title: QKI_Input_Rep1

data_processing:
Sequencing reads were trimmed with Trimmomatic (v0.36) to remove adaptors and low quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 genome with Bowtie2 (v2.2.9) with default parameters.
PCR duplicate reads were removed with Samtools (v0.1.19) rmdup.
Reads were extended to 250 bp (to approximate fragment length) with UCSC tools bedextendranges.
For each ChIP antibody, reads for each sample were randomly down-sampled to equal numbers using the GNU shuf utility.
MeCP2 ChIP-seq and input reads were quantified in mm10 RefSeq gene bodies (excluding the first 3 kb, which is relatively depleted for MeCP2 binding and DNA methylation, and thus excluding genes less than 4.5 kb in length) using Bedtools map (v2.26)
Assembly: mm10
Supplementary files format and content: tad-delimited text file with raw MeCP2 ChIP and input read counts in gene bodies excluding the first 3kb (TSS +3kb to TTS)

source_name: Forebrain

extract_protocol:
Forebrain (cortex + hippocampus) was dissected from 8-to-11-week-old male MeCP2 QKI and WT mice and flash frozen. Tissue was homogenized in 1% formaldehyde and cross-linked by rotating for 10 minutes at room temperature. Cross-linking was quenched with 125mM glycine for 5 minutes at room temperature. Tissue was pelleted by spinning at 500 x g for 5 minutes at 4°C, washed once with PBS, and spun again at 500 x g for 5 minutes at 4°C. Cells were lysed by resuspending in Buffer L1 (50 mM HEPES pH 7.5, 140mM NaCl, 1 mM EDTA pH 8, 1 mM EGTA pH 8, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1X protease inhibitors) and rotating for 10 minutes at 4°C. Nuclei were pelleted by spinning at 500 x g for 5 minutes at 4°C, then washed by rotating for 10 minutes at 4°C in Buffer L2 (10 mM Tris pH 8, 200 mM NaCl, 1X protease inhibitors). Nuclei were pelleted by spinning at 500 x g for 5 minutes, then resuspended in Buffer LB3 (10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-Lauroylsarcosine, 1X protease inhibitors). Chromatin was sonicated in a Diagenode Bioruptor (High power, 65 cycles, 30 seconds on, 45 seconds off). Insoluble material was removed by spinning at 16,000 x g for 10 minutes at 4°C, and Triton X-100 was added to soluble chromatin to a final concentration of 1%. Chromatin was pre-cleared for two hours with Protein A Dynabeads, then incubated with Protein A Dynabeads conjugated to MeCP2 antibody [Chen et al 2003] overnight at 4°C. Beads were washed at 4°C twice with Low Salt Buffer (20 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with High Salt Buffer (20 mM Tris pH 8, 500 mM NaCl, 2 mM EDTA, 1% Triton X-100, 0.1% SDS), twice with LiCl Wash Buffer (10 mM Tris pH 8, 1 mM EDTA, 1% NP-40, 250 mM LiCl, 1% sodium deoxycholate) and once with TE Buffer (50 mM Tris pH 8, 10 mM EDTA). Chromatin was eluted off beads in TE Buffer with 1% SDS at 65°C for one hour, and crosslinking was reversed overnight at 65°C. Chromatin was treated with RNase A for 30 minutes at 37°C and Proteinase K for 2 hours at 55°C. DNA was phenol-chloroform extracted and purified with the QIAGEN PCR purification kit.
Libraries were generated using the NuGEN Ovation Ultralow System V2 following manufacturer instructions.

value: Forebrain

value: 8-11 weeks


title: WT_Input_Rep2

status: Public on Oct 15 2023

type: SRA

city: Roslindale

first: Tess

last: Whitwam

address: 41 Brookdale Street

country: USA

institute: Harvard University

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: tissue

tag: Sex

value: Male

tag: developmental stage

tag: genotype

value: WT

tag: strain

tag: chip antibody


title: dbdb AAV9_null_1

city: Wuhan

first: Saiyang

last: Xie

address: Jiefang Road 238

country: China

institute: Wuhan university

library_source: transcriptomic

data_processing:
Raw sequencing reads containing more than 2-N bases were first discarded. Subsequently, the raw reads were trimmed of adaptors and low-quality bases using a FASTX-Toolkit (v.0.0.13; http://hannonlab.cshl.edu/fastx toolkit/).
In addition, short reads of less than 16 nt were dropped to retain clean reads, which were subsequently aligned to the GRch38 genome by HISAT2 . Uniquely mapped reads were ultimately used to calculate read number and paired-end fragments per kilobase of exon per million fragments mapped (FPKM) for each gene.
The software DEseq2, which is specifically used to analyze the differential expression of genes, was applied to screen the RNA-seq data for DEGs. The results were analyzed based on the fold change (FC≥2 or ≤0.5) and false discovery rate (FDR<0.05) to determine whether a gene was differentially expressed.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample

molecule: total RNA

source_name: Left ventricular tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 6000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: Left ventricular tissue

value: db/db

tag: treatment


title: dbdb AAV9_USP28_1


title: WT_dLGN_P16_Rep1

data_processing:
Reads were trimmed with Trimmomatic (v0.36) to remove Illumina adaptors and low-quality sequence (settings: LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:50).
Trimmed reads were mapped to the mm10 Refseq transcriptome and genome using STAR (v2.5.2b).
Reads were counted in the full gene body (TSS to TTS of longest isoform, in order to include intronic reads) using Subread featureCounts.
Differential expression was performed with the R package edgeR (v3.34.1) or DESeq2 (v1.34.0).
Genes with low counts were filtered by keeping only genes with rowSums(cpm(y)>1) >= (number of samples per group). Differentially expressed genes were defined by an FDR < 0.05 with no fold-change cut-off. For DESeq2 analyses, shrinkage of effect sizes was performed using lfcshrink and the apeglm method following differential expression analysis
Assembly: mm10
Supplementary files format and content: tad-delimited text file with raw counts in exons for each sample

source_name: dLGN

extract_protocol:
dLGN and visual cortex were dissected from littermate male mice (WT or QKI) and flash frozen. After collecting all replicates, tissue was homogenized in TRIzol reagent, and RNA was chloroform extracted and then purified using the Qiagen RNeasy Micro Kit with on-column DNase treatment according to the manufacturer’s instructions.
Total RNA (150-200 ng for dLGN libraries, 500 ng for visual cortex libraries) was used to generate libraries following rRNA depletion (NEBNext, E6310X) according to the manufacturer’s instructions (NEBNext, E7420).

value: dLGN


title: control [1312908]

city: WenZhou

first: Zheng

last: GongWei

address: OuHai ChaShan

institute: WenZhou Medical University

description:
otu_table.c.relative.txt
otu_table.f.relative.txt
otu_table.g.relative.txt
otu_table.k.relative.xls
otu_table.o.relative.xls
otu_table.p.relative.xls

data_processing:
library strategy: 16S_rRNA
After trimming off the barcodes and primers, paired-end sequences were assembled with FLASH (v1.2.7).
The assembled raw tags were quality controlled with Fastp (v0.23.1) to obtain high-quality clean tags
Chimeric sequences were further removed from clean tags using vsearch (v2.22.1)
Supplementary files format and content: otu_table.c.relative.txt: class level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.f.relative.txt: family level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.g.relative.txt: genus level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.k.relative.xls: kingdom level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.o.relative.xls: order level OTU(Operational Taxonomic Units) abundance table
Supplementary files format and content: otu_table.p.relative.xls: phylum level OTU(Operational Taxonomic Units) abundance table

organism: Homo sapiens

source_name: fecal samples

extract_protocol:
Qiagen Gel Extraction Kit (Qiagen, Germany)
TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA)

value: fecal samples

tag: subject status

value: matched controls


title: QKI_MeCP2_ChIPseq_Rep3

value: QKI

value: MeCP2 (Chen et al., 2003)


title: QKI_input_Rep3


title: QKI_Input_Rep2


title: WT_Input_Rep3


title: control [1339346n]

data_processing:
Raw transcriptomic sequencing data were qualified using the FastQC
Ensembl human reference genome (http://asia.ensembl.org/info/data/ftp/index.html, file name: Homo_sapiens.GRCh37.75.cdna.all.fa) was used for alignment and annotation.
The Hisat2 (v2.0.5) tool was used to establish index for reference genome, and align reads to the reference genome. The FeatureCounts (v1.5.0-p3) method was used to summarize read counts for each gene.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: blood

extract_protocol:
QIAzol and miRNeasy Mini Kit (Qiagen, CA, USA)
TruSeq® DNA PCR-Free Sample Preparation Kit (Illumina, USA)

value: blood

value: control


title: control [1336408n]


title: WT_Input_Rep1


title: Control_3

value: Wild Type


title: QKI_MeCP2_ChIPseq_Rep2


title: control [1332881n]


title: QKI_MeCP2_ChIPseq_Rep1


title: control [1336037n]


title: dbdb AAV9_null_3


title: Control_2


title: WT_MeCP2_ChIPseq_Rep2


title: WT_MeCP2_ChIPseq_Rep1


title: control [1331432n]


title: Baso.Nb.B7hi.Lung#2_RNA-seq

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: Lung

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: age

value: 6 weeks old

value: Lung

tag: cell type

value: Basophils

tag: sorting markers

value: Tissue finely mince and digested in collagenase IV (400 U/mL) + Dispase (0.1% w/v) for 30 minutes


title: MC.Nb.B7hi.Lung#2_RNA-seq

value: Mast Cells


title: control [1331868n]


title: MC.Nb.B7hi.Lung#1_RNA-seq


title: Baso.Nb.B7hi.Lung#1_RNA-seq


title: control [1329305n]


title: KO_3_Olfm4 WT

city: Guang zhou

first: ming'qiang

last: lai

address: Sha Tai Road 1023

institute: Southern Medical University

data_processing:
cutadapt version 1.11 and Hisat2 version 2.1.0
The adapter and low-quality reads were filtered out through cutadapt (version 1.11).
Clean reads were mapped to the mm10 reference genomes by Hisat2 (version 2.1.0), allowing up to two mismatches
These genes were subjected to alignment against public protein databases;NR(RefSeq non-redundant proteins). Featurecount(v1.6.0) was used for transcript abundance estimation and normalization of expression values as FPKM (Fragments per kilobase of transcript per million fragments mapped)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BAT brown adipose tissue

extract_protocol:
Total RNA was extracted using the RNAprep Pure Kit DP432 (TIANGEN Biotech Co.,Ltd., Beijing, China), following the manufacturer’s instructions. 1 μg of total RNA was used.
Illumina's VAHTS mRNA-seq V8 Library Prep Kit is used to construct RNA libraries, following the manufacturer’s instructions.

