title: Input_ADE_d6H+

description:
Library name: Sample 20
Input fragmented chromatin from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Positive Population)

data_processing:
For each sample (ADE D3-6 ChIP-seq and ADE Day 6 inputs), multiple raw .Fastq files were merged together and mapped to the mouse genome (mm9) using bowtie2 with the following options (--local -D 20 -R 3 -N 1 -L 20 -i S,1,0.50) (PMID - 22388286). Using the HOMER package (PMID - 20513432), SAM files were converted into tag directories and multi-mapping reads were removed using makeTagDirectory (parameters: -unique -fragLength 150). Mapped regions that, due to fragment processing, extended beyond the end of the chromosomes were removed using removeOutOfBoundsReads.pl. For visualisation, genome browser files (.bigWig) were generated using makeUCSCfile with the following options (-bigWig -fsize 1e20) with normalisation (-norm) set to 4M and 10M reads for H3K4me3 and H3K27me3 respectively.
Assembly: mm9
Supplementary files format and content: .bigWig files contain information on both the genomic distribution and signal strength of the mapped reads (representative of the sample composition). .bigWig files are in an indexed binary format.

extract_protocol:
Native ChIP was performed on 0.5–1M flow sorted ADE cells and immunopurified with either anti-H3K4me3 (07–473; Millipore) or anti-H3K27me3 (07–449; Millipore) as previously described (PMID: 27723457).
ChIP libraries were prepared according to (PMID: 22855832) with modifications described in (PMID: 27723457). Independent replicate sample libraries (n = 2/3) were combined into equimolar pools prior to sequencing. Library PCRs were supplemented with 2× SYBR dye (Sigma S9430) so that amplification could be monitored by quantitative PCR on a Roche LightCycler 480. ChIP/Input libraries were sequenced individually or as multi-sample pools distinguished using single end barcoding primers (NEBNext multiplex oligos for Illumina, set 1-4). Libraries were sequenced on an Illumina Hi-seq 4000 system following the standard Illumina protocol to generate single-end 42 or 49 bp reads (BGI or The Danish National High-Throughput DNA Sequencing Centre).

tag: chip antibody


title: Input_ADE_d6H-

status: Public on Jan 13 2025

type: SRA

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
Library name: Sample 19
Input fragmented chromatin from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Negative Population)

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

source_name: Hex-RS; Gsc-GFP (B6) Dual Fluoresecent Reporter mESCs

growth_protocol: Dual reporter ESCs were cultured in ESC medium + LIF as previously described (PMID: 27723457) and differentiated according to our standard ADE differentiation protocol (PMID: 26840225). To generate sufficient cells for Fluorescence Activated Cell Sorting (FACS), ADE differentiation was performed in T75 flasks alongside a 6-well plate that was analysed by flow cytometry at ADE day 6 to monitor differentiation.

tag: cell line

tag: cell type

tag: treatment

value: ADE Differentiation


title: Embryo 2, control unoperated, 6h

status: Public on Jan 14 2025

city: Aberdeen

first: Lynda

last: Erskine

address: Foresterhill

department: School of Medicine, Medical Sciences and Nutrition

institute: University of Aberdeen

description:
Library name: E2-Control
Column name in Normalised_Counts_Sex.txt: E2.Control

library_source: transcriptomic

data_processing:
To assess the quality of the sequencing data, the reads were analysed with FastQC (version 0.11.8). All samples were shown to have a majority of high-quality reads and no evidence of adapter contamination. To remove any lower quality sequences, TrimGalore! (version 0.6.4)  was used to filter the reads with a phred quality score threshold of 30.
Reads were aligned to the chicken genome using HISAT2 (version 2.1.0) and SAMtools (version 1.9) used to process the alignments. Reads were quantified at gene regions using FeatureCounts (subread version 1.6.2) utilising the parameter to split multi-mapped reads as a fraction across all genes that they align to, and the parameter for stranded analysis.
Assembly: GRCg6a
Supplementary files format and content: tab-delimited text file includes normalised counts for each sample

molecule: total RNA

organism: Gallus gallus

source_name: optic cup

growth_protocol: Fertilised Dekalb white chicken eggs were incubated on their side in a humidified incubator at 37˚ C until Hamburger and Hamilton (HH) 23 (~E4).

