title: H9 STB TEAD1 KO #3 RNA-seq rep 1

city: Saint Louis

first: Shuhua

last: Fu

state: MO

address: 660 S. Euclid Avenue Campus Box 8103

institute: Washington University in St. Louis

data_processing:
AIAP (v1.0) was applied, with command line as "bash ATAC_IAP_v1.1.sh -g hg38 -r PE", the pipeline does the alignment, peak-calling, normalized abundance measurements etc
RNA-seq analysis pipeline (https://github.com/Zhang-lab/RNA-seq_QC_analysis) was applied, with command line as "bash rna_v4.sh -g hg38 -r PE", the pipeline dose the alignment, read counting and gene and transcript quantification
RUVr was applied with k=1
Genome_build: hg38
Supplementary_files_format_and_content: AIAP (v1.0) was applied, with command line as "bash ATAC_IAP_v1.1.sh -g hg38 -r PE", the pipe does the alignment, peak-calling, normalized abundance measurements etc

source_name: human syncytiotrophoblast

extract_protocol:
Total RNA was isolated using the E.Z.N.A. total RNA kit I.
Library construction was performed using the SMARTer Directional cDNA Library Construction Kit

value: STB

value: human syncytiotrophoblast


title: H9 STB TEAD1 KO #3 RNA-seq rep 2

status: Public on Apr 11 2022

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue

tag: cell line


title: Tissue_Age_Associated_Me_20121

type: genomic

city: Philadelphia

first: Wanding

last: Zhou

state: PA

address: 3501 Civic Center Blvd

department: Pathology and Lab Medicine

institute: Children's Hospital of Philadelphia

description:
Tissue Biology
204875570048_R06C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
SeSAMe software v1.10
20210916_GEO_processed_matrix.csv (Normalized average Beta)
20210916_GEO_signal_intensity_matrix.csv (Unmethylated and methylated signal intensities)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: Liver, Mouse DNA, Tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated from tissue samples using the AllPrep DNA/RNA Mini Kit (QIAGEN)

tag: Sex

value: Male

tag: site

value: Lab 1

tag: strain

value: Liver

tag: sorted cell type

tag: treatment

tag: pathology

value: Normal


title: BR298 Pre-Tx

city: Pittsburgh

first: Jishnu

last: Das

address: 203 Lothrop Street

department: Immunology

institute: University of Pittsburgh

data_processing:
RNA libraries generated using TruSeq Stranded Total RNA with Ribo-Zero Globin (Illumina, San Diego, CA) according to the manufacturer’s protocol. The libraries were validated using Fragment Analyzer (Agilent, Santa Clara, CA) and sequenced using Nextseq 500 platform (Illumina, San Diego, CA) to generate 75 bp paired end reads, up to 40 million reads per sample
The generated reads were pre-processed using FastQC (v0.10.1) and aligned to the human reference gtf annotation file ( GRCh37.68 genome using STAR)
Transcript abundances were quantified and normalized using RSEM.
Assembly: grch37.68
Supplementary files format and content: genes.results provides gene count matrix
Supplementary files format and content: isoforms.results provides isoform count matrix

source_name: whole blood (PBMC)

extract_protocol:
Trizol.
Illumina sequencing protocols.

tag: clinical metadata (time-point)

value: Pre-Tx


title: Tissue_Age_Associated_Me_20187

description:
Tissue Biology
204875570045_R04C02

value: Female


title: H9 STB TEAD1 KO #2 RNA-seq rep 1


title: Tissue_Age_Associated_Me_20170

description:
Tissue Biology
204875570023_R06C01


title: H9 STB TEAD1 KO #1 RNA-seq rep 2


title: BR309 Pre-Tx


title: BR288 Pre-Tx


title: Tissue_Age_Associated_Me_20071

description:
Tissue Biology
204875570045_R02C01


title: H9 STB TEAD1 KO #2 RNA-seq rep 2


title: BR334 Pre-Tx


title: BR338 Pre-Tx


title: BR287 Pre-Tx


title: BR337 Pre-Tx


title: H9 STB TEAD1 KO #1 RNA-seq rep 1


title: BR335 Pre-Tx


title: BR339 Pre-Tx


title: Tissue_Age_Associated_Me_20101

description:
Tissue Biology
204875570014_R05C02


title: BR323 Pre-Tx


title: BR331 Pre-Tx


title: Developmental_Biology_22292

description:
Tissue Biology
204879580022_R03C02

source_name: Fetal Liver, Embryonic DNA, Tissue

value: Fetal Liver


title: H9 STB WT RNA-seq rep 2


title: Developmental_Biology_22300

description:
Tissue Biology
204879580043_R05C01


title: BR311 Pre-Tx


title: BR322 Pre-Tx


title: H9 STB WT RNA-seq rep 1


title: Developmental_Biology_22276

description:
Tissue Biology
204879580021_R05C01


title: Developmental_Biology_22283

description:
Tissue Biology
204879580021_R06C02


title: BR324 Pre-Tx


title: BR314 Pre-Tx


title: BR313 Pre-Tx


title: BR347 Pre-Tx


title: H9 hTSC TEAD1 KO #3 RNA-seq rep 2

source_name: human trophoblast stem cells

value: hTSCs

value: human trophoblast stem cells


title: Developmental_Biology_22270

description:
Tissue Biology
204879580020_R05C02


title: H9 hTSC TEAD1 KO #3 RNA-seq rep 1


title: BR312 Pre-Tx


title: H9 hTSC TEAD1 KO #2 RNA-seq rep 2


title: BR305 Pre-Tx


title: BR303 Pre-Tx


title: BR302 Pre-Tx


title: BR304 Pre-Tx


title: BR294 Pre-Tx


title: Developmental_Biology_22256

description:
Tissue Biology
204879580009_R03C02

value: Mixed


title: Developmental_Biology_22250

description:
Tissue Biology
204879580009_R03C01


title: Developmental_Biology_22244

description:
Tissue Biology
204879580008_R03C02


title: H9 hTSC TEAD1 KO #1 RNA-seq rep 2


title: H9 hTSC TEAD1 KO #2 RNA-seq rep 1


title: H9 hTSC WT RNA-seq rep 2


title: H9 hTSC TEAD1 KO #1 RNA-seq rep 1


title: H9 hTSC WT RNA-seq rep 1


title: Treated_3

city: Houston

first: Xin

last: Li

state: TX

address: One Baylor Plz

department: Pharmacology & Chemical Biology

institute: Baylor College of Medicine

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
FeatureCounts was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and every sample
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Molm13 cells

growth_protocol: Molm13 cells (105 cells/ml) were cultured in RPMI-1640 medium containing 10%FBS and 1% pen-strep cocktail

extract_protocol:
RNA was extracted using RNeasy mini kit (#74104, Qiagen) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Molm13 cells were treated with vector/compound 1 for 4 days in control/treatment group.

value: Blood

value: MLL-r leukemia cells

value: Treated


title: BR292 Pre-Tx


title: BR291 Pre-Tx


title: BR293 Pre-Tx


title: BR261 Pre-Tx


title: Treated_2


title: BR259 Pre-Tx


title: BR255 Pre-Tx


title: BR254 Pre-Tx


title: BR256 Pre-Tx


title: BR260 Pre-Tx


title: BR258 Pre-Tx


title: BR262 Pre-Tx


title: BR306 Pre-Tx


title: BR253 Pre-Tx


title: Developmental_Biology_22262

description:
Tissue Biology
204879580020_R03C01


title: BR252 Pre-Tx


title: BR251 Pre-Tx


title: Untreated_3

value: Untreated


title: Treated_1


title: Untreated_2


title: BR250 Pre-Tx


title: BR249 Pre-Tx


title: BR248 Pre-Tx


title: BR247 Pre-Tx


title: BR245 Pre-Tx


title: BR246 Pre-Tx


title: BR244 Pre-Tx


title: BR243 Pre-Tx


title: NKG2D--SSD3

city: Zurich

first: Lukas

middle: Simon

last: Rindlisbacher

address: Winterthurerstrasse 190

department: Experimental Immunology

country: Switzerland

institute: University Zurich

description:
Klrk1 -/- fed with SSD
NKG2D--SSD3 [normalized count]

data_processing:
Quality control with Fastqc and FastqScreen
Alignment using STAR aligner
Read count extraction and normalization were performed using FeatureCountsApp
Differential gene expression analysis with DESeq2
Assembly: GENCODE/GRCm39/Annotation/Release_M26-2021-04-20
Supplementary files format and content: tab-delimited .txt file including normalized counts for each sample

source_name: Liver

extract_protocol:
Total RNA of whole liver was isolated using the Qiagen RNeasy Micro kit according to the manufacturers’ protocol.   The Novaseq 6000 (Illumina, Inc, California, USA) was used for cluster generation and sequencing according to standard protocols. Sequencing was single end 100bp.
Illumina Truseq mRNA following manufactor's protocol

value: Whole liver isolates

tag: genotype

value: Klrk1 KO

value: SSD


title: NKG2D--SSD2

description:
Klrk1 -/- fed with SSD
NKG2D--SSD2 [normalized count]


title: BR242 Pre-Tx


title: placenta, SARS #3

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw read counts were quantified using HTSeq-count v0.11.2.
For sample 27-32, the raw gene counts were down-sampled such that the human gene counts are comparable in these samples.
Genome_build: hg19
Supplementary_files_format_and_content: plain txt file storing read counts per gene per sample

source_name: placenta

growth_protocol: Term placentas were digested in Accutase into 50-100 cell clusters, RBCs were lysed, and clusters were cultured on Matrigel coated plates in DMEM+10%FBS+1%Pen/strep+1%Glutamax

extract_protocol:
For FFPE placenta samples, total RNA samples were prepared using the Qiagen RNeasy FFPE kit (Cat# 38673604), followed by DNaseI treatment using manufacturer’s instructions. For ex vivo placental cell clusters, total RNA was extracted using Trizol (Thermo Fisher Scientific) followed by ezDNAse treatment (Thermo Fisher Scientific) per manufacturer’s instructions. Ex vivo placental cell clusters were further cleaned using RNAClean XP beads (Beckman Coutler) per manufacturer’s instructions.
RNAseq libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

treatment_protocol: Placental cell clusters were treated with MOCK or SARS-CoV-2 (isolate USA-WA1/2020; MOI=1) for 24 hours

value: Term placenta digested into cell clusters ex vivo

tag: maternal health status

value: COVID-, healthy


title: placenta, SARS #2


title: placenta, SARS #1


title: NKG2D--NCD3

description:
Klrk1 -/- fed with NCD
NKG2D--NCD3 [normalized count]

value: Liver

value: NCD


title: BR240 Pre-Tx

value: Pre-Tx


title: placenta, MOCK #3

value: MOCK


title: NKG2D--NCD2

description:
Klrk1 -/- fed with NCD
NKG2D--NCD2 [normalized count]


title: Untreated_1


title: placenta, MOCK #2


title: H9 STB TEAD1 KO #3 ATAC-seq rep 2

library_source: genomic

extract_protocol:
ATAC-seq: ATAC-seq was performed as previously described with minor modifications. Cells were harvested by TrypLE Express dissociation and centrifuged at 500 RCF for 5 minutes at 4°C. The supernatant was aspirated. Cells were washed once with cold PBS. Cell pellets were then lysed in 100 µL ATAC-seq RSB [10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2] containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin by pipetting up and down and incubating on ice for 3 minutes. 1 mL of ATAC-seq RSB containing 0.1% Tween-20 was added and mixed with the lysis reaction. Nuclei were then pelleted by centrifuging at 800 RCF for 5 minutes at 4°C. Supernatant was removed, and the nuclear pellets were resuspended in 20 µL 2x TD buffer [20mM Tris pH 7.6, 10mM MgCl2, 20% Dimethyl Formamide]. Nuclei were counted, and 50,000 counted nuclei were then transferred to a tube with 2x TD buffer filled up to 25 µL. 25 µL of transposition mix [2.5 µL Transposase (100nM final) (Illunina, 20034197, 16.5 µL PBS, 0.5 µL 1% Digitonin, 0.5 µL 10% Tween-20, 5 µL H2O) was then added. Transposition reactions were mixed and incubated at 37°C for 30 minutes with gentle tapping every 10 minutes. Reactions were cleaned up with the Zymo DNA Clean and Concentrator-5 kit (Zymo Research, D4014).
The ATAC-seq library was prepared by amplifying for 9 cycles on a PCR machine. The PCR reaction was purified with Ampure XP beads using double size selection following the manufacturer’s protocol, in which 27.5 µL beads (0.55X sample volume) and 50 µL beads (1.55X sample volume) were used based on 50 µL PCR reaction. The ATAC-seq libraries were quantitated by Qubit assays and sequenced on an Illumina NextSeq platform.

