title: ChREBP6, Biological rep6

description: Liver-specific ChREBP overexpression

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene1.0ST (Affymetrix) at 45°C for 17 hours

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V15 of Ensembl ID was used for annotation.

source_name: liver specific ChREBP overexpressing mice 6

label_protocol: 50 ng of total RNA is reverse transcribed following the Ovation  PicoSl System (Tecan). Briefly, the resulting double strand cDNA is used for amplification based on SPIA technology. After purification according to Nugen protocol, 5.5 ug of Sens Target DNA are fragmented and biotin labelled using Encore Biotin Module kit (Nugen). After control of fragmentation using Bioanalyzer 2100, cDNA is then hybridized to GeneChip® MouseGene1.0 ST (Affymetrix) at 45°C for 17 hours

value: 10 weeks


title: Normal 3

status: Public on Apr 15 2022

type: RNA

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

country: France

institute: INSERM

description: Normal liver tissue from 55 weeks old C57BL/6J mice

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® MouseGene2.0ST (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V21 was used for annotation.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Normal  liver tissue 3

label_protocol: 250 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: Extraction of total RNA was performed with SV total RNA isolation system from Promega.

tag: strain

tag: gender

value: Male

tag: age

value: 55 weeks

tag: tissue

value: Liver


title: Mouse brain tissue - dCA1 - CNTRL15

type: SRA

city: Munich

first: Elisabeth

last: Binder

address: Kraepelinstr. 2-10

country: Germany

institute: Max Planck Institute of Psychiatry

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL15-AK_S78

library_source: transcriptomic

data_processing:
Quality Control of sequencing data with FastQC v0.11.4
Adapter trimming with cutadapt
Extraction of unique molecular identifiers (UMIs) with UMI-tools v0.5.4
Alignment of reads to reference genome using STAR v2.6.0a
Deduplication of reads with UMI-tools
Quantification of gene expression with featureCounts v1.6.4
Normalization with DESeq2 v1.30.1 in R v4.0.5
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited file with raw counts of all samples
Supplementary_files_format_and_content: Tab-delimited files with normalized (DESeq2 vsd) counts per brain region

source_name: Mouse brain tissue - dCA1

growth_protocol: C57Bl/6 adult male mice were group-housed, a maximum of 4 animals per cage, in a room with a 12-hour light–dark cycle, room temperature (RT) 20–24 °C, and relative humidity 45–65%. Animals were used as approved by the Government of Upper Bavaria.

extract_protocol:
Brains were perfused, extracted and kept in -80oC until further use. The brain regions were extracted by punching of coronal sections following the Paxinos stereotaxic coordinates. RNA was extracted from each brain region of each animal using an automated Chemagic 360 instrument with an integrated dispenser and the chemagic RNA Tissue Kit (CMG-1212) in Paxgene tubes following manufacturer’s instructions.
Messenger RNA sequencing libraries were prepared using the QuantSeq 3’ mRNA Fwd kit (Lexogen) following manufacturer’s instructions with the addition of unique molecular identifiers (UMIs- UMI Second Strand Synthesis Module for QuantSeq FWD) for tagging of individual transcripts. Libraries were single-end sequenced on a whole Flow Cell of an Illumina HiSeq4000 sequencer using 75bp long reads for a total coverage of an average of 10M reads per library.

treatment_protocol: Animals were treated with 10mg/kg dexamethasone or saline 0.9% intraperitoneally for 4 hours.

tag: animal

tag: Sex

value: male

value: 3 month

tag: treatment

value: Vehicle

tag: mouse_weight (g)

tag: researcher

tag: plate

tag: lane

value: G

tag: row

tag: rin

tag: cryostat


title: Mouse brain tissue - dCA1 - DEX10

description:
dCA1_deseq2_expression_vsd.txt
dCA1-DEX10-AK_S28

value: Dexamethasone

value: C


title: Sample 8: IM-0223 EV

type: protein

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

country: USA

institute: Saint John's Cancer Institute

description: control

data_processing:
RPPA slides were assayed with 306 antibodies, analyzed by Array-Pro Analyzer 6.3 then by SuperCurve_1.5.0 via SuperCurveGUI_2.1.1
RPPA Core Facility at the University of Texas MD Anderson Cancer Center
Ratio was calculated as follow: (expression of gene X in OV-  expression of gene X in contorl EV)/expression of gene X in control EV
Fold Change worksheet reports test/control (i.e., EV/OV) ratios.

molecule: protein

organism: Homo sapiens

source_name: Melanoma cells (cultured(

growth_protocol: Cell lines were grown until 80% confluency and dettached using cell stripper non-enzimatic solution. Cells were washed with PBS and pelleted. Protein extraction were as described in extract protocol.

extract_protocol: Protein extractions, quantification, and downstream RPPA analysis were performed by CCSG-supported RPPA Core Facility at the University of Texas MD Anderson Cancer Center.

tag: cell line

tag: passages after establishing stable clones

tag: transfected vector

value: Control empty vector


title: Sample 7: IM-0223 EV

description: control


title: Mouse brain tissue - dCA1 - CNTRL14

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL14-AK_S13

tag: strain

value: A


title: ChREBP5, Biological rep5

description: Liver-specific ChREBP overexpression

source_name: liver specific ChREBP overexpressing mice 5

tag: gender


title: Sample 6: DP-0574 ILF2-OV

description: test


title: Sample 12: IM-0223 ILF2-OV

description: test


title: Mouse brain tissue - dCA1 - CNTRL10

description:
dCA1_deseq2_expression_vsd.txt
dCA1-CNTRL10-AK_S24

tag: age


title: Sample 5: DP-0574 ILF2-OV

description: test


title: Sample 4: DP-0574 ILF2-OV

description: test


title: Sample 3: DP-0574 EV

description: control


title: Sample 2: DP-0574 EV

description: control


title: ChREBP4, Biological rep4

description: Liver-specific ChREBP overexpression

source_name: liver specific ChREBP overexpressing mice 4

tag: tissue


title: Mouse brain tissue - CER - DEX4

description:
CER_deseq2_expression_vsd.txt
CER-DEX4-AK_S71

source_name: Mouse brain tissue - CER

tag: animal


title: Mouse brain tissue - CER - DEX1

description:
CER_deseq2_expression_vsd.txt
CER-DEX1-AK_S11

tag: Sex


title: Sample 1: DP-0574 EV

description: control


title: Sample 10: IM-0223 ILF2-OV

description: test


title: ChREBP3, Biological rep3

description: Liver-specific ChREBP overexpression

source_name: liver specific ChREBP overexpressing mice 3


title: Mouse brain tissue - CER - DEX15

description:
CER_deseq2_expression_vsd.txt
CER-DEX15-AK_S19

tag: treatment

value: B


title: ATAC_NALM6_CONTROL_Rep4

city: Memphis

first: Daniel

last: Savic

state: Tennessee

address: 262 Danny Thomas Pl

department: Pharmaceutical Sciences

institute: St. Jude Children's Research Hospital

library_source: genomic

data_processing:
Trimming was performed with trim_galore
Mapping was performed with Bowtie2
Peak calling was performed using MACS2 using the default q value of 0.05
Assembly: hg19
Supplementary files format and content: MACS2 narrowPeak bed files

molecule: genomic DNA

source_name: Nalm6 (ALL cell line)

growth_protocol: Cells were maintained in standard culture conditions with RPMI-1640 supplemented with 10% FBS, 2mM Glutamine and Pen/Step

extract_protocol: Cells were processed according to fast-atac protocol

treatment_protocol: Cell were treated with L-asparaginase at a concentration of 1IU/ml for 4 hours

tag: disease state

value: ALL

value: No treatment control


title: ChREBP2, Biological rep2

description: Liver-specific ChREBP overexpression

source_name: liver specific ChREBP overexpressing mice 2


title: ATAC_NALM6_CONTROL_Rep3


title: Mouse brain tissue - CER - DEX14

description:
CER_deseq2_expression_vsd.txt
CER-DEX14-AK_S46

tag: mouse_weight (g)

tag: researcher

value: E


title: ATAC_NALM6_CONTROL_Rep1


title: ATAC_NALM6_CONTROL_Rep2


title: Mouse brain tissue - CER - DEX11

description:
CER_deseq2_expression_vsd.txt
CER-DEX11-AK_S65

tag: plate

tag: lane

value: F


title: ATAC_NALM6_LASP_Rep4

value: LASP (1IU/ml, 4hrs)


title: ChREBP1, Biological rep1

description: Liver-specific ChREBP overexpression

source_name: liver specific ChREBP overexpressing mice 1

value: Male

value: 10 weeks


title: ATAC_NALM6_LASP_Rep3


title: Mouse brain tissue - CER - CNTRL4

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL4-AK_S72

tag: row

tag: rin


title: ATAC_SUPB15_CONTROL_Rep4

source_name: SUPB15 (ALL cell line)

tag: cell line


title: ATAC_NALM6_LASP_Rep2


title: ATAC_NALM6_LASP_Rep1


title: GFP6, Biological rep6

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 6

value: Liver


title: Mouse brain tissue - CER - CNTRL1

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL1-AK_S10

value: male

tag: cryostat


title: ATAC_SUPB15_CONTROL_Rep2


title: ATAC_SUPB15_CONTROL_Rep3


title: GFP5, Biological rep5

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 5


title: GFP4, Biological rep4

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 4


title: ATAC_SUPB15_CONTROL_Rep1


title: GFP3, Biological rep3

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 3


title: Mouse brain tissue - CER - CNTRL15

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL15-AK_S18

value: 3 month


title: Mouse brain tissue - CER - CNTRL14

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL14-AK_S50

value: Vehicle


title: ATAC_SUPB15_LASP_Rep4


title: ATAC_SUPB15_LASP_Rep3


title: GFP1, Biological rep1

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 1


title: miRNA-seq PAMK replicate 2

city: Guangzhou

first: Yugu

last: Li

address: Wushan street

country: China

institute: South China Agricultural University

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Supplementary files format and content: excel,expression profiles

source_name: miRNA-seq PAMK2

growth_protocol: MTEC1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in 5% CO2 at 37C

extract_protocol:
For miRNA-SEQ, approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

treatment_protocol: PAMK(50 μg/ml) for 12h affected the proliferation of MTEC1 cells

value: MTEC1 cell

tag: cell type

value: mouse medullary thymic epithelial cell line 1 cell

tag: genotype

value: WT

value: PAMK


title: ATAC_SUPB15_LASP_Rep1


title: miRNA-seq PAMK replicate 3

source_name: miRNA-seq PAMK3


title: ATAC_SUPB15_LASP_Rep2


title: miRNA-seq PAMK replicate 1

source_name: miRNA-seq PAMK1


title: Mouse brain tissue - AMY - DEX9

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX9-AK_S36

source_name: Mouse brain tissue - AMY

tag: strain

value: Dexamethasone

value: D


title: miRNA-seq Control replicate 3

source_name: miRNA-seq Control3

value: control


title: GFP2, Biological rep2

description: Liver-specific GFP overexpression

source_name: liver specific GFP overexpressing mice 2

tag: gender

tag: age


title: Mouse brain tissue - AMY - DEX7

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX7-AK_S5

tag: animal

value: A


title: SUPB15_LASP_Rep2

data_processing:
Reads were mapped to the human genome using BWA
Peak calling was performed using MACS2 using the default q value of 0.05
Final differential binding analysis was performed using DiffBind in R
Assembly: hg19
Supplementary files format and content: text file of compiled counts and narrowPeak files for each experimental sample

