix of UMI counts per gene for each cell.
Supplementary_files_format_and_content: The information (cell stage, batch…) of each cell barcode in the quantification matrix file.

organism: Dictyostelium discoideum AX4

source_name: Vegetative cells

growth_protocol: We cultured te strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin.

extract_protocol:
Cells were dissociated into single cells from different stages by physical pipetting with PBS + 0.04% BSA. The cell numbers were counted using a microscope.
Cell from each sample were subject to Chromium Single Cell Gene Expression kit V3 (10x Genomics) for library construction according to the manufacturer’s instructions.

tag: developmental stage

value: Vegetative


title: Total mRNAs ZT66 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T18.H2


title: CYP-Leaf-Rep2


title: Total mRNAs ZT66 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T18.C3


title: Total mRNAs ZT66 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T18.H1


title: 10 min post infection, T4motB 2


title: Vegetative stage replicate 2 [NovaSeq]

description:
V2
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv


title: Total mRNAs ZT66 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T18.C2


title: 10 min post infection, T4motB 1


title: Vegetative stage replicate 1 [NovaSeq]

description:
V1
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv


title: Total mRNAs ZT63 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T15.H3


title: 5 min post infection, Vector 2


title: Total mRNAs ZT66 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T18.C1


title: Total mRNAs ZT63 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T15.H2


title: Total mRNAs ZT63 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T15.H1


title: Total mRNAs ZT63 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T15.C3


title: Total mRNAs ZT63 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T15.C2


title: Total mRNAs ZT60 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T12.H1


title: Total mRNAs ZT60 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T12.H3


title: Total mRNAs ZT60 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T12.H2


title: Total mRNAs ZT63 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T15.C1


title: 8_A3 2+4

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

institute: Lille University

description: SAMPLE 8

hyb_protocol: Agilent-072363 Whole Human Genome Microarray 8x60K v3 were scanned on an Agilent G2505B scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: UCA1 siRNA transfected cells

label_protocol: manufacturer's instructions

growth_protocol: OAW42 R cells were grown in DMEM medium supplemented with 4500 mg/l glucose, 2 mM Glutamax™, 1 mM sodium pyruvate, 10% fetal calf serum, 33 mM sodium bicarbonate and 20 UI/l recombinant human insulin

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: RNA extraction occurred 24h after exponentially growing cells were transfected with indicated siRNAs: Lincode Non-targeting Pool; D-001320-10-05 for control siRNA; Lincode UCA1 targeting siRNAs number 2 and number 4 (Dharmacon). Transfeciton reagent: InterferIn, as per manufacturer's protocol, 20 nM final siRNA concentraiton in 25 cm2 culture flasks.

value: chemoresistant ovarian cancer cell line

tag: genotype/variation

value: UCA1 siRNA transfected cells


title: Total mRNAs ZT60 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T12.C3

tag: treatment


title: 5 min post infection, Vector 1


title: 0 min post infection, Vector 2


title: 5 min post infection, T4motB 1


title: 7_A2 2+4

description: SAMPLE 7


title: Streaming stage replicate 2 [NovaSeq]

description:
St2
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_4_stage.tsv

source_name: Streaming cells

value: Streaming


title: Slug stage replicate 3 [NovaSeq]

description:
Slug3
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv

source_name: Slug cells

value: Slug


title: Slug stage replicate 2 [NovaSeq]

description:
Slug2
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv


title: Streaming stage replicate 3 [NovaSeq]

description:
St3
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_4_stage.tsv


title: 0 min post infection, Vector 1


title: Total mRNAs ZT60 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T12.C2

tag: tissue


title: Total mRNAs ZT60 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T12.C1


title: Total mRNAs ZT72 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T01.C3


title: 0 min post infection, T4motB 2


title: Streaming stage replicate 1 [NovaSeq]

description:
St1
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_4_stage.tsv


title: 5 min post infection, T4motB 2


title: Total mRNAs ZT72 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T01.C2


title: Fruiting stage replicate 3 [NovaSeq]

description:
F3
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv

source_name: Fruiting stage cells

value: Fruiting


title: Total mRNAs ZT72 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T01.C1


title: Total mRNAs ZT48 heat rep 3

description:
Total mRNAs (transcriptome)
TOT.T0.H3


title: 0 min post infection, T4motB 1


title: Total mRNAs ZT48 heat rep 2

description:
Total mRNAs (transcriptome)
TOT.T0.H2


title: Fruiting stage replicate 1 [NovaSeq]