extract_protocol:
RNA was prepared using TRIzol (Fisher Scientific) followed by purification and removal of genomic DNA using the Qiagen RNeasy mini kit with on-column DNase I digestion (Qiagen), according to the manufacturers’ instructions.
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit with unique dual indices and sequenced on an Illumina NextSeq 500 with v2.5 chemistry and 75 bp paired end reads.

treatment_protocol: Lenses were removed from one eye of HH23 (~E4) chicken embryos. The eggs were windowed and the membranes around the eye removed. Using forceps, a slit was made in the dorsal side of the eye and the lens grasped and gently removed. The eggs were sealed and reincubated for 6 hours. The retinas were dissected from the operated and contralateral, unoperated eyes and collected individually in RNAlater. Paired samples of operated and contralateral (unoperated) retinas were collected, with 5 biological replicates from different embryos.

tag: tissue

value: optic cup

tag: genotype

value: WT

value: control

tag: batch


title: H3K4me3_ChIP_ADE_d5G-

description:
Library name: Sample 14
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC Negative Population)

value: Hex-RS; Gsc-GFP (B6) Dual Fluoresecent Reporter mESCs

value: ADE Day 5 GSC Negative Population

value: anti-H3K4me3 (07–473; Millipore)


title: H3K4me3_ChIP_ADE_d5Ghigh

description:
Library name: Sample 16
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC High Population)

value: ADE Day 5 GSC High Population


title: H3K4me3_ChIP_ADE_d6H+

description:
Library name: Sample 18
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Positive Population)


title: Embryo 1, control unoperated, 6h

description:
Library name: E1-Control
Column name in Normalised_Counts_Sex.txt: E1.Control


title: H3K4me3_ChIP_ADE_d6H-

description:
Library name: Sample 17
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Negative Population)


title: H3K4me3_ChIP_ADE_d4G+

description:
Library name: Sample 13
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 4 GSC Positive Population)

value: ADE Day 4 GSC Positive Population


title: H3K4me3_ChIP_ADE_d4G-

description:
Library name: Sample 12
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 4 GSC Negative Population)

value: ADE Day 4 GSC Negative Population


title: H3K4me3_ChIP_ADE_d3G-

description:
Library name: Sample 10
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 3 GSC Negative Population)

value: ADE Day 3 GSC Negative Population


title: H3K27me3_ChIP_ADE_d6H+

description:
Library name: Sample 9
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Positive Population)

value: anti-H3K27me3 (07–449; Millipore)


title: H3K27me3_ChIP_ADE_d6H-

description:
Library name: Sample 8
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 6 GSC Positive HHEX Negative Population)


title: H3K4me3_ChIP_ADE_d5Glow

description:
Library name: Sample 15
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC Low Population)

value: ADE Day 5 GSC Low Population


title: H3K4me3_ChIP_ADE_d3G+

description:
Library name: Sample 11
H3K4me3 ChIP-seq from ADE differentiated cells (ADE Day 3 GSC Positive Population)

value: ADE Day 3 GSC Positive Population


title: H3K27me3_ChIP_ADE_d5Ghigh

description:
Library name: Sample 7
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC High Population)


title: H3K27me3_ChIP_ADE_d5Glow

description:
Library name: Sample 6
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC Low Population)


title: H3K27me3_ChIP_ADE_d4G+

description:
Library name: Sample 4
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 4 GSC Positive Population)


title: 4sU_ADE_d4G-_rep1

description:
Library name: Sample 7
4sU-seq. 4sU labelled RNA isolated from ADE differentiated cells (ADE Day 4 GSC Negative Population)

library_source: other

data_processing:
Mapping and manipulation of 4sU-seq data from the ADE differentiation. Following demultiplexing (performed by the sequencing facility - BGI), .Fastq files were aligned to the mouse genome (mm9 build) using Bowtie2 v2.2.6 for paired-end sequence data with default settings. The resulting .SAM alignment files were converted into tag directories using the HOMER package (v4.8) using the ‘makeTagDirectory’ function with the following parameters (-format sam -flip –sspe; PMID: 20513432). Genomic intervals that extended beyond the end of the chromosomes were removed using the ‘removeOutOfBoundsReads.pl’ function. Strand-specific browser track files in .bigWig format were generated per replicate using ‘makeUCSCfile’ with the following parameters (-fsize 1e20 -strand +/− -norm 5e7 -lastTag -color 25,50,200).
Assembly: mm9
Supplementary files format and content: .bigWig files contain information on both the genomic distribution, strand-specific expression and signal strength of the mapped reads (representative of the sample composition). .bigWig files are in an indexed binary format.

