title: WT Mid Colon Rep2

description: A05d_EKDL210002228-1a-AK6502-AK6656_H3VG7DSX2_L4


title: WT Mid Colon Rep1

status: Public on Apr 28 2023

type: SRA

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description: A02a_EKDL210002225-1a-AK4939-AK6653_H3VG7DSX2_L1

library_source: transcriptomic

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

molecule: total RNA

organism: Mus musculus

source_name: Mid Colon

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq Stranded mRNA kit, then run on an Illumina Novaseq 6000 (2x150 cycles, paired end, dual index).

treatment_protocol: Mice were treated with a single i.p. injection of 3mg tamoxifen to induce floxing of the Apc allele in the whole body via the ROSACreER allele. Tissues were harvested on Day4.

tag: Sex

value: Male

tag: tissue

value: Mid Colon

tag: genotype

value: WT

tag: treatment

tag: time

value: Day 4


title: WT Stomach Antrum Rep1

description: A11a_EKDL210002225-1a-AK368-AK6662_H3VG7DSX2_L1

source_name: Stomach Antrum

value: Stomach Antrum


title: CS13_B_1_9

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

data_processing:
The reads were aligned onto the grapevine 12x reference genome PN40024 using TopHat v2.0.6 with default parameters
Mapped reads were used to reconstruct the transcripts using Cufflinks v2.0.2 and the reference genome annotation V1
The normalized expression of each transcript was calculated as RPKM (Reads Per Kilobase per Million mapped reads) for each sample.
Genome_build: 12X reference genome PN400024
Supplementary_files_format_and_content: tab delimited text file containing the normalized reads counts RPKM  for all the samples.

organism: Vitis vinifera

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2013 - Crop thinned 50%

growth_protocol: Vineyard Features: Vitis vinifera cultivar Cabernet Sauvignon (clone FPS 8 grafted on 5C rootstock and planted in 1997) was grown nearby Modesto (USA, CA) in sandy clay loam in an east-west orientation with 10 foot row spacing and 5 foot vine spacing.

extract_protocol:
Total RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) following the manufacturer’s instructions with some modifications (Fasoli et al., 2012). RNA quality and quantity were determined using a Nanodrop 2000 spectrophotometer (Thermo Scientific) and a Bioanalyzer Chip RNA 7500 series II (Agilent).
206 non-directional cDNA libraries were prepared from 2.5 μg of total RNA using the Illumina TruSeq RNA Sample preparation protocol (Illumina Inc., San Diego, CA, USA). Library quality was determined using the Agilent High Sensitivity DNA kit on the Agilent 2100 bioanalyzer, and the quantity was determined by quantitative PCR using the KAPA Library Quantification kit (KapaBiosystems).

treatment_protocol: Cluster thinning treatments: Moderate thinning (50% crop load reduction) was achieved removing clusters to maintain one cluster per shoot; severe thinning (75% crop load reduction) consisted in mantaining one cluster every other shoot; control (0% crop load reduction) was unthinned vines.

tag: cultivar

value: Cabernet Sauvignon

value: grape berry pericarp

tag: year

tag: time point

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 50%


title: WT Lung Rep4

description: H06a_EKDL210002225-1a-AK6542-AK6733_H3VG7DSX2_L1

source_name: Lung

value: Lung


title: CS13_B_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS13_C_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2013 - Crop thinned 75%

value: Crop thinned 75%


title: WT Lung Rep3

description: H05d_EKDL210002228-1a-AK6541-AK6732_H3VG7DSX2_L4

value: Female


title: CS13_C_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Lung Rep1

description: A09a_EKDL210002225-1a-AK6506-AK6660_H3VG7DSX2_L1


title: WT Lung Rep2

description: D11c_EKDL210002227-1a-AK5143-AK6694_H3VG7DSX2_L3


title: CS13_B_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: CS13_C_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_B_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: CS13_B_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: WT Spleen Rep1

description: A07a_EKDL210002225-1a-AK6504-AK6658_H3VG7DSX2_L1

source_name: Spleen

value: Spleen


title: CS13_C_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: WT Liver Rep2

description: D05d_EKDL210002228-1a-AK6518-AK6688_H3VG7DSX2_L4

source_name: Liver

value: Liver


title: WT Liver Rep3

description: D07c_EKDL210002227-1a-AK6520-AK6690_H3VG7DSX2_L3


title: CS13_C_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Liver Rep1

description: A05a_EKDL210002225-1a-AK6502-AK6656_H3VG7DSX2_L1


title: WT Liver Rep4

description: H02a_EKDL210002225-1a-AK5141-AK6729_H3VG7DSX2_L1


title: CS13_C_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: WT Kidney Rep4

description: H03a_EKDL210002225-1a-AK4946-AK6730_H3VG7DSX2_L1

source_name: Kidney

value: Kidney


title: CS13_B_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: CS13_B_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: CS13_B_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: WT Kidney Rep3

description: E05d_EKDL210002228-1a-AK6524-AK6699_H3VG7DSX2_L4


title: CS13_B_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: WT Kidney Rep2

description: D08c_EKDL210002227-1a-AK6521-AK6691_H3VG7DSX2_L3


title: WT Esophagus Rep4

description: H01a_EKDL210002225-1a-AK4007-AK6728_H3VG7DSX2_L1

source_name: Esophagus

value: Esophagus


title: CS13_C_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: CS13_C_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Kidney Rep1

description: A06a_EKDL210002225-1a-AK6503-AK6657_H3VG7DSX2_L1


title: CS13_C_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_B_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: WT Esophagus Rep3

description: D06c_EKDL210002227-1a-AK6519-AK6689_H3VG7DSX2_L3


title: WT Esophagus Rep1

description: A04a_EKDL210002225-1a-AK6501-AK6655_H3VG7DSX2_L1


title: WT Esophagus Rep2

description: C05d_EKDL210002228-1a-AK6512-AK6678_H3VG7DSX2_L4


title: WT Brain Rep4

description: H07a_EKDL210002225-1a-AK6543-AK6734_H3VG7DSX2_L1

source_name: Brain

value: Brain


title: CS13_B_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS13_C_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: CS13_C_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: WT Brain Rep2

description: A10d_EKDL210002228-1a-AK4947-AK6661_H3VG7DSX2_L4


title: WT Bladder Rep3

description: G05d_EKDL210002228-1a-AK6535-AK4643_H3VG7DSX2_L4

source_name: Bladder

value: Bladder


title: CS13_B_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: CS13_B_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: WT Bladder Rep4

description: H05a_EKDL210002225-1a-AK6541-AK6732_H3VG7DSX2_L1

value: Male


title: CS13_B_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS13_C_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: WT Bladder Rep2

description: D10c_EKDL210002227-1a-AK963-AK6693_H3VG7DSX2_L3


title: WT Bladder Rep1

description: A08a_EKDL210002225-1a-AK6505-AK6659_H3VG7DSX2_L1


title: CS13_C_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: Apc Stomach Corpus Rep5

description: H12a_EKDL210002225-1a-AK323-AK6739_H3VG7DSX2_L1

source_name: Stomach Corpus

value: Stomach Corpus

value: RosaCreER Apc fl/fl (new)


title: CS13_C_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: Apc Stomach Corpus Rep3

description: F03b_EKDL210002226-1a-AK5849-AK5791_H3VG7DSX2_L2

value: Day 4


title: CS13_B_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: Apc Stomach Corpus Rep4

description: G06d_EKDL210002228-1a-AK6536-AK6721_H3VG7DSX2_L4


title: CS13_B_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: CS13_B_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2013 - Crop thinned 50%


title: Apc Stomach Corpus Rep1

description: B03a_EKDL210002225-1a-AK5151-AK6665_H3VG7DSX2_L1


title: WT Brain Rep3

description: D12d_EKDL210002228-1a-AK5147-AK6695_H3VG7DSX2_L4

value: WT


title: Apc Stomach Corpus Rep2

description: E06c_EKDL210002227-1a-AK6525-AK6700_H3VG7DSX2_L3

value: RosaCreER Apc fl/fl (new) Rosa-tom/+


title: CS13_B_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2013 - Crop thinned 50%

value: Cabernet Sauvignon

value: grape berry pericarp


title: CS13_C_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2013 - Crop thinned 75%


title: CS13_C_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2013 - Crop thinned 75%


title: Apc Stomach Antrum Rep2

description: B11a_EKDL210002225-1a-AK5154-AK6672_H3VG7DSX2_L1

source_name: Stomach Antrum

value: Stomach Antrum


title: Apc Stomach Antrum Rep4

description: F11d_EKDL210002228-1a-AK5162-AK6715_H3VG7DSX2_L4


title: CS13_C_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2013 - Crop thinned 75%

value: Crop thinned 75%


title: WT Brain Rep1

description: A06d_EKDL210002228-1a-AK6503-AK6657_H3VG7DSX2_L4

source_name: Brain

value: Female


title: Apc Stomach Antrum Rep3

description: F02c_EKDL210002227-1a-AK5144-AK6707_H3VG7DSX2_L3


title: Apc Stomach Antrum Rep1

description: A08b_EKDL210002226-1a-AK6505-AK6659_H3VG7DSX2_L2


title: CS13_C_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2013 - Crop thinned 75%


title: CS13_B_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2013 - Crop thinned 50%

value: Crop thinned 50%


title: Apc Spleen Rep5

description: F07b_EKDL210002226-1a-AK1613-AK6711_H3VG7DSX2_L2

source_name: Spleen

value: Spleen


title: Apc Spleen Rep3

description: C07d_EKDL210002228-1a-AK6514-AK6680_H3VG7DSX2_L4


title: CS12_C_1_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: CS12_C_2_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Apc Spleen Rep1

description: A04b_EKDL210002226-1a-AK6501-AK6655_H3VG7DSX2_L2


title: Apc Proximal SI Rep2

description: E06d_EKDL210002228-1a-AK6525-AK6700_H3VG7DSX2_L4

source_name: Proximal SI

value: Proximal SI


title: CS12_B_3_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: Apc Proximal SI Rep1

description: E04c_EKDL210002227-1a-AK6523-AK6698_H3VG7DSX2_L3


title: CS12_B_1_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: CS12_C_3_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: CS12_B_2_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: CS12_C_2_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Apc Mid Colon Rep4

description: F06d_EKDL210002228-1a-AK6531-AK6710_H3VG7DSX2_L4

source_name: Mid Colon

value: Mid Colon


title: Apc Mid Colon Rep5

description: H11a_EKDL210002225-1a-AK136-AK6738_H3VG7DSX2_L1


title: Apc Mid Colon Rep3

description: F02b_EKDL210002226-1a-AK5144-AK6707_H3VG7DSX2_L2


title: Apc Lung Rep5

description: F09b_EKDL210002226-1a-AK6533-AK6713_H3VG7DSX2_L2

source_name: Lung

value: Lung


title: Apc Mid Colon Rep1

description: B02a_EKDL210002225-1a-AK4937-AK6664_H3VG7DSX2_L1


title: CS12_B_2_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: CS13_B_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2013 - Crop thinned 50%


title: CS12_C_1_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: Apc Spleen Rep4