growth_protocol: Nalm6 and SUPB15 were maintained in standard culture conditions with RPMI-1640 supplemented with 10% FBS, 2mM Glutamine and Pen/Step

extract_protocol:
Cells were cross-linked, lysed, and sonicated according to the ENCODE project ChIPseq guidelines (https://www.encodeproject.org/about/experiment-guidelines/). 5ug of ATF4 antibody was used for IP
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell were treated with L-asparaginase at a concentration of 1IU/ml for 2 hours

value: ALL

tag: chip antibody

value: ATF4 Rabbit mAb (Cell singal #11815)

value: LASP (1IU/ml, 2hrs)


title: SUPB15_NT_Rep2

tag: treatment


title: SUPB15_LASP_Rep1


title: DND41_LASP_rep3

data_processing:
data processing was performed using the WARDEN RNA-seq pipeline on http://www.stjude.cloud
Assembly: hg19
Supplementary files format and content: text file of raw counts for each rep

source_name: ALL cell line

growth_protocol: Cell lines were maintained in standard culture conditions with RPMI-1640 supplemented with 10% FBS, 2mM Glutamine and Pen/Step

extract_protocol:
RNA was extracted from cell lines using the RNAeasy Plus Mini Kit (Qiagen, Cat#74136)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LASP treated, 4hrs

tag: replicate


title: Mouse brain tissue - AMY - DEX6

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX6-AK_S26

tag: Sex

tag: mouse_weight (g)

value: C


title: DND41_LASP_rep2


title: miRNA-seq Control replicate 2

source_name: miRNA-seq Control2


title: SUPB15_NT_Rep1


title: miRNA-seq Control replicate 1

source_name: miRNA-seq Control1


title: DND41_LASP_rep1


title: Mouse brain tissue - AMY - DEX3

description:
AMY_deseq2_expression_vsd.txt
AMY-DEX3-AK_S67

tag: researcher

tag: plate

value: F


title: DND41_NT_rep3

value: No treatment control


title: DND41_NT_rep1


title: DND41_NT_rep2


title: Mouse brain tissue - AMY - CNTRL9

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL9-AK_S40

value: male

value: 3 month

tag: lane

tag: row


title: PR8/3841: C57BL/6 4dpi

city: Shanghai

first: Qi

last: Wang

address: Anshun Road 350

institute: Shanghai Institute of Biological Products

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to virus genome using bowtie 1.1.2 with perfect match.
Genome_build: AF389115.1, AF389116.1, AF389117.1, AF389118.1, AF389119.1, AF389120.1, AF389121.1 and AF389122.1.
Supplementary_files_format_and_content: mapping results files generated by bowtie1.1.2
The column headers are query_id, strand, reference_id, start_position, read_sequences, respectively.

source_name: lung

extract_protocol:
Total RNAs were extracted from the lung tissues of C57BL/6 mice 4 days post infection using TRIzol reagent.
Total RNA was extracted from mice lung tissue using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: infection

tag: tissue

value: lung

tag: molecule subtype

value: small RNA


title: PR8-WT: C57BL/6


title: Mouse brain tissue - AMY - CNTRL7

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL7-AK_S4

value: Vehicle

tag: rin

tag: cryostat


title: CEM_LASP_rep3

tag: cell line

value: CEM


title: Mouse brain tissue - CER - CNTRL11

description:
CER_deseq2_expression_vsd.txt
CER-CNTRL11-AK_S64

source_name: Mouse brain tissue - CER

tag: strain

tag: age


title: CEM_LASP_rep2


title: CEM_LASP_rep1


title: CEM_NT_rep3


title: Mouse brain tissue - AMY - CNTRL6

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL6-AK_S27

tag: animal


title: Mouse brain tissue - AMY - CNTRL3

description:
AMY_deseq2_expression_vsd.txt
AMY-CNTRL3-AK_S66

tag: treatment


title: CEM_NT_rep1

tag: replicate


title: Pre-BötC targeted punch-outs

city: Solna

first: Wiktor

middle: Samuel

last: Phillips

address: Visionsgatan 18

country: Sweden

institute: Karolinska Institutet

description: Dissociated cells harvested from brain tissue puncouts containing the pre-Bötzinger complex. Mice aged post-natal day 4, pooled sample of biopsies from 10 littermates. Final library was split across two lanes of Illumina HiSeq 2500 rapid run flow cell.

data_processing:
Illumina software was used for basecalling.
Raw reads were first pre-processed similar to Hochgerner et al  (https://doi.org/10.1038/s41598-017-16546-4 ). In brief, reads with UMIs containing any bases of Phred score <17 were rejected. Reads with less than 3 Gs following the 6bp UMI were filtered out. Poly-A tails were trimmed and, afterwards, only reads with at least 25 remaining cDNA bases were kept.
Pre-filtered reads were aligned and counted with zUMIs (Parekh et al. 2018). Detected barcodes were filtered according to the barcode combinations dispensed during library tagmentation. Total reads per cell were adaptively downsampled to within 3 times the median absolute deviation.
Genome_build: mm39
Supplementary_files_format_and_content: RDS (Rdata) file containing a data structure that holds the deduplicated molecule counts matrix. For layout of the data structure see the Wiki of zUMIS:  https://github.com/sdparekh/zUMIs/wiki/Output#structure-of-the-output-dgecounts-object-in-project_namedgecountsrds We used automatically downsampled intron + exon features for analysis (e.g. "AllCounts$umicount$inex$downsampling$downsampled_" )
Supplementary_files_format_and_content: text file deliminted by newlines containing a list of the barcodes used during library generation

source_name: Brainstem ventrolateral medulla

extract_protocol:
We cut transverse medullary tissue slices of 300µm thickness, with the pre-BötC approximately centered in the rostral-caudal axis of the slice according to anatomical landmarks. Circular punchouts (⌀ 690µm) were cut from the ventral-lateral border on both sides of each slice, centered over the approximate location of the pre-BötC in the transverse plane. We enzymatically dissociated the punchouts with pronase at room temperature for 25 minutes. The tissue was titurated and protease action was then inhibited with 1% fetal bovine serum (FBS). Cells were pelleted via centrifugation, resuspended and then cryopreserved in methanol (Alles et al. 2017). Methanol fixed samples were later rehydrated in PBS, pooled into a single tube, stained with Hoechst dye, and counted. Cells were finally dispensed via limiting dilution into a 9600 microwell array for STRT-seq-2i library preparation.
Single-cell cDNA libraries were prepared according to the methods described for STRT-seq-2i (For detailed description see Hochgerner et al. https://doi.org/10.1038/s41598-017-16546-4 )

value: Brainstem - ventrolateral medulla

tag: cell type

value: mixed


title: CEM_NT_rep2


title: RNA-seq: AMLN diet DKO rep3

city: Philadelphia

first: Bridget

last: Gosis

state: PA

address: 1819 Montrose St.

department: Perelman School of Medicine

institute: University of Pennsylvania

description: RNA_seq_expressionvalues_allgenotypes.csv

data_processing:
The HiSeq Control Software was used for image analysis and base calling.
Illumina’s bcl2fastq 2.17 software was used to make FASTQ files.
Trimmomatic (v0.32) was used to trim the adaptors and remove low-quality sequencing reads.
STAR v2.6.0c was used to align reads to the mm9 mouse genome assembly.
Samtools view was used to filter aligned reads without a mapped mate and alignments with mapq score below 10(-F 4 -q 10).
Counts per gene were quantified using Rsubread package’s featureCounts function with Ensembl v.67 mm9 gene annotation file. Genes with <1 count per million (CPM) in less than a quarter of samples were removed.
Limma  voom function was used to log2 transform and normalize the count matrix
Limma was used to fit a linear model and perform differential gene expression analysis, creating log2(fold change) values between different genotypes. P-values were adjusted for multiple comparisons with the Benjamini–Hochberg procedure.
Specific data processing steps applicable to different samples, as indicated for each sample.
Genome_build: mm9
Supplementary_files_format_and_content: RNA-seq: Normalized expression values csv file
Supplementary_files_format_and_content: ChIP-seq: bigWig files indicating strength of binding
Supplementary_files_format_and_content: ChIP-seq: peak text files

source_name: Liver tissue

growth_protocol: Flcnlox/lox mice on normal chow were injected with either AAV8-TBG-GFP or -Cre to yield Control and LiFKO mice. Flcnlox/lox; Tfe3-/Y (a whole body deletion of Tfe3) mice were also injected with  AAV8-TBG-Cre to yield Flcn/Tfe3 double knock-out (DKO) mice.

extract_protocol:
Mice were fasted for 4-6 hours before sacrifice, and livers were then harvested. RNA was extracted using Trizol.
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina. Sequencing was then done on an Illumina HiSeq 4000 or equivalent using a 2x150 base pair paired end method.

treatment_protocol: ~1 week after virus injection, mice were fed a total of 17-18.5 weeks of normal chow or AMLN diet.

tag: diet intervention

value: 17-18.5 weeks AMLN diet

tag: genotype

value: DKO

tag: aav8 injection

tag: feeding state when sacrificed

value: 4-6h fast


title: single-cell_VT_HSV2_Treg

city: Seattle

first: Brianna

middle: R

last: Traxinger

state: Washington

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

institute: Fred Hutch

description: 5' Transcriptome

data_processing:
Samples were processed using CellRanger pipline
FASTQ files were processed with CellRanger software and corresponding sample sheet
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated values with abundance measurements for each target.