value: STB

value: human syncytiotrophoblast


title: SiHa cells, shSYT7, 1

type: RNA

city: Nanning

first: Junying

address: 6 Shuangyong Road,

country: China

institute: First Affiliated Hospital of Guangxi Medical University

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing:
RMA normalization.
After examining signal histogram and relative log expression plot as sufficient quality control, we performed the correlation analysis, principal component analysis, and differential expression analysis, such as volcano plot, hierarchical clustering, etc.

label: biotin

source_name: SiHa cells, shSYT7

label_protocol: Standard Affymetrix protocol.

growth_protocol: a 5% CO2 incubator at 37 °C.

extract_protocol: Trizol (Sigma) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Lentiviral shRNA vectors targeting SYT7 (shSYT7) were constructed by Shanghai Biosciences Co. Ltd. (Shanghai, China). The SYT7 targeting sequences were synthesized and cloned into the backbone vector BR-V108 (Shanghai Biosciences Co. Ltd., Shanghai, China). 293T cells (Supplied by Chinese Academy of Science) seeded in a 10-cm dish were used for co-transfection with 3rd generation packaging system to produce the lentivirus. Briefly, BR-V108-RNAi (10 μg), pHelper X2 (7.5 μg), and pHelper 2.G (5 μg) were added and resuspended in 500 μL Opti-MEM R1 media and keep at room temperature for 5 mins. Meanwhile, 60 μL of transfection reagent PEI (PEI 25K™, CAS No. 23966-1) was added to another 500 μL Opti-MEM R1 media for 5 mins room temperature incubation. Then the two combinations were mixed and rest at room temperature for another 20 mins before adding to 293T cells for virus packaging under 37℃ incubation which last for 48-72h. Virus was harvested by ultracentrifugation. The negative control group was transfected with negative lentivirus shCtrl, while the test group (shSYT7) was transfected with shSYT7. Fresh media with virus was used to replace previous media and incubate at 37℃ for 18-20h of lentiviral infection, then refresh media with normal media without virus. After 72 h of lentiviral infection, the expression of the green fluorescent protein (GFP) was examined in SiHa and HeLa cells under a fluorescence microscope to evaluate the infection efficiency. The MOI of transfection is 10/HeLa or SiHa.

value: SiHa

value: cervical cancer cells

value: SYT7 knockdown


title: SiHa cells, shCtrl, 2

source_name: SiHa cells, shCtrl

value: shCtrl

value: control


title: SiHa cells, shCtrl, 5


title: SiHa cells, shCtrl, 1


title: SiHa cells, shSYT7, 3


title: NKG2D--NCD1

description:
Klrk1 -/- fed with NCD
NKG2D--NCD1 [normalized count]


title: SiHa cells, shSYT7, 2


title: H9 STB TEAD1 KO #3 ATAC-seq rep 1


title: NKG2D--SSD1

description:
Klrk1 -/- fed with SSD
NKG2D--SSD1 [normalized count]


title: placenta, MOCK #1


title: H9 STB TEAD1 KO #2 ATAC-seq rep 1


title: NKG2D--NCD4

description:
Klrk1 -/- fed with NCD
NKG2D--NCD4 [normalized count]


title: H9 STB WT ATAC-seq rep 2


title: H9 STB TEAD1 KO #2 ATAC-seq rep 2


title: placenta, I_4

value: FFPE placenta

value: COVID-, other inflammatory pathology


title: H9 STB WT ATAC-seq rep 1


title: BR241 Pre-Tx


title: C57BL6J-SSD4

description:
C57BL6J fed with SSD
C57BL6J---SSD4 [normalized count]

value: Whole liver isolates

value: WT


title: BR181 Pre-Tx


title: placenta, I_3


title: C57BL6J-SSD3

description:
C57BL6J fed with SSD
C57BL6J-SSD3 [normalized count]

value: SSD


title: H9 EVT WT ATAC-seq rep 2

source_name: human extravillous trophoblast

value: EVT

value: human extravillous trophoblast


title: H9 EVT TEAD1 KO #2 ATAC-seq rep 1


title: C57BL6J-SSD5

description:
C57BL6J fed with SSD
C57BL6J-SSD5 [normalized count]

value: Liver


title: H9 EVT TEAD1 KO #2 RNA-seq rep 2


title: H9 EVT TEAD1 KO #2 RNA-seq rep 1


title: H9 EVT TEAD1 KO #3 RNA-seq rep 1


title: placenta, I_1


title: placenta, I_2


title: C57BL6J-SSD2

description:
C57BL6J fed with SSD
C57BL6J-SSD2 [normalized count]


title: placenta, C_4

value: COVID-, healthy


title: C57BL6J-SSD1

description:
C57BL6J fed with SSD
C57BL6J-SSD1 [normalized count]


title: H9 EVT TEAD1 KO #3 RNA-seq rep 2


title: H9 EVT TEAD1 KO #1 RNA-seq rep 1


title: C57BL6J-NCD5

description:
C57BL6J fed with NCD
C57BL6J-NCD5 [normalized count]

value: NCD


title: H9 EVT TEAD1 KO #1 RNA-seq rep 2


title: C57BL6J-NCD3

description:
C57BL6J fed with NCD
C57BL6J-NCD3 [normalized count]


title: placenta, C_2


title: H9 EVT TEAD1 KO #3 ATAC-seq rep 1


title: H9 EVT WT RNA-seq rep 1


title: placenta, C_1


title: H9 hTSC TEAD1 KO #3 ATAC-seq rep 1

value: hTSCs

value: human trophoblast stem cells


title: C57BL6J-NCD1

description:
C57BL6J fed with NCD
C57BL6J-NCD1 [normalized count]


title: H9 hTSC TEAD1 KO #2 ATAC-seq rep 2


title: H9 hTSC TEAD1 KO #2 ATAC-seq rep 1


title: H9 hTSC WT ATAC-seq rep 2


title: PA M5

first: John

last: Morrow

address: 650 W 168th Street

department: Medicine

institute: College of Physicians and Surgeons of Columbia University

data_processing:
raw sequencing reads were mapped to the mouse genome version GRCm39 (m27) using Salmon (Version 1.5.1) to obtain transcript abundance counts
transcript abundance counts were condensed to the gene level using tximport (version 1.20.0)
DESeq2 (version 1.32.0) was used on genes with more than 10 counts to do differential gene expression analysis
PCA using the top 5000 genes with large CV was done to detect outliers for samples with >6 median absolute deviations from the median
Assembly: GRCm39 (M27)
Supplementary files format and content: .txt files with counts for each sample

source_name: heart

extract_protocol:
Cardiac samples were preserved in RNAlater, frozen, and shipped to Genewiz (South Plainfield, NJ) on dry ice. RNA was extracted and reverse-transcribed after polyA selection to complementary DNA for sequencing on an Illumina NovaSeq platform
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

tag: age

value: 12 weeks

value: wild type


title: H9 EVT WT ATAC-seq rep 1


title: placenta, C_3


title: H9 EVT WT RNA-seq rep 2


title: H9 hTSC WT ATAC-seq rep 1


title: AN naïve hPSC ATAC-seq rep 2

data_processing:
AIAP (v1.0) was applied, with command line as "bash ATAC_IAP_v1.1.sh -g hg38 -r PE", the pipe does the alignment, peak-calling, normalized abundance measurements etc
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: bedGraph

source_name: human embryonic stem cells

value: hPSCs

value: human embryonic stem cells

value: AN


title: PA M3


title: H9 hTSC TEAD1 KO #3 ATAC-seq rep 2


title: placenta, P_14

value: FFPE placenta

value: COVID+


title: PA M2


title: placenta, P_13


title: PA M4


title: AN naïve hPSC ATAC-seq rep 1


title: placenta, P_11


title: C57BL6J-NCD2

description:
C57BL6J fed with NCD
C57BL6J-NCD2 [normalized count]

value: Whole liver isolates

value: WT


title: placenta, P_12


title: H9 naïve hPSC ATAC-seq rep 2


title: PA M1


title: H9 naïve hPSC ATAC-seq rep 1


title: placenta, P_10


title: U251 cells 10nM (-)-SDS-1-021 treated, collected at 6h, polysomal RNA, biological replicate 2

city: Bethesda

first: Uma

middle: T

last: Shankavaram

state: MD

address: 9000 Rockville Pike

department: NCI

institute: NIH

data_processing:
RSEM
Assembly: hg38

molecule: polyA RNA

source_name: U251 glioblastoma cell line

growth_protocol: U251 cell line was  maintained in DMEM (Invitrogen) + 10% FBS (Invitrogen) and grown at 37°C, 5%CO2/95% air

extract_protocol:
Cells were incubated in 0.1 mg of cycloheximide/mL for 10 minutes before collection. Cytoplasmic RNA was obtained by lysing cells in 1.5 mL of polysome buffer [15 mmol/L Tris-HCl (pH 7.5), 300 mmol/L NaCl, 15 mmol/L MgCl2, 1% Triton X100, 0.1 mg/mL cycloheximide, and 1 mg/mL heparin]. After 10 minutes on ice, lysates were centrifuged (10,000 × g for 10 minutes), and the resulting cytosolic supernatant was layered onto a 10% to 50% sucrose gradient. Gradients were then centrifuged at 35,000 rpm for 3 hours at 4°C in an SW41Ti rotor and polysome-bound fractions were collected using an ISCO Density Gradient Fractionation System (ISCO, Lincoln, NE) with continuous monitoring based on A254. The RNA in each fraction was extracted using TRIzol LS (Invitrogen).  Excess heparin was removed by two rounds of LiCl precipitation.  The resulting RNA was DNase digested using the on-column RNA clean up protocol with the QIAGEN RNeasy Mini Kit.
200ng RNA was used as the input for mRNA capture with oligo-dT coated magnetic beads.  The mRNA was fragmented followed by random-primed cDNA synthesis. The resulting double-strand cDNA was used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification to generate a sequencing ready library.  The final library was then quantitated by qPCR before cluster generation and sequencing on the Illumina HiSeq4000 sequencer.

treatment_protocol: Cells were grown to ∼80% confluence in 150-mm2 tissue culture dishes and treated with 10nM (-)-SDS-1-021 or an equivalent volume of vehicle (DMSO).

value: Glioblastoma


title: U251 cells 10nM (-)-SDS-1-021 treated, collected at 6h, polysomal RNA, biological replicate 3


title: U251 cells vehicle treated, collected at 6h, polysomal RNA, biological replicate 3


title: PA F5


title: U251 cells 10nM (-)-SDS-1-021 treated, collected at 6h, polysomal RNA, biological replicate 1


title: U251 cells vehicle treated, collected at 6h, polysomal RNA, biological replicate 2


title: placenta, P_15


title: U251 cells vehicle treated, collected at 6h, polysomal RNA, biological replicate 1


title: placenta, P_9


title: PA F4


title: PW030-705 (NextSeq)

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

data_processing:
Raw data obtained from the Illumina NextSeq 500 was trimmed and aligned as described in Yuan et al (2018). For each read with a unique, strand specific alignment to exonic sequence, we constructed an address comprised of the CB, UMI barcode, and gene identifier. Raw data obtained from the Illumina NovaSeq 6000 was first corrected for index swapping to avoid cross-talk between sample index sequences as described in Szabo et al. 2019. The resulting address file only contained the addresses from reads with corresponding single index. We combined the addresses from the NextSeq 500 and the corrected addresses from the NovaSeq 6000 to generate a digital gene expression matrix and filter CBs as described previously (Yuan et al. 2018). Briefly, reads with the same CB, UMI and aligned gene were collapsed and sequencing errors in the CB and UMI were corrected to generate a preliminary matrix of molecular counts for each cell. Then we removed CBs 1) with excessive (> 10%) molecules expressed from mitochondrial genome, 2) where the ratio of molecules aligning to whole gene bodies (including introns) to molecules aligning exclusively to exons was >1.5, and 3) for which the average number of reads per molecule or average number of molecules per gene deviated by >2.5 standard deviations from the mean for a given sample.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files that contain the gene expression counts of each individual cell.