description: E10c_EKDL210002227-1a-AK5847-AK6703_H3VG7DSX2_L3


title: CS12_C_3_12

source_name: Cabernet Sauvignon berry sample collected at time point 12 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: CS12_B_3_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: CS13_B_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2013 - Crop thinned 50%


title: CS12_C_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: Apc Lung Rep3

description: E07d_EKDL210002228-1a-AK6526-AK2651_H3VG7DSX2_L4


title: Apc Lung Rep4

description: E12d_EKDL210002228-1a-AK5999-AK6705_H3VG7DSX2_L4


title: CS12_C_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Apc Proximal SI Rep3

description: F01b_EKDL210002226-1a-AK5157-AK6706_H3VG7DSX2_L2


title: Apc Lung Rep2

description: B09a_EKDL210002225-1a-AK6510-AK6670_H3VG7DSX2_L1


title: CS12_C_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: Apc Lung Rep1

description: A06b_EKDL210002226-1a-AK6503-AK6657_H3VG7DSX2_L2


title: Apc Spleen Rep2

description: B07a_EKDL210002225-1a-AK1412-AK6371_H3VG7DSX2_L1

source_name: Spleen


title: CS12_B_3_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: Apc Liver Rep5

description: F05b_EKDL210002226-1a-AK6530-AK6709_H3VG7DSX2_L2

source_name: Liver

value: Liver


title: YW3 (Wt3)

city: Grand Forks

first: Alexei

last: Tulin

state: NORTH DAKOTA

address: 501 N Columbia Rd, Columbia Hall Rm 1733B

department: Biomedical Science

country: USA

institute: University of North Dakota

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the Drosophila melanogaster (DM6) genome assembly using CLC genomics workbench.
Data were filtered using Filter BAM tools in galaxy using filiter on read mapping quality of >=20 on phred scale
Peaks were called using MACS version 2.1.1.20160309 (in Galaxy) with default settings: FDR (q-value cuttoff for peak detection) at 0.05, Band width for picking regions to compute fragment size (147)
Genome_build: DM6
Supplementary_files_format_and_content: Bigwig files were generated using BamCompare tools in Galaxy with default parameters.
Supplementary_files_format_and_content: Peak text files (tabular format)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole 3rd instar larvae

growth_protocol: Flies were bred in a tube for an 8-hour period, and the eggs laid were allowed to grow at room temperature.  The 3rd instar larvae at 12hrs stage were collected using 15% sucrose solution.  About 0.20g of larvae was collected.

extract_protocol:
Lysates were clarified from sonicated nuclei and Jig-DNA complexes were isolated with anti-GFP antibody.
Libraries were prepared by Novogene.

value: whole 3rd instar larvae

tag: strain

value: wildtype


title: CS12_B_2_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: Apc Liver Rep3

description: B05a_EKDL210002225-1a-AK6507-AK6667_H3VG7DSX2_L1

value: Male

value: RosaCreER Apc fl/fl (new)


title: Apc Mid Colon Rep2

description: E05c_EKDL210002227-1a-AK6524-AK6699_H3VG7DSX2_L3

value: Day 4


title: Apc Liver Rep4

description: E08c_EKDL210002227-1a-AK6527-AK6701_H3VG7DSX2_L3

value: RosaCreER Apc fl/fl (new) Rosa-tom/+


title: Apc Liver Rep2

description: A07d_EKDL210002228-1a-AK6504-AK6658_H3VG7DSX2_L4


title: CS12_B_1_10

source_name: Cabernet Sauvignon berry sample collected at time point 10 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon


title: YW2 (Wt2)


title: Apc Liver Rep1

description: A02b_EKDL210002226-1a-AK4939-AK6653_H3VG7DSX2_L2


title: YW1 (Wt1)


title: Apc Kidney Rep5

description: F06b_EKDL210002226-1a-AK6531-AK6710_H3VG7DSX2_L2

source_name: Kidney

value: Kidney


title: CS12_B_1_11

source_name: Cabernet Sauvignon berry sample collected at time point 11 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: grape berry pericarp


title: Apc Kidney Rep1

description: A03b_EKDL210002226-1a-AK5159-AK6654_H3VG7DSX2_L2


title: CG1 (JIG-GFP1)

value: JIG-GFP


title: CS12_C_1_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2012 - Crop thinned 75%

value: Crop thinned 75%


title: Apc Esophagus Rep4

description: F04b_EKDL210002226-1a-AK6529-AK6708_H3VG7DSX2_L2

source_name: Esophagus

value: Female

value: Esophagus


title: Apc Esophagus Rep5

description: H06d_EKDL210002228-1a-AK6542-AK6733_H3VG7DSX2_L4


title: Apc Kidney Rep4

description: E09c_EKDL210002227-1a-AK6528-AK6702_H3VG7DSX2_L3


title: Apc Esophagus Rep2

description: B04a_EKDL210002225-1a-AK6347-AK6666_H3VG7DSX2_L1


title: CG3 (JIG-GFP3)


title: CG2 (JIG-GFP2)


title: Apc Kidney Rep3

description: B07d_EKDL210002228-1a-AK1412-AK6371_H3VG7DSX2_L4


title: Apc Kidney Rep2

description: B06a_EKDL210002225-1a-AK6508-AK6668_H3VG7DSX2_L1


title: CS12_C_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Apc Esophagus Rep3

description: E07c_EKDL210002227-1a-AK6526-AK2651_H3VG7DSX2_L3


title: CS12_C_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: Apc Brain Rep4

description: F07d_EKDL210002228-1a-AK1613-AK6711_H3VG7DSX2_L4

source_name: Brain

value: Brain


title: CS12_B_2_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 2) over ripening season 2012 - Crop thinned 50%

value: Crop thinned 50%


title: Apc Brain Rep3

description: F01c_EKDL210002227-1a-AK5157-AK6706_H3VG7DSX2_L3


title: CS12_B_1_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: Apc Brain Rep5

description: F10b_EKDL210002226-1a-AK5846-AK6714_H3VG7DSX2_L2


title: CS12_C_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Apc Bladder Rep4

description: E11c_EKDL210002227-1a-AK5156-AK6704_H3VG7DSX2_L3

source_name: Bladder

value: Bladder


title: Apc Bladder Rep5

description: F08b_EKDL210002226-1a-AK6532-AK6712_H3VG7DSX2_L2


title: CS12_C_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: CS12_C_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: Apc Bladder Rep3

description: D07d_EKDL210002228-1a-AK6520-AK6690_H3VG7DSX2_L4


title: Apc Esophagus Rep1

description: A01b_EKDL210002226-1a-AK5140-AK242_H3VG7DSX2_L2


title: BC8

city: CDMX

first: Luis

middle: Alonso

last: Herrera Montalvo

state: CDMX

address: Av. San Fernando 22

department: Investigación

country: Mexico

institute: Instituto Nacional de Cancerología-Instituto de Investigaciones Biomédicas

data_processing:
The quality of the sequencing files was determined with the reports generated with the FastQC
Filtering of low-quality reads and adapter removal was performed with trimmomatic v.0.39
Reads were mapped to the human reference with STAR aligner v.2.7.1a
Gene expression quantification was done with featureCounts from the rsubread package on the STAR bam files
Gene expression quantification was also done by aligning to the transcriptome withSalmon v.0.14.1 l
All gene quantifications were done on gencode v31 annotations
Differential expression analysis was performed with DEseq2
Assembly: Reads were mapped to the human reference genome assembly version hg38
Supplementary files format and content: Differential expression tables from DESeq2 are included in .csv format. There are 2 tables from 2 different counting pipelines: STAR aligner v.2.7.1a and Salmon v.0.14.1 for comparison and validation

molecule: polyA RNA

organism: Homo sapiens

source_name: Biopsy from primary mammary adenocarcinoma (thick needle)

extract_protocol:
RNA was isolated using the AllPrep kit (QIAGEN, No. 80204); RNA concentration and quality analysis (RIN value) were performed by Tape Station 2200 bioanalyzer (Agilent Technologies)
1 ug of RNA with RIN associated greater than 8.0 were used to generate sequencing libraries using the TruSeq Stranded mRNA library prep kit from illumina according to the manufacturer’s instruction

tag: disease

value: Breast Cancer

tag: molecular subtype

value: Luminal A

tag: group

value: Nonresponder

value: Neoadjuvant Chemotherapy


title: Apc Brain Rep1

description: A07b_EKDL210002226-1a-AK6504-AK6658_H3VG7DSX2_L2

value: Male

value: RosaCreER Apc fl/fl (new)


title: CS12_B_3_9

source_name: Cabernet Sauvignon berry sample collected at time point 9 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: Apc Bladder Rep2

description: B08a_EKDL210002225-1a-AK6509-AK6669_H3VG7DSX2_L1

value: Day 4


title: CS12_B_1_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon


title: Apc Bladder Rep1

description: A05b_EKDL210002226-1a-AK6502-AK6656_H3VG7DSX2_L2


title: CS12_B_3_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: Nthy-ori 3-1, BDE209, 27 Days, rep 3

city: Jinan

first: Xinpei

last: Wang

address: #44 Wenhua West Road

country: China

institute: Shandong University

data_processing:
This project uses the filtering software SOAPnuke developed by BGI independently for filtering.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
We used Bowtie2 to map the clean reads to the reference gene sequence (transcriptome), and then used RSEM to calculate the gene expression level of each sample.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Thyroid

extract_protocol:
Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Thyroid

tag: cell line

value: Nthy-ori 3-1

tag: cell type

value: normal thyroid follicular epithelial cell line

value: WT

value: BDE209, 27 days


title: CS12_B_2_8

source_name: Cabernet Sauvignon berry sample collected at time point 8 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: tissue

value: grape berry pericarp


title: Apc Brain Rep2

description: B10d_EKDL210002228-1a-AK4945-AK6671_H3VG7DSX2_L4

tag: Sex

value: Brain

tag: genotype


title: Nthy-ori 3-1, BDE209, 27 Days, rep 2

tag: treatment


title: Nthy-ori 3-1, BDE209, 27 Days, rep 1


title: CS12_C_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2012 - Crop thinned 75%

tag: cultivar

value: Crop thinned 75%


title: CS12_C_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2012 - Crop thinned 75%

tag: year


title: CS12_C_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2012 - Crop thinned 75%

tag: time point


title: Nthy-ori 3-1, DMSO, 27 Days, rep 3

value: DMSO, 27 days


title: Nthy-ori 3-1, DMSO, 27 Days, rep 2


title: IP_cortex_male_Pb_3

city: Ann Arbor

first: Maureen

last: Sartor

state: MI

address: 100 Washtenaw Ave

department: Computational Medicine and Bioinformatics

institute: University of Michigan

data_processing:
assessed for quality (FastQC v0.11.8)
adapter sequence trimmed (TrimGalore v0.4.5)
aligned to mm10 with Bowtie2 (v2.3.4.1)
Duplicate reads were marked with Picard (v2.20.2) and filtered out with samtools (v1.2)
ENCODE blacklisted regions were removed with bedtools (v2.28.0)
reads were used for peak calling with macs2 (v2.1.2)
Using DiffBind (Stark and Brown, 2011, Ross-Innes et al., 2012), consensus peaks (overlapping in at least 66% of samples in each comparison group) were exacted
Individual consensus peaks were counted using 100 bp and normalized using library size
Assembly: mm10
Supplementary files format and content: bedGraph, RPKM of merged paired end files
Library strategy: hMeDIP-seq

source_name: Cortex

growth_protocol: Virgin a/a females (6-8 weeks old) were randomly assigned to one of three exposure groups. Animals were maintained on phytoestrogen-free modified AIN-93 chow (Envigo Td.95092, 7% corn oil diet, Harlan Teklad) and housed in polycarbonate-free cages.