description:
F1
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv


title: 4_A3 NT

description: SAMPLE 4

source_name: Control siRNA transfected cells

value: Control siRNA transfected cells


title: Total mRNAs ZT48 heat rep 1

description:
Total mRNAs (transcriptome)
TOT.T0.H1


title: Total mRNAs ZT48 control rep 3

description:
Total mRNAs (transcriptome)
TOT.T0.C3


title: EHF IKO 4

city: Heidelberg

first: John

last: Mariadason

state: Victoria

address: Austin Health, 145 Studyley Road

department: Gastrointestinal Cancers

country: Australia

institute: Olivia Newton-John Cancer Research Institute

data_processing:
STAR version  020201 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outSAMtype BAM Unsorted --sjdbOverhang 100 --outFilterMatchNminOverLread 0.5 --outFilterScoreMinOverLread 0.5
featureCounts (Subread-1.6.1 ) -t exon -g gene_name -s 0
Genome_build: GRCm38
Supplementary_files_format_and_content: Feature count data in GTF format

growth_protocol: The colon was removed from 6 week old mice, opened, washed in warm PBS and incubated  in pre-warmed Buffer 1 (PBS 93%, 0.5M EDTA 3%, RNA secure 4%,), at 37°C on a shaker for 10 minutes. Samples were then vortexed, the smooth muscle removed, and the epithelial cells pelleted by centrifugation at 1400g for 5 minutes at 4°C. The pellet was washed in 1-2mL of Buffer 2 (PBS 96%, RNA secure 4%), centrifuged at 17,000 rpm for 1 minute, and pellets snap-frozen on dry ice and stored at -80

extract_protocol:
RNA was extracted from isolated epithelial cells or tissue using the ReliaPrep RNA Tissue Miniprep System (Promega, USA) as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colonic epithelium

value: 6 weeks

value: Ehf intestinal knockout

value: Tamoxifen


title: 6_M2 2+4

description: SAMPLE 6


title: Slug stage replicate 1 [NovaSeq]

description:
Slug1
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv

value: WT


title: EHF IKO 3


title: Total mRNAs ZT48 control rep 2

description:
Total mRNAs (transcriptome)
TOT.T0.C2

value: Seedlings


title: stationary_minus_rep1

city: HONG KONG

first: Huan

last: ZHONG

state: HONG KONG

address: T1012 CHA CHI-MING SCIENCE TOWER

department: BIOLOGY

country: Hong Kong

institute: HKBU

data_processing:
The bioinformatic analysis was conducted using our home-made pipeline, TagSeqTools36. Tagged and non-tagged reads were differentiated using the TagSeek module with default setting (similarity=12). Two sets of reads generated from the TagSeek step were subjected to TagSeqQuant for alignment to both the reference genome and transcriptome of E. coli strain K-12 substrain MG165537, with the default alignment parameters of minimap2
Genome_build: E. coli strain K-12 substrain MG1655
Supplementary_files_format_and_content: excel files including comparisons between different samples

organism: Escherichia coli

source_name: E. coli K-12 stain MG1655

growth_protocol: grown in Luria-Bertani (LB) broth under aeration at 37 °C to an OD600 of 1.9

extract_protocol:
Total RNA was extracted according to the method described by Winz et al, 2017
For each RNA sample, 1 μg poly(A)-tailed RNA was used to prepare a library using the Nanopore Direct RNA Sequencing Kit (RNA-0002) following the manufacturer’s instructions (Oxford Nanopore Technologies, Oxford, UK). Each library was loaded onto a flow cell (R9.4) and sequenced on the sequencing device GridION.

value: E. coli K-12 stain MG1655

tag: phase

value: stationary minus


title: 3_A2 NT

description: SAMPLE 3


title: stationary_minus_rep2


title: Total mRNAs ZT48 control rep 1

description:
Total mRNAs (transcriptome)
TOT.T0.C1

source_name: Arabidopsis seedlings

value: Day 13 after sowing

tag: genotype

value: Control (22°C)