source_name: Human glioma slice culture treated with RO4929097 (NextSeq)

growth_protocol: Acute slices were generated from a surgical resection specimen collected from an adult patient with radiographic and intraoperative histopathological characteristics consistent with primary HGG, (the final diagnosis was Glioblastoma, IDH-wildtype, WHO grades IV). The surgically excised specimen was immediately placed in a sterile 50mL canonical tube ¾ filled ice-cold high-sucrose low-sodium artificial cerebrospinal fluid (ACSF) solution containing 210 mM sucrose, 10 mM glucose, 2.5 mM KCl, 1.25 mM NaH2PO4, 0.5 mM CaCl2, 7 mM MgCl2 and 26 mM NaHCO3, and were kept on ice for transportation (transit time was approximately 10 minutes from operating room to laboratory). Preparation of ex vivo tissue slices was modified from methods described previously (Stoppini et al. 1991 & Gähwiler et al. 1997 Köhlinge et al. 1999, Shimizu et al. 2011, and Ting et al. 2018). Briefly, the tissue specimen was placed in ice-cold ACSF solution and 500 um slices were generated using a tissue chopper (McIlwain TC752). The slices were immediately transferred to the ice-cold ACSF solution in 6-well plates using a sterile plastic Pasteur pipette half filled with ice-cold ACSF solution followed by a 15 minutes recovery in ACSF to reach room temperature. Slices were then placed on top of a porous membrane insert (0.4 um, Millipore). The membrane inserts were placed into 6-well plates containing 1.5 ml maintenance medium consisted of F12/DMEM (Gibco) supplemented with N-2 Supplement (Gibco) and 1% penicillin/streptomycin (Sigma). To ensure proper diffusion into the slice, culture medium was placed under the membrane insert without bubbles. A drop of 10 ul of culture medium was added directly on top of each slice to prevent the slice surface from drying.

extract_protocol:
Collected slices were dissociated using Adult brain dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions.
Dissociated cells from each slice were subjected to microwell-based single-cell RNA-seq (Yuan & Sims 2016) as previously described (Yuan et al. 2018) with modifications to the reverse transcription step and the sequencing method. Once the RNA-capture step was finished, sealing oil was flushed out of the devices by pipetting 1ml wash buffer supplemented with 0.04 U/μl RNase inhibitor (Thermo Fisher Scientific) and then beads were extracted from the device and resuspended in 200 ul of reverse transcription mixture. Bead-suspensions were divided into 50ul aliquots and placed into PCR tubes (Corning) followed by incubation at 25°C for 30 min and at 42°C for 90 min in a thermocycler. For sequencing, we pooled all libraries derived from the same donor, each of which was barcoded with a unique Illumina sample index. The pooled library sequenced on 1) an Illumina NextSeq 500 with an 8-base index read, a 21-base read 1 containing cell-identifying barcodes (CB) and unique molecular identifiers (UMIs), and a 63-base read 2 containing the transcript sequence, and 2) an Illumina NovaSeq 6000 with an 8-base index read, a 26-base read 1 containing CB and UMI, and a 91-base read 2 containing the transcript sequence.\

treatment_protocol: The slices were first rested for 6 hours with the maintenance medium in a humidified incubator at 37℃ and 5% CO2. Then, the medium was replaced with pre-warmed medium containing 5 uM Etoposide (Tocris Bioscience, 100 mM stock) or 50 nM RO4929097 (Selleck Chem, 10 mM stock), or corresponding volume of vehicle (DMSO). Slices were cultured with the treatment medium in a humidified incubator at 37℃ and 5% CO2 for 18 hrs before being collected for dissociation.

tag: drug treatment

value: glioma slice culture


title: PW030-703 (NextSeq)

source_name: Human glioma slice culture treated with etoposide (NextSeq)

value: Etoposide 5 uM


title: PA F3


title: placenta, P_8


title: placenta, P_7


title: PA F2


title: placenta, P_6


title: axe1-5 HK27me3 -JA 2

city: Egham

first: Alessandra

last: Devoto

address: Egham Hill

department: Biological Sciences

country: United Kingdom

institute: Royal Holloway, University of London

data_processing:
fastq files trimmed using Trimmomatic (version 0.36.5 for Galaxy) using the sliding window option with default parameters
Reads were aligned to the TAIR10 assembly of the A. thaliana genome with Bowtie for Illumina with default parameters
Peak calling of ChIP-enriched fragments was performed using MACS (version 1.4.2) against input reads. The effective genome size was set to 1.35e+08 with lower and upper mfold bound limits of 5 and 50, respectively
Genome_build: TAIR10
Supplementary_files_format_and_content: Peak txt files

organism: Arabidopsis thaliana

source_name: Whole seedlings

growth_protocol: A. thaliana seedlings were stratified in for 3 days at 4ºC in the dark and plated onto 1% Murashige & Skoog medium supplemented with 1% sucrose, 0.8% phytoagar and buffered to pH 5.8 under 16hr light/8 hr dark cycles for 12 days at 22ºC

extract_protocol:
Cross-linking of DNA-protein performed on fresh tissue and then sonicated to approx. 200 bp
ChIP DNA libraries were prepared according to Illumina TruSeq® ChIP Sample Preparation Kit (Part No: IP-202-1012). The protocol was optimized for 5–10 ng input ChIP DNA with an average final library size of 350-500 bp

treatment_protocol: 12 days old seedlings were transferred to plates containing 50 µM MeJA or mock plates without MeJA and sampled after 3 hours

value: Whole seedlings

value: mock

tag: chip antibody

value: H3K27me3 (Sigma Aldrich 07-449)


title: PW030-701 (NextSeq)

source_name: Human glioma slice culture treated with vehicle (DMSO) (NextSeq)

value: DMSO (vehicle control)


title: PA F1

value: heart


title: placenta, P_4


title: Chow M5

value: 12 weeks


title: PW030-702 (NextSeq)


title: placenta, P_3


title: placenta, P_2


title: DR5 HK27me3 -JA 2


title: DR5 HK27me3 +JA 2

value: jasmonate


title: Chow M3

value: wild type


title: placenta, P_1


title: Chow M1


title: SKOV3nACs1

city: Hangzhou

first: Yiyan

last: Zheng

address: Zhiqiang Road 428

institute: Westlake Laboratory of Life Sciences and Biomedicine

description: Next generation RNA-seq data

data_processing:
trim_galore (version 0.6.4)
bowtie2 (version 2.4.2)
hisat2 (version 2.2.0)
htseq-count (version 0.13.5)
edgeR
Assembly: Human: GRCh38.104

source_name: ovarian cancer cell line

growth_protocol: Ovarian cancer cell lines were cultured with RPMI-1640 media supplemented with 10% FCS, and 5% Penicillin-Streptavidin.

extract_protocol:
Cells were scrapped from the 6 well plate and the total RNA was extracted with a Qiagen RNeasy Plus mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were grown in a 6 well tissue culture plate from Corning at approximately 80% confluency before harvested for total RNA extraction.

value: ovarian cancer cell line

tag: genotype/variation

value: sparsely grown SKOV3 cells with nAC probe


title: SKOV3nAC3

description: Next generation RNA-seq data

value: confluent SKOV3 with nAC probe


title: SKOV3nAC1

description: Next generation RNA-seq data


title: SKOV3nACs2

description: Next generation RNA-seq data


title: SKOV3nAC2

description: Next generation RNA-seq data


title: SKOV3nACs3

description: Next generation RNA-seq data


title: axe1-5 H4ac -JA 2

value: H4ac (Sigma Aldrich 06-866)


title: OVCA4322

description: Next generation RNA-seq data

value: OVCA432 cell without nAC probe


title: OVCA4323

description: Next generation RNA-seq data


title: axe1-5 H4ac +JA 2


title: placenta, P_5

value: FFPE placenta

value: COVID+


title: placenta, H_2


title: Chow F5


title: OVCA4321

description: Next generation RNA-seq data


title: axe1-5 HK27me3 +JA 2


title: Chow M4


title: OVCA432nAC3

description: Next generation RNA-seq data

value: OVCA432 cell with nAC probe expression


title: placenta, H_1


title: Healthy

city: Singapore

first: Christine

last: Cheung

state: Singapore

address: 59 Nanyang Drive

country: Singapore

institute: Lee Kong Chian School of Medicine

data_processing:
Raw sequencing data was also processed by NovogeneAIT Genomics (Singapore) using CellRanger (10x Genomics) with reads mapped to the human genome assembly (GRCh38).
Genome_build: GRCh38
Supplementary_files_format_and_content: Filtered feature-barcode matrices containing detected cellular barcodes
Supplementary_files_format_and_content: Feature.tsv and barcode.tsv files containing corresponding row and column indices for respenctive data matrix

source_name: PBMC

extract_protocol:
Cryopreserved PBMCs were thawed in a 37C water bath and resuspended in Iscove’s Modified Dulbecco’s Medium (Gibco) supplemented with 10% heat inactivated FBS. PBMCs were then pelleted out of solution by centrifuging at 300g for 5 minutes. Cell number and viability percentage were determined using Trypan blue and an automated cell counter (Countess II, Thermo Fisher Scientific). NAFLD PBMCs were pooled from 2 NAFLD patients while healthy PBMCs were pooled from 4 healthy individuals with each individual contributing about 200,000 cells each. Final PBMCs pools were pelleted down at 300g for 5 minutes and resuspended in PBS with 0.04% BSA to give a final concentration of ~1200 cells/ul.
Cell suspensions were then loaded onto 10X Genomics Chromium Controller chip by facility personnel at Single-cell Omics Centre (SCOC), Genome Institute Singapore (GIS). NAFLD and healthy PBMC pools were prepared as separate scRNA-seq libraries using Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) by SCOC GIS and the final ready-to-sequence libraries were handed over with quantification and quality assessment reports from Bioanalyzer Agilent 2100 using the High Sensitivity DNA chip (Agilent Genomics). NAFLD and healthy PBMC libraries were pooled equimolarly and sent for sequencing by NovogeneAIT Genomics (Singapore).

value: Peripheral blood mononuclear cells


title: DR5 H4ac +JA 2

value: Whole seedlings


title: DR5 H4ac -JA 2

value: mock


title: Chow M2


title: OVCA432nAC2

description: Next generation RNA-seq data


title: FLV


title: axe1-5 input -JA 2


title: Chow F3


title: Chow F2


title: Chow F1


title: axe1-5 input +JA 2


title: DR5 input -JA 2


title: OVCA432nAC1

description: Next generation RNA-seq data


title: H9 hTSC TEAD1 CUT&Tag rep 3

data_processing:
Library strategy: CUT&Tag
AIAP (v1.0) was applied, with command line as "bash ATAC_IAP_v1.1.sh -g hg38 -r PE", the pipe does the alignment, peak-calling, normalized abundance measurements etc
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: bedGraph

extract_protocol: CUT&Tag: CUT&Tag was performed as previously described. Briefly, 200,000 cells per sample were washed in Wash Buffer [1 mL 1 M HEPES pH 7.5 (Sigma Aldrich, H3375), 1.5 mL 5 M NaCl (Sigma Aldrich, S5150), 12.5 μL 2 M Spermidine (Sigma Aldrich, S2501), 1 Roche Complete Protease Inhibitor EDTA-Free tablet (Sigma Aldrich, 5056489001), and bring the final volume to 50 mL with dH2O], captured with Concanavalin A beads (Bangs Laboratories, BP531), and incubated with primary antibody at 4°C overnight. The cells were then incubated with secondary antibody at room temperature for an hour. The following antibodies were used: TEAD1 (Cell Signaling Technology, 12292S); guinea pig-anti-rabbit (Antibodies online, ABIN101961). After washing off the unbound antibodies with Dig-Wash Buffer [mix 400 μL 5% Digitonin (EMD Millipore, 300410) with 40 mL Wash Buffer], the pA-Tn5 adapter complex (kindly provided by Dr. Steve Henikoff) were added at 1:200 and incubated at room temperature for an hour. The cells were washed again with Dig-300 Buffer [1 mL 1 M HEPES pH 7.5, 3 mL 5 M NaCl, 12.5 μL 2 M Spermidine, 100 μL 5% Digitonin, 1 Roche Complete Protease In-hibitor EDTA-Free tablet, and bring the final volume to 50 mL with dH2O], and incubat-ed in 300 μL Tagmentation Buffer [5 mL Dig-300 Buffer and 50 μL 1 M MgCl2 (Sigma Aldrich, M8266)] per sample at 37°C for an hour. The reaction was stopped and the DNA solubilized by adding 10 μL 0.5 M EDTA (Research Organics, 3002E), 3 μL 10% SDS (Sigma Aldrich, L4509), and 2.5 μL Proteinase K (Thermo Fisher, EO0492) per sample, and incubated at 50°C for an hour. The DNA was then extracted, excess RNA digested with RNase A (Thermo Fisher, EN0531), and PCR amplified with i5 and i7 in-dexing primers. The PCR product was cleaned up with AMPure XP beads, and the size distribution and concentration were confirmed using Tapestation.