extract_protocol:
The AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Cat. #80224) was used to extract DNA from blood and cortex tissue
For each sample, a total of 750 ng of genomic DNA was sheared by adaptive focused acoustics, using the Covaris S220 (Covaris). This sheared DNA was blunt-ended and phosphorylated. A single A-nucleotide was then added to the 3’-end of the fragments in preparation for ligation of adapter duplex with a T overhang. The ligated fragments were cleaned using Qiagen’s MinElute PCR purification columns. DNA standards for hMeDIP-seq (Diagenode, 5-hmC, 5-mC, & cytosine DNA standard pack for hMeDIP, cat # AF-107-0040) were added to each sample before denaturation and resuspension in ice-cold immunoprecipitation buffer (10 mM Sodium Phosphate pH 7.0, 140 mM NaCl, 0.05% Triton X-100). A 10% volume was input before 2 µg of a 5-hmC-specific antibody (Active Motif, Cat # 39791) was added for immunoprecipitation overnight at 4°C with rotation. Dynabeads Protein-G (Invitrogen) were added to the immunoprecipitation to perform the pull-down of 5-hmC-enriched fragments. The 5-hmC-enriched DNA fragments were then released from the antibody by digestion with Proteinase K (Ambion).The libraries were pooled and then sequenced on a NovaSeq6000 instrument.

treatment_protocol: Exposures were 5 mg DEHP/kg chow/day, 32 ppm Pb-acetate drinking water, or control (DEHP- and Pb-free).Exposure began two weeks prior to mating with virgin a/a males (7-9 weeks old) and continued until offspring weaning at postnatal day 21 (PND 21). DEHP and Pb exposures were conducted ad libitum. DEHP was dissolved in corn oil and used to create a 7% corn oil for chow. Assuming pregnant and nursing female mice weigh roughly 25 g and eat, on average, 5 g of chow per day, the resulting exposure level of 5 mg/kg-day reflects human-relevant exposures (Chang et al., 2017). Pb-acetate drinking water was prepared with distilled drinking water, with a concentration of 32 ppm to model human-relevant perinatal exposure.

value: Cortex

value: wildtype a/a

tag: age

value: 5 months

value: Pb

tag: chip antibody

value: 5-hmC-specific (Active Motif, Cat # 39791)


title: IP_cortex_male_Pb_4

value: Male


title: IP_cortex_male_Pb_1


title: IP_cortex_male_Pb_2


title: IP_cortex_male_Pb_6


title: IP_cortex_male_Pb_5


title: IP_cortex_male_DEHP_7

value: DEHP


title: IP_cortex_male_DEHP_6


title: IP_cortex_male_DEHP_3


title: IP_cortex_male_DEHP_4


title: IP_cortex_male_DEHP_2


title: Nthy-ori 3-1, DMSO, 27 Days, rep 1


title: IP_cortex_male_DEHP_1


title: CS12_B_3_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 3) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon

tag: time point replicate

tag: day after veraison

tag: sugar content (g/100ml)

value: Crop thinned 50%


title: CS12_B_2_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: treatment (cluster thinning)


title: IP_cortex_male_control_6

tag: strain

value: Control


title: CS12_B_1_7

source_name: Cabernet Sauvignon berry sample collected at time point 7 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: CS12_C_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: IP_cortex_male_control_4


title: IP_cortex_male_control_2


title: IP_cortex_male_DEHP_5


title: IP_cortex_male_control_3


title: IP_cortex_male_control_5


title: CS12_C_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: CS12_C_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: IP_cortex_female_Pb_6

value: Female


title: IP_cortex_female_Pb_5


title: IP_cortex_male_control_1


title: IP_cortex_female_Pb_3


title: IP_cortex_female_Pb_4


title: CS12_B_3_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: CS12_B_1_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: CS12_B_2_6

source_name: Cabernet Sauvignon berry sample collected at time point 6 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: IP_cortex_female_DEHP_2


title: IP_cortex_female_DEHP_3


title: scRNA-seq of the whole wt stembryos at 96h, rep1

city: Lausanne

first: Lucille

last: Lopez-Delisle

address: Station 19

country: Switzerland

institute: EPFL

library_source: transcriptomic single cell

data_processing:
All scripts are available on https://github.com/lldelisle/scriptsForRekaikEtAl2022
The cellranger pipeline version 6.0 (10x Genomics) was used with the default parameters on each fastq pair of scRNAseq datasets to perform the alignment, applying filtering and count barcodes and UMIs. Alignment was performed against the mouse reference genome mm10 and a modified gtf file based on Ensembl version 98 (https://doi.org/10.5281/zenodo.4456701). Each gene-cell count matrix was then analyzed using Seurat version 4.0.2 (Stuart et al. 2019). A Seurat object was generated by filtering out barcodes with less than 200 identified gene and genes identified in less than 3 cells. Then a further filtering was applied to remove low quality cells as well as doublets. For each dataset, the mean RNA count was used and cells with either less than 40% of the mean? or more than 2.5-fold the mean were remove. In addition, cells with more than 8% or less than 0.05% mitochondrial counts were removed. Each dataset was then normalized using the NormalizeData command, the 3000 most variable features were identified, and cell cycle was scored (using the 2019 updated gene list from Seurat). Then, all individual datasets were merged into a single Seurat object. The merged dataset was then normalized, the 3000 most variable features were identified. Then data scaling was performed using the ScaleData command using the percentage of mitochondrial count and cell cycle score.
Assembly: mm10
Supplementary files format and content: combined.96h.120h.rds: final R object containing filtered cells with expressions, clustering, projection etc. savec with saveRDS
Supplementary files format and content: filtered_feature_bc_matrix.tar: tar archive with output of cellranger (raw counts, gene names and cell names)
Supplementary files format and content: metadata.csv.gz: comma separated table containing metadata for each cell (clustering, sample of origin etc)
Supplementary files format and content: raw_counts.csv.gz: comma separated table contaiing the raw counts (genes as row and cells as columns)

source_name: stembryo

extract_protocol:
48 to 96 gastruloids were collected 96h or 120h after aggregation and washed twice in 1ml of PBS. Gastruloids were dissociated in 100ul of Stempro Accutase© for 5 minutes at 37°C, full dissociation was ensured by mechanical dissociation (pipetting) and verified to ensure absence of doublet cells. Then gastruloid cells were washed twice in 500ul PBS, and resuspended in an adequate volume of PBS 0.04%BSA at 106 cells/ml. All centrifugation steps were done for 5 minutes at 350G in DNA low binding Eppendorf tubes. Single cell suspensions were filtered using Flowmi Cell Strainer 40um and then were subjected to single cell RNAseq using the 10x genomics platform (V3, and V3.1 chemistry) following manufacturer’s recommendation.
cDNA preparations were performed according to 10x Genomics recommendations and was amplified for 10 to 12 cycles. And sequenced on a Hiseq 4000 with the cbot2 chemistry. At least 2 replicates were performed for each time points. In addition, a third 120h timepoint was generated by dissection in two portions to separate the anterior and posterior halves and each portion was analyzed separately by single cell RNAseq.

value: stembryo

value: mES cells

value: wt

tag: stage (in_hours_after_aggregation)


title: IP_cortex_female_DEHP_5


title: IP_cortex_female_DEHP_1


title: scRNA-seq of the whole wt stembryos at 96h, rep2

tag: cell line


title: IP_cortex_female_control_6


title: IP_cortex_female_DEHP_4


title: CS12_C_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2012 - Crop thinned 75%

value: grape berry pericarp


title: CS12_C_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2012 - Crop thinned 75%

value: Crop thinned 75%


title: scRNA-seq of the whole wt stembryos at 120h, rep2


title: IP_cortex_female_control_5


title: IP_cortex_female_control_4


title: scRNA-seq of the whole wt stembryos at 120h, rep1


title: CS12_C_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: Epithelium cell_rep2

city: San Diego

first: Wendy

last: Huang

state: CA

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

description: Nuclear RNA and genomic DNA

data_processing:
All the GRID-seq libraries were sequenced with single-end 100 bp reads on HiSeq400 (Illumina, 200 million reads/sample). Raw reads were firstly evaluated by FastQC and trimmed by Cutadapt to get high-quallity clean reads, and those clean reads  were then filtered out if the length were below 85 bp as suggested according to previous report (Li et al., 2017; Zhou et al., 2019).
The designed linker sequence of GRID-seq library were identified identified by matefq in GridTools (Zhou et al., 2019) and the paired reads consisting of transcribed RNA and genomic DNA were then seprated. Paired RNA and DNA reads were then mapped to the mouse genome (GRCm38/mm10) by BWA respectively. Read counts were generally summarized into 1kb genomic bins for downstream analyses.
Assembly: GRCm38/mm10
Supplementary files format and content: Processed data are in gzipped tsv (*.xbed.bgz) recording: RNA_Chrom, RNA_Start, RNA_End, DNA_Chrom, DNA_Start, DNA_End, RNA_Strand, DNA_Strand.
Library strategy: GRID-seq

source_name: Epithelium cells

extract_protocol:
Two independent biological replicates (5-10 x106) were crosslinked with disuccinimidyl glutarate (DSG) and formaldehyde. DNA in isolated nuclei were digested with AluI. A biotinylated bivalent linker was ligated to chromatin-associated RNA (with the ssRNA stretch on the linker) and nearby fragmented genomic DNA and captured by streptavidin microbeads for library construction.
To amplify each library, 20 μl of PCR amplification mix (9.4 μl of H2O, 5 μl of DNA sample, 4 μl of 5× Phusion HF Buffer, 40 pmol dNTP, 5 pmol Primer#1, 5 pmol Primer#2, 0.4 U Phusion High-Fidelity DNA Polymerase (Thermo Fisher)) was prepared. PCR primers consist of Primer#1 (5′-AATGATACGGCGACCACCGAGATCTACACBBBBBACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′ (BBBBB: 5 nt barcode for multiplexing libraries)) and Primer#2 (5′-CAAGCAGAAGACGGCATACGAGACGTGTGCTCTTCCGATCT-3′). PCR was performed initially for 30 seconds at 98°C, and then 16 cycles of 10 sec denaturation at 98°C, 30 sec annealing at 65°C, and 15 sec extension at 72°C. The PCR product was resolved by native 10% polyacrylamide gel and the band of 194 bp in size was recovered.Sequencing was performed on HiSeq400 (Illumina, 200 million reads/sample).