value: BAT brown adipose tissue

tag: strain background


title: KO_1_Olfm4 WT


title: MC.Tongue#1_RNA-seq

source_name: Tongue

value: Tongue


title: case [1327338p]

value: case


title: Ctrl_3_Olfm4 WT

value: Ctrl


title: Control_1

value: Left ventricular tissue


title: MC.Palate#2_RNA-seq

source_name: Palate

value: Palate


title: MC.Palate#1_RNA-seq


title: WT_MeCP2_ChIPseq_Rep3

value: Forebrain

value: Male

value: 8-11 weeks

value: WT


title: Ctrl_2_Olfm4 WT


title: MC.Sp#2_RNA-seq

source_name: Spleen

value: Spleen


title: MC.Tongue#2_RNA-seq


title: KO_2_Olfm4 WT


title: case [1326041p]

value: blood


title: MC.Fat#2_RNA-seq

source_name: Fat

value: 6 weeks old

value: Fat


title: MC.Fat#1_RNA-seq


title: control [1326212n]

value: control


title: Ctrl_1_Olfm4 WT


title: MC.BM#2_RNA-seq

source_name: Bone Marrow

value: Bone Marrow


title: control [1324576n]


title: LSM14B_KO_MII_Rep3

city: Jinan

first: Yanling

last: Wan

address: Medicine west wenhua road

institute: Center for Reproductive Medicine, Shandong University

data_processing:
The DESeq2 package (version 1.38.3) was utilized to identify differentially expressed genes (DEGs) between the two groups (3 replicates in each group).
Genes were defined as DEGs when logFC ≥ 2 and logFC ≤ −2, with a P value cutoff of 0.05. To perform Gene Ontology (GO) and pathway enrichment analyses, clusterProfiler (version 4.0.5) and Metascape were employed.
Assembly: mm10
Supplementary files format and content: The DESeq2 package (version 1.38.3) was utilized to identify differentially expressed genes (DEGs) between the two groups (3 replicates in each group).

source_name: oocyte

growth_protocol: Mice housing and all experimental protocols were approved by the Regional Ethics Committee of Shandong University.

extract_protocol:
We carried out the amplification by the Smart Seq2 method. An Oligo dT primer wa s introduced to the reverse transcription reaction for first strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production.
purification step to clean up the production. Then the cDNA production was checked by Qubit ® 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2kbp. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A tailing, adapter ligation, PCR amplification and library validation.

treatment_protocol: Fifteen oocytes at each of the three stages (GV, MI, MII) were collected from wild-type and Lsm14b-/- mice  respectively, with three replicates per sample. After  washing three times in phosphate-buffered saline (PBS), the samples were collected in tubes with lysis component and ribonuclease inhibitor and then transferred to -80°C freezer with liquid nitrogen.

value: oocyte

tag: cell line

value: MII


title: MC.BM#1_RNA-seq

value: Mast Cells


title: B.PC.BM#4_RNA-seq

value: B cells

value: GFPhi CD138+ MHCIIlo (dump:NK1.1- TCRb- Gr1- CD11b-)


title: case [1324273p]

value: case


title: case [1324765p]


title: MC.Sp#1_RNA-seq


title: LSM14B_KO_MII_Rep1


title: proB.FrD.BM#3_RNA-seq


title: MC.BM#3_RNA-seq


title: LSM14B_KO_MII_Rep2


title: LSM14B_WT_MII_Rep3


title: proB.FrD.BM#2_RNA-seq


title: case [1323238p]


title: MAIT.SeT.3d.Lu#3_RNA-seq

value: 9 weeks old

value: Lung

value: ab T cells


title: proB.FrD.BM#1_RNA-seq


title: case [1323118p]


title: MAIT.SeT.3d.Lu#1_RNA-seq


title: LSM14B_WT_MII_Rep1


title: LSM14B_KO_MI_Rep3

value: MI


title: LSM14B_WT_MII_Rep2


title: MAIT.SeT.3d.Lu#2_RNA-seq


title: case [1322936p]


title: MAIT.Th#3_RNA-seq

source_name: Thymus

value: Thymus


title: B.PC.BM#3_RNA-seq


title: MAIT.Lv#3_RNA-seq

source_name: Liver

value: Liver


title: case [1324132p]

value: blood


title: LSM14B_WT_MI_Rep3


title: MAIT.Th#1_RNA-seq


title: control [1322807n]


title: case [1322935p]


title: LSM14B_KO_MI_Rep2


title: control [1322654n]


title: B.PC.BM#2_RNA-seq

value: 6 weeks old


title: MAIT.Lv#2_RNA-seq


title: MAIT.Lu#2_RNA-seq


title: case [1322533p]


title: MAIT.Lv#1_RNA-seq


title: case [1322424p]


title: MAIT.Lu#1_RNA-seq


title: MAIT.Lu#3_RNA-seq


title: LSM14B_KO_MI_Rep1


title: LSM14B_WT_MI_Rep2


title: T8.LCMV.d32.Sp#7_RNA-seq

value: 12 weeks old

value: Spleen


title: T8.LCMV.d32.Sp#8_RNA-seq


title: MAIT.Sp#2_RNA-seq


title: MAIT.Th#2_RNA-seq


title: LSM14B_KO_GV_Rep3

value: GV


title: control [1321644n]

value: control


title: T8.LCMV.d32.Sp#6_RNA-seq


title: case [1321638p]


title: T8.LCMV.d32.Sp#5_RNA-seq


title: LSM14B_KO_GV_Rep2

value: oocyte


title: T8.LCMV.d32.SG#1_RNA-seq

source_name: Salivary Gland

value: Salivary Gland


title: LSM14B_KO_GV_Rep1


title: LSM14B_WT_GV_Rep3


title: case [1321623p]


title: case [1321612p]


title: T8.LCMV.d32.Lv#3_RNA-seq


title: T8.LCMV.d32.SG#4_RNA-seq


title: T8.LCMV.d32.Sp#3_RNA-seq


title: MAIT.Sp#1_RNA-seq


title: T8.LCMV.d32.Kd#5_RNA-seq

source_name: Kidney

value: Kidney


title: case [1320908p]


title: LSM14B_WT_GV_Rep2


title: T8.LCMV.d32.Kd#4_RNA-seq


title: LSM14B_WT_MI_Rep1


title: case [1319398p]


title: LSM14B_WT_GV_Rep1


title: case [1320471p]


title: T8.LCMV.d32.Kd#3_RNA-seq


title: T8.LCMV.d32.Fat#4_RNA-seq

value: Fat


title: T8.LCMV.d32.Lv#1_RNA-seq


title: Colon_GsMTx4_R3

first: Xiuli

last: Zuo

address: 107 Wenhuaxi Road

institute: Shandong University

data_processing:
Reads generated with Illumina NovaSeq 6000 Sequencing System were further filtered by Cutadapt. The parameters were as follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases.
Then sequence quality was verified using FastQC, including the Q20, Q30, and GC-content of the clean data.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was used according to the RNA-seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: colon

value: WT

value: 2.5% DSS in drinking water for 7 days, with intravenous injection of 10 mg/kg GsMTx4 on days 2, 4, and 6.


title: T8.LCMV.d32.Bl#5_RNA-seq

source_name: Blood

value: Blood

value: ab T cells


title: Colon_GsMTx4_R2


title: T8.LCMV.d32.Fat#3_RNA-seq


title: T8.LCMV.d32.Bl#6_RNA-seq


title: case [1319334p]

value: case


title: T8.LCMV.d32.SG#3_RNA-seq


title: control [1319014n]


title: SM92_infested_2

city: Hyderabad

first: Ramesh

middle: Venkata

last: Sonti

state: Telangana

address: Habsiguda

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

description:
Samples were collected 72 hours post infestation or at corresponding time from uninfested plants. SM is susceptible to YSB and SM92 is tolerant to YSB,
sm92_raw_gene_counts.txt

data_processing:
The raw data was obtained, and the quality was assessed using FastQC.
Adapters and low-quality reads were trimmed using Trim Galore!
RNA-STAR was used to align the trimmed reads to the rice genome (MSU Rice Genome Annotation Project - version 7)
Reads that mapped to the genes were quantified using featureCounts
Differential gene expression was obtained using the R library DEseq2
Assembly: MSU Rice Genome Annotation Project - version 7
Supplementary files format and content: Format: txt; Description: Raw gene counts as obtained using FeatureCounts

organism: Oryza sativa

source_name: Stem tissue

growth_protocol: Rice plants were grown in Indian Institute of Rice Research, Hyderabad field till the booting stage at which the infestation was performed.

extract_protocol:
Total RNA was extracted from all the samples usign Qiagen RNeasy RNA isolation kit with on-column DNase treatment. The integrity of RNA samples were tested using Bioanalyzer 2100 and quantified using Qubit fluoromter 4.0.
1 µg of total RNA samples was used for library preparation for each sample using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant; ssRNA-seq (reversely stranded)

treatment_protocol: YSB larvae were manually infested onto the tillers of SM and SM92 at the booting stage of the plants.

value: Stem tissue

value: YSB

tag: time

value: 72 hours


title: Colon_DSS_R3

value: 2.5% DSS in drinking water for 7 days.


title: Colon_GsMTx4_R1


title: SM92_infested_1


title: T8.LCMV.d32.Bl#3_RNA-seq

value: 12 weeks old


title: control [1318973n]

value: blood


title: control [1316883n]

value: control


title: SM92_uninfested_2

value: Control


title: T8.IEL.LCMV.d32.SI#5_RNA-seq

source_name: Small Intestine

value: 6 weeks old

value: Small Intestine


title: SM92_uninfested_1


title: case [1316766p]

source_name: blood


title: Colon_Control_R3

value: Normal drinking water.


title: Colon_DSS_R2

value: colon


title: case [1315658p]


title: case [1315846p]


title: Colon_DSS_R1

value: WT


title: SM_infested_2

description:
Samples were collected 72 hours post infestation or at corresponding time from uninfested plants. SM is susceptible to YSB and SM92 is tolerant to YSB,
sm_raw_gene_counts.txt

value: SM


title: T8.IEL.LCMV.d32.SI#4_RNA-seq


title: Colon_Control_R2


title: Colon_Control_R1


title: SM_infested_1


title: MC.Sk.F#3_RNA-seq

source_name: Skeleton

value: Skeleton

value: Mast Cells


title: control [1314524n]


title: control [1315626n]


title: MC.Sk.F#2_RNA-seq


title: SM_uninfested_2


title: SM_uninfested_1


title: Adipoq-Cre; Pak4 flox/flox, n 3 [KO_C]

city: Jeonju-si

first: Byung-Hyun

last: Park

address: 567 Baekje-daero, Deokjin-gu

country: South Korea

institute: Jeonbuk National University Medical School

data_processing:
bcl2fastq2-v2.20.0 package was used for basecalling.
Quality check of basecalling was done using FastQC v0.11.7 by calculating phred quality score.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1
Transcript assembly and calculation of normalized Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were done using StringTie v2.1.3b.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: eWAT

extract_protocol:
Epididymal white adipose tissues were excised from mice and stored in RNAlater solution. Total RNA was extracted using Trizol.
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA LT Sample Prep Kit (#RS-122-2001)

value: eWAT

value: adipocytes

value: Adipose tissue-specific Pak4 KO


title: T8.LCMV.d32.Bl#4_RNA-seq

value: Blood

value: ab T cells


title: Adipoq-Cre; Pak4 flox/flox, n 2 [KO_B]


title: MC.Sk.F#1_RNA-seq


title: control [1314353n]


title: T8.IEL.LCMV.d32.SI#3_RNA-seq


title: MC.Sk.M#3_RNA-seq


title: RNA-Seq: TE3 Cells treated with DMSO for 12 hours rep2

city: Worcester

first: Rui

last: Li

state: Massachusetts

address: 364 Plantation Street, LRB

department: MCCB

institute: University of Massachusetts Medical School

description: DMSO for control

data_processing:
The analysis were performed on the OneStopRNASeq platform.
Specifically, paired-end RNASeq reads were aligned to human genome hg38 with STAR
Gene expression were quantified with featureCounts
Genome annotation file used was Gencode(v34)
Differential analysis processed with DESeq2
Assembly: hg38
Supplementary files format and content: excel: count and TPM

source_name: Breast cancer cells

growth_protocol: Grown in DMEM (high glucose) supplemented with 5% FBS

extract_protocol:
RNA was collected using the RNA miniprep kit by BioBasic (Catalogue number: BS88136)
As per KAPA Stranded mRNA Hyper prep polyA selected kit with 201-300 bp insert size (KAPA Biosystems, Wilmington, MA) using 250 ng total RNAs as input.
library quality and quantity was analyzed by Agilent Technologies 4200 station and Qubit 3.0(Thermo Fisher Scientific Inc, Waltham, MA)Fluorometer.