source_name: vaginal tissue

extract_protocol: RNA was extracted using 10x genomics protocols

treatment_protocol: Cells were sorted from the vaginal-draining lymph nodes or vaginal tissue from FoxP3GFP mice on day 7 after either intravaginal HSV-2 infection or mock infection

value: vaginal tissue

tag: phenotype

value: live+CD45+CD45.2 iv label-CD4+FoxP3+

value: s.c. medroxyprogesterone acetate, intravaginal HSV-2 infection


title: RNA-seq: AMLN diet DKO rep2


title: 697_LASP_rep3

value: LASP treated, 4hrs


title: single-cell_LN_uninfected_Treg

description: 5' Transcriptome

source_name: vaginal-draining lymph nodes

value: vaginal-draining lymph nodes

value: s.c. medroxyprogesterone acetate, PBS mock intravaginal mock


title: 22_HSV-2pos_gVT

description: 3' Transcriptome

data_processing:
The RNA-seq data were aligned to the mouse genome (reference sequence mm10) using STAR (v2.4.2a) and gene expression quantification was performed using RSEM (v1.2.22). Genes with less than seven nonzero read counts were discarded, leaving 12,317 expressed genes for the analysis. Libraries (samples) with less than 2,000,000 reads; 9,000 detected genes; and an exon rate < 75% were also removed. Twenty-one of the 22 prepared libraries passed these quality criteria.   Raw count data from RSEM was imported into R. The edgeR Bioconductor package was used to calculate normalization factors, followed by the voom transformation from the limma Bioconductor package for normalization. Statistical analyses were performed with the limma R package. A linear model was fitted to each gene, and empirical Bayes moderated t-statistics were used to assess differences in expression. We subsetted the whole dataset into one subset corresponding to the cell type Treg & the treatment HSV-2+, and looked at the constrast between vaginal tract and lymph node. Intraclass correlations were estimated to account for measures originating from the same mice. An absolute log2-fold change cutoff of 1 and a false discovery rate (FDR) cutoff of 5% were used to determine differentially expressed genes (DEGs). Gene set enrichment analysis (GSEA) was performed using the R function Camera implemented within the limma R package. An FDR cut-off of 5% was used to determine significant gene sets
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated values; count data

extract_protocol:
cells were sorted into SMART-seq v4 Ultra Low Input (Takara Bio USA, San Jose, California) lysis buffer and reverse transcription was performed followed by PCR amplification to generate full length amplified cDNA. Sequencing libraries were constructed using the NexteraXT DNA sample preparation kit (Illumina) to generate Illumina-compatible barcoded libraries.  Libraries were pooled and quantified using a Qubit® Fluorometer (Life Technologies).
Dual-index, single-read sequencing of the pooled libraries was carried out on a HiSeq2500 sequencer (Illumina) with 58-base reads, using HiSeq v4 Cluster and SBS kits (Illumina) with a target depth of 5 million reads per sample.  FASTQs were aligned to a mouse reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count.  QC and metrics analysis was performed using the Picard family of tools

value: live+CD45+CD4+FoxP3+ CD45.2 iv label -

value: s.c. medroxyprogesterone acetate, intravaginal HSV-2

tag: mouse

value: g


title: single-cell_LN_HSV2_Treg

description: 5' Transcriptome

tag: tissue

value: s.c.medroxyprogesterone acetate, intravaginal HSV-2 infection


title: RNA-seq: AMLN diet LiFKO rep3

value: LiFKO


title: 20_HSV-2pos_gLN

description: 3' Transcriptome


title: 697_LASP_rep1


title: 18_HSV-2pos_fVT

description: 3' Transcriptome

value: f


title: PR8/3841: BALB/c 4dpi

extract_protocol:
Total RNAs were extracted from the lung tissues of BALB/c mice 4 days post infection using TRIzol reagent.
Total RNA was extracted from mice lung tissue using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

value: BALB/c

tag: infection

value: lung

tag: molecule subtype

value: small RNA


title: RNA-seq: AMLN diet DKO rep1

value: 17-18.5 weeks AMLN diet

value: DKO


title: 697_NT_rep2

value: No treatment control


title: 697_NT_rep3


title: 16_HSV-2pos_fLN

description: 3' Transcriptome


title: 697_NT_rep1


title: 697_LASP_rep2


title: 14_HSV-2pos_eVT

description: 3' Transcriptome

value: e


title: RNA-seq: AMLN diet Control rep3

value: Control

value: 4-6h fast


title: RNA-seq: AMLN diet Control rep2


title: 12_HSV-2pos_eLN

description: 3' Transcriptome


title: RNA-seq: AMLN diet LiFKO rep2


title: 10_HSV-2pos_dVT

description: 3' Transcriptome

value: d


title: REH_LASP_rep2

value: REH

value: LASP treated, 4hrs


title: RNA-seq: AMLN diet Control rep1


title: RNA-seq: AMLN diet LiFKO rep1


title: RNA-seq: Normal chow LiFKO rep3

value: 17-18.5 weeks normal chow


title: REH_LASP_rep1


title: 8_HSV-2pos_dLN

description: 3' Transcriptome

value: s.c. medroxyprogesterone acetate, intravaginal HSV-2


title: RNA-seq: Normal chow LiFKO rep2


title: 6_none_cLN

description: 3' Transcriptome

value: s.c. medroxyprogesterone acetate, PBS mock intravaginal

value: c


title: REH_NT_rep3


title: RNA-seq: Normal chow LiFKO rep1

value: LiFKO


title: 4_none_bLN

description: 3' Transcriptome

value: b


title: REH_LASP_rep3


title: REH_NT_rep2


title: RNA-seq: Normal chow Control rep3


title: 2_none_aLN

description: 3' Transcriptome

value: a


title: hTSC, SP600125, rep 3

city: London

first: Miguel

last: Branco

address: 4 Newark Street

country: United Kingdom

institute: Blizard Institute

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped using HISAT2 v2.0.5 with --no-softclip and --no-unal. Reads with MAPQ<2 were removed.
Raw read counts for each gene were extracted using the RNA-seq quantitation pipeline.
Differentially expressed genes were identified using DESeq2.
Gene expression values for each sample were generated using the variance-stabilizing transformation in DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix containing normalised (variance-stabilizing transformation) gene expression values
Supplementary files format and content: List of differentially expressed genes with padj<0.05 and >2-fold difference.

source_name: hTSC CT27

growth_protocol: Human trophoblast stem cells were grown on plates coated either with 5–10 µg/mL collagen IV or 0.5 µg/mL iMatrix 511. Medium comprised DMEM/F12 supplemented with 1% KSR, 0.5% Penicillin-Streptomycin, 0.15% BSA, 1% ITS-X supplement, 200 µM L-ascorbic acid, 2.5 µM Y27632, 5 µM A83-01, 2 µM CHIR99021, 50 ng/ml EGF and 0.8 mM valproic acid.

extract_protocol:
RNA was extracted with QIAGEN's AllPrep DNA/RNA Mini Kit, and treated with Ambion's TURBO DNA-free Kit.
10-100 ng total RNA was treated with the NEBNext rRNA Depletion Kit. Library was generated with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina.

treatment_protocol: Cells were treated with either 10 µM SP60015 or DMSO control for 96 hours.

value: hTSC CT27

value: Human trophoblast stem cells


title: RNA-seq: Normal chow Control rep1


title: hTSC, SP600125, rep 2


title: He_Thi_20W_21

city: Shinjuku-ku

first: Fumihiko

last: Takeuchi

state: Tokyo

address: 1-21-1 Toyama

department: Research Institute

country: Japan

institute: National Center for Global Health and Medicine

hyb_protocol: RNA samples were prepared and analyzed using the Rat GE 4x44K v3 Microarray (Agilent Microarray Design ID 028282).

scan_protocol: Arrays were scanned using the G2539A scanner (Agilent) until 2011.07.01 and the G2600D scanner (Agilent) from 2014.06.19.

data_processing: The scanned images were processed using the Feature Extraction software (Agilent). The signal intesity was transformed by the logarithm of base 2.

organism: Rattus norvegicus

source_name: heart, Chlorothiazide 20 milligram per kilogram per day

label_protocol: The RNA samples were labeled using the Low Input Quick Amp Labeling Kit  (Agilent). cRNA samples were prepared with a template of 100 ng of total RNA and labeled with Cy3.

extract_protocol: Tissues were obtained from male rats at 16 weeks old. The RNA was extracted using RNeasy kit (Qiagen) or AllPrep DNA/RNA Mini Kit (Qiagen).

value: heart

tag: Sex

value: male

value: 16 weeks

value: WKY/Izm

tag: individual

tag: array

tag: scan date

tag: compound

value: Chlorothiazide

tag: dose


title: PR8/3841:293T

description: Total RNA was extracted from 293T cells using TRIzol reagent.

source_name: 293T cells

extract_protocol:
Total RNA was extracted from 293T cells or mice lung tissue using TRIzol reagent.
Small RNA libraries were constructed by  the TruSeq Small RNA Sample Preparation Kit of Illumina from total RNA.

tag: cell line

value: 293T cells

tag: influenza a virus (iav) infection


title: PR8/3841:AGO-IP (293T)

description: Small RNA (AGO-IP) was extracted from 293T cells using TRIzol reagent.


title: hTSC, DMSO, rep 3

tag: cell type

tag: treatment

value: DMSO


title: SHS170

type: genomic

city: Davis

first: Hong

last: Ji

address: County Rd 98 & Hutchison Drive

institute: University of California Davis

description: Nasal epithelial cells obtained by nasal brushing

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 and EPIC Beadchip using standard Illumina protocol

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

data_processing: Minfi and RnBeads

label: Cy5 and Cy3

source_name: Nasal epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted using Qiagen Allprep micro kit according to manufacturer’s  instructions.

tag: cohort

value: GSEP

tag: age

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore

value: Nasal epithelial cells


title: PMG84U

city: los angeles

first: Shubhamoy

last: Ghosh

address: 650 Charles E Young  Dr East

department: Pediatrics

institute: University of California Los Angeles

data_processing:
Demultiplexed fastq files were analysed using miRDeep2 package. Adapters were trimmed from miRNA sequences and  aligned using Bowtie aligner against the hg38 referece.
Genome-aligned reads were matched to known human miRNAs from miRBase version 21  and quantified using the script quantifier.pl
ggplot2 was used for visulazation of RNAseq data
Genome_build: mm10
Supplementary_files_format_and_content: Expression Matrix

source_name: Extracellular Vesicles from plasma of pregnant women

growth_protocol: Maternal blood samples colleted at different trimesters of pregnancy

extract_protocol:
secretory Extracellular Vesicles were isolated from maternal blood samples. Total RNA was extracted from isolated sEVs and miRNA library were prepared using miRNeasy Mini Kit (Qiagen)
for library prep 6µl of total RNA extracted from sEVs were used.  Libraries were prepared using NEB Next Multiplex small RNA Library prep kit (NEB E7300S)

treatment_protocol: Maternal blood samples collected from normal pregnancy and pregnany with Gestetional diabetes or  Ischemic placental disease

tag: trimester

tag: complecation

value: IPD


title: He_Thi_20W_23

tag: tissue

tag: Sex

tag: strain

tag: individual

tag: array

tag: scan date


title: He_Thi_20W_20

tag: compound

tag: dose


title: He_Thi_20W_19

tag: age


title: REH_NT_rep1

tag: cell line

value: REH

tag: treatment

value: No treatment control

tag: replicate


title: PLH87K


title: SHS169

tag: cohort

value: F

tag: race (b=black, o=other)

value: b

tag: shs (1=exposed to 2nd smoke)

tag: cell type


title: SHS173

tag: asthma severity (1=severe)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: SHS183

tag: Sex


title: SHS154


title: SHS168


title: He_Thi_20SP_22

tag: tissue

tag: strain

value: SHRSP/Izm

tag: individual

tag: array


title: SHS162

tag: age


title: PHV89T

tag: trimester

tag: complecation


title: SHS159


title: SHS181


title: RNA-seq: Normal chow Control rep2

tag: diet intervention

value: 17-18.5 weeks normal chow

tag: genotype

value: Control

tag: aav8 injection

tag: feeding state when sacrificed

value: 4-6h fast


title: SHS166

tag: cohort

tag: race (b=black, o=other)

tag: shs (1=exposed to 2nd smoke)

tag: cell type


title: hTSC, DMSO, rep 2

tag: cell line

value: hTSC CT27

value: Human trophoblast stem cells

tag: treatment


title: hTSC, DMSO, rep 1


title: SHS161

tag: Sex

tag: asthma severity (1=severe)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: hTSC, CUT&Tag, JunD