molecule: other

extract_protocol:
4sU incubation was performed in ADE differentiation medium (ADEM; see PMID: 26840225) from the T75 flasks to be used for FACS sorting. To obtain the ADEM, 15 ml of ADEM was pipetted from each T75 flask, flasks were returned to the incubator and the extracted ADEM was pooled and centrifuged at 1000 g for 5 mins to remove cell debris. In the following steps, flasks were treated in the same order for every action taken in batches of up to 6 flasks to avoid timing differences between flasks. After aspiration, 5 ml pooled ADEM (negative control; 1-2 flasks per sort) or 5 ml pooled ADEM containing 500 μM 4sU were added and flasks were then returned to the incubator. After exactly 20 mins, flasks were aspirated, washed with 10 ml PBS (Merck, D8537), aspirated again and incubated for 3 min at 37°C in 2 ml per flask of attenuated trypsin (0.025% (v/v) trypsin (Thermo Fisher Scientific, 15090–046), 1.27 mM EDTA, and 1% (v/v) Chicken serum (Merck C5405) in PBS (Merck D8537)). Cells were then released from the flask by tapping and attenuated trypsin was inactivated by adding 8 ml ice-cold flow cytometry buffer (FC buffer - 10% FCS in PBS). Cell suspensions from all flasks with the same treatment in the batch were then pooled, pipetted repeatedly to obtain a single cell suspension, counted using a hemocytometer (Neubauer) and stored on ice. This process was repeated when required (for day 3 & day 4 samples) until a sufficient number of cells were obtained for the sorting procedure 100M cells). All centrifugation steps hereafter were performed at 400 g for 3 mins. Samples were centrifuged, aspirated, resuspended in ice-cold FC buffer at 1-1.5 x 107 cells/ml and passed through a cell strainer (Corning, 352235). Negative control cells were not sorted and kept on ice during the sorting procedure. 4sU-labelled cells were sorted on a BD FACSAriaIII into 5 ml Falcon tubes (Corning) at 4°C containing 1 ml of ice-cold FC buffer. After sorting 1 million cells, the tube was transferred to ice in the dark and replaced with a fresh 5 ml Falcon tube containing 1 ml of ice-cold FC buffer and this process was repeated until all 4sU-labelled cells were sorted. Samples were centrifuged, resuspended in 100 μl of ice-cold PBS and cells from the same population were pooled to obtain an equal number of cells for each population, equivalent to the population that generated the lowest number of cells and an identical number of cells was taken from the unsorted and unlabelled negative control sample. All samples were then transferred to 1.5 ml DNA LoBind tubes (Eppendorf, Enfield, CT 06082), added up to 1 ml using ice-cold PBS, centrifuged, aspirated and agitated to resuspend cells in the remaining PBS (<10 μl). Cells were lysed by adding 1 ml of Trizol reagent (Thermo Fisher Scientific) equilibrated to RT. After 5 mins of incubation at RT, samples were stored at -20 ºC. 4sU incorporated RNAs were isolated as previously described (PMID: 32439634; as adapted from PMID: 25811895).
Ribosomal RNA was depleted from the purified RNA using the low-input RiboMinus eukaryote system v2 kit according to the manufacturer's instructions (Ambion A15027). Libraries were constructed using the NEBNext Ultra II directional RNA library preparation kit for Illumina according to the protocol for ribosome-depleted RNA and with an 11-min RNA fragmentation step (NEB E7760). Library PCRs were supplemented with 2× SYBR dye (Sigma S9430) so that amplification could be monitored by quantitative PCR on a Roche LightCycler 480. Individual libraries were pooled into two six-sample equimolar pools containing the indexes 3-8 (NEBNext multiplex oligos for Illumina, set 1, E7335) and deep-sequenced at BGI on a HiSeq4000 (paired-end 100-bp reads).


title: H3K27me3_ChIP_ADE_d3G+

description:
Library name: Sample 2
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 3 GSC Positive Population)


title: H3K27me3_ChIP_ADE_d5G-

description:
Library name: Sample 5
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 5 GSC Negative Population)


title: KOBQ3

type: RNA

city: Nagasaki

first: Koji

last: Ando

state: Nagasaki

address: 1-12-7 Sakamoto

department: hematology

country: Japan

institute: Nagasaki University

description: KOB with JQ1

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Processed signal intensities were normalized by the global scaling method.  A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor.