treatment_protocol: 2.5x10^5 cells per condition were plated and 24 hours after plating the respective treatments were added for 12 hours at which time-point RNA was collected.

value: Triple negative breast cancer cells

tag: parental cell line

tag: passages


title: RNA-Seq: TE3 Cells treated with DMSO for 12 hours rep3

description: DMSO for control


title: RNA-Seq: TE3 Cells treated with DMSO for 12 hours rep1

description: DMSO for control


title: case [1313636p]

value: blood

value: case


title: Pak4 flox/flox, n 3 [WT_C]


title: case [1313438p]


title: MC.Sk.M#1_RNA-seq


title: MC.To.F#3_RNA-seq

source_name: Tongue

value: Tongue


title: MC.Sk.M#2_RNA-seq

value: 6 weeks old


title: RNA-Seq: TE3 Cells treated with 10 uM BI-79327 for 12 hours rep3

description: BI-749327- TRPC6 inhibitor (MedChem express)


title: Pak4 flox/flox, n 2 [WT_B]


title: MC.To.F#2_RNA-seq


title: Pak4 flox/flox, n 1 [WT_A]


title: RNA-Seq: TE3 Cells treated with 10 uM BI-79327 for 12 hours rep2


title: RNA-Seq: TE3 Cells treated with 10 uM BI-79327 for 12 hours rep1


title: case [1311926p]


title: case [1311467p]


title: MC.To.F#1_RNA-seq


title: case [1313791p]


title: Adipoq-Cre; Pak4 flox/flox, n 1 [KO_A]


title: MC.To.M#3_RNA-seq


title: ID1_KO_2_TAM

city: Beijing

first: Yang

last: Chen

address: 1 Xian Nong Tan Street

institute: Peking Union Medical Collage

data_processing:
Agilent 2100 Bioanalyzer  used for basecalling.
Raw data (raw reads) were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
If it was transcript-level quantification, FPKM and read counts value of each transcript (protein_coding) was calculated using bowtie2 and eXpress. DEGs were identified using the DESeq (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: TAMs isolated from tumors of Id1-Lyz-KO mice in the s.c. tumor model

growth_protocol: 6×10^5 MC38 cells were mixed with 2×10^5 control or Id1-ko TAMs  and implanted to the C57BL/6J mice.

extract_protocol:
Subcutaneous tumors of the two groups were separated and digested into single cells using IV collagenase and DNASE I.TAM cells were then isolated using CD11b and F4/80 magnetic microbeads.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAMs


title: control [1310251n]

value: control


title: MC.To.M#2_RNA-seq


title: ID1_KO_1_TAM


title: case [1308827p]


title: C57_3_TAM

source_name: TAMs isolated from tumors of Id1f/f mice in the s.c. tumor model


title: MC.To.M#1_RNA-seq


title: case [1249448p]


title: case [1309866p]


title: control [1312908n]


title: arabidopsis thaliana seedlings_3, traffic noise, 48h

city: Daejeon

first: Seyun

last: Kim

address: Daehak-ro 291

institute: KAIST

description: Arabidopsis thaliana seeds exposed to traffic noise (average 75 dB) for 48h

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to TAIR10.1 (NCBI) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text files include read count values for each Sample

organism: Arabidopsis thaliana

source_name: whole seedlings

growth_protocol: Wild-type seeds of Arabidopsis thaliana were seeded on half-strength MS-agar plates (MS 2.2 g, MES 0.5 g, phytoAgar 8 g, distilled water 1L, pH 5.7) (Duchefa M0222.0050, M1503.0250, P1003.1000). Plates were sealed with 3M micropore tape to prevent dehydration and wrapped in aluminum foil to block light.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: To collect urban traffic noise, sound recording was performed in Gangnam area with high traffic density by using iPhone 13 (Apple, Inc). To block external noise interference, the noise treatments were performed in a custom-made, sound-proof facility by using the inote BT-V3 speaker system (Fusionfnc, Inc). For the untreated control groups, the seeds were exposed to the same experimental conditions with background white noise at average 10 dB.

value: whole seedlings

value: wild-type

value: traffic noise for 48h


title: C57_2_TAM


title: case [1240831p]


title: ID1_KO_3_TAM


title: arabidopsis thaliana seedlings_1, traffic noise, 48h


title: SH4_3

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
Clean reads were obtained after the removal of reads containing adapter and ploy-N and having low quality.
HISAT2 was used to align the clean reads to the reference genome.
Differential expression was assessed using DESeq by using read counts as input.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Text file for FPKM values of each gene

source_name: ESCC cells

extract_protocol:
TRIzol extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ESCC

value: silenced LINK-A#2

value: LINK-A knockdown


title: ES-2+exosome

type: RNA

city: Suita

first: Aasa

last: Shimizu

state: Osaka

address: 2-2, Yamadaoka

country: Japan

institute: Osaka University

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: ovarian cancer cell line

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: RNA was prepared using the Rneasy Mini kit (Purchased from QIAGEN, 74104) following the manufacturer's recommendations.

tag: gender

value: female

value: Ovarian cancer cell line ES-2

value: exosome


title: arabidopsis thaliana seedlings_3, control white noise, 48h

description: Arabidopsis thaliana seeds exposed to background white noise (average 10 dB) for 48h

tag: tissue

value: control white noise for 48h


title: SH4_2


title: C26 cells, exercise [EXP0226]

city: Planegg

first: Maximilian

middle: Michael

last: Saller

state: Bavaria

address: Fraunhoferstraße 20

department: Department of Orthopedics and Trauma Surgery

country: Germany

institute: LMU Hospital

data_processing:
pseudoaligned to the mouse reference genome (version GRCm39.106) with kallisto (version 0.48)
Assembly: GRCm39.106
Supplementary files format and content: summarized experiment

molecule: polyA RNA

source_name: cancer

growth_protocol: C26 cells were cultured in high glucose DMEM (# 41966 Gibco) supplemented with 10% of foetal bovine serum (Life Technologies) and Pen/Strep solution (penicillin 100U/ml and streptomycin 0.1mg/mL, Gibco). Cell culture was maintained at 37°C with a humidified atmosphere of 5% CO2. Low‑passage cell lines were used.

extract_protocol:
To identify transcriptional changes after one bout of exercise, approximately 100 mg of cancer tissue was cut‑off on dry ice, transferred to TRIzol (Invitrogen), homogenized three times at 4,000 rpm for 10 seconds two times using a high throughput tissue homogenizer (Precellys 24, Bertin Technologies). The homogenates were then centrifuged at 14,000 g for 1 minute at 4°C to remove tissue debris. Total RNA was isolated from the Trizol homogenates using the Direct-zol™ RNA MiniPrep Kit (Zymo Research) and RNA integrity was validated using BioAnalyzer (Agilent).
cDNA sequencing libraries were generated with the CORALL mRNA-Seq V2 (Lexogen) according to the manufacturers’ protocol. All libraries were sequenced on the same run using a NEXTSEQ™1000 device (Illumina) with a read length of 50 bp and a sequencing depth of approximately 20 million reads per sample.

treatment_protocol: To initiate a tumour, we injected a C26 cell suspension subcutaneously, dorsally into 3-month-old mice. Tumour-bearing mice received 100,000 C26 cells in PBS and were divided in two different groups: rest (control, n=3 females, 2 males) and exercise (n=3 females & 3 males). When C26 mice had lost 10% of their body weight when compared to the day of inoculation (D0), they performed one bout of exercise in the morning and immediately after that we collected the C26 tumour and a serum samples.

value: BALB/c

tag: Sex

value: male

value: cancer

value: C26 colon carcinoma cells

value: wildtype

value: one bout of expercise


title: C26 cells, exercise [EXP0224]


title: C26 cells, rest [EXP0227]

value: rest


title: SH4_1


title: arabidopsis thaliana seedlings_2, control white noise, 48h

value: whole seedlings


title: C26 cells, rest [EXP0225]


title: ES-2+exosome+siRNA

value: exosome containing Met-targetting siRNAs

value: Met knockdown


title: Uterine artery endothelial cells, PFOS- Treated, Replicate 4

city: Madison

first: Sathish

last: Kumar

state: WI

address: 2015 Linden Dr

department: Comparative Biosciences

institute: University of Wisconsin

data_processing:
Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8)
Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt ) were aligned to reference genome using Hisat2 software
The transcript abundances for each sample was estimated with StringTie, and the FPKM value for gene and transcript level were calculated with R package Ballgown
The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of those sequences
rMATS was used to detect alternative splicing events and plots
Assembly: GRCh37
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample

source_name: Uerine artery endothelial cells

growth_protocol: hUAECs cultured in endothelial cell medium containing 5% fetal bovine serum, endothelial growth supplements, and 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from the cells using an RNeasy mini kit (Qiagen) and 1-2 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq library was prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina) as per manufacturer's instruction.

treatment_protocol: The cells were treated with PFOS for 24 hours at a concentration of 10 µmol/L

value: Female

tag: condition

value: Pregnant

value: Uerine artery endothelial cells

value: WT

value: 24H PFOS- 10 uM


title: arabidopsis thaliana seedlings_2, traffic noise, 48h

tag: genotype

value: wild-type

value: traffic noise for 48h


title: Uterine artery endothelial cells, PFOS- Treated, Replicate 2


title: arabidopsis thaliana seedlings_1, control white noise, 48h

value: control white noise for 48h


title: SH2_3

value: ESCC

value: silenced LINK-A#1

value: LINK-A knockdown


title: C26 cells, exercise [EXP0223]

tag: strain

value: BALB/c

value: male

value: cancer

value: C26 colon carcinoma cells

value: wildtype


title: Uterine artery endothelial cells, PFOS- Treated, Replicate 1


title: C57_1_TAM

value: TAMs


title: C26 cells, exercise [EXP0222]

value: female

value: one bout of expercise


title: SH2_2


title: Uterine artery endothelial cells, Vehicle- Treated, Replicate 4

value: Female

value: Pregnant

value: Uerine artery endothelial cells

value: 24H DMSO


title: ES-2

value: Ovarian cancer cell line ES-2

value: control


title: Uterine artery endothelial cells, Vehicle- Treated, Replicate 3

value: WT


title: C26 cells, exercise [EXP0221]


title: 1 hour after -Pi, biol repl 2

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

data_processing:
The RNA-seq raw reads were mapped to the C. glabrata genome downloaded from the Candida Genome Database (CGD, RRID:SCR_002036, version s02-m02-r09), using Bowtie v1.1.1 (RRID:SCR_005476) with the option ‘-m 1 --best –strata’
The resulting SAM files were sorted using Samtools v1.2 and the number of reads per transcript was counted using Bedtools2 with the option ‘bedtools coverage -a BAM_file -b genome_annotation.bed -S -s sorted -g Chrom.length’, using gene features for C. glabrata downloaded from CGD, version s02-m07-r04
The trimmed mean of M-values (‘TMM’) method in the EdgeR package was used to calculate the normalization factors for scaling the raw library sizes. Then, normalized read counts were log2 transformed and used for downstream analyses.
Assembly: CGD, s02-m07-r04
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes normalized and log2 transformed counts for each sample

organism: Nakaseomyces glabratus

growth_protocol: C. glabrata wild type cells were grown in SC overnight, diluted into fresh SC the next morning to OD600 = 0.1, grown for another 2-3 hours until the culture reached mid-log phase (OD600∼0.6). At this point, two biological replicates of pre-starvation samples were collected using a cold methanol quenching method (Pieterse et al. 2006; Zhou and O’Shea 2011).