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using SEACR v1.2 with normalisation to IgG and relaxed mode.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 100 bp bin size.
Assembly: hg38, mm10
Supplementary files format and content: Bigwig tracks
Supplementary files format and content: Peaks, bed format
Library strategy: CUT&Tag

extract_protocol:
Cells were bound to BioMagPlus Concanavalin A coated magnetic beads and incubated overnight with primary antibodies. Samples were washed and incubated with secondary antibody (Guinea Pig anti-Rabbit IgG ABIN101961) for 1 hr, then washed and incubated with pA-Tn5 loaded with Illumina NEXTERA adapters, followed by tagmentation. Adapter-ligated DNA was released with proteinase K and phenol/chloroform extracted.
NEXTERA-tagmented libraries were amplified using NEBNext HiFi 2x PCR Master mix.

treatment_protocol: EVT differentiation was performed in matrigel, in DMEM/F12 supplemented with 0.1 mM 2-mercaptoethanol, 0.5% Penicillin-Streptomycin, 0.3% BSA, 1% ITS-X, 100 ng/ml NRG1, 7.5 μM A83-01, 2.5 μM Y27632 and 4% KSR. NRG1 was exlcuded from the medium from day 3, and KSR from day 6. Cells were collected on day 8.

tag: antibody

value: anti-JunD (Cell Signalling D17G2)


title: PET67Q

tag: trimester

tag: complecation


title: hTSC, CUT&Tag, IgG

value: Rabbit IgG (Santa Cruz sc-2027)


title: PXW81E

value: GDM


title: He_Thi_20SP_19

tag: tissue

value: heart

value: male

tag: age

value: 16 weeks

tag: strain

tag: individual

tag: array

tag: scan date

tag: compound

value: Chlorothiazide

tag: dose


title: He_Thi_20SP_20


title: PLC79F


title: SHS152

tag: cohort

value: GSEP

tag: race (b=black, o=other)

tag: shs (1=exposed to 2nd smoke)

tag: cell type

value: Nasal epithelial cells


title: SHS139

tag: Sex

value: F

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)


title: SHS136

value: b

tag: asthma severity (1=severe)

tag: allergyscore


title: hTSC, CUT&Tag, H3K4me1, rep 2

tag: cell line

tag: antibody

value: anti-H3K4me1 (Abcam ab8895)


title: PCJ88V

tag: trimester

tag: complecation


title: hTSC, SP600125, rep 1

tag: treatment


title: PRN85I_GDM


title: hTSC, CUT&Tag, H3K4me1, rep 1


title: SHS150

tag: age


title: SHS146

value: M


title: He_Thi_20SP_21

tag: tissue

tag: strain

value: SHRSP/Izm

tag: individual

tag: array

tag: scan date

tag: compound


title: PPR84F_GDM


title: He_Hyd_10W_16

source_name: heart, Hydralazine 10 milligram per kilogram per day

tag: Sex

value: WKY/Izm

value: Hydralazine

tag: dose


title: He_Hyd_10W_14


title: He_Hyd_10W_15


title: PSJ84R_GDM


title: hTSC, CUT&Tag, H3K27ac, rep 2

value: hTSC CT27

tag: cell type

value: Human trophoblast stem cells

value: anti-H3K27ac (Active Motif 39034)


title: SHS129

tag: cohort

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)


title: SHS138

tag: allergy (1=yes)

tag: allergyscore


title: hTSC, CUT&Tag, cJun

tag: cell line

tag: antibody

value: anti-cJun (Cell Signalling 60A8)


title: He_Hyd_10SP_16

tag: tissue

value: heart

tag: age

tag: strain


title: He_Hyd_10SP_15

value: male

tag: individual

tag: array

tag: scan date


title: PRL80T_GDM

tag: trimester

tag: complecation

value: GDM


title: He_Hyd_10W_13

tag: Sex

value: 16 weeks

tag: compound

tag: dose


title: SHS128

tag: cohort

value: GSEP

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: cell type


title: hTSC, CUT&Tag, H3K27ac, rep 1

tag: cell line

tag: antibody

value: anti-H3K27ac (Diagenode C15410196)


title: EVT, CUT&Tag, IgG

source_name: hTSC BTS5

value: hTSC BTS5

value: Extravilous trophoblast differentiatied from hTSCs

tag: treatment

value: EVT differentiation

value: Rabbit IgG (Santa Cruz sc-2027)


title: PFP80Z_GDM


title: PSN79O_GDM


title: He_Hyd_10SP_14

tag: tissue

tag: age

tag: strain

value: SHRSP/Izm


title: He_Hyd_10SP_13

tag: individual

tag: array

tag: scan date


title: hTSC, CUT&RUN, TFAP2C

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using SEACR v1.2 with normalisation to IgG and relaxed mode.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 100 bp bin size.
Assembly: hg38
Supplementary files format and content: Bigwig tracks
Supplementary files format and content: Peaks, bed format
Library strategy: CUT&RUN

source_name: hTSC CT29

extract_protocol:
Cells were bound to BioMagPlus Concanavalin A coated magnetic beads and incubated overnight with primary antibodies, then washed and incubated with pA-Mnase followed by digestion (100mM CaCl2) and reaction arrest in digitonin/EGTA STOP buffer. DNA was extracted using phenol/chloroform.
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit.

value: hTSC CT29

value: anti-TFAP2C (Santa Cruz sc-12762)


title: SHS132

tag: Sex

value: M

value: b

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore

value: Nasal epithelial cells


title: PRA77U_GDM

tag: trimester

tag: complecation


title: PTA81A_CON

value: NORM


title: EVT, CUT&Tag, H3K27ac

value: anti-H3K27ac (Active Motif 39034)


title: hTSC, CUT&RUN, TEAD4

value: Human trophoblast stem cells


title: SHS124

tag: cohort

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)


title: PTG80I_CON


title: SHS122

value: F

tag: cell type


title: He_Ena_20W_7

source_name: heart, Enalapril 20 milligram per kilogram per day

tag: tissue

value: heart

value: male

value: 16 weeks

value: WKY/Izm

tag: compound

value: Enalapril

tag: dose


title: He_Ena_20W_8

tag: age

tag: strain

tag: individual


title: SHS119

value: GSEP

tag: Sex


title: He_Ena_20W_6

tag: array

tag: scan date


title: PEH80C_CON


title: SHS121

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: He_Ena_20W_5


title: NP4

tag: trimester

value: NP

tag: complecation


title: NP3


title: hTSC, CUT&RUN, GATA3

tag: cell line

tag: antibody

value: anti-GATA3 (Santa Cruz sc-268)


title: SHS116

tag: cohort

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: cell type


title: He_Ena_20SP_12

tag: tissue

tag: age

tag: strain

value: SHRSP/Izm

tag: compound

tag: dose


title: SHS110

tag: Sex

tag: ecat exposure>=40 (1=yes)


title: He_Ena_20SP_9

tag: individual

tag: array

tag: scan date


title: NP5

tag: trimester

tag: complecation


title: hTSC, ChIP, Input

data_processing:
Adaptors and low-quality base calls were trimmed using Trim Galore v0.6.5 with default parameters.
Trimmed reads were mapped to hg38 using bowtie2 v2.4.1 with default paramaters. Reads with MAPQ<2 were removed.
Peaks were called using MACS2 v2.1.1 with -q 0.05 and --broad.
BigWig tracks were generated using the bamCoverage function of deepTools2.0, with CPM normalisation and 100 bp bin size.
Assembly: hg38
Supplementary files format and content: Bigwig tracks
Supplementary files format and content: Peaks, broadPeak format

extract_protocol:
Cells were fixed with 1% formaldehyde for 12 mins, followed by chromatin extraction and sonication. Immunoprecipitation was performed with 10 µg of chromatin for 2.5 µg of anti-H3K27ac or H3K4me3 antibody. DNA was purified using the GeneJET PCR purification kit (Thermo Fisher).
Libraries were prepared from 1-5 ng of DNA using the NEBNext ultra II DNA library prep kit.

tag: cell line

value: hTSC CT27

tag: antibody

value: none (input)


title: PEW80F.cord

value: Cord

value: IPD


title: SHS107

tag: cohort

tag: race (b=black, o=other)

value: b

tag: asthma severity (1=severe)

tag: allergy (1=yes)

tag: allergyscore

value: Nasal epithelial cells


title: hTSC, ChIP, H3K4me1

tag: cell type

value: Human trophoblast stem cells

value: anti-H3K4me1 (Abcam ab8895)


title: PNC75Z.cord


title: He_Ena_20SP_11

tag: tissue

value: heart

tag: age

tag: strain

tag: compound


title: He_Ena_20SP_10

tag: Sex

value: male

tag: individual

tag: dose


title: He_Cds_5W-9

source_name: heart, Candesartan 5 milligram per kilogram per day

value: 16 weeks

tag: array

tag: scan date

value: Candesartan


title: He_Cds_5W-8

value: WKY/Izm


title: PNC75Z.4th

tag: trimester

value: Del

tag: complecation


title: hTSC, ChIP, H3K27ac

tag: cell line

tag: antibody

value: anti-H3K27ac (Diagenode C15410196)


title: SHS104

tag: cohort

value: GSEP

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)


title: PNC75Z.2nd


title: PNC75Z.3rd


title: He_Cds_5W-10

tag: tissue

tag: age


title: Fertile control_5

city: Jette

first: Margo

last: Willems

state: Brussels

address: Laarbeeklaan 103

department: Reproduction, genetics and regenerative medicine

country: Belgium

institute: Vrije Universiteit Brussel

data_processing:
basecalling: Illumina bcl2fastq
alignment to human genome hg19 using STAR
expression was quantified using htseq-count
Assembly: hg19
Supplementary files format and content: count files per sample

source_name: testicular biopsy

growth_protocol: Testis tissue was snap-frozen in liquid nitrogen after biopsy and stored at -80°C until RNA extraction

extract_protocol:
RNA was extracted using the Rneasy Micro kit (Qiagen), accoring to the manufacturer's guideline (RNA extraction from tissue)
KAPA RNA HyperPrep Kit with RiboErase (HMR) from Roche Diagnostics

value: testis

tag: fibrosis status

value: Non-fibrotic tissue


title: SHS023

tag: Sex

tag: cell type


title: SHS102

value: F

tag: allergy (1=yes)

tag: allergyscore


title: SHS114


title: Fertile control_3


title: He_Cds_5SP-9

tag: strain

value: SHRSP/Izm

tag: individual

tag: array

tag: scan date

tag: compound

tag: dose


title: He_Cds_5SP-8


title: ESS059_A1

tag: cohort

value: ESS

tag: race (b=black, o=other)