value: hTSCs

value: human trophoblast


title: H9 hTSC TEAD1 CUT&Tag rep 2


title: Jade2_KO4_RNA_Seq

city: Beijing

first: yongqing

last: liu

address: 38 Xue Yuan Road

department: Department of Biochemistry and Molecular Biology

institute: Peking University Health Science Center

data_processing:
Illumina NovaSeq sequencer and software used for sequencing and basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference genome of mm10 using HISAT2.
Transcript assembly were performed using Cufflink. DEG analyses were performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include p-value or q-value for each Sample.

source_name: Hippocampus

growth_protocol: Hippocampal tissues from 8-week old control and Jade2-KO mice

extract_protocol:
Hippocampal tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NEBNext Ultra RNA Library Prep Kit for Illumina (Cat#E7530S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Hippocampus

value: 8 weeks

value: Jade2 knockout


title: H9 hTSC TEAD1 CUT&Tag rep 1

source_name: human trophoblast stem cells


title: HEYnAC2

description: Next generation RNA-seq data

value: HEY cell with nAC probe expression


title: Jade2_KO3_RNA_Seq


title: HEYnAC1

description: Next generation RNA-seq data

value: ovarian cancer cell line


title: axe1-5 HK27me3 -JA 1

value: H3K27me3 (Sigma Aldrich 07-449)


title: DR5 input +JA 2

value: jasmonate


title: Day 18 rep 2

data_processing:
Library strategy: Targeted DNA sequencing
AIAP (v1.0) was applied, with command line as "bash ATAC_IAP_v1.1.sh -g hg38 -r PE", the pipe does the alignment, peak-calling, normalized abundance measurements etc
Genome_build: hg38
Supplementary_files_format_and_content: bigWig
Supplementary_files_format_and_content: bedGraph

extract_protocol:
CRISPR: Genomic DNA (gDNA) was isolated using the QIAamp DNA Blood Maxi Kit (Qiagen, 51192) as per the manufacturer’s instructions. The gDNA concentrations were quanti-tated by Nanodrop.
For PCR amplification, 252 μg of DNA was amplified per sample using the MyTaq Red Mix (Bioline, 25043). Reactions were set up in 384-well plates, using 200 ng of gDNA in 12 μL of reaction mix per well. Primers used for gDNA ampli-fication were Fwd 5’ tgtggaaaggacgaaacacc 3’ and Rev 5’ cggactagccttattttaacttgc 3’. PCR cycling condition is as follows: an initial 2 minutes at 94 °C; followed by 15 seconds at 94 °C, 15 seconds at 56 °C, 30 seconds at 72 °C, for 30 cycles; and a fi-nal 5 minutes extension at 72 °C. P5/P7 primers were synthesized at Integrated DNA Technologies (IDT). PCR products were purified using the Agencourt AMPure XP SPRI beads (Beckman Coulter, A63880) according to manufacturer’s instructions. Samples were sequenced on a NovaSeq S4 2X150 platform (Illumina).


title: Jade2_KO2_RNA_Seq


title: Chow F4

value: heart

value: 12 weeks

value: wild type


title: Day 18 rep 1


title: Jade2_KO1_RNA_Seq


title: Day 12 rep 2


title: DR5 HK27me3 -JA 1


title: Control_4_RNA_Seq


title: axe1-5 HK27me3 +JA 1


title: NCG MDA-231ba429C

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

data_processing:
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
aligned reads are summarized to gene-level counts by the featureCounts tool
Genome_build: GRCh38_ens92_ercc_sirv

source_name: human mammary tumor cell line

growth_protocol: cells were grown in DMEM media supplemented with 10% FBS, 1 mM sodium pyruvate, 4 mM glutamine, 1% antibiotic/antimycotic and 60ug/ml puromycin (InvivoGen, San Diego, CA). RNA was extracted from sub-confluent cells

extract_protocol:
RNA extracted using mirVana miRNA Isolation Kit following the manufacturer's protocol
KAPA stranded Illumina kits for the RNA-seq library preparation, which include procedures of RNA fragmentation, random hexamer primed first strand cDNA synthesis, dUTP based second strand cDNA synthesis, end-repairing, A-tailing, adaptor ligation and library PCR amplification. Library prep performed by Arraystar Inc (Rockville, MD)

value: stably transfected with vector containing miR-200b, miR-200a and miR-429


title: Control_3_RNA_Seq


title: NCG MDA-231ba429A


title: NCG MDA-231ba429B


title: NCG MDA-231ba429D


title: HEYnAC3

description: Next generation RNA-seq data


title: axe1-5 H4ac -JA 1

value: H4ac (Sigma Aldrich 06-866)


title: Day 12 rep 1


title: Control_2_RNA_Seq


title: NCG MDA-231c141F

value: stably transfected with vector containing miR-200c and miR-141


title: axe1-5 H4ac +JA 1

value: Whole seedlings


title: Day 6 rep 2


title: DR5 H4ac -JA 1

value: mock


title: Day 6 rep 1

value: hTSCs


title: Day 0 rep 3

value: human trophoblast


title: NCG MDA-231c141E


title: DR5 H4ac +JA 1


title: RAW264.7, sh-lncRNA-SNHG1, 2

city: Zhengzhou

first: Chunling

last: Hu

address: No. 1 Jianshe East Road

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: gene_expression.txt (Matrix table with raw gene counts for every gene and every sample)

source_name: RAW264.7, sh-lncRNA-SNHG1

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: RAW264.7 cells transfected with no-targeting siRNA or shRNA against SNHG1

value: leukemia cells in mouse macrophage


title: RAW264.7, sh-lncRNA-SNHG1, 3


title: Day 0 rep 2


title: axe1-5 input -JA 1


title: NCG MDA-231c141D


title: axe1-5 input +JA 1


title: Day 0 rep 1


title: NCG MDA-231c141C


title: RAW264.7, sh-lncRNA-SNHG1, 1


title: PW030-705 (NovaSeq)

source_name: Human glioma slice culture treated with RO4929097 (NovaSeq)

value: glioma slice culture


title: DR5 input -JA 1


title: DR5 input +JA 1


title: RAW264.7, NC3

value: Control


title: Control_1_RNA_Seq

value: Hippocampus

value: 8 weeks


title: PW030-702 (NovaSeq)

source_name: Human glioma slice culture treated with vehicle (DMSO) (NovaSeq)

value: DMSO (vehicle control)


title: PW030-703 (NovaSeq)

source_name: Human glioma slice culture treated with etoposide (NovaSeq)

value: Etoposide 5 uM


title: NCG MDA-231EV2

value: stably transfected with empty vector


title: RAW_Fn

city: Guangzhou

first: Songhe

last: Guo

state: Guangdong

address: No.132 Waihuandong Road, University Town

institute: Sun Yat-sen University

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

growth_protocol: RAW 264.7 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma),
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS

value: monocyte macrophage

value: WT

value: RAW264.7 cells treated with Fn(MO1:1:10) for 24h


title: NCG MDA-231EV1


title: NCG MDA-231EV


title: RAW_C

value: RAW264.7 cells treated with PBS for 24h


title: RAW264.7, NC2


title: TLSC H3K27me3

city: GuangZhou

first: Hanwen

last: Yu

state: GuangDong

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-*Sen Road, Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: SUN YAT-SEN UNIVERSITY

description: TLSC H3K27me3

data_processing:
The bioinformatics analysis of CUT&Tag datasets generated in this study or downloaded from publicly available repositories and data portals were performed by custom shell scripts in which raw data were first trimmed and filtered by TrimGalore with default parameter. Qualified read pairs were then aligned to mouse genome (mm10) by Bowtie2 (release 2.4.1). Biological and optical duplicates were removed with Sambamba (release 0.7.1). Last we used MACS2 (release 2.2.7.1; parameters for narrow peaks such as H3K27ac and H3K4me3: -p 0.05 -g mm -f BAMPE; broad peaks such as H3K27me3, H3K4me1, H3K79me2, H3K79me3 and H3K4me3: --broad --broad-cutoff 0.05 -g mm -f BAMPE; ATAC-seq: --broad --broad-cutoff 0.05 -g mm -f BAMPE) to call peaks. The highly reproducible peaks were identified by package IDR, which is a uniﬁed approach to measure the reproducibility of ﬁndings identiﬁed from replicate experiments and provide highly stable thresholds based on reproducibility.
Assembly: mm10
Supplementary files format and content: peak bed files.
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.
Library strategy: CUT&Tag-sequencing

source_name: mouse embryonic stem cells

growth_protocol: Mouse ESCs were cultured in N2B27 medium comprising 10ng/ml of LIF, 1 μM PD03, 3 μM CHIR9901 (Nichols and Ying, 2006) or in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 100 μg/ml L-ascorbic acid, 100 µM 2-mercaptoethanol and 10 ng/ml LIF. The medium was changed every another day. Mouse TLSCs were cultured in the TLSC medium (TLSCM) comprising KnockOut medium, 20% KnockOut serum replacement, 1× non-essential amino acids solution, 2 mM L-glutamine, 50 μg/ml BSA, 100 µM 2-mercaptoethanol, 10 ng/ml IL6, 10 ng/ml sIL-6R, 100 μg/ml L-ascorbic acid, 2 μM SGC0946, 2 μM A366, 3 μM AS8351, and primocin. The medium was changed every another day. When passaging, cells were dissociated by 0.05% Trypsin-EDTA into single cells and re-plated every three days at a ratio of 1:10 - 1:12 (for mESCs) or 1:4 - 1:6 (for TLSCs).

extract_protocol:
A hyperactive pA-Tn5 transposon for the illumina platform was first generated. Cells were harvested and washed twice. Then the nuclei were isolated by ice-cold NE1 buffer and re-suspended in wash buffer. 10 μl of activated concanavalin A beads were added per sample and incubated at room temperature for 10 minutes. Primary antibody (1:50 dilution of anti-IgG, anti-H3K4me1, H3K4me3, H3K27me3, H3K27ac and H3K9me2) incubation was performed on a rotator at 4°C overnight. To increase the number of protein A binding sites, a secondary antibody (such as guinea pig anti-Rabbit IgG antibody for a rabbit primary antibody, and rabbit anti-mouse IgG for a mouse primary antibody) was diluted 1:100 in wash buffer and incubated at RT for 1h. After removing unbound antibodies, cells were mixed with 1:100 dilution of pA-Tn5 (0.04 µM) and incubated at room temperature for 1 hour on rotator. Next, cells were re-suspended in 300 µl tagmentation buffer and incubated at 37 °C for 1 h. To stop tagmentation, 10 µl 0.5 M EDTA, 3µl 10% SDS and 2.5 µl of 20 mg/mL Proteinase K was added to sample, which was incubated overnight at 37 °C. DNA was extracted by PCI and dissolved in 30 μl TE buffer.
To amplify libraries, we added P5 primer, P7 primer (Vazyme, catalog. no. TD202), TruePrep Amplify Enzyme (Vazyme catalog. no. TD601) and performed PCR with the conditions below: 72°C for 3 minutes; 98°C for 30 seconds; 18 cycles of 98°C for 15 seconds, 63°C for 15 seconds; 72°C for 5 minutes. Post-PCR clean-up was performed by adding 1.2 volume of DNA clean beads (Vazyme, catalog. no. N411) and libraries were eluted in 20 μl nuclease-free water.

treatment_protocol: 2C::GFP+/SGC cells were cultured in in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 100 μg/ml L-ascorbic acid,  100 µM 2-mercaptoethanol and 10 ng/ml LIF, under treatment with SGC0946 (2 µM). 2C::GFP+/SA cells were cultured in in KnockOut medium comprising 20% KnockOut serum replacement, 1X non-essential amino acids solution, 2 mM L-glutamine, 100 μg/ml L-ascorbic acid, 50 μg/ml BSA, 100 µM 2-mercaptoethanol and 10 ng/ml IL6/sIL-6R, under treatment with SGC0946 (2 µM) and AS8351 (3 μM).