tag: cell type

value: Epithelium cells

value: untreated


title: CS12_B_3_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 3) over ripening season 2012 - Crop thinned 50%

tag: tissue


title: IP_cortex_female_control_2

value: Cortex

tag: Sex

value: wildtype a/a


title: IP_cortex_female_Pb_2

value: 5 months

value: Pb


title: Epithelium cell_rep1

description: Nuclear RNA and genomic DNA


title: IP_cortex_female_control_3

value: 5-hmC-specific (Active Motif, Cat # 39791)


title: 5113_Malat1_SI_IEC_Het

data_processing:
Paired-end reads were aligned to the mouse mm10 genome with the STAR aligner version 2.6.1a using the parameters: "--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000".
Uniquely mapped reads overlapping with exons were counted using featureCounts for each gene in the GENCODE.vM19 annotation
Differential expression analysis was performed using DESeq2 (v1.18.1 package) , including a covariate in the design matrix to account for differences in harvest batch
FASTQ files from RNA-seq were used to analyze alternative splicing events via rMATS v4.1.0 using the parameters: “-t paired --nthread 4 --readLength 100 --cstat 0.0001 --libType fr-firststrand”
Candidates corresponding to each type of alternative splicing patterns with FDR greater than 0.05 were filtered out
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized Deseq count for each gene/Sample

source_name: small intestine_ileum epithelium

growth_protocol: All mice were raised in Specific Pathogen Free (SPF) facility on normal diet. 9-11 week old animals were used for experiments.

extract_protocol:
RNA were isolated using Qiagen Rneasy mini kit (74106)
Ribosome-depleted RNAs were used to generate the cDNA libraries using the KAPA Hyper Prep Kit (KR0961) according to the instructions. Briefly, DNA was end-repaired and A-tailing to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. Post-liagation clean was used to remove the extra adapters. Then the adapter ligation DNA was PCR amplified with Illumina primers for 8 cycles, follwed with post-ampilcation clean with KAPA pure beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 4000 following the manufacturer's protocols.

treatment_protocol: No treatment. Steady state mice were harvest at 9-11 week old.

value: steady state


title: IP_blood_male_Pb_4

source_name: Blood

value: Blood

value: Male


title: IP_blood_male_Pb_6


title: CS12_B_1_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon

value: Crop thinned 50%


title: IP_blood_male_Pb_5


title: IP_blood_male_Pb_3


title: CS12_C_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2012 - Crop thinned 75%


title: CS12_C_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: IP_blood_male_Pb_1


title: 3534_Malat1_SI_IEC_WT


title: IP_blood_male_DEHP_6

value: DEHP


title: CS12_C_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: IP_blood_male_DEHP_5


title: CS12_B_3_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: CS12_B_2_5

source_name: Cabernet Sauvignon berry sample collected at time point 5 (replicate 2) over ripening season 2012 - Crop thinned 50%


title: IP_cortex_female_control_1

source_name: Cortex

value: Female

value: Control


title: IP_blood_male_DEHP_2


title: 4589_Malat1_LI_IEC_KO

source_name: Colon epithelium


title: IP_blood_male_DEHP_1


title: 3534_Malat1_LI_IEC_WT


title: IP_blood_male_control_5


title: CS12_B_2_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 2) over ripening season 2012 - Crop thinned 50%

value: grape berry pericarp


title: IP_blood_male_control_6


title: IP_blood_male_Pb_2


title: IP_blood_male_control_4


title: CS12_B_1_4

source_name: Cabernet Sauvignon berry sample collected at time point 4 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: 3532_Malat1_LI_IEC_KO


title: IP_blood_male_control_2


title: CS12_C_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2012 - Crop thinned 75%

value: Crop thinned 75%


title: 3532_Malat1_SI_IEC_KO


title: IP_blood_male_control_3


title: IP_blood_male_control_1


title: IP_blood_male_DEHP_4


title: IP_blood_male_DEHP_3


title: Ythdf2 cKO, IR, m6A IP, r3, MeRIP-seq

city: Shanghai

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

data_processing:
Raw reads were trimmed with Trimmomatic-0.39, then aligned to mouse genome and transcriptome (mm10)
Mapped reads were separated by strands with samtools
m6A peaks on each strand were called using MACS (version 2)
Significant peaks with q < 0.01 identified by MACS2 were considered
Peaks identified in at least three biological replicates were merged using bedtools (v.2.26.0)
Assembly: mm10
Supplementary files format and content: text files includes read counts for each Sample, narrowPeak (except for Input sample)
Library strategy: MeRIP-seq

source_name: MC38 tumors

growth_protocol: CD11b+ myeloid cells were sorted from MC38 tumors or blood of MC38 tumor-bearing mice

extract_protocol:
total RNA was harvested using Rneasy mini plus kit (Qiagen), followed by mRNA isolation using Dynabeads™ mRNA Purification Kit,M6A-IP was performed
RNA libraries for RNA-seq were prepared using SMARTer® Stranded Total RNA-Seq Kit (TaKaRa)

treatment_protocol: MC38 tumors were received irradition (20 Gy, one dose), three days after IR, cells were collected

value: MC38 tumors

value: CD11b+ myeloid cells

tag: genotype

value: Ythdf2 cKO

value: Irradiation

tag: antibody

value: EpiMark N6-Methyladenosine Enrichment Kit


title: IP_blood_female_Pb_5

value: wildtype a/a

value: 5 months

tag: treatment

value: Pb


title: Ythdf2 cKO, IR, m6A IP, r2, MeRIP-seq


title: CS12_C_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2012 - Crop thinned 75%

tag: cultivar

tag: year


title: IP_blood_female_Pb_6

value: Blood

tag: age

value: 5-hmC-specific (Active Motif, Cat # 39791)


title: 4591_Malat1_LI_IEC_WT

value: steady state


title: CS12_C_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2012 - Crop thinned 75%

value: Cabernet Sauvignon

tag: time point


title: IP_blood_female_Pb_1

tag: chip antibody


title: IP_blood_female_Pb_2


title: Ythdf2 cKO, IR, m6A IP, r1, MeRIP-seq


title: IP_blood_female_Pb_3


title: Ythdf2 cKO, Control, m6A IP, r3, MeRIP-seq


title: CS12_B_2_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 2) over ripening season 2012 - Crop thinned 50%

tag: time point replicate

tag: day after veraison

value: Crop thinned 50%


title: IP_blood_female_DEHP_5

value: Female

value: DEHP


title: IP_blood_female_DEHP_4


title: Ythdf2 cKO, Control, m6A IP, r2, MeRIP-seq

value: Control


title: Ythdf2 cKO, Control, m6A IP, r1, MeRIP-seq


title: CS12_C_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2012 - Crop thinned 75%

value: grape berry pericarp

tag: sugar content (g/100ml)

tag: treatment (cluster thinning)

value: Crop thinned 75%


title: IP_blood_female_DEHP_2

source_name: Blood

tag: strain


title: IP_blood_female_Pb_4


title: IP_blood_female_DEHP_1


title: IP_blood_female_control_6


title: IP_blood_female_control_5


title: WT, IR, m6A IP, r2, MeRIP-seq

value: MC38 tumors

value: CD11b+ myeloid cells

value: WT


title: IP_blood_female_control_4


title: CS12_C_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: IP_blood_female_control_2


title: IP_blood_female_control_3


title: WT, IR, m6A IP, r1, MeRIP-seq

value: Irradiation

value: EpiMark N6-Methyladenosine Enrichment Kit


title: CS12_B_1_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 1) over ripening season 2012 - Crop thinned 50%


title: CS12_B_3_3

source_name: Cabernet Sauvignon berry sample collected at time point 3 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: IP_blood_female_control_1

value: wildtype a/a

value: 5 months


title: CS12_B_3_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 3) over ripening season 2012 - Crop thinned 50%


title: input_cortex_male_Pb_5

description: Processed data file is on IP sample

value: Cortex

value: Male

value: Pb

value: none (input)


title: input_cortex_male_Pb_4

description: Processed data file is on IP sample


title: CS12_B_2_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 2) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon

value: Crop thinned 50%


title: input_cortex_male_Pb_6

description: Processed data file is on IP sample


title: IP_blood_female_DEHP_3

value: Blood

value: Female

value: DEHP

value: 5-hmC-specific (Active Motif, Cat # 39791)


title: input_cortex_male_Pb_3

description: Processed data file is on IP sample


title: WT, Control, m6A IP, r2, MeRIP-seq

value: MC38 tumors

value: Control


title: WT, Control, m6A IP, r3, MeRIP-seq

value: CD11b+ myeloid cells

value: WT


title: CS12_B_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: grape berry pericarp


title: input_cortex_male_Pb_2

description: Processed data file is on IP sample

source_name: Cortex

value: wildtype a/a


title: input_cortex_male_Pb_1

description: Processed data file is on IP sample

value: 5 months


title: WT, IR, m6A IP, r3, MeRIP-seq

value: Irradiation

value: EpiMark N6-Methyladenosine Enrichment Kit


title: input_cortex_male_DEHP_7

description: Processed data file is on IP sample

value: Cortex

value: Male


title: input_cortex_male_DEHP_6

description: Processed data file is on IP sample

value: none (input)


title: CS12_C_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2012 - Crop thinned 75%

value: Cabernet Sauvignon

value: Crop thinned 75%


title: CS12_C_1_2

source_name: Cabernet Sauvignon berry sample collected at time point 2 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: CS12_C_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2012 - Crop thinned 75%


title: Ythdf2 cKO, IR, Input, r3, MeRIP-seq

value: Ythdf2 cKO


title: 5112_Malat1_SI_IEC_KO

source_name: small intestine_ileum epithelium

value: steady state


title: input_cortex_male_DEHP_5

description: Processed data file is on IP sample

value: DEHP


title: CS12_C_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2012 - Crop thinned 75%


title: WT, Control, m6A IP, r1, MeRIP-seq

source_name: MC38 tumors

value: MC38 tumors


title: input_cortex_male_DEHP_3

description: Processed data file is on IP sample


title: input_cortex_male_DEHP_4

description: Processed data file is on IP sample


title: Ythdf2 cKO, IR, Input, r2, MeRIP-seq


title: Ythdf2 cKO, IR, Input, r1, MeRIP-seq


title: input_cortex_male_DEHP_2

description: Processed data file is on IP sample


title: IP_cortex_female_Pb_1

value: Female

value: Pb

value: 5-hmC-specific (Active Motif, Cat # 39791)


title: input_cortex_male_DEHP_1

description: Processed data file is on IP sample


title: Ythdf2 cKO, Control, Input, r3, MeRIP-seq

value: CD11b+ myeloid cells

value: Control


title: Ythdf2 cKO, Control, Input, r2, MeRIP-seq


title: CS12_B_2_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 2) over ripening season 2012 - Crop thinned 50%

value: grape berry pericarp

value: Crop thinned 50%


title: input_cortex_male_control_5

description: Processed data file is on IP sample

value: wildtype a/a

value: 5 months


title: input_cortex_male_control_6

description: Processed data file is on IP sample

value: Cortex

value: Male


title: input_cortex_male_control_4

description: Processed data file is on IP sample

value: none (input)


title: input_cortex_male_control_1

description: Processed data file is on IP sample


title: Ythdf2 cKO, Control, Input, r1, MeRIP-seq


title: input_cortex_male_control_2

description: Processed data file is on IP sample


title: input_cortex_male_control_3

description: Processed data file is on IP sample


title: WT, IR, Input, r3, MeRIP-seq

value: WT

value: Irradiation


title: WT, IR, Input, r2, MeRIP-seq


title: input_cortex_female_Pb_5

description: Processed data file is on IP sample


title: WT, IR, Input, r1, MeRIP-seq


title: Rectum WT Rep1

source_name: Rectum

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 2 x 2mg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues at the noted distances along the intestine were harvested after 4 days.