value: b


title: SHS003

value: Nasal epithelial cells


title: ESS093_A1

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)


title: Fertile control_4

tag: tissue


title: PGC81D.cord

tag: trimester

value: Cord

tag: complecation

value: IPD


title: ESS097_A1

tag: age

tag: Sex

tag: ecat exposure>=40 (1=yes)


title: PNC75Z.1st


title: Fertile control_2

tag: fibrosis status


title: Fertile control_1


title: PGC81D.3rd


title: He_Cds_5SP-7

value: heart

value: male

tag: strain


title: ESS061_A1

tag: allergy (1=yes)

tag: allergyscore

tag: cell type


title: ESS053_A1


title: ESS063_A1


title: He_Cds_5SP-10

value: 16 weeks

tag: individual

tag: array

tag: scan date

tag: compound

value: Candesartan


title: ESS055_A1

tag: cohort

tag: race (b=black, o=other)

tag: asthma severity (1=severe)


title: He_Cds_5W-7

tag: tissue

value: WKY/Izm

tag: dose


title: PGC81D.4th

tag: trimester

value: Del

tag: complecation


title: ESS049_A1

tag: age

tag: Sex

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)


title: Sertoli cell only_3

tag: fibrosis status


title: Sertoli cell only_5


title: PGC81D.2nd


title: PWZ84A.cord


title: ESS047_A1

value: o

tag: allergy (1=yes)

tag: allergyscore

tag: cell type


title: Sertoli cell only_1


title: Sertoli cell only_2


title: Sertoli cell only_4


title: hTSC, ChIP, H3K4me3

tag: cell line

value: hTSC CT27

value: Human trophoblast stem cells

tag: antibody

value: anti-H3K4me3 (Diagenode C15410003)


title: PGC81D.1st


title: PWZ84A.3rd


title: He_Car_50W_1

source_name: heart, Carvedilol 50 milligram per kilogram per day

tag: strain

tag: individual

tag: array

tag: scan date

tag: compound

value: Carvedilol


title: ESS041_A1

tag: cohort

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)


title: He_Car_50W_4

tag: tissue

tag: Sex

tag: age

tag: dose


title: He_Car_50W_3


title: SHS111

value: GSEP

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)


title: ESS045_A1

value: ESS

value: b

tag: allergyscore

tag: cell type


title: He_Car_50SP_4

tag: strain

value: SHRSP/Izm


title: He_Car_50W_2

tag: individual


title: Testis atrophy_3

value: testis

tag: fibrosis status

value: Fibrotic tissue


title: PWZ84A.4th

tag: trimester

tag: complecation

value: IPD


title: PMD88R.cord

value: Cord


title: He_Car_50SP_2

value: heart

value: male

value: 16 weeks

tag: array

tag: scan date

tag: compound


title: PMD88R.4th

value: Del


title: Testis atrophy_5

tag: tissue


title: ESS039_A1

tag: cohort

tag: Sex

value: F

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

value: Nasal epithelial cells


title: PWZ84A.2nd


title: ESS035_A1

tag: age

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)


title: Testis atrophy_4


title: PWZ84A.1st


title: ESS033_A1

tag: allergy (1=yes)

tag: allergyscore

tag: cell type


title: He_Car_50SP_1

tag: strain

tag: individual

tag: dose


title: He_Car_50SP_3

tag: array


title: ESS025_A1


title: Testis atrophy_2

tag: fibrosis status


title: PMD88R.1st

tag: trimester

tag: complecation


title: Testis atrophy_1

tag: tissue


title: He_Aml_20W_9

source_name: heart, Amlodipine 20 milligram per kilogram per day

tag: Sex

value: WKY/Izm

tag: scan date

tag: compound

value: Amlodipine


title: ESS027_A1

tag: cohort

tag: age

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)


title: ESS029_A1

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: ESS019_A1

tag: cell type


title: ESS023_A1


title: Klinefelter syndrome_2


title: He_Aml_20W_8

tag: strain

tag: individual

tag: array

tag: dose


title: ESS021_A1


title: Klinefelter syndrome_5

tag: tissue

tag: fibrosis status


title: PMD88R.3rd

tag: trimester

tag: complecation


title: X85WD

value: GDM


title: Klinefelter syndrome_4


title: Klinefelter syndrome_3


title: He_Aml_20W_7

tag: Sex

tag: scan date

tag: compound


title: He_Aml_20Sp_8

tag: age


title: X85W3


title: ESS011_A1

tag: cohort

value: ESS

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)


title: BiPNT.D3(-SGC).ATAC-seq

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 ensembl v79) transcriptome using rsem (version 1.3.1)
The gene expression level was calculated by using  RSEM
The RNA-seq data processing was performed as described45. To analyze the regular gene expression, the reads were aligned to the reference transcriptome by RSEM46 and bowtie2 (—bowtie2— bowtie2-sensitivity-level very_sensitive —no-bam-output —estimate -rspd) using the index built by RSEM with the mouse genome, mm10, and Ensembl gene annotation track v79
Assembly: mm10

source_name: epiblast stem cell

growth_protocol: EpiSCs were cultured and maintained in N2B27 medium with Activin A (20ng/ml, PeproTech), bFGF (15ng/ml, PeproTech) and XAV939 (1uM, Selleck) on fetal bovine serum (FBS, NATOCOR)-coated dishes. For induction of BVSC double positive (BV+SC+) cells, the EpiSCs containing BVSC reporter were cultured in iCD1 medium which comprised of Vitamin C (50 μg/ml, Sigma), bFGF (10 ng/ml, PeproTech), LiCl (5 mM, Sigma), LIF (1000 U/ml, Millipore) and CHIR99021 (1 μM, synthesized in GIBH), with the addition of BMP4 (5-10 ng/ml,  R&D Systems), EPZ5676 (2.5 μM, Selleck ) and EPZ6438 (1 μM, TargetMol) for 3 days, and then in N2B27 medium with 2i (PD0325901, 1uM, synthesized in GIBH; CHIR99021, 3uM, synthesized in GIBH) and Vitamin C (50 μg/ml, Sigma) for another 3 days.  Fluorescence-activated cell sorting (FACS) was performed with a FACSAriaIII (BD) cell sorter for purifying BV+SC+ cells.

extract_protocol:
Genomic DNA
Total RNAs were extracted as described above. The VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina (VAHTS, #NR603) was used for RNA library preparation. In brief, 1 μg total RNAs were hybridized with the rRNA probe (H/M/R) and digested by RNase H to remove ribosomal RNAs. After DNase I digestion, the ribosomal-depleted RNAs were fragmented at 94°C for 8min. Then the first-strand and second-strand cDNAs were synthesized successively using the provided reagents. The cDNA was purified by VAHTS DNA Clean Beads (VAHTS, #NR411), followed by end repaired, dA-tailing, adapter ligation, and second strand cDNA digestion. After two-round of purification, the cDNAs was PCR-amplified and purified by VAHTS DNA Clean Beads. High- throughput sequencing was performed using Illumina HiSeq Xten (Illumina) platform with PE150 (pair-end sequencing, 150 bp reads).

tag: cell type

value: epiblast stem cell


title: Klinefelter syndrome_1


title: He_Aml_20W_10

tag: strain


title: ESS015_A1

value: b

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: ESS017_A1


title: ESS009_A1


title: X85W2


title: X85W1


title: mTSC, CUT&Tag, IgG, rep 2

source_name: mTSC EGFP

tag: cell line

value: mTSC EGFP

value: Mouse trophoblast stem cells

tag: antibody

value: Rabbit IgG (Santa Cruz sc-3888)


title: He_Aml_20Sp_9

tag: tissue

value: SHRSP/Izm

tag: individual

tag: array

tag: dose


title: FaDu cells, normal control, biol rep 2 [NC_NC2]

city: Beijing

first: Wei

last: Gu

address: Shuaifuyuan No.1

department: Otolaryngology Head and Neck Surgery

institute: Peking Union Medical College Hospital

data_processing:
hisat2 2.0.5
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes gene counts for all samples.

source_name: Pharynx

growth_protocol: The human HPSCC cell line FaDu was purchased from Shanghai GeneChem Co., Ltd. Cells were maintained in Minimum Essential Medium (MEM, Thermo) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37°C in a humidified atmosphere of 5% CO2 in compressed air.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent (Invitrogen) according to the manufacturer’s instructions. A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Pharynx

value: FaDu

value: Squamous Cell Carcinoma cell

tag: genotype

value: WT

tag: treatment


title: T00306996

hyb_protocol: The fragmented cRNA was hybridized overnight at 37C in hybridization buffer in an Innova 4080 shaking incubator (New Brunswick, Edison, NJ) at 300 rpm.

scan_protocol: Images were captured on an Axon GenePix Scanner (Arlington, TX) using GenePix Pro 6.0 Software and were analyzed using CodeLink Expression Analysis Software.

data_processing: Expression values were globally normalized to the median expression value of the whole rat probes. Signal smaller than or equal to 0.23 is weak and such probes should be discarded.

source_name: kidney, Candesartan 5 milligram per kilogram per day

label_protocol: All reagents were provided in the CodeLink Expression Assay Kit. cRNA synthesis was performed according to the manufacturer's instructions using 2 ug of total RNA and labeled with Cy5.

extract_protocol: Tissues were obtained from male rats at 16 weeks old. Total RNA was extracted using RNeasy maxi kit (Qiagen).

value: kidney

tag: Sex

value: male

tag: age

value: 16 weeks

tag: scandate

tag: compound

value: Candesartan


title: He_Aml_20Sp_7

value: heart

tag: scan date

value: Amlodipine


title: ESS013_A1

tag: cohort

value: ESS

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: cell type

value: Nasal epithelial cells


title: BiPNT.D3(+SGC).ATAC-seq

value: epiblast stem cell


title: FaDu cells, normal control, biol rep 1 [NC_NC1]

tag: cell line


title: FaDu cells, normal control, biol rep 3 [NC_NC3]

tag: tissue


title: ESS005_A1

value: F

value: b

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: PVA80N.3rd

tag: trimester

tag: complecation

value: GDM


title: FaDu cells, AMIGO2 knockdown & CAPN2 overexpress, biol rep 1 [KD_OE1]

value: Pharynx

tag: genotype

value: AMIGO2 knockdown & CAPN2 overexpress

tag: treatment


title: He_Aml_20Sp_10

tag: Sex

tag: age

tag: strain

value: SHRSP/Izm

tag: individual

tag: array

tag: dose


title: FaDu cells, AMIGO2 knockdown & CAPN2 overexpress, biol rep 3 [KD_OE3]

value: FaDu

value: Squamous Cell Carcinoma cell


title: PVA80N.5th

value: Cord


title: T00306993

source_name: kidney, Solvent A (PEG300 EtOH NaHCO3)

value: kidney

value: male

value: 16 weeks

value: WKY/Izm

tag: scandate

tag: compound

value: Solvent A (PEG300 EtOH NaHCO3)


title: mTSC, CUT&Tag, IgG, rep 1

tag: cell line

value: mTSC EGFP

tag: cell type

value: Mouse trophoblast stem cells

tag: antibody

value: Rabbit IgG (Santa Cruz sc-3888)