title: 2_M2 NT

description: SAMPLE 2


title: 5_A1 2+4

description: SAMPLE 5


title: EHF IKO 1

tag: age


title: 1_A1 NT

description: SAMPLE 1

tag: cell type


title: EHF IKO 2


title: stationary_plus_rep3

value: stationary plus


title: SB-1197 Tumor 16S rRNA

city: Stony Brook

first: Jinyu

last: Li

address: 101 Nicolls Rd

department: Cancer Center

institute: Stony Brook University

data_processing:
Salmon (version 0.10.2) was used to process RNA-seq data. Human genome assembly GRCh37 was used as reference. After alignment, DEseq2 was used to concatenate all individual samples and run comparative analysis. For 16S rRNA data, llumina Miseq paired-end reads were aligned to human reference genome hg19 with Bowtie2. SINA/SILVA classifier was used for classification. Operational taxonomic units (OTUs) were produced by binning sequences with identical taxonomic assignments.
Genome_build: hg19
Supplementary_files_format_and_content: concatenated results from Salmon for each sample, OTUs

source_name: colorectal

extract_protocol:
DNA and RNA was extracted from the archived frozen tissues using the Qiagen Allprep DNA/RNA/miRNA kits (Qiagen,  Hilden, Germany) according to the manufacturer’s protocol.  DNA and RNA was extracted from sections of FFPE tumor and non tumor samples using the Qiagen Allprep DNA/RNA FFPE (Qiagen, Hilden, Germany) kits according to the manufacturer’ protocol except that xylene was used to de-paraffinize the FFPE samples.
RNA sequence libraries were prepared with the Kapa RNA kit with RiboErase (Roche Sequencing and Life Science Kapa Biosystems, Wilmington, MA) according to the manufacturer’s protocol. 16S rRNA libraries were constructed by generating broad-range PCR amplicons using barcoded primers that target the V3V4 variable region of the 16S rRNA gene: primers 338F (5’ ACTCCTACGGGAGGCAGCAG) and 806R (5’ GGACTACHVGGGTWTCTAAT), Illumina paired-end sequencing was performed on the Miseq platform with versions v2.4 of the Miseq Control Software and of MiSeq Reporter, using a 600 cycle version 3 reagent kit.

tag: sample type

value: Tumor

tag: molecule subtype

value: rRNA


title: SB-1026 Non-tumor 16S rRNA

value: Non-tumor


title: Fruiting stage replicate 2 [NovaSeq]

description:
F2
mRNA
scRNA-seq
processed data file: raw_sc_Dicty_4_stage.tsv
processed data file: raw_sc_Dicty_3_stage.tsv
processed data file: raw_sc_Dicty_3_stage_ds.tsv
processed data file: normalized_sc_Dicty_4_stage.tsv
processed data file: normalized_sc_Dicty_3_stage.tsv
processed data file: normalized_sc_Dicty_3_stage_ds.tsv
processed data file: Metadata_Dicty_4_stage.tsv
processed data file: Metadata_Dicty_3_stage.tsv
processed data file: Metadata_Dicty_3_stage_ds.tsv


title: SB-1026 Tumor 16S rRNA


title: SB-912 Tumor 16S rRNA


title: stationary_plus_rep2


title: SB-950 Tumor 16S rRNA


title: SB-647 Non-tumor 16S rRNA


title: stationary_plus_rep1


title: SB-906 Non-tumor 16S rRNA


title: Control-OIL 4

value: Wild-type

value: Sunflower Oil


title: Control-OIL 3


title: exponential_minus_rep2

growth_protocol: grown in Luria-Bertani (LB) broth under aeration at 37 °C to an OD600 of 0.32

value: exponential minus


title: SB-597 Non-tumor 16S rRNA


title: SB-597 Tumor 16S rRNA


title: exponential_minus_rep1


title: SB-457 Tumor 16S rRNA (descending colon)


title: SB-457 Tumor 16S rRNA (ascending colon)


title: SB-460 Non-tumor 16S rRNA


title: SB-457 Non-tumor 16S rRNA (descending colon)


title: SB-457 Non-tumor 16S rRNA (ascending colon)


title: exponential_plus_rep2

value: exponential plus


title: exponential_plus_rep1


title: SB-110 Non-tumor 16S rRNA


title: SB-647 Tumor 16S rRNA


title: Ovotestis mix scRNA-seq

city: Wuhan

first: Xin

last: Wang

address: No.299 Bayi Road, Wuchang District

department: College of Life Sciences

institute: Wuhan University

data_processing:
Raw sequencing data were demultiplexed using CellRanger (CellRanger v 3.1.0) with default parameters  to get Fastq files.
Reads were aligned to reference genome (M_albus_1.0) using STAR of CellRanger.
Barcode and UMI counting were performed to generate feature-barcode matrices by CellRanger count application.
Single cell data was filtered with Seurat package (v3.1.0) with default parameters.
Genome_build: monopterus albus NCBI genome build 1.
Supplementary_files_format_and_content: Matrix table with raw gene UMIs for every gene and every cell.