tag: celltype

value: mouse embryonic stem cells

value: H3K27me3(Millipore, 07-449)

value: TLSC medium


title: N2_JM03 rep1

status: Public on Apr 10 2022

city: shanghai

first: song

last: zhouzhi

address: Lingyun Road, Xuhui District

institute: East China University of Science and Technology

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include TPM values for each sample.

organism: Caenorhabditis elegans

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain/genotype


title: osm-9_JM03 rep2


title: osm-9_Control rep1


title: N2_JM03 rep2


title: osm-9_JM03 rep1


title: N2_Control rep3


title: NCG MDA-231EV3


title: osm-9_JM03 rep3


title: N2_JM03 rep3


title: RAW264.7, NC4

tag: cell type


title: osm-9_Control rep2


title: N2_Control rep1


title: N2_Control rep2


title: knock-out C

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Basecalling was conducted with the Illumina bcl2fastq 2.18.0.12 pipeline
Skewer (v0.2.2; Jiang et al, 2014; PMID: 24925680) was used to trim low quality bases from the 3’ end of reads.
Trimmed reads were then mapped to the Gencode (v37) human transcriptome using Kallisto (Bray et al, 2016; PMID: 27043002). Data were read into R, followed by aggregation of transcript level counts to gene level count data for downstream analysis.
Assembly: Gencode (v37) human transcriptome
Supplementary files format and content: ECHS1_KO_countmatrix.tsv  count matrix tab separated values

source_name: fibroblasts from ECHS1D patient “C”

growth_protocol: 143BTK- osteosarcoma cells (ATCC CRL-8303) were cultured in glucose free DMEM media supplemented with 10 mM galactose, 5% (v/v) dialyzed fetal calf serum (dFCS), 50 units/mL penicillin, 50 μg/mL streptomycin, 50 μg/mL uridine and 1x GlutaMAXTM (ThermoFisher Scientific, Waltham, MA, USA) (GAL media) at 37°C/5% CO2. 143BTK- cells were used in accordance with Deakin University Human Research Ethics Committee approval (2019-087).

extract_protocol:
Total RNA was extracted using the RNeasy Plus Kit with on-column DNA elimination (Qiagen) according to manufacturer’s instructions.
Transcriptome-wide mRNA sequencing was performed by the Australian Genome Research Facility (Melbourne, Australia) from four independent experiments (n=4). RNA purity and integrity were confirmed by BioAnalyser (Agilent, CA). Libraries were prepared using the Ribo-zero Gold protocol (Illumina) and assessed by Bioanalyser DNA 1000 chip (Agilent).

treatment_protocol: ECHS1-deficient 143BTK- osteosarcoma cells were generated by transformation with recombinant lentiCRISPR v2 vector containing the sgRNA ECHS1 target 5’-TGC AAA GGC CTT ATC CCC GC-3’ [31, 32]. HEK293T cells were transfected with recombinant lentiCRISPR v2-ECHS1, pSPAX2 (Addgene 12259) and VSV-G (Addgene 8454) to generate infectious viral particles, which were subsequently combined with 5 µL/mL polybrene (Sigma-Aldrich) to infect 143BTK- cells. Transformed cells were selected with 1 µg/mL puromycin and cell clones generated by limiting dilution.  Disruption of the ECHS1 gene was confirmed by PCR amplification of the target region using primers (forward 5’-GGT CAC ACT GTA TCC ACC G-3’ and reverse 5’-CCT TGA CAC ACA CAA AGC C-3’) with OneTaq Hot Start DNA Polymerase (New England Biolabs, Ipswich, MA, USA) and subsequent ligation of the PCR products into the pGEM-T Easy vector. Transformed bacterial colonies were picked and plasmid clones sequenced to confirm editing of both ECHS1 alleles.

tag: echs1 construct

value: knock-out


title: knock-out D

source_name: fibroblasts from ECHS1D patient “D”


title: knock-out B

source_name: fibroblasts from ECHS1D patient “B”


title: control C

value: control


title: knock-out A

source_name: fibroblasts from ECHS1D patient “A”


title: PW030-701 (NovaSeq)

tag: tissue


title: control B


title: control D


title: control A


title: microgila BV2 cells-NC-Control_rep3

city: Luzhou

first: Qiu

last: Xiancheng

address: No.25 of Taiping Street

institute: Southwest medical college

data_processing:
bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using hisat2 v2.2.0 with parameters --dta -p 10
Counts were calculated using featurecounts with parameters -t exon -T 10 -p -g gene_id -f. Normalized counts were calculated using DESeq2.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include deseq2 output for each group
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Microglia BV2 cells

growth_protocol: BV2 mouse microgial cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) containing 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin, and maintained under normal conditions with 37℃ and 5% CO2.

extract_protocol:
Microglia were seeded in a 6-well plate, and after 12h for complete cell wall adhesion, Oxy-Hb stimulated the cells and reached the scheduled stimulation time. Cellular RNA was extracted using RNAeasy Isolation Reagent (#R701-02, Vazyme Biotech Co., Ltd) according to the manufacturer's instructions.
The Universal V6 RNA-seq Library Prep Kit for Illumina (#NR604-02, Vazyme Biotech Co., Ltd) was used for library preparation. Briefly, the samples were normalized at a 500 ng/ml concentration. First, samples were subjected to a tagmentation redaction, indexed, and PCR amplified. Libraries were then purified with VAHTS DNA Clean Beads (#N411-02, Vazyme Biotech Co., Ltd). QC checks for the library preparations included electrophoresis (Agilent Technologies 2100 Bioanalyzer) or library quantification.

treatment_protocol: One replicate was oxyhemoglobin treated for 12 hours or 24 hours.

value: Microglia BV2 cells


title: microgila BV2 cells-NC-24H_rep2

value: 10mM oxyhemoglobin for 24 hr


title: microgila BV2 cells-NC-24H_rep3


title: microgila BV2 cells-NC-Control_rep1


title: osm-9_Control rep3

value: Control


title: microgila BV2 cells-NC-Control_rep2


title: microgila BV2 cells-NC-24H_rep1


title: microgila BV2 cells-NC-12H_rep3

value: 10mM oxyhemoglobin for 12 hr


title: microgila BV2 cells-NC-12H_rep2


title: microgila BV2 cells-NC-12H_rep1


title: microgila BV2 cells-BAK1-KD-Control_rep2


title: microgila BV2 cells-BAK1-KD-24H_rep3


title: microgila BV2 cells-BAK1-KD-Control_rep1


title: microgila BV2 cells-BAK1-KD-12H_rep3


title: microgila BV2 cells-BAK1-KD-Control_rep3


title: microgila BV2 cells-BAK1-KD-24H_rep2


title: microgila BV2 cells-BAK1-KD-12H_rep2


title: microgila BV2 cells-BAK1-KD-12H_rep1


title: microgila BV2 cells-BAK1-KD-24H_rep1


title: P8T1_DN

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

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 rattus norvegius reference rn6 genome using the STAR RNA-Seq aligner (2.7.0f), and HTS. 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.
RNA-Seq: Raw read counts for individual genes were extracted using --quantMode GeneCounts in STAR using the UCSC rn6 refGene annotation file
Genome_build: rn6
Supplementary_files_format_and_content: RNA-Seq: Tab-separated file of the raw read counts of each samples for each gene.

organism: Rattus norvegicus

source_name: DN cells from Tumor in NMU treated Sprague Dawley rats

growth_protocol: To induce tumors, virgin Sprague Dawley rats were injected 1-3 times with 50mg/kg N-nitroso N-methylurea (NMU) intraperitoneally at ages 35-53 days

extract_protocol:
Tumor tissue was dissociated to a single-cell suspension in a collagenase solution (2mg/ml collagenase in DMEM/F12 (Life Technologies) with constant stirring at 37'C for 1-2 hours. Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on Illumina Illumina NextSeq 500 or NovaGene ...

treatment_protocol: In the immunotherapy cohort, animals were followed by weekly inspections and treatment with LY2157299, anti-PD-L1 mAb, the combination or vehicle initiated when palpable tumors were detected

tag: fraction

value: DN

value: Vehicle

tag: cohort

value: Immunotherapy

tag: ratid

tag: tumorid

tag: tissuetype

value: Tumor


title: F_H460_2

first: shali

last: shao

address: longhang road

institute: jinshan hospital of fudan university

data_processing:
DESeq2  1.18.1/edegR 3.20.9/ fastp 0.20.0/HISAT2 2.1.0/ HTSeq 0.10.0
Sequence reads were trimmed for ow-quality sequence using fastp software
Trimmed sequence reads were mapped to reference genes using HISAT2 software
Read count extraction and analysis were performed using HTSeq software
Supplementary files format and content: the excel includes the differentially expressed genes

source_name: Lung

growth_protocol: The H460 cells were cultured in complete RPMI-1640 medium  with 10% fetal bovine serum (FBS)  at 37°C under 5% CO2

extract_protocol:
the total RNA was extracted from cells using TRIzol (Invitrogen)
Library construction and sequencing were performed by HaploX Genomics Center (Jiangxi, China)

treatment_protocol: The cells were seeded in the 6-well plates. After 24 hours of incubation, the cells were treated with the 20μM  fluoxetine for the next 24 hours

value: Lung

tag: cell line

value: H460 cell line

value: Carcinoma

tag: treatment

value: 20μM  fluoxetine


title: H460_3

tag: genotype

value: WT


title: F_H460_3


title: H460_2


title: F_H460_1


title: P6T1_CD45

source_name: CD45 cells from Tumor in NMU treated Sprague Dawley rats


title: H460_1


title: P6T1_DN


title: P5T2_DN


title: P5T3_CD45


title: P8T1_CD45


title: P5T1_CD45


title: P39T1_DN


title: P5T2_CD45


title: P39T1_CD45


title: P5T1_DN


title: P38T2_DN


title: P35T1_CD45


title: P29T1_DN


title: P36T3_CD45


title: P27T1_DN


title: P29T1_CD45


title: P33T1_DN


title: P26T2_Ep

source_name: Ep cells from Tumor in NMU treated Sprague Dawley rats

value: Ep


title: P27T1_CD45


title: P27T1_Ep


title: P33T1_CD45


title: P29T1_Ep


title: P26T2_CD45


title: P24T2_DN


title: P22T1_DN

value: LY


title: P22T1_CD45


title: P23T2_CD45


title: P17T3_CD45


title: P23T1_DN


title: P17T3_DN


title: P24T2_CD45


title: P36T3_DN


title: P19T2_CD45


title: P14T1_CD45


title: CMC_scRNA-seq_B16F10

city: Seoul

first: YOON-SEOB

last: KIM

state: Korea (the Republic of)

address: Banpodaero 222

country: South Korea

institute: The Catholic University of Korea

data_processing:
Libraries were sequenced on HiSeq 2500 instruments
Using CellRanger 3.0.0 pipeline (10X Genomics), fastq data was aligned to a mouseh genome reference (mm10) and the unique molecular identifier (UMI) counts was quantified .
The raw gene expression matrix from the CellRanger pipeline was filtered using the Seurat R package (version 3.0) and selected according to the following criteria: cells with > 3000 genes, and < 7,000 genes, and < 0.2% of mitochondrial gene expression in UMI counts.
After filtering step, the raw gene expression matrix was normalized to the total UMI counts per cell and transformed to the natural log scale.
Further clustering and analysis were done under Seurat pipeline
Genome_build: mm10
Supplementary_files_format_and_content: Supplementary_files_format_and_content: Tab-deliminated text file containing the raw gene expression (UMI_raw_counts.txt) and the normalized gene expression (Natural_log_UMI_matrix.txt) for QC filtered cells, and cell annotation file.

source_name: melanoma cell line

extract_protocol:
The cells were washed in PBS (0.04% BSA) and resuspended at a concentration of ~1000 cells/μl.
The cells were used for generating scRNA-seq libraries using Chromium Single-cell 3' Reagent Kits v2 (10x Genomics, Pleasanton, CA) according to the manufacturer’s protocol.