title: FaDu cells, AMIGO2 knockdown & CAPN2 overexpress, biol rep 2 [KD_OE2]

tag: tissue


title: PVA80N.4th

value: Del


title: FaDu cells, AMIGO2 knockdown, biol rep 3 [KD_NC3]

value: AMIGO2 knockdown


title: mTSC, CUT&Tag, H3K4me3, rep 2

value: anti-H3K4me3 (Abcam ab8580)


title: PVA80N.1st

value: GDM


title: FaDu cells, AMIGO2 knockdown, biol rep 2 [KD_NC2]

value: Pharynx


title: ESS007_A1

tag: cohort

value: ESS

value: F

tag: race (b=black, o=other)

value: b

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore

value: Nasal epithelial cells


title: T00306995

value: kidney

tag: Sex

tag: age

tag: strain

value: Candesartan


title: PMD88R.2nd

tag: trimester

tag: complecation

value: IPD


title: T00306987

value: male

value: 16 weeks

value: SHRSP/Izm

tag: individual

tag: scandate

tag: compound

tag: dose


title: T00306994

tag: tissue

value: WKY/Izm

value: Solvent A (PEG300 EtOH NaHCO3)


title: mTSC, CUT&Tag, H3K4me3, rep 1

tag: cell line

value: mTSC EGFP

tag: cell type

value: Mouse trophoblast stem cells

tag: antibody


title: PRD82D.cord

value: Cord


title: mTSC, CUT&Tag, H3K4me1, rep 1

value: anti-H3K4me1 (Abcam ab8895)


title: mTSC, CUT&Tag, H3K4me1, rep 2


title: ESS001_A1

tag: cohort

value: M

tag: race (b=black, o=other)

tag: asthma severity (1=severe)

tag: shs (1=exposed to 2nd smoke)


title: ESS003_A1

value: ESS

tag: Sex

tag: ecat exposure>=40 (1=yes)

tag: allergy (1=yes)

tag: allergyscore


title: PVA80N.2nd

tag: trimester

tag: complecation

value: GDM


title: ChIP-seq: GSC6 sh HOXA-AS2 H3K27me3

city: Clermont-Ferrand

first: franck

last: court

address: 28 Place Henri Dunant

institute: GReD CNRS

data_processing:
ChIP-seq R1 reads were mapped to the human genome (hg19) using Bowtie2 (v 2.3.4.3).
Alignments were filtered according to their quality (Mapq>30) using SamTools (v 1.9).
ChIP-seq signals coverage were generated with Bamcoverage (v 3.1.3) (options: normalizeUsing RPKM, extendReads 200, ignoreDuplicates, binSize 20).
Assembly: hg19 (GRCh37)
Supplementary files format and content: coverage signal; bigwig.

source_name: Glioblastoma stem cell

growth_protocol: Glioblastoma stem cells were cultured in Neurobasal Medium supplemented with B27 1%; N2 0.5%; bFGF 0.05% and EGF 0.005% at 37°C in 5% CO2 humidified incubator. Culture medium was replaced twice a week and when spheres became large and numerous, they were enzymatically dissociated with accutase. Glioblastoma stem cell cultures were characterized by assessing self renewal, differentiation and tumorigenic ability as well as their expression of stemness markers (CD133, SOX2). Finally, all cultures were also classified according to Verhaak's classification of glioblastomas using the method of classification to nearest centroids (ClaNC) with a 840 gene signature.

extract_protocol:
ChIP-seq were performed on native chromatin isolated from frozen GSC pellets.
Library preparation and sequencing on NovaSeq 6000 (Illumina) were performed by IntegraGen SA, according to the manufacturer’s recommendations.

treatment_protocol: SMART vector targeting HOXA-AS2 (V3SH11246-245298993) was purchased from GE Healthcare (Little Chalfont, UK). Viral particles were produced and concentrated by the Vectorology platform of Montpellier (Biocampus, Montpellier, France). GSCs were infected using a multiplicity of infection of 10 and processed 120 h later for ChIP-seq analysis.

value: Glioblastoma stem cells:GSC6

tag: treatment

tag: chip antibody

value: H3K27me3 (Millipore 07-449)


title: mTSC, CUT&Tag, H3K27ac, rep 1

value: anti-H3K27ac (Abcam ab4729)


title: T00306988

value: kidney

tag: age

tag: strain

tag: individual

tag: scandate

tag: compound

value: Candesartan

tag: dose


title: ChIP-seq: GSC6 sh HOXA-AS2 H3K4me3

tag: cell type

value: H3K4me3 (Diagenode 03-050)


title: mTSC, CUT&Tag, H3K27ac, rep 2

tag: cell line

tag: antibody


title: ChIP-seq: GSC6 sh HOXA-AS2 H3K27ac

value: H3K27ac (Abcam Ab4729)


title: PRD82D.1st


title: FaDu cells, AMIGO2 knockdown, biol rep 1 [KD_NC1]

tag: tissue

value: Pharynx

value: FaDu

value: Squamous Cell Carcinoma cell

tag: genotype

value: AMIGO2 knockdown


title: T00275968

source_name: kidney, Enalapril 20 milligram per kilogram per day

tag: Sex

value: male

value: 16 weeks

value: WKY/Izm

value: Enalapril


title: T00275966

source_name: kidney, Hydralazine 10 milligram per kilogram per day

value: SHRSP/Izm

value: Hydralazine


title: PLJ81T.5th

source_name: Extracellular Vesicles from plasma of pregnant women

value: Cord

value: GDM


title: PRD82D.4th

value: Del


title: 0220L P6

city: San Diego

first: Andre

middle: Alberto

last: Weber

address: 9500 Gilman Dr. La Jolla

institute: UCSD

data_processing:
Image deconvolution, quality value calculation, and the mapping of exon reads and exon junctions were performed at the UCSD sequencing core. Base calling was performed using bcl2fastq (v2.17.1.14; Illumina). RNA sequencing reads were aligned Q20 to the mice genome (mm10) with STAR (v2.2.0c)58 with default parameters, only uniquely alienable reads were used for downstream analysis. Gene expression values were calculated using HOMER by quantifying strand-specific reads across annotated gene exons (RefSeq) and reported as fragments per kilobase of exon per million mapped reads.
Assembly: mm10
Supplementary files format and content: One excel file containing results from all samples.

source_name: Liver

extract_protocol:
RNA was extracted using Trizol. 1 ug of total RNA was used for the construction of sequencing libraries.
The sequencing library was prepared using the Illumina TruSeq RNA Sample Prep Kit (FC-122-1001; Illumina, San Diego, CA) with 1 ug of total RNA. The sequencing was performed on an NovaSeq 6000 sequencer in the IGM Genomics Center at UCSD.

treatment_protocol: Neonatal mice was treated for 21 days with Triclosan at 120 ppm in the breastmilk of lactating females

value: Liver

value: 21 days

value: TCS breastmilk


title: PRD82D.2nd


title: TGF-β treated rep 2

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Basecalls performed using Real-Time Analysis (RTA) software
Reads were aligned to the hg38 reference genome using STAR (version 2.5.1a) (Dobin et al., 2013). Reads were assigned to genes using the Gencode gene annotation (Release 35 (GRCh38.p13)) and counts generated using HTSeq (version 0.12.4) (Anders et al., 2015).
Differential gene expression was analysed via EBSeq in R (Leng et al., 2013)
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and sample

source_name: Primary Human Fibroblasts

growth_protocol: Fibroblasts were grown in culture using a standard explant protocol (Schneider and Mitsui, 1976). Cells were subsequently cultured in DMEM-GlutamaxTM supplemented with 10% v/v fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin. Cells were maintained at 37 °C, 5% CO2 in a humidified incubator and passaged at 80-90% confluency with 1x TrypLE Express. Cell culture medium was replaced every 2 days, and experiments conducted on cells between passages P4-P7.

extract_protocol:
RNA was extracted and purified using RNeasy Mini Kit (Qiagen). RNA libraries were prepared using the TruSeq stranded total RNA with Ribo-Zero Human/Mouse/Rat library prep kit (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were exposed to MMWs for 5 h/day, 46.8 J cm-2 doses for 2 days

value: Patient-derived primary human fibroblasts

value: TGF-beta treated for 2 days


title: ChIP-seq: GSC6 sh HOXA-AS2 Input

value: Glioblastoma stem cells:GSC6


title: T00306985

value: kidney

value: Solvent A (PEG300 EtOH NaHCO3)


title: PLJ81T.4th


title: T00306984

value: male


title: MMW-exposed rep 2

value: MMW exposed for 2 days


title: 0220L P3

value: Regular breastmilk


title: T00275928

source_name: kidney, Solvent C (0.5% MC)

value: 16 weeks

value: Solvent C (0.5% MC)


title: 0220L P4


title: PRD82D.3rd


title: PLJ81T.3rd


title: 0220L P1


title: 0220L P2


title: TGF-β treated rep 1


title: PLJ81T.2nd


title: T00275965

value: WKY/Izm

value: Hydralazine


title: lncRNA-seq PAMK replicate 3

data_processing:
Transcripts Assembly: Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used Bowti2 and Hisat2 to sequence the genome. Using StringTie to assemble a mapping read of each sample and a transcription combination of the sample, Samples were merged to reconstruct a comprehensive transcriptome using perl scripts. After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts
LncRNA identification: First of all, transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC and CNCI to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed. The remaining transcripts were considered as lncRNAs.
Supplementary files format and content: excel,expression profiles

source_name: lncRNA-seq PAMK3

extract_protocol:
After total RNA was extracted, all ribosomal RNA in total RNA was removed. After that, the RNA was broken into segments and connected with sequencing connectors for PCR amplification and sequencing library construction, and finally for machine sequencing. The sequencing platform was Illumina Novaseq™ 6000 and the sequencing model was PE150.rRNA removal library construction method was adopted for sequencing, and the expression level of lncRNA and mRNA could be detected during the whole sequencing process.
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure

value: MTEC1 cell

value: mouse medullary thymic epithelial cell line 1 cell

value: WT

value: PAMK


title: PLJ81T.1st

value: GDM


title: 0220L P5

value: Liver

value: 21 days

value: TCS breastmilk


title: Control rep 2

value: Patient-derived primary human fibroblasts

value: Untreated


title: T00275931

source_name: kidney, Carvedilol 50 milligram per kilogram per day

value: kidney

value: male

value: SHRSP/Izm

value: Carvedilol


title: T00275927

value: 16 weeks

value: Solvent C (0.5% MC)


title: T00275932


title: PPF87I.cord

value: Cord

value: NORM


title: X85WC


title: MMW-exposed rep 1

value: MMW exposed for 2 days


title: PPF87I.4th

value: Del


title: T00275925

value: WKY/Izm


title: lncRNA-seq PAMK replicate 2

source_name: lncRNA-seq PAMK2

value: MTEC1 cell

value: mouse medullary thymic epithelial cell line 1 cell

value: WT

value: PAMK


title: PPF87I.3rd


title: Control rep 1

value: Patient-derived primary human fibroblasts


title: NALM6_LASP_Rep1

data_processing:
Reads were mapped to the human genome using BWA
Peak calling was performed using MACS2 using the default q value of 0.05
Final differential binding analysis was performed using DiffBind in R
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files for each experimental sample