organism: Monopterus albus

source_name: Ovotestis

extract_protocol:
Gonads were collected and washed. Samples were minced with sterilized scissors after washing, then were digested in collagenase type IV, trypsin, and Deoxyribonuclease I.  After stopping digestion,  single cells were obtained by strainers for library preparation with Chromium single-cell 3′ reagent kits V3.
Chromium single-cell 3′reagent kits V3 were used for scRNA-seq library preparation with Chromium Controller.

value: gonad

value: adult

value: untreated


title: SB-074 Non-tumor 16S rRNA


title: SB-086 Tumor 16S rRNA


title: Control-TMX 1

value: Colonic epithelium

value: 6 weeks

value: Tamoxifen


title: Control-TMX 3


title: Control-OIL 1


title: SB-912 Non-tumor 16S rRNA


title: SB-950 Non-tumor 16S rRNA


title: Control-TMX 2


title: SB-052 Tumor 16S rRNA


title: CHIR_SP_1

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

institute: Anhui University

data_processing:
Integrative Genomcs Viewer software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragment Per Kilobase of exon model per Million mapped reads(FPKM) were calculated using a standard protocol from GENERGY BIO company. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library of GENERGY BIO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: 46c mouse  embryonic stem cells

extract_protocol:
Culture medium were removed, washed by PBS, and RNA was harvested using Trizol reagent. MGI2000 was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard BGI protocols

treatment_protocol: 46C mouse ESCs cultured in serum-containing medium supplemented with 3 µM CHIR or 3 µM CHIR plus 8 µM Spautin-1 (CHIR_SP) for 24 h

value: embryonic stem cells


title: exponential_plus_rep3

value: E. coli K-12 stain MG1655


title: Control-TMX 4


title: SB-086 Non-tumor 16S rRNA


title: SB-052 Non-tumor 16S rRNA


title: SB-039 Tumor 16S rRNA


title: Control-OIL 2


title: SB-039 Non-tumor 16S rRNA


title: SB-014 Tumor 16S rRNA


title: CHIR_1

source_name: 46c mouse embryonic stem cells


title: SB-014 Non-tumor 16S rRNA


title: SB-074 Tumor 16S rRNA


title: NKT cell PLZFon Medp-Seq

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

data_processing:
Reads are aligned to the Mouse reference genome (mm10) using bwa, before identifying enriched regions and comparing them between the two conditions using the MeDIPS R package
The Integrative Genomics viewer (IGV; version mm10) was then used to present the data by converting the output from the analysis pipeline into browser extensible data (BED) files.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including values for each Sample and for indicated position on mouse chromosomes : row counts, RPKM and RMS.edgeR statistics are also provided (edgeR.logFC  edgeR.logCPM edgeR.p.value) for PLZF_ON vs WT samples

source_name: NKT cells

extract_protocol:
freshly sorted thymic CD1-tetramer positive NKT cells from PLZFON and WT mice were digested with GenDNA Digestion Buffer and Proteinase K for 12 to 18 h at 50 °C with shaking. Genomic DNA extracted from each sample was fragmented by sonication with a Diagenode Bioruptor to produce a median fragment length of 180-230 bp.
iDeal Library Preparation Kit (Diagenode)

value: NKT thymocytes


title: NKT cell WT Medip-Seq


title: NKT cell PLZFon Medp-Seq input


title: CHIR_SP_2


title: Liver_Low Isoleucine_Refed_s9NL1

city: Madison

first: Cara

middle: Leanne

last: Green

state: Wisconsin

address: 2214 Kendall Ave

department: Medicine

institute: University of Wisconsin-Madisin

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
9N

data_processing:
To remove any genes that exhibited no or a very low number of mapped reads, only genes that had more than 1 count per million in at least 4 samples across all treatments were retained for further analysis. This resulted in a total of 14211 unique genes. Raw counts were normalized using the trimmed mean of M values (TMM normalization) (Robinson and Oshlack 2010). Differential gene expression was modeled using the edgeR package (Robinson, McCarthy et al. 2010) in R (version 3.5.3) and pairwise comparisons were conducted between Fasted Control or Refed Ctrl AA and either Low AA or Low Ile. To control for type I errors, the Benjamini Hochberg adjusted p-value was used (5% FDR). We tested for over-representation of gene ontology (GO) terms or KEGG pathways in each comparison, using the limma package (Ritchie, Phipson et al. 2015).
Supplementary_files_format_and_content: raw counts and statistical analysis