extract_protocol:
Briefly, 5 mL of culture was added directly into 7.5 mL of pre-chilled methanol (−50°C) and incubated in an ethanol-dry ice bath at that temperature for at least 20 min. When all samples were in the ethanol-dry ice bath for > 20 minutes, cells were collected by centrifugation and quickly washed with ice-cold water to remove the methanol and resuspended in RNAlater solution (Qiagen, 76104) for at least 2 hours. Cells were centrifuged to remove the RNAlater, flash-frozen in liquid nitrogen and stored at -80 C until RNA-extraction. For each sample, ∼5x10^7 cells were collected and total RNA was extracted using a MasterPure Yeast RNA purification kit (Biosearch Technologies, MPY03100) following the manufacturer’s protocol.
RNA-seq libraries were prepared with the TruSeq RNA Library Preparation Kit v2 (Illumina) with the mRNA purification option.

treatment_protocol: The remaining culture was collected by filtration, washed with equal volume of pre-warmed no phosphate SC media and then released into the pre-warmed no phosphate SC. After 1 hour incubation with shaking at 30 C, three biological replicates of the starved samples were collected in the same way as above.

value: 1 hour of -Pi starvation


title: 1 hour after -Pi, biol repl 3


title: Uterine artery endothelial cells, PFOS- Treated, Replicate 3

value: 24H PFOS- 10 uM


title: C26 cells, exercise [EXP0219]

value: BALB/c


title: SHC_3

value: ESCC


title: SH2_1

value: silenced LINK-A#1

value: LINK-A knockdown


title: 1 hour after -Pi, biol repl 1


title: before starvation, biol repl 1


title: SHC_2


title: C26 cells, rest [EXP0218]

value: cancer

value: C26 colon carcinoma cells

value: wildtype

value: rest


title: before starvation, biol repl 2


title: Uterine artery endothelial cells, Vehicle- Treated, Replicate 2

value: Female


title: Uterine artery endothelial cells, Vehicle- Treated, Replicate 1

value: Pregnant


title: SHC_1


title: C26 cells, rest [EXP0217]

value: male


title: C8

status: Public on Oct 14 2023

city: Chicago

first: Paul

middle: W.

last: Burridge

state: IL

address: 320 East Superior Street

institute: Northwestern University

data_processing:
Using SOAPnuke, sequence files were trimmed for adaptors, low-quality reads, and N reads.
Clean sequencing reads were mapped to the GRCh38 reference genome using STAR and counted using RSEM.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel Workbook includes TPM gene counts for each sample

growth_protocol: On d16, hiPSC-derived cardiomyocytes were dissociated and plated in 6-well plate at 1 x 106 cells per well. On d20, RBAI media was exchanged for MMc, MMc-glu, MMc-no FA, MMc-CD, MMs, MMs-glu, MMs-no FA, MMs-CD, or RBAI for 13 days. Cells were maintained in humidified atmosphere with 5% CO2, atmospheric O2, at 37C. On d33, cells were collected for RNA extraction.

extract_protocol:
RNA was extracted using 350 µL/well of TRIzol Reagent. RNA was then purified using the Direct-zol RNA MicroPrep kit, including on-column Dnase digestion to remove genomic DNA.
RNA libraries for RNA-seq were prepared using eukaryotic mRNA library preparation (poly A enrichment)

value: hiPSC derived cardiomyocyte

value: MMc-CD


title: C9

value: RBAI


title: C7

value: WT

value: MMc-no FA


title: C6

value: MMc-glu


title: C26 cells, rest [EXP0220]

value: BALB/c


title: C3

value: MMs-no FA


title: C4

value: MMs-CD


title: C2

value: MMs-glu


title: C1

value: MMs


title: B9


title: B8


title: B6


title: C5

value: MMc


title: A8


title: B1


title: B2


title: B4


title: A7


title: A3


title: A6


title: A4


title: A1


title: A2


title: A5


title: CYFIP2ArpinARPC1A-Exp2

city: Paris

first: Laura

last: Courtois

address: 25 rue d'Ulm

country: France

institute: Institut Curie

data_processing:
RNA sequencing data were analyzed using the BlueBee Genomics Plateform (Lexogen, Vienna, Austria).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include counts for each sample

extract_protocol:
Total RNA from cell lines was extracted by NucleoSpin RNA Plus Kit (Macherey-Nagel)
Library preparation was performed using QuantSeq 3’ mRNA-Seq reverse (REV) Library Prep Kit (Lexogen, Vienna, Austria) using 150 ng of total RNA, and according to manufacturer’s instruction.


title: CYFIP2ArpinARPC1A-Exp3


title: CYFIP2ARPC1A-Exp1


title: CYFIP2ARPC1A-Exp3


title: CYFIP2ArpinARPC1A-Exp1


title: CYFIP2Arpin-Exp3


title: CYFIP2ARPC1A-Exp2


title: CYFIP2Arpin-Exp2


title: B7


title: B5


title: ArpinARPC1A-Exp2


title: CYFIP2Arpin-Exp1


title: ArpinARPC1A-Exp1


title: CYFIP2-Exp3


title: CYFIP2-Exp2


title: CYFIP2-Exp1


title: ARPC1A-Exp1


title: ARPC1A-Exp2


title: ARPC1A-Exp3


title: Arpin-Exp3

value: Arpin


title: Arpin-Exp2


title: Arpin-Exp1


title: MCF10Aparental-Exp3


title: STB_1049_CoV_NI_3

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

institute: UCSD

data_processing:
Quality control was performed using FastQC (v.0.11.8) and multiQC (v.1.11).
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v.2.7.3a; Dobin et al., 2013) and annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation; Liao et al., 2014). The STAR parameters used were: –runMode alignReads –outSAMmode Full –outSAMattributes Standard –genomeLoad LoadAndKeep –clip3pAdapterSeq AGATCGGAAGAGC –clip3pAdapterMMp 1. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id.
Ensembl genes without at least two samples with 10 or more reads were removed from analysis.
Ensembl gene ID’s were converted to HGNC gene symbols using BiomaRt (v. 2.42.1). Normalization was performed using the R (v.3.6.3) package DESeq2 (v.1.28.1; Love et al., 2014).
Assembly: GRCh38.p10 (GENCODE release 26)
Supplementary files format and content: Kallol_et_al_raw_counts_10212022.csv : comma separated values file contains raw counts from all 53 samples
Supplementary files format and content: Kallol_et_al_filt_norm_10212022.csv : comma separated values file contains DESeq2 normalized counts from all 53 samples

growth_protocol: The two human TSC lines used in this study were derived in our lab following a modified protocol from Okae et al. and previously characterized through both transcriptomic and functional studies [31]. TSC were cultured on collagen IV-coated plates using a modified Okae media, composed of 2uM CHIR990021, 500nM A83-01, 1uM SB431542, 5uM Y-27362, 0.8mM valproic acid sodium, 100ng/ml FGF2, 20ng/ml Noggin, and 50ng/ml HGF (“TSC media”) [32]. Cells were passaged using TrypLE as previously described [30]. TSC were differentiated into either EVT or STB using protocols as previously described [30, 31]. For EVT differentiation, TSC were plated at a density of 5,000 cells/well onto a 96-well plate, pre-coated with 20µg/ml fibronectin in EVT differentiation media. On day 3, EVT medium was replaced with media without NRG1, and Matrigel concentration was reduced from 2% to 0.5% until day 5. For STB differentiation, TSC were plated at a density of 2,000 cells/well onto 96-well plate coated with 2.5µg/ml of collagen IV in TSC media. The next day, STB differentiation media (containing forskolin) was added and changed on day 3. Samples were collected on day 5 for EVT and day 6 for STB to confirm differentiation. TSC and TSC-derived EVT (day 5) and STB (day 6) were subjected to viral infection.

extract_protocol:
Total RNA was extracted from cells using the Nucleospin® (Macherey-Nagel, USA) kit. Total RNA was quantified using Qubit fluorometer (Thermo Fisher Scientific, USA) and quality controlled on an Agilent Tapestation (Agilent, Santa Clara, USA).
RNA-seq libraries were prepared using the Ribo-Zero Plus rRNA Depletion kit (Illumina) followed by TruSeq Stranded Total RNA kit (Illumina) at the IGM Genomics Center at UC San Diego. Libraries were pooled and sequenced on NovaSeq 6000 S1 Flow Cell (Illumina) to an average depth of 23 million uniquely mapped reads.

treatment_protocol: Undifferentiated TSC and TSC-derived EVT (d5) and STB (d6) were infected with SARS-CoV-2 USA-WA1/2020 strain, obtained from BEI Resources (NR-52281) at MOI = 1. After 1h incubation at room temperature, the viral inoculum was removed, and cells were washed twice with PBS to remove unbound virus, followed by addition of fresh TSC, EVT, or STB media, containing either vehicle (DMSO) or 500nM of remdesivir (considered time = 0h). Cell lysates and culture supernatants were collected at 0h, 2h, 10h, 24h and 48h post-infection. All infections with SARS-CoV-2 were performed in a Biosafety Level 3 (BSL3) laboratory under the approval of the Sanford Burnham Prebys Medical Discovery Institute Biosafety Committee.