source_name: Nalm6 (ALL cell line)

growth_protocol: Nalm6 were maintained in standard culture conditions with RPMI-1640 supplemented with 10% FBS, 2mM Glutamine and Pen/Step

extract_protocol:
Cells were cross-linked, lysed, and sonicated according to the ENCODE project ChIPseq guidelines (https://www.encodeproject.org/about/experiment-guidelines/). 5ug of ATF4 antibody was used for IP
Libraries were prepared for sequencing using standard Illumina protocols

value: ALL

value: ATF4 Rabbit mAb (Cell singal #11815)

value: LASP (1IU/ml, 2hrs)


title: NALM6_LASP_Rep2


title: lncRNA-seq Control replicate 1

source_name: lncRNA-seq Control1

value: control


title: PPF87I.2nd


title: NALM6_NT_Rep2


title: T00275923

value: kidney

value: male


title: lncRNA-seq Control replicate 2

source_name: lncRNA-seq Control2


title: NALM6_NT_Rep1


title: PPF87I.1st


title: PET80M_cord


title: Stromal cell scRNAseq [Ai9-lib1]

city: Saint Louis

first: Christopher

middle: A

last: Miller

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St Louis

description: 10x Genomics 3' GEX V3.1

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10 with addition of Ai9 transgene sequence obtained from Addgene plasmid 22799 sequence 115994 positions 3897-6222 (https://www.addgene.org/22799/sequences/) as described here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr
Supplementary files format and content: h5 matrix file of gene expression

source_name: bone marrow

extract_protocol:
Lineage- (CD45, Gr-1, B220, CD3, Ter119, CD11b) and Pdgfb+ cells were sorted from total bone marrow cells from one male and one female Osx-Cre, Ai9 mice
Library was performed according to the manufacter’s instructions (single cell 3’ GEX v3.1 protocol, 10x Genomics).

value: bone marrow

value: stromal cell

value: Lineage- Pdgfrb+ stromal cells

value: Osx-Cre, Ai9


title: PET80M_4th

value: Del

value: NORM


title: lncRNA-seq PAMK replicate 1

source_name: lncRNA-seq PAMK1

value: MTEC1 cell


title: lncRNA-seq Control replicate 3

source_name: lncRNA-seq Control3

value: mouse medullary thymic epithelial cell line 1 cell


title: PET80M_3rd


title: T00275926

value: 16 weeks

value: WKY/Izm

value: Carvedilol


title: RS411_LASP_rep3

city: Memphis

first: Daniel

last: Savic

address: 262 Danny Thomas Pl

institute: St. Jude Children's Research Hospital

data_processing:
data processing was performed using the WARDEN RNA-seq pipeline on http://www.stjude.cloud
Genome_build: hg19
Supplementary_files_format_and_content: text file of raw counts for each rep

source_name: ALL cell line

extract_protocol:
RNA was extracted from cell lines using the RNAeasy Plus Mini Kit (Qiagen, Cat#74136)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: LASP treated, 4hrs

tag: replicate


title: RS411_LASP_rep1


title: RS411_NT_rep3

value: No treatment control


title: T00275924

value: Solvent C (0.5% MC)


title: RS411_LASP_rep2


title: T00275922

source_name: kidney, Chlorothiazide 20 milligram per kilogram per day

value: SHRSP/Izm

value: Chlorothiazide


title: T00275920

source_name: kidney, Solvent B (NaOH)

value: kidney

value: male

value: Solvent B (NaOH)


title: T00275918


title: T00275921


title: PET80M_1st

tag: trimester


title: PET80M_2nd

tag: complecation


title: MEF Claspin(f/-) release

city: Tokyo

first: Chi-Chun

last: Yang

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

data_processing:
CLC Genomics Workbench 21
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Mouse GRCm39

source_name: MEF Claspin(f/-)

growth_protocol: MEF cells were cultured at 37 °C in a 5% CO2 humidified incubator in Dulbecco’s modified Eagle’s medium (high glucose) (Nacalai Tesque Inc.) supplemented with 15% fetal bovine serum (HANA-NESCO), 2 mM L-glutamine (Gibco), 1% sodium pyruvate (Nacalai Tesque Inc.), 100 U/ ml penicillin and 100 μg /ml streptomycin.

extract_protocol: RNA was isolated from Claspin (f/-) MEFs grown under three different conditions (grown asynchronously, grown in serum-free medium for 24 hr, and grown in serum-free medium for 24 hr and released into growth by addition of serum for 14 hr) by using RNA purification kit (QIAGEN).

treatment_protocol: MEF cells treated ±Ad-Cre cultured in the  ±serum medium for 24 hr and realeaed cells by adding serum and harvested cell in 14 hr

value: MEF Claspin(f/-)

value: Mouse Embryonic Fibroblast

value: Claspin(f/-)

tag: treatment

value: relase from serum starvation


title: MEF Claspin(-/-) release

value: Claspin(-/-)

value: relase from serum starvation with Ad cre


title: MEF Claspin(f/-) serum starvation

value: serum free medium


title: T00275914

value: 16 weeks

value: WKY/Izm


title: T00275917


title: T00275916


title: PAP91E.2nd

source_name: Extracellular Vesicles from plasma of pregnant women

value: NORM


title: RS411_NT_rep2

value: No treatment control


title: RS411_NT_rep1


title: MEF Claspin(-/-)

value: serum containing medium with Ad-Cre


title: MEF Claspin(f/-)

value: serum containing medium


title: T00275910

source_name: kidney, Hydralazine 10 milligram per kilogram per day

value: SHRSP/Izm

value: Hydralazine


title: SUPB15_LASP_rep3

value: LASP treated, 4hrs


title: MEF Claspin(-/-) serum starvation

value: serum free medium with Ad-Cre


title: C3 K0+ S1PR1 overexpression

city: Charleston

first: Alhaji

middle: Harune

last: Janneh

state: SC

address: 86 Jonathan Lucas Street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

description:
B16 S1PR1 OE cell line tail vein injection
HR3

data_processing:
Raw data from illumina was transformed to Sequenced Reads by CASAVA base recognition (Base  Calling)
Raw data was filtered by Novogene Corporation Inc. according to the following steps; 1) reads containing adaptors were removed, and 2)reads containing bases that could not be determined were also removed.
STAR software was used to align reads to reference genome
FPKM was used to estimate gene expression levels. This method considers both sequencing depth and gene length on counting of fragments. (Mortazavi et al. 2008, https://doi.org/10.1038/nmeth.1226)
The readcount from Gene Expression Analysis was used to determine the differential expression analysis
Genome_build: Mus Musculus(GRCm38/mm10)
Supplementary_files_format_and_content: xls file that include FPKM values, gene names, gene id, gene_chr, gene_start, gene_end, gene_strand, gene_biotype, and gene descriptions for each Sample

source_name: Lung

growth_protocol: B16 melanoma cells were maintained in RPMI growth media, supplemented with 10% FBS, 1%Penicillin streptomyocin(100x), and plasmocin prophylactic.

extract_protocol:
Total RNA was extracted from mice lungs using QIAzol Lysis Reagent(Qiagen, Cat No./ID: 79306) and processed as per manufacturer’s instructions.
RNA libraries were prepared using standard Illumina protocols from Novogene Corporation Inc.(Sacramento, CA 95826)

treatment_protocol: Mice in three groups (WT+Vector, WT+S1PR1 OE, and C3 KO + S1PR1 OE), were injected with either Vector or S1PR1 overexpression B16 melanoma cells and euthanized after 21-30 days.

value: lung tissue


title: PEW85X.cord

data_processing:
Demultiplexed fastq files were analysed using miRDeep2 package. Adapters were trimmed from miRNA sequences and  aligned using Bowtie aligner against the hg38 referece.
Genome-aligned reads were matched to known human miRNAs from miRBase version 21  and quantified using the script quantifier.pl
ggplot2 was used for visulazation of RNAseq data
Genome_build: mm10
Supplementary_files_format_and_content: Expression Matrix

extract_protocol:
secretory Extracellular Vesicles were isolated from maternal blood samples. Total RNA was extracted from isolated sEVs and miRNA library were prepared using miRNeasy Mini Kit (Qiagen)
for library prep 6µl of total RNA extracted from sEVs were used.  Libraries were prepared using NEB Next Multiplex small RNA Library prep kit (NEB E7300S)

value: Cord


title: PAP91E.1st


title: SUPB15_LASP_rep2


title: Wildtype+ S1PR1 overexpression

description:
B16 S1PR1 OE cell line tail vein injection
HR2

value: wild type


title: SUPB15_NT_rep3


title: T00275913

value: kidney

value: male

value: Solvent B (NaOH)


title: T00275909


title: PEW85X.3rd


title: PEW85X.4th

value: Del


title: T00275906

source_name: kidney, Amlodipine 20 milligram per kilogram per day

value: 16 weeks

value: Amlodipine


title: SUPB15_LASP_rep1


title: Wildtype+ Vector

description:
B16 vector cell line tail vein injection
HR1


title: T00275907


title: PEW85X.1st

value: NORM


title: PEW85X.2nd


title: WT-MOLM13-DRIPc-seq-2

city: Hangzhou

first: Huacheng

last: Luo

state: Zhejiang

address: No. 150, Fucheng Road, Qiantang District

institute: Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences

data_processing:
Standard Illumina software base-calling and quality-control filtering was applied Sequences (Paired end)
Paired end HiC-seq and scRNA-seq and scATAC-seq reads from mice were aligned to the mm9 genome assembly using BWA, and NG capture-C-seq, ChIP-seq, DRIP-seq and DRIPc-seq reads from human cells were aligned to the hg19 genome assembly using BOWTIE2 default parameters.
Peak calling was performed using MACS algorithm (version 2.1.1)
Genome coverage tracks were created using deepTools version 3.0
Assembly: mm9, hg19
Supplementary files format and content: tab-delimited text files include FPKM values for scRNA-seq and scATAC-seq Samples and peaks for DRIP-seq , DRIPc-seq, ChIP-seq, NG-capture-C and HIC-seq.

source_name: MOLM13 leukemia cells

growth_protocol: Total bone marrow cells were isolate from WT and Hottip-Tg mice, and sorted with Lin-, Sca1+ and Kit+ markers.  Human MOLM13 leukemia cells were culture at RMPI1640 medium with 10% FBS media.