organism: Homo sapiens

source_name: KOB, 18hr, JQ1, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: KOB  cells were cultured in RPMI 1640 supplemented with 20% (v/v) fetal bovine serum (FBS) and 1 ng/mL interleukin-2 (IL-2; Cosmo Bio Co., Tokyo, Japan) in a T-75 flask. ST-1 cells were cultured under the same conditions but without IL-2.

extract_protocol: the Pure Link RNA Mini Kit (Invitrogen, Carlsbad, CA, USA) was used to isolate the total RNA, which was then purified using DNase I.

treatment_protocol: KOB or ST1 with JQ1 or DMSO, respectively, and cultured in RPMI 1640 medium supplemented with 10% heat-inactivated fetal bovine serum.  Cultures were incubated at 37°C for 16 hours in a 5% CO2 humidified incubator.

value: Cell line

tag: gender

value: ATL derived cell lines


title: KOBD3

description: KOB with DMSO

source_name: KOB, 18hr, DMSO, replicate 3


title: KOBD1

description: KOB with DMSO

source_name: KOB, 18hr, DMSO, replicate 1


title: KOBQ2

description: KOB with JQ1

source_name: KOB, 18hr, JQ1, replicate 2


title: STD3

description: ST1 with DMSO

source_name: ST1, 18hr, DMSO, replicate 3


title: KOBQ1

description: KOB with JQ1

source_name: KOB, 18hr, JQ1, replicate 1


title: STD2

description: ST1 with DMSO

source_name: ST1, 18hr, DMSO, replicate 2


title: control 5, biol rep 5, 5 dpf, 5 fish pooled

city: Ghent

first: Michiel

last: Vanhooydonck

address: Corneel Heymanslaan  10

department: Biomolecular medicine

country: Belgium

institute: Ghent University

data_processing:
Read quality was verified using FastQC v0.11.9 (default values)
followed by adapter trimming with Trim Galore v0.6.6 (default values)
FeatureCounts package from SubRead v2.0.0 was used for count estimation per gene (default values)
Duplication levels were evaluated using the DupRadar package (default values)
along with additional control statistics provided by MultiQC v1.9 (default values)
Assembly: GRCz11
Supplementary files format and content: Tab-delimited text file includes ra counts for each sample

organism: Danio rerio

source_name: pool of 5 whole embryos

growth_protocol: Embryos were grown at 27°C in E3 medium with methylene blue until 5 days post fertilization (dpf). At 1 and 3 dpf, medium was refreshed.

extract_protocol:
the Rneasy® minikit (Qiagen) was used following manufacturers guidelines
the TruSeq Stranded Total RNA kit (Illumina) was used following manufacturers guidelines, 200 ng of total mrRNA was used for the consctruction of the sequencing libraries

value: pool of 5 whole embryos

value: wild type

tag: age

value: 5 days post fertilization


title: control 3, biol rep 3, 5 dpf, 5 fish pooled


title: control 4, biol rep 4, 5 dpf, 5 fish pooled


title: control 2, biol rep 2, 5 dpf, 5 fish pooled


title: qKO 3, biol rep 3, 5 dpf, 5 fish pooled

value: qKO


title: qKO 4, biol rep 4, 5 dpf, 5 fish pooled


title: STQ2

description: ST1 with JQ1

source_name: ST1, 18hr, JQ1, replicate 2


title: qKO 2, biol rep 2, 5 dpf, 5 fish pooled


title: STQ1

description: ST1 with JQ1

source_name: ST1, 18hr, JQ1, replicate 1


title: H3K27me3_ChIP_ADE_d4G-

description:
Library name: Sample 3
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 4 GSC Negative Population)

value: ADE Differentiation


title: STD1

description: ST1 with DMSO

source_name: ST1, 18hr, DMSO, replicate 1


title: qKO 5, biol rep 5, 5 dpf, 5 fish pooled


title: control 1, biol rep 1, 5 dpf, 5 fish pooled


title: KOBD2

description: KOB with DMSO

source_name: KOB, 18hr, DMSO, replicate 2


title: H3K27me3_ChIP_ADE_d3G-

description:
Library name: Sample 1
H3K27me3 ChIP-seq from ADE differentiated cells (ADE Day 3 GSC Negative Population)

value: Hex-RS; Gsc-GFP (B6) Dual Fluoresecent Reporter mESCs


title: HepG2_NTC_3

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression of liver cancer cell lines treated with nonsense-siRNA, replicate 3