value: Rectum

tag: time

value: Day 4


title: Rectum WT Rep3


title: Rectum WT Rep2


title: CS12_B_3_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 3) over ripening season 2012 - Crop thinned 50%

value: Cabernet Sauvignon


title: input_cortex_female_Pb_6

description: Processed data file is on IP sample

value: Female


title: input_cortex_female_Pb_3

description: Processed data file is on IP sample

value: Pb


title: Colon 50% WT Rep2

source_name: Colon 50%

value: Colon 50%


title: WT, Control, Input, r3, MeRIP-seq

value: MC38 tumors

tag: cell type

value: CD11b+ myeloid cells


title: Colon 50% WT Rep3

tag: tissue


title: input_cortex_female_Pb_2

description: Processed data file is on IP sample

tag: Sex


title: input_cortex_female_Pb_4

description: Processed data file is on IP sample


title: input_cortex_female_Pb_1

description: Processed data file is on IP sample


title: input_cortex_female_DEHP_5

description: Processed data file is on IP sample

value: DEHP


title: input_cortex_female_DEHP_4

description: Processed data file is on IP sample


title: CS12_B_1_1

source_name: Cabernet Sauvignon berry sample collected at time point 1 (replicate 1) over ripening season 2012 - Crop thinned 50%

value: grape berry pericarp

value: Crop thinned 50%


title: input_cortex_female_DEHP_3

description: Processed data file is on IP sample

value: wildtype a/a

value: 5 months


title: WT, Control, Input, r2, MeRIP-seq

tag: genotype

value: Control


title: Colon 50% WT Rep1


title: input_cortex_female_DEHP_2

description: Processed data file is on IP sample

value: Cortex

value: none (input)


title: WT, Control, Input, r1, MeRIP-seq

value: WT

tag: antibody


title: input_cortex_female_DEHP_1

description: Processed data file is on IP sample

tag: treatment


title: input_cortex_female_control_6

description: Processed data file is on IP sample


title: Kidney cortex, PTKO AA 4wk rep3

city: Stony Brook

first: Sandeep

last: Mallipattu

state: NY

address: 101 Nicolls Road

department: Department of Medicine

institute: Stony Brook University

data_processing:
Raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
Raw RNA-seq data was quantified to gene-level counts using Kallisto (Bray et al., 2016) with the ARCHS4 pipeline (Lachmann et al., 2017)
Raw counts were normalized to log10-Counts Per Million (logCPM) by dividing each column by the total sum of its counts followed by the application of a log10-transform.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file containing RPKM values for all samples

source_name: Kidney cortex

extract_protocol:
Mice were perfused with PBS, kidneys removed and stored in RNAlater. RNA was extracted using the RNeasy kit (Qiagen) and DNase treated.
cDNA was prepared using TruSeq Stranded Total RNA Sample Preparation kit (Illumina, San Diego, CA), according to the manufacturer’s instructions.

value: AA 4wk

value: Kidney cortex


title: Colon 10% WT Rep2

source_name: Colon 10%

value: Male

value: Colon 10%

value: Day 4


title: Colon 10% WT Rep3


title: input_cortex_female_control_4

description: Processed data file is on IP sample

value: Female


title: Kidney cortex, PTKO AA 4wk rep2


title: input_cortex_female_control_3

description: Processed data file is on IP sample


title: Colon 10% WT Rep1


title: input_cortex_female_control_1

description: Processed data file is on IP sample


title: input_cortex_female_control_2

description: Processed data file is on IP sample


title: SI 90% WT Rep4


title: Kidney cortex, fl/fl AA 4wk rep3


title: input_blood_male_Pb_6

description: Processed data file is on IP sample

source_name: Blood

value: Blood

value: Pb


title: input_blood_male_Pb_5

description: Processed data file is on IP sample


title: SI 90% WT Rep3


title: input_blood_male_Pb_3

description: Processed data file is on IP sample


title: input_blood_male_Pb_2

description: Processed data file is on IP sample


title: input_blood_male_Pb_4

description: Processed data file is on IP sample


title: SI 90% WT Rep2


title: input_blood_male_Pb_1

description: Processed data file is on IP sample


title: Kidney cortex, fl/fl AA 4wk rep2


title: SI 90% WT Rep1


title: Kidney cortex, fl/fl AA 4wk rep1


title: Kidney cortex, PTKO AA 2wk rep3

value: AA 2wk


title: input_blood_male_DEHP_6

description: Processed data file is on IP sample

value: DEHP


title: input_blood_male_DEHP_5

description: Processed data file is on IP sample


title: input_cortex_female_control_5

description: Processed data file is on IP sample


title: input_blood_male_DEHP_4

description: Processed data file is on IP sample


title: Kidney cortex, PTKO AA 2wk rep2


title: input_blood_male_DEHP_3

description: Processed data file is on IP sample


title: SI 75% WT Rep2


title: Kidney cortex, PTKO AA 2wk rep1


title: input_blood_male_DEHP_1

description: Processed data file is on IP sample


title: Kidney cortex, PTKO AA 4wk rep1


title: SI 75% WT Rep1


title: input_blood_male_control_6

description: Processed data file is on IP sample


title: Kidney cortex, fl/fl AA 2wk rep3


title: input_blood_male_DEHP_2

description: Processed data file is on IP sample


title: SI 50% WT Rep3


title: input_blood_male_control_4

description: Processed data file is on IP sample


title: Kidney cortex, fl/fl AA 2wk rep2


title: SI 50% WT Rep2


title: input_blood_male_control_3

description: Processed data file is on IP sample


title: input_blood_male_control_2

description: Processed data file is on IP sample


title: Kidney cortex, fl/fl AA 2wk rep1


title: SI 50% WT Rep1


title: input_blood_female_Pb_5

description: Processed data file is on IP sample


title: SI 75% WT Rep3


title: SI 25% WT Rep3


title: input_blood_male_control_1

description: Processed data file is on IP sample


title: input_blood_female_Pb_6

description: Processed data file is on IP sample


title: Kidney cortex, PTKO DMSO rep3

value: DMSO


title: input_blood_female_Pb_4

description: Processed data file is on IP sample

value: wildtype a/a


title: input_blood_female_Pb_3

description: Processed data file is on IP sample

value: 5 months


title: SI 25% WT Rep2


title: Kidney cortex, PTKO DMSO rep1


title: input_blood_female_Pb_1

description: Processed data file is on IP sample


title: input_blood_female_Pb_2

description: Processed data file is on IP sample


title: SI 25% WT Rep1


title: input_blood_male_control_5

description: Processed data file is on IP sample

value: Control


title: SI 10% WT Rep3


title: Kidney cortex, fl/fl DMSO rep2


title: input_blood_female_DEHP_4

description: Processed data file is on IP sample


title: SI 10% WT Rep2


title: Kidney cortex, fl/fl DMSO rep1


title: input_blood_female_control_6

description: Processed data file is on IP sample


title: input_blood_female_DEHP_1

description: Processed data file is on IP sample


title: Kidney cortex, PTKO DMSO rep2


title: SI 10% WT Rep1


title: Rectum Apc Rep2

value: Rectum

value: VilCreER Apcfl/fl


title: input_blood_female_control_1

description: Processed data file is on IP sample

value: none (input)


title: input_blood_female_control_3

description: Processed data file is on IP sample


title: input_blood_female_control_2

description: Processed data file is on IP sample


title: Rectum Apc Rep1


title: Colon 50% Apc Rep3

value: Colon 50%


title: Kidney cortex, fl/fl DMSO rep3

value: Kidney cortex


title: input_blood_female_DEHP_5

description: Processed data file is on IP sample


title: Colon 50% Apc Rep2


title: input_blood_female_DEHP_3

description: Processed data file is on IP sample


title: input_blood_female_DEHP_2

description: Processed data file is on IP sample


title: Colon 50% Apc Rep1


title: input_blood_female_control_5

description: Processed data file is on IP sample


title: mouse FGF/Nrg1

city: UTRECHT

first: PHILIP

last: LIJNZAAD

state: Utrecht

address: HEIDELBERGLAAN 25

department: Single Cell Facility

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

data_processing:
10x genomics cellranger version 6.1.1  was used for all the analysis steps from fastq.gz to count tables
Assembly: For the mouse samples, the 10x genomics genome refdata-gex-mm10-2020-A (which is Mus musculus, GRCm38, patchlevel 6 and gencode version M23). For the Acomys samples, a custom genome was used.
Supplementary files format and content: 10x genomics cellranger 6.1.1 hdf5 file. For details see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/h5_matrices

source_name: ear pinna skin

extract_protocol:
Tissue was dissociated into single cell suspension using Protease from B. Licheniformis and Dounce homogenizer. Red blood cells were removed with RBC lysis buffer. Centrifugation steps were performed at 300g 5min. Cells were resuspended in PBS/BSA 0.04%
The barcoding of individual transcripts from single cells, followed by cDNA amplification and library construction, were performed using 10X Genomics reagents and 10X Chromium Controller, according to the manufacturer’s user guide nr. CG000315 (“Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index), RevC”).

treatment_protocol: pERK, FGFR and ErbB2 inhibitors were injected from D12 to D15, similarly to DMSO control;  micro-beads soaked with either PBS, recombinant FGF-2/NRG-1 were implanted locally at D10.

value: healing ear punch


title: 5018_SI_EDTA

data_processing:
the single-end raw reads of two repeats of each example were mapped to the mouse genome (GENCODE assembly GRCm38) by bowtie2 (Version 2.3.4.1) in the local mapping mode with parameter “--local”, followed by PCR deduplication by SAMTools (Version 1.9) with the utility markedup
Assembly: mm10
Supplementary files format and content: bigwig files were generated using bamCoverage function in deepTools

source_name: small intestine

extract_protocol:
Intestine tissues were first incubated in 5 mM EDTA in HBSS containing 1 mM DTT for 20 min at 37°C with shaking, and then incubated in a second wash of 5 mM EDTA in HBSS without DTT for 20 min at 37°C with agitation. Suspended cells from the EDTA washes were pooled as enriched “intestine epithelial cells”.
ATAC-seq libraries were generated as described by J. D. Buenrostro, B. Wu, H. Y. Chang, W. J. Greenleaf, ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21 29 21-21 29 29 (2015).