extract_protocol:
RNA samples extracted with Trizon and treated with Dnase I.  ChIP Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with CTCF, SA1, SA2, RAD21, H3K4me3 and H3K27me3 antibody (antibody: Anti-CTCF, Cell Signaling Technology, Cat# 2899; Anti-SA1, Abcam, Cat# ab4457; Anti-SA2, Abcam, Cat# ab4464;  Anti-RAD21, Abcam, Cat# ab992;  Anti-H3K4me3, Millipore, Cat No. 04-745;   Anti-H3K27me3, Millipore, Cat No. 07-449).  ATAC-seq samples derived according to Nextera Tn5 Transposase kits. DNA:RNA immunoprecipitation sequencing (DRIP-seq) was performed as described previously with s9.6 antibody (Anti-DNA-RNA Hybrid [S9.6] Antibody, Kerafast, Cat# ENH001).  NG-Capture-C assay was performed as previously described. Hi-C assay was performed to generate a genome-wide interaction as described previously with Arima-HiC Kit (Cat: A410030) (https://arimagenomics.com/) with minor modifications. Single cells were generated using Chromium Controller (10x Genomics), and scRNA-seq and scATAC-seq libraries were constructed using chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to the manufacturer’s recommendations.
RNA-seq libraries were prepared according to TruSeq Stranded mRNA Library Prep (#20020594).  ChIP-seq libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Library Preparation Kit (#IP-202-1012). ATAC-seq libraries were prepared according to Nextera DNA Library Prep Kit (#FC-121-1030). NG-Capture-C-seq libraries were prepared according to  using the Herculase II PCR kit (Agilent). . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Immediately extract RNA from LK, LSK cells and MOLM13 AML cells without any treatment

tag: cell types

value: Human-derived acute myeloid leukemia

value: peripheral blood

value: Library strategy:DRIPc-seq


title: T00275905

tag: age

value: WKY/Izm


title: Nalm6_LASP_rep3


title: HOTTIP-KO-MOLM13-DRIP-seq-2

tag: strain

value: Library strategy:DRIP-seq


title: SUPB15_NT_rep2

value: No treatment control


title: Nalm6_LASP_rep2

value: LASP treated, 4hrs


title: T00275904

tag: individual


title: T00275903

source_name: kidney, Enalapril 20 milligram per kilogram per day

tag: scandate

value: Enalapril


title: Nalm6_LASP_rep1


title: HOTTIP-KO-MOLM13-DRIPc-seq-2


title: WT-MOLM13-DRIP-seq-2


title: SUPB15_NT_rep1


title: T00247073

source_name: kidney, H2O

tag: compound


title: Control replicate B

city: Chicago

first: Kyle

last: Mangano

state: Illinois

address: 900 S Ashland Ave, MBRB Rm 3056

institute: University of Illinois at Chicago

data_processing:
Library strategy: Ribosome profiling (Ribo-seq)
For replicate B samples, a custom script was used to demultiplex the samples, remove the linker barcode and any nts 3' of the linker barcode, and then remove 5 nts from the 3' end and 2 nts from the 5' end, which were added as part of the library design
For replicate A samples, samples were not multiplexed, but the same custom script was used to identify and remove the 3’ adapter sequence and then remove 1 nt from the 5’ end.
Bowtie2 (v2.2.9) within the GALAXY pipeline first aligned the trimmed reads to the non-coding RNA sequences
Trimmed and filtered reads were written to a samplename.fastq.gz file to be deposited as raw data.
The remaining unmapped reads were aligned to the reference MG1655 genome (GenBank ID U00096.3) again using Bowtie2 (v2.2.9)
Reads of length 23-40 nts were considered in subsequent analysis.
The ribosome P-site was assigned 15 nucleotides from the 3' end of the reads.
Scripts can be found at https://github.com/mmaiensc/RiboSeq
Genome_build: genbank id: U00096.3
Supplementary_files_format_and_content: For each sample, wig files for the positive and negative genomic strands are deposited. The first column denotes the genomic position of the P-site assigned ribosomes, and the second column is the coverage in reads per million (RPM). RPM is calculated as the raw reads assigned to each position, divided by the total aligned reads to the genome after ncRNA filtering, in millions.

organism: Escherichia coli

source_name: exponential growth phase culture

growth_protocol: The cultures were grown overnight in LB medium supplemented with chloramphenidol (30 mg/ml). Cultures were diluted 200-fold into conical baffled 1-litre flasks containing 150 mL of LB supplemented without antibiotics and with 0.2% glucose. Cultures were grown at 37 °C with vigorous shaking.

extract_protocol:
When the culture density reached A600 of ∼0.4 cells were harvested by rapid filtration, frozen in liquid nitrogen, and processed for ribosome profiling.
The library for next-generation sequencing was prepared using size-selected RNA fragments ranging in size from 20 to 46 nt.  Replicate A samples followed the library construction protocol described in Ingolia, et al., 2009. Replicate B followed the library construction protocol described in McGlincy and Ingolia, 2017.

treatment_protocol: When the culture density reached A600 of ∼0.4, for EVN-samples, 20 mg/mL EVN solution in 100% ethanol was added to the cultures to a final concentration of 50 µg/mL (100X MIC) and incubation with shaking continued for 4 min.

tag: growth phase

value: exponential


title: T00247072

value: SHRSP/Izm

tag: dose


title: Evernimicin replicate B


title: Nalm6_NT_rep2

tag: cell line


title: Nalm6_NT_rep3


title: Control replicate A


title: Evernimicin replicate A


title: Drosophila_melanogaster_control_RIP_RNA_rep3

city: Toronto

first: Howard

middle: D

last: Lipshitz

state: ON

address: 1 King's College Circle

department: Molecular Genetics

country: Canada

institute: University of Toronto

description: This sample is total RNA isolated from synthetic antibody control (antibody C1) RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.

hyb_protocol: Hybridization was performed following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 6.0).

scan_protocol: Arrays were scanned with a GenePix4000B microarray scanner system (Molecular Devices, Inc., Sunnyvale, CA, USA), and scanned images were initially quantified using Nimblescan (Roche) according to the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 6.0).

data_processing: The raw data (.pair files) were normalized with ArrayStar 11 (DNASTAR) software using the RMA quantile method, and signal intensities were log2-transformed. For normalization, RIN RIP samples were normalized together with control RIP samples.

organism: Drosophila melanogaster

source_name: synthetic antibody control (antibody C1) RIP from w1118 0-3 hour embryo

label_protocol: Labelling was performed following the protocol described in the NimbleGen Array User's Guide (Gene Expression Arrays, version 6.0).

growth_protocol: The following fly strains were used: w1118. Stocks were maintained at 25 degrees C.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) according to the manufacturer's protocol.

tag: developmental stage

value: 0-3 h embryo


title: Nalm6_NT_rep1


title: Drosophila_melanogaster_control_RIP_RNA_rep2

description: This sample is total RNA isolated from synthetic antibody control (antibody C1) RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.


title: Drosophila_melanogaster_control_RIP_RNA_rep1

description: This sample is total RNA isolated from synthetic antibody control (antibody C1) RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.


title: Drosophila_melanogaster_anti-RIN_RIP_RNA_rep3

description: This sample is total RNA isolated from anti-RIN (antibody D072) RIPs from 0-3 hour w1118 embryos. It is the third of three biological replicates.

source_name: anti-RIN (antibody D072) RIP from w1118 0-3 hour embryo


title: T00247069

tag: tissue

value: kidney

value: male


title: T00247074


title: CBS-/-(8) CBS8-5

status: Public on Apr 14 2022

city: Moscow

first: Alexander

middle: Pertovich

last: Rezvykh

state: Moscow

address: Vavilova, 32

department: Russian Academy of Sciences

country: Russia

institute: Engelhardt Molecular Biology Institute

data_processing:
Read trimming (Trimmomatic)
Short read alignment (STAR)
Alignment file sorting and indexing (samtools)
Read counting (featureCounts)
Assembly: Dm6
Supplementary files format and content: First column: Flybase gene identifier, second column — counts per million (non-normalized gene expression value)

molecule: polyA RNA

source_name: mixed

extract_protocol:
Three biological replicates of 5-day-old naive males were collected for each transcriptome analysis. For each replicate, total RNA was isolated from approximately 100 heads of naïve males collected by decapitation of Drosophila male on an ice-cooled surface. The extraction was made using RNAzol RT (Molecular Research Center, USA) according to the company’s protocol. The concentration and quality of RNA was determined via Qubit Fluorometer (Invitrogen) and an Agilent BioAnalyzer 2100 respectively using RNA 6000 nano kit. For each of three biological replicates taken for libraries 100 heads were collected. For libraries RNA with Integrity Number (RIN) no less than 8 was taken.
Illumina NEB Next Ultra II Directional RNA Library Prep Kit (NEB, USA) was used for mRNA libraries preparation. The sequencing was performed on the Illumina NextSeq 500 platform. For each library sequencing provided around 15-20 million reads.

value: mixed

tag: cell type

value: bulk

tag: genotype

value: no

tag: time

value: Day 5


title: CBS-/-(5) CBS5-3


title: CBS-/-(8) CBS8-2


title: CSE-/- CSE-1

description: CSE-/-

value: CSE-/-


title: CBS-/-(8) CBS8-1


title: Drosophila_melanogaster_anti-RIN_RIP_RNA_rep2

description: This sample is total RNA isolated from anti-RIN (antibody D072) RIPs from 0-3 hour w1118 embryos. It is the second of three biological replicates.


title: CSE-/- CSE-3

description: CSE-/-


title: CBS-/-CSE-/-(2) BE2-4


title: T00247068

city: Shinjuku-ku

first: Fumihiko

last: Takeuchi

address: 1-21-1 Toyama

institute: National Center for Global Health and Medicine

tag: Sex

value: 16 weeks


title: Drosophila_melanogaster_anti-RIN_RIP_RNA_rep1

description: This sample is total RNA isolated from anti-RIN (antibody D072) RIPs from 0-3 hour w1118 embryos. It is the first of three biological replicates.


title: T00247070


title: E12.5 Wnt1cre; Rosa26Dlx2/- mouse embryonic maxillary prominence_rep3

city: Shanghai

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.

source_name: maxillary prominence

growth_protocol: Rosa26CAG-LSL-Dlx2-3xFlag mouse model was developed by Shanghai Model Organisms Center, Inc. This model was generated by CRISPR/Cas9 system in C57BL/6J mouse background. Wild-type C57BL/6J mouse were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine.

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from 7 littermates. For each genotype, three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On Embryo 12.5, pregnant female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: maxillary prominence

value: embryo 12.5

value: Wnt1cre; Rosa26Dlx2/-


title: E12.5 wild-type mouse embryonic maxillary prominence_rep1

value: wild type


title: E12.5 Wnt1cre; Rosa26Dlx2/-  mouse embryonic maxillary prominence_rep1


title: CSE-/- CSE-4

description: CSE-/-


title: CBS-/-CSE-/-(1) BE1-2


title: CBS-/-CSE-/-(2) BE2-2


title: WT 58492-1

description: WT

value: WT


title: CBS-/-CSE-/-(1) BE1-1


title: E12.5 wild-type mouse embryonic maxillary prominence_rep2


title: CBS-/-CSE-/-(1) BE1-3


title: WT 58492-3

description: WT


title: E12.5 wild-type mouse embryonic maxillary prominence_rep3


title: E12.5 Wnt1cre; Rosa26Dlx2/- mouse embryonic maxillary prominence_rep2