tag: phenotype

value: highly metastatic subclone


title: CMC_scRNA-seq_B16F0

value: parental


title: OE_SLAM_wt_4hr

city: Rehovot

first: Noam

last: Stern-Ginossar

address: 234 herzel

department: Molecular Genetics

country: Israel

institute: Weizmann Institute

description:
OE_SLAMseq_cds_reads.csv.gz
OE_wt_HL.csv.gz

data_processing:
The reads of the ribo-seq libraries were trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et al., plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et al. to get all the breakpoints.
Assembly: Host: Human hg19 (GRCh37); Chlorocebus sabaeus genome and annotation ENSEMBL release 99; Mesocricetus auratus genome and annotation ENSEMBL release 104; Virus Genbank NC_045512.2.
Supplementary files format and content: *.csv: Comma-separated files of the cytosolic to nuclear ratio of transcripts, half-life of transcripts, and the read counts of all transcripts in each experiment (either for coding RNAs or for all transcripts).
Library strategy: SLAM-seq

source_name: Human

extract_protocol:
For RNA-seq, cells were harvested with Tri-Reagent (Sigma-Aldrich), total RNA was extracted, and poly-A selection was performed using Dynabeads mRNA DIRECT Purification Kit (Invitrogen). For ribosome profiling, medium was aspirated from dishes, which were immediately placed on ice and rinsed with 10 ml ice-cold PBS supplemented with drugs used in pretreatment of the cells. PBS was aspirated and 800 μl ice-cold lysis buffer (20 mM Tris, pH 7.4, 250 mM NaCl, 15 mM MgCl2, 1 mM dithiothreito, 0.5% Triton X-100 and 24 U / ml Turbo DNase (Ambion, AM2239), along with any drugs used for sample treatment) was dripped onto dishes. Cells were scraped and the lysate was removed and incubated 10 min on ice. The lysate was then clarified by centrifugation for 10 min at 20,000 × g, 4°C and ∼1.1 ml supernatant was recovered.
RNA-seq: mRNA sample was subjected to DNaseI treatment and 3’ dephosphorylation using FastAP Thermosensitive Alkaline Phosphatase (Thermo Scientific) and T4 PNK (NEB) followed by 3’ adaptor ligation using T4 ligase (NEB). The ligated products used for reverse transcription with SSIII (Invitrogen) for first strand cDNA synthesis. The cDNA products were 3’ ligated with a second adaptor using T4 ligase and amplified for 8 cycles in a PCR for final library products of 200-300bp.

treatment_protocol: For Ribo-seq libraries, all samples were treated with 100μg/mL CHX for 1 minute. Cells were placed on ice immediately after treatment, washed twice with PBS containing 100μg/mL CHX.

tag: hours post infection


title: Nsplmt_Ham_day3_3

data_processing:
The reads of the ribo-seq libraries were trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et al., plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et al. to get all the breakpoints.
Assembly: Host: Human hg19 (GRCh37); Chlorocebus sabaeus genome and annotation ENSEMBL release 99; Mesocricetus auratus genome and annotation ENSEMBL release 104; Virus Genbank NC_045512.2.
Supplementary files format and content: *.csv: Comma-separated files of the cytosolic to nuclear ratio of transcripts, half-life of transcripts, and the read counts of all transcripts in each experiment (either for coding RNAs or for all transcripts).

organism:
Mesocricetus auratus
Severe acute respiratory syndrome coronavirus 2

source_name: Hamster + Virus

value: Lung tissue

tag: infection


title: P26T2_DN


title: OE_SLAM_wt_3hr_B


title: WT_Ham_day3_3


title: OE_SLAM_RK_4hr

description:
OE_SLAMseq_cds_reads.csv.gz
OE_rk_HL.csv.gz


title: OE_SLAM_wt_2hr_A


title: Nsplmt_Ham_day3_2


title: WT_Ham_day3_2


title: OE_SLAM_wt_0hr


title: OE_SLAM_wt_3hr_A


title: OE_SLAM_wt_2hr_B


title: WT_Ham_day3_1


title: P13T1_CD45


title: Nsplmt_Ham_day3_1


title: MOCK_Ham_day3_3


title: MOCK_Ham_day3_2


title: OE_SLAM_RK_3hr_B


title: OE_SLAM_RK_3hr_A


title: 48_WT_ruxo_B

organism:
Homo sapiens
Severe acute respiratory syndrome coronavirus 2

source_name: Human + Virus


title: P10T1_DN


title: OE_SLAM_RK_2hr_B

description:
OE_SLAMseq_cds_reads.csv.gz
OE_gfp_HL.csv.gz


title: MOCK_Ham_day3_1


title: OE_SLAM_GFP_4hr


title: 48_WT_ruxo_A


title: OE_SLAM_GFP_3hr_B


title: OE_SLAM_RK_2hr_A


title: C9T2_Ep

value: Characterization


title: OE_SLAM_RK_0hr


title: 48_WT_noruxo_B


title: OE_SLAM_GFP_2hr_B

description:
OE_SLAMseq_cds_reads.csv.gz
OE_del_HL.csv.gz


title: OE_SLAM_GFP_3hr_A


title: 48_WT_noruxo_A


title: 48_del_ruxo_B


title: 48_del_ruxo_A


title: OE_SLAMdel_3hr_B


title: OE_SLAM_del_4hr


title: 48_del_noruxo_B


title: OE_SLAM_GFP_2hr_A


title: 24_WT_noruxo_A


title: OE_SLAM_GFP_0hr


title: OE_SLAMdel_0hr

description:
OE_SLAMseq_cds_reads.csv.gz
cyt2nuc_ratios.csv.gz


title: 24_WT_ruxo_A


title: 24_WT_ruxo_B


title: 24_del_noruxo_B


title: 24_WT_noruxo_B


title: OE_SLAMdel_3hr_A


title: 0_WT_ruxo_B


title: Frac_NSP1wt_B_Total

description:
Fractionation_csv_reads.csv.gz
cyt2nuc_ratios.csv.gz


title: Frac_NSP1wt_C_Total


title: Frac_NSP1wt_B_Cytosol


title: 48_del_noruxo_A


title: 24_del_noruxo_A


title: 0_WT_noruxo_B


title: Frac_NSP1wt_C_Cytosol


title: 24_del_ruxo_B


title: 0_WT_ruxo_A


title: Frac_NSP1wt_A_Cytosol


title: 0_del_ruxo_A


title: 24_del_ruxo_A


title: Frac_NSP1del_C_Total


title: Frac_NSP1wt_C_Nucleus


title: OE_SLAMdel_2hr_B


title: Frac_NSP1wt_A_Nucleus


title: OE_SLAMdel_2hr_A


title: 0_del_noruxo_B


title: Frac_NSP1wt_A_Total


title: 0_del_noruxo_A


title: 0_WT_noruxo_A


title: TotalRNA_Mock_A_rep1

data_processing:
The reads of the ribo-seq libraries were trimmed to remove the linker CTGTAGGCACCATCAAT by using cutadapt. For the Shishkin protocol libraries the linker was AGATCGGAAGAGCACACGT.
Reads aligned to hg19 based rRNA and tRNA reference were removed. Then reads were aligned to combined reference of the host and the virus.
Reads that failed to align to genome, were aligned to the host transcriptome and to the viral breaking points according to strong break point at Kim et al., plus few breakpoints from our STAR runs.
The alignments above were made with Bowtie1. In the ribo-seq libraries the p-site was calculated as an offset (adjusted to the read length) from the read start site.
The STAR alignment was made with the flags recommended by Kim et al. to get all the breakpoints.
Assembly: Host: Human hg19 (GRCh37); Chlorocebus sabaeus genome and annotation ENSEMBL release 99; Mesocricetus auratus genome and annotation ENSEMBL release 104; Virus Genbank NC_045512.2.
Supplementary files format and content: *.csv: Comma-separated files of the cytosolic to nuclear ratio of transcripts, half-life of transcripts, and the read counts of all transcripts in each experiment (either for coding RNAs or for all transcripts).
Library strategy: Ribo-seq


title: Frac_NSP1wt_B_Nucleus


title: TotalRNA_Mock_A_rep2


title: Frac_NSP1del_C_Cytosol


title: Frac_NSP1del_B_Nucleus


title: TotalRNA_7hpi_wt_rep1


title: Frac_NSP1del_B_Total


title: Frac_NSP1del_C_Nucleus


title: Frac_NSP1del_A_Total


title: TotalRNA_7hpi_del_rep2


title: TotalRNA_7hpi_wt_rep2


title: Frac_NSP1del_B_Cytosol


title: TotalRNA_4hpi_wt_rep2


title: Frac_GFP_B_Total


title: TotalRNA_4hpi_del_rep2


title: 0_del_ruxo_B


title: TotalRNA_4hpi_del_rep1


title: RP_FP_WT7_A


title: Frac_NSP1del_A_Nucleus


title: Frac_NSP1del_A_Cytosol


title: RP_FP_WT4_B


title: TotalRNA_4hpi_wt_rep1


title: Frac_GFP_A_Cytosol


title: Frac_GFP_A_Nucleus


title: Frac_GFP_A_Total


title: RP_FP_WT4_A


title: RP_FP_mock_B_2


title: TotalRNA_7hpi_del_rep1


title: RP_FP_delta7_A


title: Frac_GFP_B_Nucleus


title: RP_FP_delta4_B


title: RP_FP_delta4_A


title: RP_FP_WT7_B


title: Frac_GFP_B_Cytosol


title: RP_mRNA_Mock_B_rep2


title: RP_mRNA_Mock_B_rep1


title: nasopharyngeal carcinoma patients with posttreatment metastasis 35

first: Jun

last: Ma

address: 651 Dongfeng Road East

institute: Sun Yat-sen University Cancer Center

description: lncRNA expression data from nasopharyngeal carcinoma with posttreatment metastasis

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering.

source_name: primary nasopharyngeal carcinoma with posttreatment metastasis

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

growth_protocol: Nasopharyngeal carcinoma biopsy samples obtained through nasopharyngoscope before treatment.

extract_protocol: Total RNA was extracted from frozen fresh tissues using the AllPrep DNA/RNA Mini Kit (QIAGEN GmbH, Hilden, Germany)

value: Nasopharyngeal carcinoma

tag: disease state


title: nasopharyngeal carcinoma patients with posttreatment metastasis 37


title: nasopharyngeal carcinoma patients with posttreatment metastasis 33


title: RP_FP_mock_B_1


title: nasopharyngeal carcinoma patients with posttreatment metastasis 38


title: nasopharyngeal carcinoma patients with posttreatment metastasis 34


title: RP_mRNA_4hpi_wt_rep1

description:
RibosomeProfiling_mRNA_cds_reads.csv.gz
Inf_wt_HL.csv.gz


title: RP_mRNA_4hpi_del_rep2

description:
RibosomeProfiling_mRNA_cds_reads.csv.gz
Inf_mock_HL.csv.gz


title: nasopharyngeal carcinoma patients with posttreatment metastasis 36


title: nasopharyngeal carcinoma patients with posttreatment metastasis 31


title: RP_mRNA_7hpi_wt_rep2


title: nasopharyngeal carcinoma patients with posttreatment metastasis 30


title: nasopharyngeal carcinoma patients with posttreatment metastasis 32


title: nasopharyngeal carcinoma patients with posttreatment metastasis 29


title: RP_FP_delta7_B


title: RP_mRNA_7hpi_wt_rep1


title: RP_mRNA_7hpi_del_rep2


title: RP_mRNA_7hpi_del_rep1


title: Inf_SLAM_SLAMseq_6hr_mock_B

description:
Infection_SLAMseq_cds_reads.csv.gz
Inf_del_HL.csv.gz


title: RP_mRNA_4hpi_wt_rep2


title: Inf_SLAM_SLAMseq_no4su_delta

description:
Infection_SLAMseq_cds_reads.csv.gz
Inf_mock_HL.csv.gz


title: Inf_SLAM_SLAMseq_6hr_mock_A

description:
Infection_SLAMseq_cds_reads.csv.gz
Inf_wt_HL.csv.gz


title: nasopharyngeal carcinoma patients without posttreatment metastasis 27

description: lncRNA expression data from nasopharyngeal carcinoma without posttreatment metastasis