value: small intestine

value: DDX5 wildtype

value: female


title: 4940_SI_EDTA


title: 5016_SI_EDTA

value: DDX5 knockout


title: input_blood_female_control_4

description: Processed data file is on IP sample

value: Blood

value: Female


title: Rectum Apc Rep3

value: Male

value: Day 4


title: Colon 10% Apc Rep3

value: Colon 10%


title: mouse PBS

value: PBS


title: 5018_LI_EDTA

source_name: Colon

value: Colon


title: 5016_LI_EDTA


title: 4941_LI_EDTA


title: 4940_LI_EDTA


title: 4941_SI_EDTA


title: SM3, sample RNA42

city: Hull

first: Lauric

last: Feugere

address: Cottingham Road

department: Biological and Marine Sciences

institute: University of Hull

description: Stress Metabolites at 27°C

data_processing:
The quality control of reads was verified with FASTQC v0.11.9 and fastp v0.23.1.
Reads were filtered and trimmed using fastp v0.23.1, to remove low quality reads, polyG, polyX, and Illumina adapter sequences. Default parameters were used along with --dup_calc_accuracy 3 --trim_poly_g --trim_poly_x
Reads were aligned to the zebrafish reference genome using STAR v2.6.1
Reads were counted by gene using STAR v2.6.1 (--runMode alignReads --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMunmapped None --outSAMattributes Standard)
Differential gene expression analysis was conducted in Bioconductor v3.11 using DESeq2 v1.28.1 in R v4.0.2.
Assembly: primary genome assembly GRCz11.104 (http://ftp.ensembl.org/pub/release-104/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz and http://ftp.ensembl.org/pub/release-104/gtf/danio_rerio/Danio_rerio.GRCz11.104.gtf.gz)
Supplementary files format and content: The files with "_ReadsPerGenes.fastp.noD.tab" name extensions are read counts per gene obtained from STAR, which were used in DESeq2 for differential expression analysis.

organism: Danio rerio

source_name: 1-dpf whole-body embryos

growth_protocol: Zebrafish eggs were sanitised with standard 0.004% bleaching protocols and maintainted in 1X E3 embryo medium. Zebrafish eggs were collected at 10 am from a population of adult zebrafish (wild-type AB) maintained at 27°C, with 14:10 light:dark cycles.  Embryos were incubated in individual 0.2 mL PCR tubes (one embryo per tube) containing 200 μL of of experimental embryo medium. Embryos were incubated in darkness in a thermal cycler with their experimental temperature protocol.

extract_protocol:
Randomised embryo samples were processed for Total RNA extraction using the TRIzol method following the manufacturer's recommendations, and followed by a DNAse I digestion step and a sodium acetate clean-up.
Total RNA samples were processed to prepare cDNA libraries using the Illumina TrueSeq stranded mRNA kit.

treatment_protocol: Two temperature protocols were used, either (i) a control constant temperature of 27°C, or (ii)  thermal stress protocol consisting of repeated heat stress with temperature fluctuations  between 27, 29, 32, 29, and 27°C, with each temperature step being maintained for 15 min for a total of 19 cycles in 24 hours. Stress metabolites were obtained by pooling stress medium from embryos that had experienced the thermal stress treatment on the day prior. Individual embryos were in experimental embryo medium (fresh medium free of metabolites or stress medium with stress metabolites, SM) and incubated with their temperature protocols for 24 hours, from 11 am (once they reached the stage of 2-3.3 hours post fertilisation) to 11 am on the next day. At 1 day post fertilisation, i.e. after 24 hours of experimental treatment, embryos were sampled by pools of 20 per condition, and snap-frozen at -80°C before total RNA extraction.

value: 1-dpf whole-body embryos

value: Wild-type Line:AB

value: 1 day post fertilisation

tag: treatment group

value: SM

value: Stress Metabolites at 27C


title: set_3_d4_RNA_S15

city: Pittsburgh

first: Daniella

last: Schwartz

state: PA

address: 200 Lothrop St

institute: University of Pittsburgh

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Reads of 50 bases were processed using the rna-seek pipeline (https://ccbr.github.io/RNA-seek/): adapter sequences were trimmed with cutadapt 1.18
Reads were mapped to the mouse transcriptome and genome mm10 or human transcriptome and genome GRCh38 (hg38) using STAR.
Gene expression values (FPKM: Fragments Per Kilobase exon Per Million mapped reads; TPM, Tags Per Million mapped reads; counts) were generated using RSEM.
Differential gene expression was calculated using DESeq2.
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: FPKM_all_samples_RSEM

source_name: In vitro differentiated Th9 (d4)

growth_protocol: Complete IMDM (10% FBS, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 55 μM 2-Mercaptoethanol

extract_protocol:
Cells were suspended in Trizol LS (Invitrogen), and total RNA extracted according to the manufacturer instruction.
Libraries for mRNA-sequencing were prepared using the NEBNext Ultra II Directional RNAseq Library preparation kit, per the manufacturer’s instructions.

treatment_protocol: Murine naïve CD4+CD62L+ cells were isolated from spleen and lymph nodes using negative selection (Miltenyi) followed by flow cytometric sorting to >95% purity. Cells were cultured at a density of 0.5 x10^6 per mL and activated with plate bound aCD3Ɛ (10 µg/mL) and aCD28 (10 µg/mL) for 3 days with polarizing cytokine and antibodies to promote the differentiation of Th9 (10 µg/mLaIFN-g, 20 ng/mL mIL-4, 10ng/mL hIL-2, 5 ng/mL hTGF-β) for 3 days. After 3 days, cells were washed and cultured without aCD3 or aCD28 but with polarizing cytokines and antibodies, and with 10 ng/mL hIL-2, in fresh media. Media, cytokines, and antibodies were changed every 2 days. Cells were collected 24h later (on d4) for analysis

value: In vitro differentiated Th9 (d4)


title: set_3_d3_RNA_S14

source_name: In vitro differentiated Th9 (d3)

treatment_protocol: Murine naïve CD4+CD62L+ cells were isolated from spleen and lymph nodes using negative selection (Miltenyi) followed by flow cytometric sorting to >95% purity. Cells were cultured at a density of 0.5 x10^6 per mL and activated with plate bound aCD3Ɛ (10 µg/mL) and aCD28 (10 µg/mL) for 3 days with polarizing cytokine and antibodies to promote the differentiation of Th9 (10 µg/mLaIFN-g, 20 ng/mL mIL-4, 10ng/mL hIL-2, 5 ng/mL hTGF-β) for 3 days.

value: In vitro differentiated Th9 (d3)


title: set_3_d8_RNA_S16

source_name: In vitro differentiated Th9 (d8)

treatment_protocol: Murine naïve CD4+CD62L+ cells were isolated from spleen and lymph nodes using negative selection (Miltenyi) followed by flow cytometric sorting to >95% purity. Cells were cultured at a density of 0.5 x10^6 per mL and activated with plate bound aCD3Ɛ (10 µg/mL) and aCD28 (10 µg/mL) for 3 days with polarizing cytokine and antibodies to promote the differentiation of Th9 (10 µg/mLaIFN-g, 20 ng/mL mIL-4, 10ng/mL hIL-2, 5 ng/mL hTGF-β) for 3 days. After 3 days, cells were washed and cultured without aCD3 or aCD28 but with polarizing cytokines and antibodies, and with 10 ng/mL hIL-2, in fresh media. Media, cytokines, and antibodies were changed every 2 days. Cells were collected 5 days later (on d8) for analysis

value: In vitro differentiated Th9 (d8)


title: set_3_naive_RNA_S13

source_name: naive T cells

treatment_protocol: Murine naïve CD4+CD62L+ cells were isolated from spleen and lymph nodes using negative selection (Miltenyi) followed by flow cytometric sorting to >95% purity.

value: naive T cells


title: Colon 10% Apc Rep1

value: VilCreER Apcfl/fl


title: C3, sample RNA37

description: Control (fresh medium at 27°C)

value: C

value: Control (fresh medium at 27C)


title: set_2_d8_RNA_S10


title: SI 90% Apc Rep3

value: Female


title: set_2_d3_RNA_S8


title: set_2_d4_RNA_S9


title: TS3, sample RNA36

description: Fresh medium with repeated heat stress

value: TS

value: Fresh medium with repeated heat stress


title: SI 90% Apc Rep2

value: Male

value: Day 4


title: set_2_naive_RNA_S7


title: Colon 10% Apc Rep2

value: Colon 10%


title: TS+SM3, sample RNA35

description: Stress Metabolites with repeated heat stress

value: 1-dpf whole-body embryos

value: Wild-type Line:AB

value: TS+SM


title: set_1_d8_RNA_S4


title: set_1_d4_RNA_S3


title: SI 75% Apc Rep3


title: set_1_naive_RNA_S1


title: SI 75% Apc Rep1


title: M2_Naive_K4me3_S18

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Reads of 50 bases were processed using the ccbr pipeliner tool (https://ccbr.github.io/pipeliner-docs/): adapter sequences were trimmed with cutadapt 1.18
Data were mapped to the mouse genome mm10 or human genome GRCh38 (hg38)  using BWAmem 0.7.17. Uniquely mapped and nonredundant reads were generated using Picard 2.17.11 and used for downstream analysis.
The aligned files were converted to bam format using SAMtools 1.6, and bigwig files were created using deepTools 3.0.1.
For downstream analysis, peaks were called using MACS v2.1.1 using a FDR 0.01 and with the input sample for background correction and using the --broad setting
Assembly: mm10 (mouse), hg38 (human)
Supplementary files format and content: bedfile, broadPeak

extract_protocol:
ChIP-seq sample preparation was performed with Covaris kit (PN 520154). Naïve T cells were cultured in vitro under Th9 promoting conditions and treated with chemical cross-linking (1% formaldehyde) on days 0, 3, 4, and 8 (murine) or days 0, 5, 8, and 15 (human). At least 0.5 million cells were used for each immunoprecipitation. After chemical chromatin cross-linking (1% formaldehyde), cells were washed and frozen at -80C. Cells were resuspended in Lysis Buffer B (Covaris) with protease inhibitors, and DNA fragmentation was performed on a Covaris Sonicator (ME220) for 8 min to an average length of 200-700 bp.  After sonication, cells were immunoprecipitated with anti-H3K27Ac (ab4729; Abcam), anti-H3K4Me1 (ab8895; Abcam), and anti-H3K4Me3 (ab8580; Abcam). Genomic DNA (input) was prepared by treating aliquots of chromatin with proteinase K, and heated for de-cross linking, followed by column-based DNA purification (28106, Qiagen).  An aliquot of chromatin underwent immunoprecipitation, after which decrosslinking was performed as above.
After recovering purified DNA, 5ng or more of DNA was used to generate libraries using the NEBNext Ultra Directional II DNA sequencing kit per the manufacturer’s instructions.