value: In vitro differentiated syncytiotrophoblast

value: Not infected

tag: infection time


title: ArpinARPC1A-Exp3


title: MCF10Aparental-Exp1


title: STB_1049_CoV_NI_2

tag: treatment


title: STB_1049_CoV_NI_1


title: STB_1049_CoV_10h_3

value: SARS-CoV-2 infection


title: STB_1049_CoV_10h_2


title: STB_1049_CoV_24h_2


title: STB_1049_CoV_10h_1


title: STB_1048_CoV_NI_3


title: STB_1049_CoV_24h_1


title: STB_1048_CoV_24h_1


title: STB_1048_CoV_NI_2


title: STB_1048_CoV_24h_2


title: STB_1048_CoV_NI_1


title: STB_1048_CoV_24h_3


title: STB_1048_CoV_10h_3


title: STB_1048_CoV_10h_2


title: STB_1048_CoV_10h_1


title: MCF10Aparental-Exp2


title: hTSC_1049_CoV_NI_2

value: trophoblast stem cell


title: STB_1049_CoV_24h_3


title: HL1_short-read_nucleoplasmfraction_rep3

first: Alexander

middle: J

last: Ruthenburg

address: 920 E. 58th Street

department: Molecular Genetics and Cell Biology

institute: University of Chicago

description:
HL1_short-read_nucleoplasmfraction_rep3
HL1_short-read_DESeq2_normalizedgenecounts.csv

data_processing:
For short-read RNA-seq, read quality and adapter content was checked using FastQC (Andrews, 2015). Reads were then aligned to reference genomes (mm10) catenated with ERCC sequences using hisat2 version 2.1.0 (Kim, 2019) with --rna-strandness R --dta options. Sam files were converted to sorted bam files using samtools (Li, 2009). StringTie (Pertea, 2015) was used to assemble transcripts from sorted bam files to obtain gtf files for each sample. These gtf files were merged using stringtie --merge --rf. This merged transcriptome gtf file was then used as a reference for re-estimation of transcripts in each of the samples using stringtie -e -B -G. Raw counts of transcript and gene abundance were obtained using prepDE.py script from StringTie. Raw counts were then used to calculate differentially expressed transcripts and genes as well as normalized transcript and gene counts using DESeq2. For long-read RNA-seq, real-time basecalling information and FASTQ files were generated with the MinKNOW software using default settings (HL1 rep1: minQ 7; HL1 rep2: minQ 9). FASTQ files generated by the MinKNOW software were concatenated and mapped to mm10+ERCC genomes using minimap2 (Li, 2018) without canonical splice sites (-ax splice -un). After sorting and indexing the BAM files (samtools), coverage analyses were performed using Stringtie2 (Kovaka, 2019) with options -A to generate gene coverage in addition to transcripts and -L to specify long reads. Replicates were then analyzed in tandem using the Stringtie --merge function (-e -B -G) to create a reference GTF with the union of transcripts between both replicates to calculate tags per million (TPM) for transcripts in individual replicates.
Assembly: mm10
Supplementary files format and content: HL1_short-read_DESeq2_normalizedgenecounts.csv is a csv file containing Deseq-normalized gene counts from three biological replicates each of chromatin and nucleoplasm fraction using short-read RNA-seq
Supplementary files format and content: HL1_long-read_StringTie_transcriptabundance.csv is a csv file containing tags per million (TPM) of transcripts in two biological replicates calculated by StringTie in the long-read RNA-seq sample

molecule: nuclear RNA

growth_protocol: HL1 mouse cardiomyocytes were grown per manufacturer instructions in supplemented Claycomb Medium (51800C-500ML) + 10% FBS (TMS-016) + 0.1mM Norepinephrine with 30mM L-ascorbic acid (A0937, A7506) + 5% L-Glutamine (G7513) in 0.1% gelatin-coated (SF008) T75 flasks. To prepare the cells for RNA harvesting, they were washed once with 1X PBS, detached with TrypLE Express (Gibco #12605010), quenched with FBE-containing media, then washed with PBS, and pelleted by centrifugation for 5 min at 250 x g

extract_protocol:
For nuclear fractionation and RNA isolation, cell pellets were resuspended in Buffer A (10 mM HEPES•KOH pH 7.5, 10 mM KCl, 10% glycerol, 340 mM sucrose, 4mM MgCl2, 1 mM DTT, 0.1% Triton X-100, 1 x Protease Inhibitor Cocktail (PIC) [1mM AEBSF, 0.8 μM aprotinin, 20 μM leupeptin, 15 μM pepstatin A, 40 μM bestatin, 15 μM E-64; from 200x DMSO stock]) to obtain nuclei. Purified nuclei were extracted with 0.5 M Urea and 0.5% NP-40 substitute to solubilize loosely bound factors from chromatin and fractionated by centrifugation (Werner, 2015;Werner, 2017). The supernatant was termed as the nucleoplasm fraction and the pellet as the chromatin fraction. 1 μL of a 1:10 diluted ERCC RNA Spike-in standards aliquot (Life Technologies 4456740) was added to each nuclear fraction prior to addition of TRIzol reagent (Life Technologies 15596026). RNA from each fraction was processed using Zymo RNA Clean & Concentrator kit (Zymo Research R1017) with on-column DNase digestion. Ribosomal RNA was removed using Ribo-zero Gold rRNA depletion kit (Illumina MRZG12324) for HL1 short-read RNA seq samples and RiboMinus kit (Invitrogen A15026) for HL1 long-read samples.
For short-read RNA-seq, 100 ng rRNA-depleted RNA from each nuclear fraction was used with the NEBNext Ultra II Directional library kit (NEB E7765S) to prepare RNA-seq libraries. RNA-seq libraries of nuclear fractions (chromatin extract and nucleoplasm extract) from three independent cultures were sequenced on the Illumina HiSeq 4000 to obtain 50bp single end reads. For long-read RNA-seq, two HAP1 long-read sequencing libraries were generated as follows. rRNA-depleted RNA was polyadenylated with E. coli Poly(A) Polymerase (M0276S) (for later priming with long read sequencing primers) and precipitated with ethanol. Polyadenylated chromatin fraction RNA was subjected to library preparation according to the Oxford Nanopore direct cDNA sequencing kit protocol (SQK:DCS109). 10-50 fmol of library was loaded onto a MinION (MIN-101B) flow cell (R9.4.1; FLO-MIN106D) and run for 48 hours.

tag: rna fraction

value: chromatin


title: HL1_short-read_nucleoplasmfraction_rep1

description:
HL1_short-read_nucleoplasmfraction_rep1
HL1_short-read_DESeq2_normalizedgenecounts.csv


title: hTSC_1049_CoV_NI_1


title: hTSC_1049_CoV_24h_3


title: HL1_short-read_chromatinfraction_rep3

description:
HL1_short-read_chromatinfraction_rep3
HL1_short-read_DESeq2_normalizedgenecounts.csv


title: Microbiota of Stool from patient HPV+10

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description:
16s rRNA v3-v4 sequencing of human Saliva
feature_table.csv

data_processing:
from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 8 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed --verbose >Log_di_cutadapt.txt
qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 261 --p-trunc-len-r 198 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 8
qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: rep_sequences.fasta: representative ASV sequences in fasta fomat (sequence names correspond to row names of the feature_table.tsv file)
Supplementary files format and content: feature_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)
paired-end (2x300) amplicon sequencing

value: Stool

tag: patient id

value: F

value: CRC+HPV

tag: crc site

value: Descending colon

tag: crc sex

value: Adenocarcinoma, NOS

tag: tumor grading

tag: tumor stage


title: HL1_short-read_chromatinfraction_rep2

description:
HL1_short-read_chromatinfraction_rep2
HL1_short-read_DESeq2_normalizedgenecounts.csv

tag: cell line


title: hTSC_1049_CoV_24h_2

tag: cell type


title: HL1_short-read_chromatinfraction_rep1

description:
HL1_short-read_chromatinfraction_rep1
HL1_short-read_DESeq2_normalizedgenecounts.csv


title: hTSC_1049_CoV_10h_2


title: hTSC_1049_CoV_10h_3


title: hTSC_1048_CoV_24h_3


title: hTSC_1048_CoV_24h_2


title: hTSC_1048_CoV_NI_2


title: hTSC_1049_CoV_NI_3


title: hTSC_1048_CoV_NI_1


title: HCT116, control siRNA

city: Yufu

first: Naoki

last: Hijiya

state: Oita

address: 1-1, Idaigaoka Hasama-machi

department: Medicine

institute: Oita University

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Version 9.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis. Analysis of the microarray images was performed with Genespring 7.3.1 Software (Agilent Technologies).

source_name: Colorectal cancer cell line

label_protocol: Cy3-labeled cRNA targets were generated using Quick Amp Labeling Kit, one-color (Agilent Technologies).

growth_protocol: All cell lines were cultured in accordance with the supplier's instructions.

extract_protocol: Total RNA for expression analysis was extracted using an RNeasy Mini kit (Qiagen).

tag: knock down

value: siCont


title: CW2, control siRNA


title: CW2, VSNL1 siRNA


title: HCT116, VSNL1 siRNA


title: hTSC_1048_CoV_10h_2


title: hTSC_1048_CoV_10h_3


title: HL1_short-read_nucleoplasmfraction_rep2

description:
HL1_short-read_nucleoplasmfraction_rep2
HL1_short-read_DESeq2_normalizedgenecounts.csv


title: hTSC_1048_CoV_10h_1


title: genomic DNA in WT cells in S phase + HU 0.2M (60 min)

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

institute: IGMM - CNRS

description: hydroxyurea 200mM

data_processing:
Basecalls were performed using HiSeq Control Software 1.5.15.1, RTA 1.13.48.0 and CASAVA version 1.8.2
Reads were aligned to the sacCer3 genome assembly using using Bowtie 2, version 2.1.0, allowing only perfect matches
bigwig files were generated with the tool "Bamcompare" from Deeptool2. Ramírez et al, (2016)
Assembly: sacCer3
Supplementary files format and content: Bigwig files for HU samples correspond to the ratio of the S+HU / G1

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: For DNA copy number analysis, S. cerevisiae cells were grown in YPAD and released from alpha-factor arrest in the presence of 200 mM HU (hydroxyurea) for 60 min.

extract_protocol:
Yeast genomic DNA was prepared using standard protocol
Libraries were constructed using standard Illumina kits (TruSeq SBS Kit v3) and protocols. Sequencer: HiSeq4000. Reads lenght: 50.

value: yeast

value: wild-type

value: S-phase + HU


title: hTSC_1049_CoV_24h_1


title: EVT_1049_CoV_NI_3

value: In vitro differentiated extravillous trophoblast


title: genomic DNA in rnh1delta rnh201delta cells in S phase + HU 0.2M (60 min)

description: hydroxyurea 200mM

value: rnh1delta rnh201delta

value: S phase + HU


title: hTSC_1049_CoV_10h_1


title: genomic DNA in WT cells synchronized in G1

description: alpha-factor synchronization


title: hTSC_1048_CoV_24h_1


title: EVT_1049_CoV_NI_2


title: EVT_1049_CoV_NI_1


title: Insulin-resistant mouse liver 3, HFD-12w group

first: Yibo

last: Wang

state: Beijin

address: 167 Beilishi Road, Xicheng District, Beijing

institute: Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences & Peking Union Medical College

description: column name: H12-3

data_processing:
Hisat2（version:2.0.4）
Adaptor sequences contained in reads were removed using trimadap, bases with a mass Q below 20 at the 3 'end were removed by seqtk trimfq (version: 1.0), i.e., the base error rate was less than 0.01, (Q = -10 logerrorratio).
Reads less than 25 in length were removed using lengthsort.pl. Ribosome RNA reads of the species to which they belonged were removed by bowtie2 (version: 2.2.6).
Genome mapping of pre-processed reads was performed applying the spliced mapping algorithm of Hisat2 (version: 2.0.4).
Stringtie (version: 1.3.0) was applied to count the number of Fragments per gene after Hisat2 alignment, then the TMM (trimmed mean of M values) method was used to normalize, and finally the FPKM value of each gene was calculated using a perl script.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample.
Supplementary files format and content: tab-delimited text files include counts for each sample.

source_name: liver

growth_protocol: All mice were housed under a 12-hour light/dark cycle at a temperature of 23 ± 1 °C and relative humidity of 50%-60%, with free access to water.

extract_protocol:
Total RNA was extracted using the MJzol Animal RNA Isolation Kit (Majorivd) and purified using RNAClean XP Kit (Beckman Coulter) and RNase-Free DNase Set (QIAGEN) according to standard operating procedures provided by the manufacturer.
The mRNA was enriched using VAHTS ® mRNA Capure Beads (Human/Mouse/Rat), and mRNA sequencing libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (Vazyme) according to standard operating procedures provided by the manufacturer.

treatment_protocol: 6-week-old mice were fed a HFD for 12 weeks to induce insulin resistance (HFD-12w group); 14-week-old mice were fed a HFD for 4 weeks to induce obesity (HFD-4w group). Control mice were fed a ND continuously for 12 weeks starting at 6 weeks of age (ND group).