source_name: Liver, Low Isoleucine Diet, Refed

growth_protocol: Diet started at 10 weeks of age

extract_protocol:
Liver tissues were harvested and snap frozen in liquid nitrogen. Transcriptional profiling: RNA was extracted from liver as previously described (Cummings et al., 2018). Concentration and purity of RNA was initially determined using a Nanodrop 2000c, and then submitted to the University of Wisconsin-Madison Biotechnology Center Gene Expression Center & DNA Sequencing Facility. RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide Rev. E.
Sample libraries were combined and striped across three lanes, the data from each lane was merged into a single sample file prior to expression estimation

treatment_protocol: Mice were placed on either a control or low isoleucine diet

value: liver

tag: Sex

value: male

value: 13 weeks

tag: diet

value: Low Isoleucine

tag: feeding state

value: Refed


title: NKT cell WT Medip-Seq input

tag: antibody


title: SB-008 Tumor 16S rRNA

value: Tumor

value: rRNA


title: Liver_Low Isoleucine_Refed_s9LL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
9L


title: SB-008 Non-tumor 16S rRNA

value: Non-tumor


title: leaf_21DAS_F1_rep3

city: Beijing

first: Wenwen

last: Liu

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
Quality control was conducted using fastp version 0.20.0 with the parameter length_required set to 150
Quantification of transcript expression was performed using Salmon version 1.0.0 against a reference transcript dataset for Arabidopsis, AtRTDv2_QUASI_19April2016 (Zhang et al., 2017) with parameters salmon index --type puff -k 31 and salmon quant -l IU --numBootstraps 30 --seqBias --validateMappings
The transcript-level quantifications were merged to the gene-level and then the length scaled transcripts per kilobase million (TPM) and estimated read counts were calculated for genes using the R package tximport version 1.12.3 with the option “lengthScaledTPM”
Genome_build: Arabidopsis Thaliana Reference Transcript Dataset 2 (AtRTD2), a comprehensive, non-redundant, high quality transcript reference dataset developed for RNA-seq analysis. It is generated by integration of transcript assemblies of ca. 8.5 billion pairs of reads from 285 RNA-seq data sets obtained from 129 RNA-seq libraries and merged along with the previous version, AtRTD (which covers TAIR10 transcripts and transcripts from Marquez et al., 2012), and Araport11 transcript assemblies
Supplementary_files_format_and_content: Matrix table with TPM value for every gene and every sample
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: seedling

growth_protocol: The plants were grown on MS plates containing 1% sucrose under long-day condition (16-h light with intensity of 18 W/m2 at 22 °C and 8-h dark at 18 °C) after surface-sterilization followed by 7-day stratification of the seeds.

extract_protocol:
flash frozen in liquid nitrogen, and RNA was extracted using an RNeasy Plant Mini Kit (Qiagen), followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Col-0 x Per-1 F1

value: the first true leaf

value: 21DAS (days after sowing)


title: leaf_21DAS_Per-1_rep1


title: leaf_21DAS_Per-1_rep3


title: leaf_21DAS_Per-1_rep2


title: SB-1230 Non-tumor 16S rRNA


title: SB-1260 Tumor 16S rRNA


title: Liver_Low Isoleucine_Refed_s9RLL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
9RL


title: SB-068 Non-tumor 16S rRNA


title: Liver_Control_Refed_s7NL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
7N

source_name: Liver, Control Diet, Refed

value: Control


title: CHIR_2


title: Liver_Low Isoleucine_Refed_s9RL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
9R


title: SB-1230 Tumor 16S rRNA


title: SB-1217 Non-tumor 16S rRNA


title: Liver_Control_Refed_s7LL1

description:
RNA quality was assayed using an Agilent RNA NanoChip, and stranded mRNA libraries with polyA enrichment were prepared as described in the Illumina TruSeq Stranded mRNA Sample Preparation Guide
7L


title: SB-1172 Tumor 16S rRNA


title: SB-1173 Non-tumor 16S rRNA


title: leaf_21DAS_F1_rep2


title: leaf_21DAS_F1_rep1


title: SB-1150 Non-tumor 16S rRNA


title: SB-1150 Tumor 16S rRNA


title: leaf_21DAS_Col-0_rep3


title: SB-002 Non-tumor 16S rRNA


title: SB-1140 Non-tumor 16S rRNA


title: SB-1260 Non-tumor 16S rRNA