title: C2, sample RNA12

description: Control (fresh medium at 27°C)

value: 1 day post fertilisation


title: TS+SM2, sample RNA9

value: Stress Metabolites with repeated heat stress


title: SI 50% Apc Rep3


title: SM2, sample RNA10

description: Stress Metabolites at 27°C

value: SM

value: Stress Metabolites at 27C


title: M2_D8_input_S10

value: In vitro differentiated Th9 (d8)


title: M2_D8_K4me3_S9


title: M2_Naive_K27Ac_S28

value: naive T cells


title: M2_Naive_input_S21


title: M2_D8_K4me1_S2


title: set_1_d3_RNA_S2

value: In vitro differentiated Th9 (d3)


title: TS2, sample RNA7

description: Fresh medium with repeated heat stress


title: SI 90% Apc Rep1

value: VilCreER Apcfl/fl


title: TS1, sample RNA6

description: Fresh medium with repeated heat stress


title: SI 50% Apc Rep2

value: Female


title: SI 50% Apc Rep1


title: TS+SM1, sample RNA5


title: SI 75% Apc Rep2


title: M2_Naive_K4me1_S1


title: M2_D4_input_S7

value: In vitro differentiated Th9 (d4)


title: M2_D8_K27Ac_S14


title: M2_D4_K4me3_S23


title: C1, sample RNA3

description: Control (fresh medium at 27°C)

value: C

value: Control (fresh medium at 27C)


title: SI 25% Apc Rep3

value: Day 4


title: M2_D4_K4me1_S22


title: SM1, sample RNA2

description: Stress Metabolites at 27°C


title: M2_D3_input_S20


title: M2_D4_K27Ac_S8


title: SI 25% Apc Rep2


title: M2_D3_K4me3_S15


title: M2_D3_K4me1_S19


title: M2_D3_K27Ac_S17


title: IC21

city: Rotterdam

first: Andre

last: Boonstra

state: Zuid-Holland

address: Wytemaweg 80

department: Gastroenterology & Hepatology

institute: Erasmus MC

data_processing:
Raw paired-end reads were aligned to human reference genome hg38 downloaded from the USCS Genome Bioinformatics site using the STAR (v.2.7.3a).
Picard tools were employed to detect at least 10 million reads in protein coding mRNA regions for downstream analysis.
Quantification of gene expression was calculated using featureCounts (v.1.4.6-p1), converted to reads per kilobase per million mapped reads (RPKM) using the R package edgeR.
Subsequently, scores were calculated for gene sets from MSigDB v7 using the R GSVA package.
Gene counts per sample were used to perform differentialgene expression analysisbetween groups using the DESeq2 package (v.1.30.1).
Assembly: human reference genome hg38
Supplementary files format and content: Excel file RPKM

source_name: Liver

extract_protocol:
Eight 10 µm-thick core needle liver biopsies were sectioned, deparaffinized, and total RNA was isolated using the RNeasy FFPE Kit (Qiagen, Germany) following the manufacturer’s instructions. rRNA was depleted using the Illumina Ribo-Zero rRNA Depletion kit (Illumina, USA) following the manufacturer’s instructions, and fragmented into approximately 300 basepairs (bp)
cDNA libraries for each sample were prepared using Illumina TrueSeq Total Gold
RNA-seq using 100 bp paired-end reads on Illumina HiSeq platform

tag: disease state

value: chronic HBV, phase IC

value: Liver


title: IC22


title: SI 10% Apc Rep3

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts


title: M1_Naive_K27Ac_S28


title: M1_Naive_K4me3_S18


title: IC23


title: SI 10% Apc Rep2


title: M1_Naive_K4me1_S1


title: IA15

value: chronic HBV, phase IA


title: M1_D8_input_S10


title: M1_D8_K4me1_S2


title: M1_D8_K4me3_S9


title: SI 10% Apc Rep1

value: Male


title: M1_D8_K27Ac_S14


title: IA13


title: Day4 M Liver Rep3

treatment_protocol: Induction of genetic recombination was performed with AAV8.TBG.Cre, administered via intravenous tail vein injections at either 6.4X10e8 GC/ml or 2X10e11 GC/ml to target mutant alleles in the liver. Tissues were harvested at the timepoints specified.

value: AAV8Cre DM-Myc/DM-Myc


title: Day4 M Liver Rep2


title: IA12


title: M1_D4_K4me3_S23


title: M1_D4_input_S7


title: M1_D4_K4me1_S22


title: Day4 M Liver Rep1


title: IA11


title: SI 25% Apc Rep1


title: M1_D3_input_S20


title: M1_Naive_input_S21


title: M1_D4_K27Ac_S8


title: Day4 Bcat+M Liver Rep5

value: AAV8Cre BcateninEx3/+ DM-Myc/DM-Myc


title: M1_D3_K4me3_S15


title: IA10


title: M1_D3_K4me1_S19


title: IA14


title: mouse2_ATAC_s03

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422
Redundant paired end (PE) reads were removed using fastquniq
PE reads of 50 bases were aligned to the mouse genome build mm10 or human build hg19 with Bowtie 0.12.8, following the guidelines presented by Buenrostro et al.
Customized python scripts were used to calculate fragment length of each pair of uniquely mapped PE reads for size distribution analysis, and to group uniquely mapped reads into bins of 0 to 175 bases and 180 to 250 bases, respectively.
UCSC Genome Browser viewable and normalized BigWig files were generated with the Hypergeometric Optimization of Motif EnRichment program (HOMER) version 4.8. Only one mapped read to each unique region of the genome that was less than 175 bp was kept and used in peak calling.
Regions of open chromatin were identified by MACS (version 1.4.2) using a p-value threshold of 1 × 10−5. Only regions called in both replicates were used in downstream analysis. Peak intensities (“tags” column) were normalized as tags per 10 million reads (RP10M) in the original library. Signal across all sites (i.e., all annotated genes and all accessible chromatin regions) was analyzed to eliminate potential bias by pre-selection.
Assembly: mm10 (mouse), hg19 (human)
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Omni-ATAC-seq sample preparation was performed as previously described. After flow cytometric sorting, 50,000 cells were lysed with 50 µl cold ATAC-Resuspension buffer (RSB) (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20) with 0.1% NP40, and 0.01% Digitonin on ice for 3 min. Lysis was stopped with 1 mL cold ATAC-RSB.
After centrifugation (500×g for 10 min), nuclei were resuspended in 50μl transposition reaction containing 2.5μl Tn5 transposase (FC-121–1030; Illumina) to tag and fragmentalize accessible chromatin. The reaction was incubated at 37°C, 400rpm for 30 min; DNA was then purified using a MinElute kit (QIAGEN) and amplified with 8–12 cycles of PCR based on the amplification curve. Samples were purified using a MinElute kit, sequenced on a NovaSeq 6000, paired end, 50 cycles


title: ENEG15

value: chronic HBV, phase ENEG


title: mouse2_ATAC_s04


title: mouse2_ATAC_s02


title: Day4 Bcat+M Liver Rep3


title: ENEG16


title: Day4 Bcat+M Liver Rep1


title: mouse1_ATAC_s04


title: mouse1_ATAC_s03


title: M1_D3_K27Ac_S17


title: ENEG14


title: Day4 Bcat+M Liver Rep2


title: mouse2_ATAC_s01


title: mouse1_ATAC_s02


title: Day4 Bcat+ Liver Rep4

value: AAV8Cre BcateninEx3/+


title: ENEG13


title: mouse1_ATAC_s01


title: Day4 Bcat+ Liver Rep3


title: Day4 Bcat+M Liver Rep4


title: ENEG11


title: Day4 Bcat+ Liver Rep2


title: Injured Young H12

city: Saint Louis

first: Jonathan

last: Kipnis

state: MO

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: RNA was isolated from 5 mice

data_processing:
Demultiplexing with custom Python and perl script
Aligned to the Ensembl release 76 top-level assembly with STAR version 2.5.1a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5
Assembly: mm10
Supplementary files format and content: raw gene counts for all cells

source_name: Spinal cord meninges

extract_protocol:
For the contusion injury, mice were anesthetized with ketamine (100 mg/kg)-xylazine (10 mg/kg) mixture. A 15-mm midline skin incision was made, and the connective tissue and muscles were bluntly dissected to expose T6-T13. Laminectomy was performed at T9 to expose the dorsal spinal cord, and the vertebral column was stabilized with angled clamps attached to the T7 and T12 transverse processes. The contusion injury was delivered using an Infinite Horizon Impactor (IH-0400 Impactor) with a force of 90 dynes. After injury, the muscles and skin were sutured separately. Mice were humanely euthanized with an intraperitoneal injection of a lethal dose of Euthasol® (10% v/v), followed by transcardiac perfusion of PBS with 5 U/mL of Heparin. Vertebral columns were obtained. The ventral bone of the vertebrae was cut laterally and was removed to expose the spinal cord. Nervous tissue was carefully dissected from the bone using fine forceps to release the dorsal root ganglia surrounded by the meninges. The meninges was cut along the ventral side and peeled from the spinal cord. Spinal cord meninges was enzymatically digested in RPMI containing 1 mg/mL collagenase VIII, 0.5 mg/mL DNase I, and 2% FBS for 30 minutes at 37°C with shaking. Samples were passed through a 70 µm filter to obtain single-cell suspensions, washed with FACS buffer, and pelleted at 380 xg for 5 minutes. Cells were resuspended in FACS buffer with 1:100 CD16/32 Fc block. They were stained with CD31, CD45, Podoplanin and Lyve1, washed, and resuspended in DAPI-containing FACS buffer. Single meningeal lymphatic endothelial cells were sorted as Live (DAPI-) CD45- CD31+ PDPN+ Lyve1+ cells using a FACS Aria II. Individual cells were sorted into 96-well plates containing 2 µL of 10X RNA lysis buffer (Takara) and 5% RNAse out (Takara) and rapidly frozen over dry ice.
Library preparation was performed with 2 µL of single cell lysates arrayed in 96-well PCR plates. ds-cDNA was prepared using a protocol adapted from the Takara-Clontech SMARTer methods. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified using a standard Illumina i7 primer to introduce an index sequence and FACSseq Lib PCR 1.0 specific to fragments containing the cell barcode added during cDNA synthesis. Fragments were sequenced on an Illumina NovaSeq.