value: liver

value: male

tag: time point

tag: diet

value: high-fat diet

value: wild type

value: PBS perfusion


title: Insulin-resistant mouse liver 2, HFD-12w group

description: column name: H12-2

tag: tissue

tag: Sex


title: Insulin-sensitive obese mouse liver 3, HFD-4w group

description: column name: H4-3

tag: genotype


title: Insulin-resistant mouse liver 1, HFD-12w group

description: column name: H12-1

tag: strain


title: HAP1_long-read_chromatinfraction_rep2

description:
HAP1_long-read_chromatinfraction_rep2
HAP1_long-read_StringTie_transcriptabundanceTPM.csv

data_processing:
For short-read RNA-seq, read quality and adapter content was checked using FastQC (Andrews, 2015). Reads were then aligned to reference genomes (hg38) catenated with ERCC sequences using hisat2 version 2.1.0 (Kim, 2019) with --rna-strandness R --dta options. Sam files were converted to sorted bam files using samtools (Li, 2009). StringTie (Pertea, 2015) was used to assemble transcripts from sorted bam files to obtain gtf files for each sample. These gtf files were merged using stringtie --merge --rf. This merged transcriptome gtf file was then used as a reference for re-estimation of transcripts in each of the samples using stringtie -e -B -G. Raw counts of transcript and gene abundance were obtained using prepDE.py script from StringTie. Raw counts were then used to calculate differentially expressed transcripts and genes as well as normalized transcript and gene counts using DESeq2. For long-read RNA-seq, real-time basecalling information and FASTQ files were generated with the MinKNOW software using default settings (HAP1 rep1: minQ 7; HAP1 rep2: minQ 7). FASTQ files generated by the MinKNOW software were concatenated and mapped to hg38+ERCC genomes using minimap2 (Li, 2018) without canonical splice sites (-ax splice -un). After sorting and indexing the BAM files (samtools), coverage analyses were performed using Stringtie2 (Kovaka, 2019 #3879) with options -A to generate gene coverage in addition to transcripts and -L to specify long reads. Replicates were then analyzed in tandem using the Stringtie --merge function (-e -B -G) to create a reference GTF with the union of transcripts between both replicates to calculate tags per million (TPM) for both genes and transcripts in individual replicates.
Assembly: hg38
Supplementary files format and content: HAP1_short-read_DESeq2_normalizedgenecounts.csv is csv file containing Deseq-normalized gene counts from three biological replicates each of chromatin and nucleoplasm fraction using short-read RNA-seq
Supplementary files format and content: HAP1_long-read_StringTie_transcriptabundance.csv is a csv file containing tags per million (TPM) of transcripts in two biological replicates calculated by StringTie in the long-read RNA-seq sample

growth_protocol: HAP1 cells were grown in IMDM media (Gibco, 12440-053), supplemented with 10% FBE (Seradigm, 3100-500) and 1% Pen/Strep (ThermoFisher 15140-122) to 80-90% confluency in T75 flasks at 37˚C. To prepare the cells for RNA harvesting, they were washed once with 1X PBS, detached with TrypLE Express (Gibco #12605010), quenched with FBE-containing media, then washed with PBS, and pelleted by centrifugation for 5 min at 250 x g.

extract_protocol:
For nuclear fractionation and RNA isolation, cell pellets were resuspended in Buffer A (10 mM HEPES•KOH pH 7.5, 10 mM KCl, 10% glycerol, 340 mM sucrose, 4mM MgCl2, 1 mM DTT, 0.1% Triton X-100, 1 x Protease Inhibitor Cocktail (PIC) [1mM AEBSF, 0.8 μM aprotinin, 20 μM leupeptin, 15 μM pepstatin A, 40 μM bestatin, 15 μM E-64; from 200x DMSO stock]) to obtain nuclei. Purified nuclei were extracted with 0.5 M Urea and 0.5% NP-40 substitute to solubilize loosely bound factors from chromatin and fractionated by centrifugation (Werner, 2015;Werner, 2017). The supernatant was termed as the nucleoplasm fraction and the pellet as the chromatin fraction. 1 μL of a 1:10 diluted ERCC RNA Spike-in standards aliquot (Life Technologies 4456740) was added to each nuclear fraction prior to addition of TRIzol reagent (Life Technologies 15596026). RNA from each fraction was processed using Zymo RNA Clean & Concentrator kit (Zymo Research R1017) with on-column DNase digestion. Ribosomal RNA was removed using RiboMinus kit (Invitrogen A15026) for HAP1 short- and long-read samples.
For short-read RNA-seq, 100 ng rRNA-depleted RNA from each nuclear fraction was used with the NEBNext Ultra II Directional library kit (NEB E7765S) to prepare RNA-seq libraries. RNA-seq libraries of nuclear fractions (chromatin extract and nucleoplasm extract) from three independent cultures were sequenced on the Illumina HiSeq 4000 to obtain 50bp single end reads. For long-read RNA-seq, two HAP1 long-read sequencing libraries were generated as follows. rRNA-depleted RNA was polyadenylated with E. coli Poly(A) Polymerase (M0276S) (for later priming with long read sequencing primers) and precipitated with ethanol. Polyadenylated chromatin fraction RNA was subjected to library preparation according to the Oxford Nanopore direct cDNA sequencing kit protocol (SQK:DCS109). 10-50 fmol of library was loaded onto a MinION (MIN-101B) flow cell (R9.4.1; FLO-MIN106D) and run for 48 hours.

value: chromatin


title: HAP1_long-read_chromatinfraction_rep1

description:
HAP1_long-read_chromatinfraction_rep1
HAP1_long-read_StringTie_transcriptabundanceTPM.csv


title: HL1_long-read_chromatinfraction_rep2

description:
HL1_long-read_chromatinfraction_rep2
HL1_long-read_StringTie_transcriptabundanceTPM.csv


title: Insulin-sensitive obese mouse liver 1, HFD-4w group

description: column name: H4-1


title: EVT_1049_CoV_24h_3

value: SARS-CoV-2 infection

tag: infection time


title: EVT_1049_CoV_10h_3

tag: treatment


title: EVT_1049_CoV_24h_1


title: Male WT mouse liver 2

city: Miyazaki

first: Narantsog

last: Choijookhuu

state: Miyazaki

address: Kiyotake

department: Anatomy

institute: University of Miyazaki

hyb_protocol: Fifteen micrograms of fragmented cRNA from each sample was hybridized to a pre-equilibrated Clariom S mouse microarray chip, which was then washed and stained.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, USA)

data_processing:
Normalization and expression value calculations were performed using Genespring. (Agilent Technologies, Santa Clara, CA, USA). Fold change 1.5 or more related to cell cycle was considered.
Summarization Algorithm: ExonSSTRMAWithoutStabilization

label: biotin

source_name: Liver

label_protocol: Amplification and biotin labeling of fragmented cDNA was performed using the biotin labeling system (WT PLUS Reagent Kit, Thermo Fisher Scientific, Rockford, IL, USA) in duplicate.

extract_protocol: Total RNA was prepared using Trizol (Invitrogen, Carlsbad, CA, USA).

value: WT

tag: age


title: Male KO mouse liver 2


title: Insulin-sensitive obese mouse liver 2, HFD-4w group

description: column name: H4-2


title: Male WT mouse liver 3


title: Male KO mouse liver 3


title: Male KO mouse liver 1


title: Control mouse liver 3, ND group

description: column name: ND-3

value: normal standard chow diet


title: Male WT mouse liver 1


title: EVT_1049_CoV_10h_2


title: EVT_1049_CoV_10h_1


title: Adult male 24hr+midL4, prg-1 DPAZ mutant, piRNA, rep 3

city: Houston

first: Jacob

middle: Manuel

last: Ortega

state: Texas

address: 6550 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

description: Small RNA sample

data_processing:
Raw data were first analyzed for quality using FastQC (Version 0.12.0).
Adapter sequences were trimmed using CutAdapt (Version 3.7).
Reads were aligned to C. elegans piRNAs (piRNAdb.cel.v1_7_6.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Aligned piRNA reads for each sample were normalized to total number of reads mapping to the C. elegans genome (per million).
Assembly: piRNAdb.cel.v1_7_6
Assembly: ce11genome
Supplementary files format and content: tab-delimited text file includes raw counts of piRNA reads
Supplementary files format and content: tab-delimited text file includes raw counts of reads aligning to C. elegans genome
Supplementary files format and content: xlsx file includes normalization of piRNA reads to the total number of reads aligning to the C. elegans genome per million

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: 20-30 male, mid-L4 stage animals were collected of each genotype from C. elegans stocks cultured at 25°C. These male animals were seperately cultured at 25°C until adulthood (24 hours past mid-L4 stage) at which point animals were collected for small RNA extraction.

extract_protocol:
Small RNAs were extracted using a mirVana miRNA isolation kit (Ambion) following manufacturers protocol. Purified small RNA samples were treated with Acid Pyrophosphotase to allow for cloning of small RNAs bearing a 5' triphosphate.
Libraries were contructured using a TruSeq Small RNA Library Preparation Kit (Illumina).

value: Whole Animal

value: prg-1 Delta PAZ-domain mutant


title: Control mouse liver 2, ND group

description: column name: ND-2


title: EVT_1048_CoV_NI_3

value: Not infected


title: HL1_long-read_chromatinfraction_rep1

description:
HL1_long-read_chromatinfraction_rep1
HL1_long-read_StringTie_transcriptabundanceTPM.csv

tag: rna fraction


title: Adult male 24hr+midL4, prg-1 DPAZ mutant, piRNA, rep 1

description: Small RNA sample


title: EVT_1048_CoV_NI_2


title: Control mouse liver 1, ND group

description: column name: ND-1


title: EVT_1049_CoV_24h_2


title: Mouse Colon, KO, rep 3 (KO3)

city: Urbana

first: Guanying

middle: Bianca

last: Xu

state: Illinois

address: 905 S Goodwin Ave Rm #472B1

department: Food Science and Human Nutrition

institute: University of Illinois at Urbana-Champaign

library_source: transcriptomic single cell

data_processing:
Reading files (150 nt in length) in FASTQ format were generated and de-multiplexed by Cell Ranger 3.1.0 (10× Genomics Cell Ranger 3.0.0) aligned with mm10 mouse reference genome.
The exonic reads uniquely mapped to the transcriptome were used for a unique mo-lecular identifier (UMI) counting. Subsequently, single cells and their UMI count matrices were imported into the R package “Seurat” (version 2.3.2) for further analysis.
Selection and filtering of the single−cell RNA sequencing data were carried out if the total UMI counts (cell counts) or the number of expressed genes (feature counts) of cells were beyond predefined thresholds, defined as the medians ± 3× the median absolute deviation (MAD).
We also discarded both the genes expressed in fewer than three cells and low−quality cells with ≤200 expressed genes. Furthermore, cells with >25% of the mitochondrial genes (markers for dead cells) were also discarded.
After the filtering process, as described above, a total of 31,798 cells collected from 6 animals were kept for subsequent analysis.
Assembly: mm10 mouse reference genome
Supplementary files format and content: The Rdata file contains the aggregated Seurat object with the following info in the metadata: 1) Orig.ident: the original identity of each Seurat object before merging; 2) nCount_RNA; 3)nFeature_RNA; 4)percent.mt: the percentage of mitochondrial RNA expressed in each cell; 5)nCount_SCT: the RNA counts after SCT transformation; 6)nFeature_SCT: the feature count after SCT transformation; 7)SCT_snn_res.0.5: cluster assignments for cells based on the SCTransform-normalized data, using the shared nearest neighbor clustering method at a resolution of 0.5.; 8)seurat_clusters; 9)genotype: WT or KO; 10) celltype: assigned manually based on cluster marker genes.
Supplementary files format and content: See above.