source_name: primary nasopharyngeal carcinoma without posttreatment metastasis


title: Inf_SLAM_SLAMseq_no4su_wt


title: RP_mRNA_4hpi_del_rep1

description:
RibosomeProfiling_mRNA_cds_reads.csv.gz
Inf_del_HL.csv.gz


title: nasopharyngeal carcinoma patients without posttreatment metastasis 28


title: nasopharyngeal carcinoma patients without posttreatment metastasis 23


title: Inf_SLAM_SLAMseq_no4su_mock


title: nasopharyngeal carcinoma patients without posttreatment metastasis 21


title: Inf_SLAM_SLAMseq_6hr_wt_B


title: nasopharyngeal carcinoma patients without posttreatment metastasis 25


title: Inf_SLAM_SLAMseq_6hr_wt_A


title: nasopharyngeal carcinoma patients without posttreatment metastasis 20


title: nasopharyngeal carcinoma patients without posttreatment metastasis 26


title: Inf_SLAM_SLAMseq_5hr_wt_A


title: nasopharyngeal carcinoma patients without posttreatment metastasis 24


title: nasopharyngeal carcinoma patients without posttreatment metastasis 22


title: Inf_SLAM_SLAMseq_5hr_mock_B


title: Inf_SLAM_SLAMseq_5hr_delta_B


title: Inf_SLAM_SLAMseq_6hr_delta_B


title: Inf_SLAM_SLAMseq_6hr_delta_A


title: nasopharyngeal carcinoma patients without posttreatment metastasis 19


title: Inf_SLAM_SLAMseq_5hr_wt_B


title: nasopharyngeal carcinoma patients 16

description: lncRNA expression data from nasopharyngeal carcinoma

source_name: primary nasopharyngeal carcinoma


title: Inf_SLAM_SLAMseq_5hr_delta_A


title: Inf_SLAM_SLAMseq_5hr_mock_A


title: Calu3_GC_WT_48hpi_A


title: Calu3_GC_WT_48hpi_B


title: nasopharyngeal carcinoma patients 15


title: nasopharyngeal carcinoma patients 17


title: nasopharyngeal carcinoma patients 07


title: nasopharyngeal carcinoma patients 18


title: nasopharyngeal carcinoma patients 13


title: nasopharyngeal carcinoma patients 10


title: nasopharyngeal carcinoma patients 11


title: nasopharyngeal carcinoma patients 14


title: nasopharyngeal carcinoma patients 03


title: Inf_SLAM_SLAMseq_4hr_wt

description:
Infection_SLAMseq_cds_reads.csv.gz
OE_wt_HL.csv.gz


title: nasopharyngeal carcinoma patients 09


title: Inf_SLAM_SLAMseq_4hr_mock


title: nasopharyngeal carcinoma patients 06


title: nasopharyngeal carcinoma patients 08


title: nasopharyngeal carcinoma patients 12


title: Inf_SLAM_SLAMseq_4hr_delta


title: Calu3_GC_WT_24hpi_B


title: Calu3_GC_WT_24hpi_A


title: nasopharyngeal carcinoma patients 05


title: Calu3_GC_WT_0hpi_B


title: Calu3_GC_Del_48hpi_B


title: Calu3_GC_WT_11hpi_B


title: Calu3_GC_Del_48hpi_A


title: Calu3_GC_WT_11hpi_A


title: Calu3_GC_Del_24hpi_A


title: Calu3_GC_Del_11hpi_A


title: Calu3_GC_WT_0hpi_A


title: nasopharyngeal carcinoma patients 01


title: nasopharyngeal carcinoma patients 02


title: nasopharyngeal carcinoma patients 04


title: Calu3_GC_Del_24hpi_B


title: Calu3_GC_Del_0hpi_A


title: Healthy controls 17

description: lncRNA expression data from nasopharyngeal mucositis

source_name: nasopharyngeal mucositis

value: nasopharyngeal mucositis

value: healthy


title: Healthy controls 14


title: Healthy controls 18


title: 338-F1_K

city: Ottawa

first: Lauren

middle: E

last: Carter

state: ON

address: 251 SIR FREDERICK BANTING

institute: Health Canada

data_processing:
Quality filtering and trimming; Bbduk (38.84); maq=12 qtrim=rl trimq=12 minlength=20 tpe tbo
Alignment; STAR (2.7.1a); OutFilterScoreMinOverLread=0.25 outFilterMatchNminOverLread=0.25
Gene reads counting; FeatureCounts (2.0.0); -p -Q=12 -C -t exon -g gene_id
Differential Expression calling; DESeq2 (1.26.0); alpha=0.05 min_reads_gene=5 min_reads_library=1000000 shrinkage=apeglm
Assembly: Rnor_6.0
Supplementary files format and content: gene counts assigned by featureCounts and differentially expressed genes assigned by DESeq2

source_name: Kidney

extract_protocol:
Kidneys were removed and flash frozen in liquid N2, RNA was harvested using QIAzol reagent. Libraries were prepared using Illumina TruSeq Stranded mRNA Sample Preparation guide (Illumina, San Diego, CA) with 250ng total RNA.
cDNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney

tag: diet

value: Diet 6 - 1.000mg/kg OTA Diet

tag: strain

value: Fischer

tag: Sex

value: Female

tag: generation

tag: dose timeline

value: In Utero to PND90


title: Healthy controls 16

tag: tissue


title: Calu3_GC_Del_11hpi_B


title: Calu3_GC_Del_0hpi_B


title: Healthy controls 10


title: 340-F1_K


title: 336-F1_K


title: Healthy controls 15


title: P8T2_Ep

tag: fraction

value: Vehicle

tag: cohort

value: Immunotherapy

value: Tumor


title: 335-F1_K


title: Healthy controls 07


title: Healthy controls 13


title: Healthy controls 12


title: Healthy controls 09


title: Healthy controls 06


title: Healthy controls 08


title: P8T2_CD45

tag: ratid

tag: tumorid


title: Healthy controls 11


title: Healthy controls 03


title: Healthy controls 02


title: Healthy controls 05


title: Healthy controls 04


title: 337-F1_K


title: P7T1_DN

value: DN

tag: tissuetype


title: P6T2_CD45

tag: treatment


title: P8T2_DN


title: 339-F1_K


title: 319-F1_K

value: Diet 5 - 0.400mg/kg OTA Diet


title: P4T1_DN


title: P7T1_CD45


title: P6T2_DN


title: 323-F1_K


title: P7T1_Ep

value: Ep


title: 315-F1_K


title: P4T1_CD45


title: 333-F1_K


title: 320-F1_K


title: 321-F1_K


title: 322-F1_K


title: P39T3_Ep


title: 332-F1_K


title: P39T3_DN


title: P36T2_DN


title: P4T1_Ep


title: 318-F1_K


title: 312-F1_K


title: 306-F1_K

value: Diet 4 - 0.160mg/kg OTA Diet


title: 307-F1_K


title: P32T1_DN


title: 300-F1_K


title: P34T1_Ep


title: 285-F1_K

value: Diet 3 - 0.064mg/kg OTA Diet


title: 304-F1_K


title: P34T1_CD45


title: 305-F1_K


title: 302-F1_K


title: P31T2_Ep


title: 308-F1_K


title: 286-F1_K


title: P32T1_Ep


title: 289-F1_K


title: 284-F1_K


title: P36T2_Ep


title: P31T3_Ep


title: 279-F1_K


title: P31T3_DN


title: Healthy controls 01


title: 280-F1_K


title: 281-F1_K


title: P31T3_CD45


title: P31T2_CD45


title: P30T2_Ep


title: P31T1_CD45


title: P34T1_DN


title: P31T2_DN


title: 268-F1_K

value: Diet 2 - 0.026mg/kg OTA Diet


title: 270-F1_K


title: Dog E - Tumor

city: Auburn University

first: Xu

last: Wang

state: AL

address: 273 CASIC Building, Auburn Research Park, 559 Devall Dr

department: Pathobiology, College of Veterinary Medicine

institute: Auburn University

data_processing:
Quality - FASTQC (v 0.10.1) was used to assess the read quality
Trimming - Trimmomatic (v 0.39) was used to remove the adapters, first leading base, and reads with a minimum length of 36 bp. After trimming, approximately 32-45 million reads remained for each sample. FASTQC was used again to confirm all bases had a Phred quality score above 28.
Mapping - Reads were mapped to the indexed canine reference genome (CanFam3.1) obtained from ENSEMBL using HiSat2 (v 2.2.1) and a table of mapped read counts was generated with Stringtie (v 1.3.3)
Differential Gene Expression Analysis - DEseq2 (v 3.14) was used to identify differentially expressed genes in tumor vs. bone. A multi-factor design was used for a paired analysis to include patient ID as a random effect in the design formula (design = ~dog + tissue source) to account for differences between individuals
Filtering - Genes with less than 1 read were excluded. To extract significant DEGs while minimizing noise, the data was filtered using a false discovery rate (FDR) less than 0.05, base mean greater than 10, and log2 fold-change greater than 1 and less than −1 (corresponding to a fold-change of 2 and −2, respectively).
Individual Level Analysis - Variance stabilizing transformation (vst) function in DEseq2 was used on the significant DEGs (padj<0.05, base mean<10, log2FC>1,<-1);  log2 fold-change values for each gene were derived by subtracting the variance stabilized transformed counts (on the log2 scale) of bone from tumor for each dog
Assembly: CanFam3.1
Supplementary files format and content: Gzipped, tab-delimiited text file inlcuding raw gene counts for every gene and every sample

organism: Canis lupus familiaris

source_name: Osteosarcoma

extract_protocol:
Bone: RNA extracted according to Nance et al (Nance R, Agarwal P, Sandey M, Starenki D, Koehler J, Sajib AM, et al. A method for isolating RNA from canine bone. Biotechniques. 2020 Jun;68(6):311–7). Osteosarcoma Tumor: RNA extracted using Tri-Reagent + mechanical homogenization
RNA sequencing libraries were produced with 500 ng of total RNA using the TruSeq PolyA library kit (Illumina) to deplete samples of any RNA aside from polyadenylated mRNA. They were pooled and sequenced on two lanes of the Illumina HiSeq v4 (PE, 50 bp, 25 M reads)

value: Osteosarcoma

tag: dog breed

value: Great Pyranees

tag: source location

value: Left distal radius


title: 278-F1_K

value: Kidney


title: 264-F1_K


title: 265-F1_K


title: P29T2_Ep


title: Dog C - Tumor

value: Doberman Pinscher


title: 299-F1_K

value: Fischer


title: Dog G - Tumor

value: Greyhound

value: Right distal tibia


title: 258-F1_K

value: Diet 1 - 0mg/kg OTA Diet (Control)

value: Female

value: In Utero to PND90


title: Dog F - Tumor

value: Golden Retriever

value: Right distal radius


title: P30T2_DN

value: DN

value: Immunotherapy

value: Tumor


title: 274-F1_K

value: Diet 2 - 0.026mg/kg OTA Diet


title: Dog B - Tumor

value: Osteosarcoma

value: Rottweiler

value: Left distal femur


title: Dog D - Tumor

value: Left proximal humerus


title: 267-F1_K

value: Kidney


title: 257-F1_K

value: Fischer


title: P28T1_Ep

value: Ep


title: 256-F1_K


title: 251-F1_K


title: P29T2_DN


title: 249-F1_K


title: P28T1_CD45


title: 260-F1_K


title: 266-F1_K


title: P29T2_CD45


title: Dog F - Bone

source_name: Bone

value: Bone

value: Phalanx P2


title: P26T1_DN


title: Dog E - Bone

value: Great Pyranees


title: 334-M1_L

value: Diet 6 - 1.000mg/kg OTA Diet

value: Male

value: In Utero to PND90


title: 275-F1_K

value: Female


title: 333-M1_L


title: Dog A - Tumor

value: Golden Retriever

value: Left distal radius


title: P24T3_CD45

value: Immunotherapy

value: Tumor


title: 326-M1_L


title: P22T2_DN

value: DN

value: LY


title: 246-F1_K

value: Diet 1 - 0mg/kg OTA Diet (Control)


title: 323-M1_L

value: Kidney

value: Diet 5 - 0.400mg/kg OTA Diet


title: Dog A - Bone


title: 245-F1_K

value: Fischer


title: Dog G - Bone

value: Bone

value: Greyhound


title: 340-M1_L


title: P26T1_Ep

value: Ep


title: 320-M1_L


title: P22T2_CD45


title: 319-M1_L


title: 339-M1_L

value: Diet 6 - 1.000mg/kg OTA Diet


title: 337-M1_L

value: Male


title: P26T1_CD45


title: 335-M1_L

value: In Utero to PND90


title: Dog D - Bone

value: Phalanx P2


title: 315-M1_L


title: Microwell-seq datasets of E12.5DayEmbryo_8

city: Hanzhou

first: Guoji

address: Yuhangtang street 866

department: Zhejiang University School of Medicine

institute: Center for Stem Cell and Regenerative Medicine

data_processing:
Base-calls were performed with Illumina bcl2fastq
Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular (UMI) barcode sequences using Drop-seq_tools-1.12. The reads quality under 10 were removed. Cellbarcode:In read1, the bases 1-6,22-27,43-48 merge (18bp)； UMI:In read1, the　bases　49-54 (6bp)
ScRNA-seq reads were aligned to the Mus_musculus.GRCm38.88 genome assembly using STAR version (2.5.2a)  with default configurations.
Next, merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags.
Last, we demultiplexed all cell barcodes taken into consideration for the analysis from the exon-tagged bam files to get a digital expression matrix based on UMI counts.The cell barcode is tagged with XC, the UMI is tagged with XM, the gene is tagged with GE.
Genome_build: Mus_musculus.GRCm38.88 genome
Supplementary_files_format_and_content: tab-delimited text files of digital expression matrix (dge) based on raw UMI counts ,columns are cells, and rows are genes.