value: Spinal cord meninges

tag: age

value: 3 months

value: Lymphatic endothelial cells

value: female

tag: sample group

value: Injured


title: Injured Young H11

description: RNA was isolated from 5 mice


title: Injured Young H10

description: RNA was isolated from 5 mice


title: Injured Young H9

description: RNA was isolated from 5 mice


title: Day4 Bcat+ Liver Rep1


title: Injured Young H7

description: RNA was isolated from 5 mice


title: Injured Young H6

description: RNA was isolated from 5 mice


title: Injured Young H4

description: RNA was isolated from 5 mice


title: Day10 WT Liver Rep3

value: WT

value: Day 10


title: Day10 WT Liver Rep2


title: Injured Young H3

description: RNA was isolated from 5 mice


title: Injured Young H1

description: RNA was isolated from 5 mice


title: Injured Young H2

description: RNA was isolated from 5 mice


title: ENEG6


title: ENEG7


title: ENEG12


title: Day10 M Liver Rep4


title: Injured Young G12

description: RNA was isolated from 5 mice


title: ENEG5


title: Injured Young G10

description: RNA was isolated from 5 mice


title: Injured Young G11

description: RNA was isolated from 5 mice


title: ENEG10


title: Day10 M Liver Rep3


title: Injured Young H8

description: RNA was isolated from 5 mice


title: ENEG4


title: Day10 M Liver Rep2


title: Injured Young G8

description: RNA was isolated from 5 mice


title: Injured Young G9

description: RNA was isolated from 5 mice


title: Injured Young H5

description: RNA was isolated from 5 mice


title: Injured Young G7

description: RNA was isolated from 5 mice


title: ENEG8


title: Day10 M Liver Rep1


title: Injured Young G6

description: RNA was isolated from 5 mice


title: ENEG9


title: Injured Young G5

description: RNA was isolated from 5 mice


title: Day10 WT Liver Rep1


title: Day10 Bcat Liver Rep3

value: AAV8Cre BcateninEx3/BcateninEx3


title: Injured Young G3

description: RNA was isolated from 5 mice


title: Injured Young G1

description: RNA was isolated from 5 mice


title: Day10 Bcat Liver Rep2


title: Injured Young G4

description: RNA was isolated from 5 mice


title: IC20


title: ENEG1


title: Day10 Bcat Liver Rep1


title: Injured Young F11

description: RNA was isolated from 5 mice


title: Injured Young G2

description: RNA was isolated from 5 mice


title: IC19


title: Injured Young F10

description: RNA was isolated from 5 mice


title: ENEG3


title: Injured Young F9

description: RNA was isolated from 5 mice


title: IC18


title: Day10 Bcat+M Liver Rep3


title: Injured Young F8

description: RNA was isolated from 5 mice


title: IC17


title: Injured Young F7

description: RNA was isolated from 5 mice


title: Day10 Bcat+M Liver Rep2


title: Injured Young F2

description: RNA was isolated from 5 mice


title: Day10 Bcat+M Liver Rep1


title: Day10 Bcat+ Liver Rep2


title: Injured Young F6

description: RNA was isolated from 5 mice


title: Injured Young F3

description: RNA was isolated from 5 mice


title: Injured Young F5

description: RNA was isolated from 5 mice


title: ENEG2


title: Injured Young F4

description: RNA was isolated from 5 mice


title: IC15


title: IC16


title: IC14


title: Day10 Bcat+ Liver Rep3


title: Injured Young E10

description: RNA was isolated from 5 mice


title: IC13


title: Injured Young E11

description: RNA was isolated from 5 mice


title: Injured Young F12

description: RNA was isolated from 5 mice


title: Day10 Bcat+ Liver Rep1


title: IC12


title: Injured Young E7

description: RNA was isolated from 5 mice


title: Injured Young E8

description: RNA was isolated from 5 mice


title: Injured Young E9

description: RNA was isolated from 5 mice


title: Injured Young E6

description: RNA was isolated from 5 mice


title: Day10 ApcM Liver Rep5

value: AAV8Cre Apcfl/fl DM-Myc/DM-Myc


title: IC11

value: chronic HBV, phase IC


title: Day10 ApcM Liver Rep3

value: Liver


title: Day10 ApcM Liver Rep4


title: Injured Young E5

description: RNA was isolated from 5 mice


title: Day10 ApcM Liver Rep2


title: IC10


title: Injured Young E3

description: RNA was isolated from 5 mice


title: Injured Young F1

description: RNA was isolated from 5 mice


title: Injured Young E12

description: RNA was isolated from 5 mice


title: IC9


title: Injured Young E4

description: RNA was isolated from 5 mice


title: Day10 ApcM Liver Rep1


title: Injured Young E2

description: RNA was isolated from 5 mice


title: Day10 Apc Liver Rep4

value: AAV8Cre Apcfl/fl


title: Injured Young D12

description: RNA was isolated from 5 mice


title: Injured Young E1

description: RNA was isolated from 5 mice


title: IC7


title: IC6


title: Day10 Apc Liver Rep3

value: Male


title: Injured Young D8

description: RNA was isolated from 5 mice


title: Injured Young D9

description: RNA was isolated from 5 mice


title: Injured Young D11

description: RNA was isolated from 5 mice


title: Injured Young D10

description: RNA was isolated from 5 mice


title: Injured Young D7

description: RNA was isolated from 5 mice


title: IC5


title: Day10 Apc Liver Rep2


title: Day10 Apc Liver Rep1


title: Injured Young D4

description: RNA was isolated from 5 mice


title: Injured Young D5

description: RNA was isolated from 5 mice


title: IC4


title: Injured Young D6

description: RNA was isolated from 5 mice


title: HEART_cKO_4

city: London

first: Athanasia

last: Stathopoulou

address: 30 Guilford Street

institute: University College London

description:
E19.8-heart
Chd7vsControl.complete_HEART_original file.xlsx

data_processing:
For SHF samples: Raw data were demultiplexed and converted to fastq files using Illumina’s bcl2fastq Conversion Software (v2.18) on BaseSpace. Reads were then aligned to the mouse reference genome (UCSC mm10) using STAR (v2.5.0b) on the BaseSpace RNA-seq alignment app (v1.1.0, Illumina). Reads per transcript were counted using HTSeq (RnaReadCounter by Illumina) and differential expression was estimated using the BioConductor package DESeq2 on BaseSpace app (v1.0.0).
For HEART samples: We built a Galaxy pipeline which first pre-processed the data, removing any Illumina adapter contamination and poor quality base-calls using fastp (v0.20.1) before aligning reads to the mouse genome (UCSC mm10) with RNA STAR (v2.7.2b). Once aligned, reads were counted for each gene using featureCounts (v1.6.4). All sequence and annotation were obtained from the Illumina iGenomes repository. Counts were then used to perform DESeq2 differential expression analysis using the BioConductor tool (v1.3.2).
Assembly: UCSC mm10
Supplementary files format and content: For SHF samples: the average FPKMs of Chd7Mut and Control groups
Supplementary files format and content: For Heart RNASeq: read count of each gene and each sample

source_name: OFT and Heart tube

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro kit, with gDNA eliminator column.
For SHF samples: Five control (Mesp1-Cre) and six cKO (Mesp1-Cre; Chd7fl/fl) samples were processed using the KAPA RNA HyperPrep Kit with RiboErase according to manufacturer’s instructions. ERCC RNA Spike-In Mix was added to all RNA samples. For HEART samples: Four control (Mesp1-Cre) and four cKO (Mesp1-Cre; Chd7fl/fl) samples were processed using the KAPA mRNA HyperPrep kit.

value: OFT and Heart tube

tag: developmental stage

value: E9.5 tissue

value: cKO


title: Injured Young D2

description: RNA was isolated from 5 mice


title: HEART_cKO_3

description:
E8.4-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: IC3


title: IC8


title: IC2


title: HEART_cKO_1

description:
E12.3-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: Injured Young C9

description: RNA was isolated from 5 mice


title: Injured Young C12

description: RNA was isolated from 5 mice


title: Injured Young D3

description: RNA was isolated from 5 mice


title: IC1


title: Injured Young C10

description: RNA was isolated from 5 mice


title: Injured Young D1

description: RNA was isolated from 5 mice


title: Injured Young C11

description: RNA was isolated from 5 mice


title: IA9

value: chronic HBV, phase IA


title: Injured Young C8

description: RNA was isolated from 5 mice

value: Spinal cord meninges


title: Injured Young C7

description: RNA was isolated from 5 mice

value: 3 months


title: HEART_control_4

description:
E19.7-heart
Chd7vsControl.complete_HEART_original file.xlsx

value: control


title: HEART_control_3

description:
E8.5-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: Injured Young C6

description: RNA was isolated from 5 mice

value: Lymphatic endothelial cells

value: female


title: Injured Young C5

description: RNA was isolated from 5 mice

value: Injured


title: Injured Young C4

description: RNA was isolated from 5 mice


title: Injured Young C3

description: RNA was isolated from 5 mice


title: IA7


title: Injured Young C2

description: RNA was isolated from 5 mice


title: IA6


title: HEART_control_2

description:
E13.3-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: HEART_control_1

description:
E18.4-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: IA5


title: Injured Young C1

description: RNA was isolated from 5 mice


title: Injured Young B12

description: RNA was isolated from 5 mice


title: HEART_cKO_2

description:
E12.7-heart
Chd7vsControl.complete_HEART_original file.xlsx


title: SHF_cKO_6

description:
NM0281_E22_4-Mu6
Chd7Mut_vs_Control.gene_exp_SHF.xlsx

source_name: Dissected distal pharyngeal apparatus, SHF


title: Injured Young B11

description: RNA was isolated from 5 mice


title: IA4


title: Injured Young B9

description: RNA was isolated from 5 mice


title: Injured Young B10

description: RNA was isolated from 5 mice


title: SHF_cKO_4

description:
NM0279_E19_8-Mut4
Chd7Mut_vs_Control.gene_exp_SHF.xlsx

value: Dissected distal pharyngeal apparatus, SHF


title: IA3


title: IA2


title: Injured Young B6

description: RNA was isolated from 5 mice


title: SHF_cKO_5

description:
NM0280_E20_4-Mut5
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: IA8


title: Injured Young B7

description: RNA was isolated from 5 mice


title: SHF_cKO_3

description:
NM0278_E12_7-Mut3
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young B5

description: RNA was isolated from 5 mice


title: SHF_cKO_2

description:
NM0277_E12_3-Mut2
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young B4

description: RNA was isolated from 5 mice


title: IA1


title: SHF_cKO_1

description:
NM0276_E8_4-Mut1
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young B3

description: RNA was isolated from 5 mice


title: IT14

value: chronic HBV, phase IT


title: Injured Young B1

description: RNA was isolated from 5 mice


title: Injured Young A12

description: RNA was isolated from 5 mice


title: SHF_control_5

description:
NM0274_E19_7-Ctr5
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: IT15


title: Injured Young A11

description: RNA was isolated from 5 mice


title: IT12


title: SHF_control_4

description:
NM0273_E18_4-Ctr4
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young B8

description: RNA was isolated from 5 mice


title: Injured Young A8

description: RNA was isolated from 5 mice


title: IT11


title: SHF_control_3

description:
NM0275_E19_9-Ctr6
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young A9

description: RNA was isolated from 5 mice


title: SHF_control_2

description:
NM0271_E13_3-Ctr2
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young A7

description: RNA was isolated from 5 mice


title: IT10


title: Injured Young A4

description: RNA was isolated from 5 mice


title: Injured Young A3

description: RNA was isolated from 5 mice


title: SHF_control_1

description:
NM0270_E8_5-Ctr1
Chd7Mut_vs_Control.gene_exp_SHF.xlsx


title: Injured Young A6

description: RNA was isolated from 5 mice


title: IT9


title: Injured Young A1

description: RNA was isolated from 5 mice


title: Injured Young B2

description: RNA was isolated from 5 mice


title: IT8


title: Injured Old H12

description: RNA was isolated from 3 mice

value: 24 months


title: Injured Young A10

description: RNA was isolated from 5 mice


title: Injured Old H11

description: RNA was isolated from 3 mice


title: Injured Old H9

description: RNA was isolated from 3 mice


title: Injured Old H8

description: RNA was isolated from 3 mice


title: Injured Old H7

description: RNA was isolated from 3 mice


title: Injured Young A5

description: RNA was isolated from 5 mice


title: IT6