source_name: Colon

extract_protocol:
Immediately after euthanasia and necropsy, whole colon tissues from WT and KO male mice (littermates, 3−month−old, male, n = 3) were washed twice with ice−cold PBS to remove fecal matter. Tissues were then opened by cutting longitudinally through the lu-men, and excess fat was removed during the process. Opened colon tissues were washed again in a clean petri dish containing ice−cold PBS and lightly swirled with forceps to re-move any remaining fecal matter. The cell isolation protocol was based on the manuscript published by Gracz et al. [1], with the modifications described below: • Epithelial cells: After washing, tissues were digested in ice−cold dissociation reagent #1 [47 mL PBS + 3 mL 0.5 M EDTA (Sigma, Livonia, MI, USA, #E9884) + 75 µL DTT (Sigma, #D0632)] for 20 min. Then, tissues were transferred to dissociation reagent #2 [47 mL PBS + 3 mL 0.5 M EDTA] for 10 min at 37 °C. After incubation, tissues with reagent were shaken for 30 s to release epithelium from the basement membrane, and remnant tissues consisting of submucosa and muscularis were removed for lamina propria digestion. The cell solution was centrifuged at 1000× g for 5 min at 4 °C to pellet the cells. Cell pellets were washed with 10 mL PBS containing 10% FBS (Sigma, Livonia, MI, USA, #F0926). The cell solution was then centrifuged again, and the pel-let was resuspended in 10 mL HBSS (Sigma, Livonia, MI, USA, #H6648) containing 8 mg Dispase (Sigma, Livonia, MI, USA, #D4693) and incubated for 10 min at 37 °C in a water bath. After incubation, the cell suspension was filtered through 70 and 40 µm nylon cell strainers (Falcon, #352350 and #352340) to exclude large clumps of cells. The filtered cell solution was pelleted again, washed with 10 mL HBSS containing 10% FBS, and then pelleted again. Finally, cells were resuspended in 1 mL RPMI 1640 (Corning Life Sciences, Corning, NY, USA, #15−040−CV) with 10% FBS. • Lamina propria cells: Remnant tissues from previous steps were transferred to diges-tion media (5 mL RPMI 1640 + 2 mg Dispase + 10 mg collagenase IV (Gibco, Grand Island, NY, USA, #17104−109) + 60 µL FBS) and cut into small pieces, incubated for 30 min at 37 °C with constant spinning. After incubation, the cell suspension was fil-tered through 70 and 40 um nylon cell strainers to exclude large clumps of cells, the same manufacturer as described before. The filtered cell suspension was pelleted again, washed with 10 mL HBSS containing 10% FBS, then pelleted again. Finally, cells were resuspended in 1 mL RPMI 1640 with 10% FBS.
[1] 21. Gracz, A.D.; Puthoff, B.J.; Magness, S.T. Identification, isolation, and culture of intestinal epithelial stem cells from murine intestine. Methods Mol. Biol. 2012, 879, 89–107. https://doi.org/10.1007/978−1−61779−815−3_6.
Cellular suspensions (~5000 cells) were loaded on a Chromium Single−Cell Instru-ment (10× Genomics) to generate single−cell GEMs. Single−cell RNAseq libraries were prepared using Chromium Single−Cell Gene Expression NextGem V3.1 and sequenced on an S4 2 × 150 nt lane in a NovaSeq 6000 platform, following the manufacturer’s protocol (10× Genomics). Sequencing and library construction were performed at the Roy. J. Carver Biotechnology Center, University of Illinois at Urbana−Champaign.

value: Colon

value: KO, Hnrnp Iflox/flox VillinCre/+


title: Adult male 24hr+midL4, prg-1 RNase mutant, piRNA, rep 3

description: Small RNA sample

value: prg-1 RNase mutant


title: Adult male 24hr+midL4, prg-1 RNase mutant, piRNA, rep 2

description: Small RNA sample


title: EVT_1048_CoV_NI_1

value: In vitro differentiated extravillous trophoblast


title: Mouse Colon, KO, rep 2 (KO2)


title: EVT_1048_CoV_24h_3


title: Mouse Colon, WT, rep 3 (WT3)

value: WT, Hnrnp Iflox/flox


title: EVT_1048_CoV_24h_2


title: Adult male 24hr+midL4, prg-1 null mutant, piRNA, rep 4

description: Small RNA sample

value: prg-1 null mutant


title: Adult male 24hr+midL4, prg-1 RNase mutant, piRNA, rep 1

description: Small RNA sample


title: Mouse Colon, KO, rep 1 (KO1)


title: Mouse Colon, WT, rep 2 (WT2)


title: EVT_1048_CoV_24h_1


title: Adult male 24hr+midL4, prg-1 null mutant, piRNA, rep 3

description: Small RNA sample


title: EVT_1048_CoV_10h_3


title: Adult male 24hr+midL4, prg-1 DPAZ mutant, piRNA, rep 2

description: Small RNA sample


title: Adult male 24hr+midL4, prg-1 null mutant, piRNA, rep 2

description: Small RNA sample


title: Mouse Colon, WT, rep 1 (WT1)


title: EVT_1048_CoV_10h_2


title: EVT_1048_CoV_10h_1


title: FFD_R32

city: Stanford

first: Weiguo

last: Fan

address: 300 Pasteur Dr., M207 Alway Bldg.

institute: Stanford University School of Medicine

data_processing:
Dropseq tools v1.1249 were used for mapping the raw sequencing data to the reference genome
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Dropseq tools v1.1249 (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using Dropseq tools v1.1249 (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 Dropseq tools v1.1249
Assembly: mm10
Supplementary files format and content: tab-delimited excel files include RPKM values for each Sample

extract_protocol:
total RNA was extracted from snap-frozen liver tissues using the RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: RAGE flox

value: FFD diet


title: Adult male 24hr+midL4, prg-1 null mutant, piRNA, rep 1

description: Small RNA sample


title: FFD_R31


title: CRAC, Rpb1, WT, S, HU, R2

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor was clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert  quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Assembly: R64
Supplementary files format and content: Bigwig files providing coverage for all samples. All values are normalized to 10,000,000 reads or to S. pombe spike-in
Library strategy: CRAC

source_name: S. cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing an HTP-tagged version of target protein were grown at 30°C to OD600=0.6 in conditional media.

extract_protocol:
Cells were broken and extracts were prepared as described in the original publication.
Library construction is described in Candelli et al., EMBO J, 2018 and in the associated manuscript.
See Aiello et al. PMID: 35839782

treatment_protocol: Cells were treated with hydroxyurea (HU) 200mM. Cells were crosslinked for 50 seconds using a W5 UV crosslinking unit (UVO3).

value: wild-type

value: yeast cell

tag: cell cycle phase

value: S-phase

value: hydroxyurea

tag: fusion tag

value: HTP tag (his-TEV-Protein A)


title: Adult male 24hr+midL4, Wild Type, piRNA, rep 3

description: Small RNA sample

value: Whole Animal

value: Wild Type


title: CRAC, Rpb1, WT, S, HU, R1


title: Adult male 24hr+midL4, Wild Type, piRNA, rep 2

description: Small RNA sample


title: FFD_R28


title: MYb115∆sgaAB_Bt_3

city: Kiel

first: Katja

last: Dierking

address: Am Botanischen Garten 9

department: Evolutionary Ecology and Genetics

institute: Kiel University

data_processing:
filtering and quality-trimming using cutadapt (https://cutadapt.readthedocs.io/en/stable/)
alignment of reads to reference genome (c_elegans_WBcel235_GCF_000002985.6) using STAR aligner (Spliced Transcripts Alignment to a Reference; https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf)
Assembly: c_elegans_WBcel235_GCF_000002985.6
Supplementary files format and content: .tsv file showing gene counts for each sample

source_name: 1 d adults grown on P. fluorescens MYb115 ∆sgaAB and infected with Bt247 from L4 to 1 d adult

growth_protocol: Roughly 500 synchronized N2 worms were raised on PFM plates inoculated with MYb115 or MYb115 ΔsgaAB (OD600 nm of 10) from L1 to L4 stage. At L4 stage worms were transferred to control plates or infection plates (microbiota mixed with Bt247 spores 1:100). Transcriptomic response was assessed 24 hours post-transfer, with three independent replicates.

extract_protocol:
Worms were washed off the plates with M9-T (M9 buffer + 0.02 % Triton X-100), followed by three gravity washing steps. The worm pellets were resuspended in 800µL TRIzol (Thermo Fisher Scientific, Waltham, MA United States). Worms were broken up prior to RNA extraction by treating the samples with four rounds of freeze-thaw cycles using liquid nitrogen and a thermo block at 46 °C. The RNA was extracted using Direct-zol™ RNA MicrolPrep (Zymo Research, R2062) and stored at -80 °C.
The RNA was processed by Lexogen (Vienna, Austria) using the 3’ mRNAseq library prep kit.
3' mRNAseq

value: whole organism

value: wild type, N2

tag: infection


title: MYb115∆sgaAB_noBt_3

source_name: 1 d adults grown on P. fluorescens MYb115 ∆sgaAB

value: not infected


title: Adult male 24hr+midL4, Wild Type, piRNA, rep 1

description: Small RNA sample


title: MYb115_Bt_3

source_name: 1 d adults grown on P. fluorescens MYb115 and infected with Bt247 from L4 to 1 d adult


title: B3

value: hiPSC derived cardiomyocyte

value: WT

value: MMs-no FA


title: HiAD_PM_R19

value: HiAD diet plus PM treatment


title: MYb115∆sgaAB_Bt_2

value: 1 d adults grown on P. fluorescens MYb115 ∆sgaAB


title: HiAD_RAGE_hepKO_RA19

value: liver

value: RAGE flox/Alb cre

value: HiAD diet


title: Adult male 24hr+midL4, prg-1 null mutant, siRNA, rep 3

description: Small RNA sample

data_processing:
Raw data were first analyzed for quality using FastQC (Version 0.12.0).
Adapter sequences were trimmed using CutAdapt (Version 3.7).
Reads were aligned to C. elegans cDNAs (Caenorhabditis_elegans.WBcel235.cdna.all.fa) and the C. elegans genome (ce11genome.fa) using a custom python script HQAlign (https://github.com/FireLabSoftware/HQAlign).
Assembly: Caenorhabditis_elegans.WBcel235.cdna.all.fa
Assembly: ce11genome
Supplementary files format and content: tab-delimited text file includes raw counts of siRNA reads mapped toC. elegans cDNAs
Supplementary files format and content: tab-delimited text file includes raw counts of reads aligning to C. elegans genome

value: prg-1 null mutant


title: Adult male 24hr+midL4, prg-1 null mutant, siRNA, rep 1

description: Small RNA sample


title: Adult male 24hr+midL4, prg-1 null mutant, siRNA, rep 2

description: Small RNA sample


title: HiAD_PM_R18

value: RAGE flox


title: MYb115∆sgaAB_noBt_2


title: TAA Male1

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

data_processing:
Cell segmentation boundaries were determined using the default MERFISH approach (Zhang et al., 2021). The Vizgen MERSCOPE data and cell boundaries were inputted to Seurat 4.2 (R package) using LoadVizgen function. Cells with less than 20 molecules were discarded. SCTransform function was used to normalize the data. Unsupervised clustering and dimensionality reduction were performed using Seurat to identify spatially-resolved cell types on the merged dataset of two control and three TAA samples.
*Molecules.txt are raw data files that contain spatial coordinates for each molecule
*Segmentation.txt are processed data files that contain spatial coordinates describing segmentation of each cell
*Matrix.txt are processed data files that contain detected transcripts in each cell.