extract_protocol:
Tissue dissociation and  single-cell lysate
Library preparations were performed with the Microwell-seq protocol

tag: age


title: P21T1_Ep


title: Dog B - Bone

value: Rottweiler


title: 321-M1_L


title: P24T3_Ep


title: 322-M1_L


title: Dog C - Bone

value: Doberman Pinscher


title: Microwell-seq datasets of E12.5DayEmbryo_7


title: AX-REG3-RESUB

first: James

middle: R

last: Monaghan

address: 360 Huntington Ave.

department: Biology

institute: Northeastern University

data_processing:
Base calling was performed on an Illumina HiSeq 3000/4000 sequencer or equivalent with HiSeq Control Software.
Sequenced reads were quality trimmed with Trimmomatic v0.38, then mapped to axolotl transcriptome AmexT_v47 and quantified at gene level using salmon v0.13.1 under Trinity v2.8.5 with parameters "--validateMappings --recoverOrphans --rangeFactorizationBins 4 --seqBias" to generate gene-level counts files
The gene-level counts matrix was generated with Trinity v2.8.5 script "abundance_estimates_to_matrix.pl"
Assembly: AMEXG_v6.0-DD
Supplementary files format and content: tab-delimited text files including gene-level counts for each sample
Supplementary files format and content: matrix file of combined gene-level counts for each sample

organism: Ambystoma mexicanum

source_name: Regenerating retina

extract_protocol:
The retinas were flash-frozen in liquid nitrogen, stored in -80 C until use, and shipped to a Genewiz sequencing facility on dry ice for total RNA extraction and sequencing. The uninjured retinas were pooled into 3 samples (4 retinas per sample, as axolotl retinas are very small). The regenerating retinas were also pooled into 3 samples, with the same animals making up each sample.
RNA libraries were prepared for sequencing using using the NEBNext Ultra II RNA Library Prep Kit for Illumina

treatment_protocol: We performed retinectomy on 12 adult axolotls. The retinas were extracted from the left eyes of anesthesized animals, and the regenerating retinas were extracted at 27 days post injury from the same animals.

value: Regenerating retina

value: regenerating 27 days post retinectomy

tag: genotype

value: leucistic

tag: tissue source

value: pooled from 4 adult axolotls (same as sample 3)


title: P19T1_Ep

value: LY

value: Immunotherapy

value: Tumor


title: AX-REG2-RESUB

value: pooled from 4 adult axolotls (same as sample 2)


title: 307-M1_L

value: Kidney

tag: diet

value: Diet 4 - 0.160mg/kg OTA Diet

value: Fischer


title: P21T1_CD45


title: P22T1_Ep

value: Ep


title: Microwell-seq datasets of E12.5DayEmbryo_9

tag: strain


title: Microwell-seq datasets of E12.5DayEmbryo_5


title: 318-M1_L

value: Diet 5 - 0.400mg/kg OTA Diet

tag: Sex

value: Male


title: 332-M1_L

value: Diet 6 - 1.000mg/kg OTA Diet

tag: generation

value: In Utero to PND90


title: 312-M1_L

tag: dose timeline


title: AX-NM3-RESUB

source_name: Retina

tag: tissue

value: Retina

value: uninjured

value: pooled from 4 adult axolotls


title: 308-M1_L


title: P17T1_Ep

tag: fraction


title: Microwell-seq datasets of E12.5DayEmbryo_6


title: P17T1_DN

source_name: DN cells from Tumor in NMU treated Sprague Dawley rats

value: DN

tag: cohort


title: P19T1_CD45

tag: ratid


title: 304-M1_L


title: 302-M1_L


title: AX-NM1-RESUB

value: leucistic


title: P16T1_CD45

value: LY

tag: tumorid


title: MGC9_CD45

source_name: CD45 cells from Mammary Gland in NMU treated Sprague Dawley rats

value: Characterization

tag: tissuetype

value: Mammary Gland


title: 306-M1_L


title: 301-M1_L


title: AX-REG1-RESUB

value: Regenerating retina

tag: treatment

value: regenerating 27 days post retinectomy

value: pooled from 4 adult axolotls (same as sample 1)


title: Microwell-seq datasets of E10.5DayEmbryo_8


title: Microwell-seq datasets of E12.5DayEmbryo_1


title: Microwell-seq datasets of E12.5DayEmbryo_2


title: 300-M1_L

value: Kidney

value: Diet 4 - 0.160mg/kg OTA Diet

value: Fischer


title: MGC7_CD45


title: Microwell-seq datasets of E12.5DayEmbryo_4


title: Microwell-seq datasets of E12.5DayEmbryo_3


title: MGC8_CD45


title: Microwell-seq datasets of E10.5DayEmbryo_9


title: AX-NM2-RESUB


title: Microwell-seq datasets of E10.5DayEmbryo_6


title: 299-M1_L

value: Male


title: 289-M1_L

value: Diet 3 - 0.064mg/kg OTA Diet


title: MGC6_CD45


title: 286-M1_L

value: In Utero to PND90


title: Feces, sep-housed, KO [18-20210603_S18]

city: Charlottesville

first: Alban

last: Gaultier

state: VA

address: 409 Lane Rd

institute: University of Virginia

description: Zymo Quick-16STM Primer Set V3-V4

data_processing:
Demultiplexed reads were preprocessed using DADA2, and the first 20 base pairs were trimmed from forward and reverse reads prior to merging.
Chimeric reads were filtered out, and taxonomic identification was performed with the standard DADA2 classifier using the 13_8 Greengenes 16S database.
Supplementary files format and content: tab separated values absolute counts of OTUs by sample with taxonomic annotations attached

source_name: Feces

growth_protocol: Fecal Pellet

extract_protocol:
ZymoBIOMICS -96 MagBead DNA kit (Zymo Research, Irvine, CA)
Dual-barcoded primers targeting the 16S V4 region

treatment_protocol: Separately Housed Cd4creAhrfl/fl or Ahrfl/fl

value: Feces

value: Separately Housed

value: Female


title: Feces, sep-housed, KO [17-20210603_S17]

description: Zymo Quick-16STM Primer Set V3-V4


title: Feces, sep-housed, KO [19-20210603_S19]

description: Zymo Quick-16STM Primer Set V3-V4


title: 285-M1_L


title: MGC5_CD45


title: Microwell-seq datasets of E10.5DayEmbryo_5


title: Feces, sep-housed, KO [20-20210603_S20]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of E10.5DayEmbryo_4


title: 284-M1_L


title: Feces, sep-housed, KO [16-20210603_S16]

description: Zymo Quick-16STM Primer Set V3-V4


title: MGC3_CD45


title: Feces, sep-housed, WT [14-20210603_S14]

description: Zymo Quick-16STM Primer Set V3-V4

value: Ahrfl/fl


title: Feces, sep-housed, WT [15-20210603_S15]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of E10.5DayEmbryo_3


title: Microwell-seq datasets of E10.5DayEmbryo_7


title: MGC2_CD45


title: Microwell-seq datasets of E10.5DayEmbryo_2


title: Feces, sep-housed, WT [13-20210603_S13]

description: Zymo Quick-16STM Primer Set V3-V4


title: 282-M1_L


title: MG_CD45

source_name: CD45 cells from Mammary Gland in Sprague Dawley rats

value: MG


title: 281-M1_L


title: Feces, sep-housed, WT [12-20210603_S12]

description: Zymo Quick-16STM Primer Set V3-V4


title: C9T1_CD45

source_name: CD45 cells from Tumor in NMU treated Sprague Dawley rats

value: Tumor


title: 279-M1_L


title: 280-M1_L


title: Microwell-seq datasets of E10.5DayEmbryo_1


title: Feces, sep-housed, WT [11-20210603_S11]

description: Zymo Quick-16STM Primer Set V3-V4


title: C9T1_Ep

source_name: Ep cells from Tumor in NMU treated Sprague Dawley rats

value: Ep

value: Characterization


title: C7T1_CD45


title: Feces, sep-housed, KO [8-20210603_S8]

description: Zymo Quick-16STM Primer Set V3-V4


title: Feces, sep-housed, KO [7-20210603_S7]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of TenDaysUterus_3

value: Uterus


title: 275-M1_L

value: Diet 2 - 0.026mg/kg OTA Diet


title: Microwell-seq datasets of TenDaysUterus_2


title: Microwell-seq datasets of AdultUterus_1


title: Feces, sep-housed, KO [10-20210603_S10]

description: Zymo Quick-16STM Primer Set V3-V4


title: Feces, sep-housed, KO [9-20210603_S9]

description: Zymo Quick-16STM Primer Set V3-V4


title: C5T1_Ep


title: Microwell-seq datasets of ThreeWeeksUterus_1


title: 267-M1_L


title: 270-M1_L


title: Microwell-seq datasets of TenDaysUterus_1


title: 274-M1_L


title: C7T1_Ep


title: 268-M1_L


title: Feces, sep-housed, WT [5-20210603_S5]

description: Zymo Quick-16STM Primer Set V3-V4


title: 265-M1_L


title: Microwell-seq datasets of NeonatalUterus_2

value: neonatal


title: Feces, sep-housed, WT [3-20210603_S3]

description: Zymo Quick-16STM Primer Set V3-V4


title: C5T1_CD45


title: C2T1_CD45


title: Feces, sep-housed, KO [6-20210603_S6]

description: Zymo Quick-16STM Primer Set V3-V4


title: C2T1_Ep


title: C3T1_Ep


title: Microwell-seq datasets of AdultUterus_2


title: Feces, sep-housed, WT [4-20210603_S4]

description: Zymo Quick-16STM Primer Set V3-V4


title: 264-M1_L

value: Kidney


title: C3T1_CD45


title: Microwell-seq datasets of FetalFemaleGonad_1


title: Feces, sep-housed, WT [2-20210603_S2]

description: Zymo Quick-16STM Primer Set V3-V4


title: 258-M1_L

value: Diet 1 - 0mg/kg OTA Diet (Control)


title: 266-M1_L

value: Fischer


title: C17T4_CD45


title: Microwell-seq datasets of AdultTestis_5

value: Testis

value: Male


title: C17T4_Ep


title: Microwell-seq datasets of AdultTestis_4


title: C11T1_Ep


title: 257-M1_L

value: In Utero to PND90


title: C11T1_CD45


title: 251-M1_L


title: 254-M1_L


title: Microwell-seq datasets of NeonatalUterus_1


title: Cecum, WT [zr4936_23V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

source_name: Cecum Contents

growth_protocol: Cecum Contents

extract_protocol:
ZymoBIOMICS -96 MagBead DNA kit (Zymo Research, Irvine, CA)
V3-V4 region Quick-16S NGS Library Prep Kit (Zymo Reseach, Irvine, CA)

value: Cecum Contents


title: Cecum, WT [zr4936_22V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Separately Housed


title: C10T6_CD45


title: Microwell-seq datasets of ThreeWeeksTestis_1


title: Feces, sep-housed, WT [1-20210603_S1]

description: Zymo Quick-16STM Primer Set V3-V4

value: Feces


title: Microwell-seq datasets of AdultTestis_1


title: Cecum, WT [zr4936_21V3V4]

description: Zymo Quick-16STM Primer Set V3-V4

value: Ahrfl/fl

value: Female


title: C10T4_Ep

value: Tumor


title: Cecum, WT [zr4936_24V3V4]

description: Zymo Quick-16STM Primer Set V3-V4


title: Microwell-seq datasets of TenDaysTestis_2


title: 256-M1_L


title: Microwell-seq datasets of AdultTestis_3


title: C10T4_CD45


title: Microwell-seq datasets of TenDaysTestis_1


title: 249-M1_L


title: C10T2_Ep

value: Ep