extract_protocol: Surgically resected ascending aorta samples from two non-aneurysmal (Control) subjects and three TAA subjects with ascending aneurysms were embedded and frozen in Optimal cutting temperature compound (OCT). OCT-embedded ascending aorta samples were cut into 10 μm sections and adhered onto the imageable area of Vizgen slides. The slides were fixed in pre-heated 4% paraformaldehyde for 30 minutes in an incubator. Subsequent slide processing was performed according to Fresh Frozen Tissue preparation protocol by Vizgen. Hybridization of custom MERFISH probes targeting 140 genes were performed by Vizgen according to the MERSCOPE User Guide.

value: ascending aorta

tag: disease state

value: TAA

value: Male

tag: ascending aorta diameter

tag: number of cells


title: Control Female

value: control (non-aneurysmal)

value: Female

value: Non-aneurysmal


title: TAA Male2


title: Control Male


title: Adult male 24hr+midL4, Wild Type, siRNA, rep 2

description: Small RNA sample

value: Whole Animal

value: Wild Type


title: MYb115_Bt_2

value: whole organism

value: wild type, N2

value: 1 d adults grown on P. fluorescens MYb115


title: HiAD_B3


title: TAA Female


title: HiAD_B2


title: Adult male 24hr+midL4, Wild Type, siRNA, rep 1

description: Small RNA sample


title: HiAD_RAGE_hepKO_RA21


title: MYb115∆sgaAB_Bt_1

value: 1 d adults grown on P. fluorescens MYb115 ∆sgaAB


description:
HAP1_short-read_nucleoplasmfraction_rep2
HAP1_short-read_DESeq2_normalizedgenecounts.csv

tag: cell line

value: chromatin


title: MYb115_noBt_2

source_name: 1 d adults grown on P. fluorescens MYb115

value: not infected


title: HiAD_B1

value: liver

value: HiAD diet


title: MYb115_noBt_3


description:
HAP1_short-read_nucleoplasmfraction_rep1
HAP1_short-read_DESeq2_normalizedgenecounts.csv


title: LoVo MET KO cells, biol rep2

city: Bologna

first: Mattia

last: Lauriola

address: Via Belmeloro 8

institute: University of Bologna

data_processing:
The softwares used for data analysis are the following (in order):  NextSeq Control Software v2.2.0.4 (base-calling);  BCL to FASTQ file converter bcl2fastq (demultiplexing);  cutadapt v1.16 (Trimming);  FastQC v0.11.7;  multiqc v1.5;  STAR v2.5.4a (Alignment);  featureCounts v1.6.2 (Counting);  DESeq2 v1.18.1 (Differential expression);
Assembly: hsa_GRCh38.96_ERCC_SIRV
Supplementary files format and content: tab-delimited text files include raw gene counts

source_name: Colon adenocarcinoma

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

extract_protocol:
Total RNA was extracted from cells using QIAzol® Lysis Reagent according to manufacturer’s instructions
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) following manufacturer's protocols

value: LoVo

value: Colon adenocarcinoma

value: MET knock out


title: HiAD_RAGE_hepKO_RA20

value: RAGE flox/Alb cre


title: MYb115∆sgaAB_noBt_1


title: Adult male 24hr+midL4, Wild Type, siRNA, rep 3

description: Small RNA sample


title: LoVo MET KO cells, biol rep1


title: MYb115_Bt_1


title: HAP1_short-read_chromatinfraction_rep2

description:
HAP1_short-read_chromatinfraction_rep2
HAP1_short-read_DESeq2_normalizedgenecounts.csv


description:
HAP1_short-read_nucleoplasmfraction_rep3
HAP1_short-read_DESeq2_normalizedgenecounts.csv


title: HAP1_short-read_chromatinfraction_rep3

description:
HAP1_short-read_chromatinfraction_rep3
HAP1_short-read_DESeq2_normalizedgenecounts.csv


title: Chow_R2

value: RAGE flox

value: Chow diet


title: LoVo cells, biol rep2

value: WT


title: HAP1_short-read_chromatinfraction_rep1

description:
HAP1_short-read_chromatinfraction_rep1
HAP1_short-read_DESeq2_normalizedgenecounts.csv


title: Chow_R3


title: LoVo cells, biol rep1


title: Chow_R1


title: MYb115_noBt_1


title: H3K27ac_rep1

status: Public on Oct 13 2023

city: Dallas

first: Miao

last: Cui

address: UT Southwestern Medical Center Department of Molecular Biology 6000 Harry Hines Blvd.

institute: UTSW

description: ChIP-seq

data_processing:
Raw reads were aligned to rat (Rn6) genome assembly using Bowtie2 (Version 2.3.4) with default parameters. MACS2 (Version 2.1.1) was applied to each sample to perform peaking calling using the “-nomodel” parameter with the input sample.
For motif analysis, chromatin peaks of NFYa ChIP were searched for known motifs in the JASPAR database using HOMER (Version 4.8) “analyzing genomic positions” function with “-size = 500”. ChIP-seq tracks were plotted using Deeptools.
Assembly: Rn6
Supplementary files format and content: Bigwig

organism: Rattus norvegicus

source_name: NRVMS

growth_protocol: NRVMs were isolated from P2-3 Sprague-Dawley rats using the Neomyt isolation kit from Cellutron Life Technologies (NC-6031). Isolated NRVMs were maintained in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796)/199 medium (Gibco, 11150-059) (3:1) with 3% fetal bovine serum (FBS) (Gemini Bio Products, 100-106), and 1% penicillin-streptomycin (Sigma, P0781). HEK 293 cells (Clontech, 632271) were maintained in DMEM with 10% FBS, and 1% penicillin-streptomycin.

extract_protocol:
Cells were detached from the plate with trypsin and fixed in 1% PFA in PBS at room temperature for 8 min then quenched with 0.125 M glycine for 10 min. Crosslinked samples were then washed with cold PBS and resuspend in Farnham Lab buffer (5mM PIPEs PH8, 85 mM KCcl, 0.5% NP40) for sonication based nuclear extraction.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB.
NEBNext Ultra II DNA Library Preparation Kit

treatment_protocol: Adenovirus expressing TY1 tagged NFYa was used to infect NRVMs for 48h. Two 15cm plates yielding 5-10 million cells were used for each ChIP sample.

tag: cell type

value: cardiomyocytes

value: Sprague-Dawley

value: Wildtype


title: H3K27ac_rep2

description: ChIP-seq


title: NFYA_rep1

description: ChIP-seq


title: input_rep2

description: ChIP-seq


title: input_rep1

description: ChIP-seq


title: modifiedRNA,4

city: Cambridge

first: Thomas

last: Mulroney

address: Tennis Court Road

country: United Kingdom

institute: University of Cambridge

library_source: other

data_processing:
Reads mapped using STAR 2.7.4a.
Subsetting non-matching SAMs.
SAM filtering for GC (>35).
Map indels and generate tables.
Assembly: FlucFS sequence ($refseq) indexed using STAR 2.7.4a --genomeSAindexNbases 4.
Supplementary files format and content: Tab delimited text files containing mutations for each sample.
Supplementary files format and content: Tab delimited text files containing summary data for each condition.
Supplementary files format and content: Tab delimited text files containing total normalised mutations for each condition.

molecule: other

organism: synthetic construct

source_name: Not applicable

extract_protocol:
Purified by phenol/chloroform extraction.
1 microgram prepared using NextFlex Rapid Directional RNA-seq kit 2.0 (Perkin Elmer)

value: Not applicable


title: modifiedRNA,2


title: modifiedRNA,3


title: unmodifiedRNA,3

value: unmodified


title: unmodifiedRNA,2


title: unmodifiedRNA,4


title: unmodifiedRNA,1


title: E110 VFC, bio rep 2

city: New haven

first: Nenad

last: Sestan

state: CT

address: 333 Cedar street

department: Neuroscience

institute: Yale University

description:
Mac_dev_column_cell_meta.tsv.gz
Mac_dev_row_genes.tsv.gz
Mac_dev_counts.mtx.gz

data_processing:
CellRanger was used for read alignment, barcode and UMI counting.
Seurat, fastMNN, and Harmony were used for batch correction.
Seurat were used for dimension reduction and clustering.
Assembly: Mmul10
Supplementary files format and content: tsv, tab-separated txt file containing gene names or cell metadata
Supplementary files format and content: mtx, sparse matrix file containing the raw UMI count data

organism: Macaca mulatta

source_name: fetal brain

extract_protocol:
Fetal macaque brains were isolated from E37 to E110, put on a dish containing PBS and sectioned. Telencephalic regions were identified and dissected using a blade. For E37-43 brains, the entire anterior and medio-posterior parts of the hemispheres were cut. Each tissue was incubated with HBSS-Papain (2 mg/ml, BrainBits) from 15 (for the early ages) to 30 (for more advanced ages) minutes at 37oC. The solution was removed and the tissue gently triturated in HBSS-DNase I 0.1mg/ml solution (StemCells) using a 2 ml pipette. Then, samples were filtered through 30 µm strain filters and the cells counted with an automatic cell counter (ThermoFisher Scientific). Samples were diluted in HBSS to 1000 cells/microliter and processed for single cell RNA-seq analysis within 20 min at Yale Center for Genome Analysis (YCGA) core facility.
GEM Generation and Barcoding. Single cell suspension in RT Master Mix is loaded on the Single Cell A Chip and partition with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 12 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence (30nt). Upon dissolution of the Gel Beads in a GEM, the primers are released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produces barcoded, full-length cDNA from poly-adenylated mRNA.   Post GEM-RT Cleanup, cDNA Amplification and library construction. Silane magnetic beads are used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA is then amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection are used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) are added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) are added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.

value: fetal brain

tag: region

value: VFC

value: Male


title: E110 STC, bio rep 2

tag: tissue

value: STC


title: E110 S1C, bio rep 2

tag: Sex


title: NFYa_rep2

description: ChIP-seq

tag: genotype


title: E110 V1C, bio rep 2


title: E110 PCC, bio rep 2

value: PCC


title: E110 OFC, bio rep 2

value: OFC


title: E110 MGE, bio rep 2

value: MGE


title: E110 MFC, bio rep 2

value: MFC


title: E110 ITC, bio rep 2

value: ITC


title: E110 IPC, bio rep 2

value: IPC


title: modifiedRNA,1


title: E110 M1C, bio rep 2


title: E110 LGE, bio rep 2

value: LGE


title: E110 DFC, bio rep 2

value: WT

value: DFC


title: E110 CGE, bio rep 2

value: CGE


title: E110 A1C, bio rep 2


title: E110 V1C, bio rep 1


title: E110 Insula, bio rep 2

value: Insula


title: E110 STC, bio rep 1


title: E110 S1C, bio rep 1


title: E110 VFC, bio rep 1


title: E110 OFC, bio rep 1


title: E110 MFC, bio rep 1