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 15, from SAS. Gene expression profiling was performed using arrays of Human HuGene-2_0-st from Thermo Fischer Scientific. A Custom CDF Version 21 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: biotin

source_name: Liver cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Subconfluent HepG2 cells were used for transfection. Cells were seeded 24 hours before transfection.

extract_protocol: Total RNA was isolated 24 hours after transfection using the NucleoSpin RNA II kit (Macherey-Nagel, Düren, Germany). Only samples with an RNA integrity number (RIN)>7 were considered for expression profiling.

treatment_protocol: SiRNAs were transfected using the Lipofectamine RNAiMAX transfection reagent (Invitrogen/Thermo Fisher) according to the manufacturer’s instructions.

tag: group

value: nonsense-siRNA treated cells


title: HepG2_MPP5_5_3

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP3 nhibition, replicate 3


title: qKO 1, biol rep 1, 5 dpf, 5 fish pooled


title: HepG2_MPP5_3_3

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP5 inhibition, replicate 3


title: STQ3

description: ST1 with JQ1

source_name: ST1, 18hr, JQ1, replicate 3


title: HepG2_NTC_2

description: Gene expression of liver cancer cell lines treated with nonsense-siRNA, replicate 2


title: HepG2_MPP5_5_2

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP3 nhibition, replicate 2


title: HepG2_UTC_1

description: Gene expression of liver cancer cell lines untreated, replicate 1

value: untreated cells


title: HepG2_NTC_1

description: Gene expression of liver cancer cell lines treated with nonsense-siRNA, replicate 1


title: HepG2_MPP5_3_2

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP5 inhibition, replicate 2


title: HepG2_MPP5_5_1

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP3 nhibition, replicate 1


title: ChIPseq-SET11-SDG2(H1866K)cd-input-rep3

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

country: USA

institute: University of California, Los Angeles

data_processing:
The ChIP-seq raw reads were filtered and trimmed using trim_galore (v0.6.5).
Mapping to the reference genome (TAIR10) with Bowtie2 (v2.1.0).
The duplicated reads were removed by using the Samtools (v1.9), and the tracks were generated by using deeptools (v3.1.3).
MACS2 (v2.2.1) was used to call peaks.
Assembly: Tair10
Supplementary files format and content: bigwig file
Supplementary files format and content: narrowPeak

organism: Arabidopsis thaliana

source_name: Arabidopsis leaf tissue

growth_protocol: Arabidopsis plants of the Columbia-0 (Col-0) ecotype were used in this study. All plants were grown under green house condition (16 hour light and 8 hour dark at 22C). Leaf tissues were collected from 4-5 week plants

extract_protocol:
Total RNA was extracted from 4-5 week old leaf tissue from each sample by using Zymo RNA extraction kit. ChIP-seq libraries were prepared by using the Ovation Ultra Low System V2 kit (NuGEN). Genomic DNA was extracted by using the CTAB-based DNA extraction.
1 ug RNA was used to prepare the RNA-seq library by following Illumina kit. Three grams of Arabidopsis leaf tissue (4-5 week old) of each sample were used for ChIP experiment. 10 minutes cross-link with 1% formaldehyde. The chromatin was sheared with Biorupter with 26 cycles. 500 ng DNA of each sample was sheared at 4°C for 2 min by using Covaris, and the WGBS library construction used Kapa DNA Hyper Kit (Roche) and TruSeq DNA UD indexes for Illumina (Illumina)

value: Leaf tissue

value: 4-5 week old

tag: ecotype


title: ChIPseq-SET11-SDG2(H1866K)cd-input-rep2


title: ChIPseq-SET11-SDG2(H1866K)cd-input-rep1


title: HepG2_MPP5_3_1

description: Gene expression of liver cancer cell lines treated with siRNA wich caused MMP5 inhibition, replicate 1


title: ChIPseq-SET11-SDG2(H1866K)cd-H3K4me3-rep4


title: HepG2_UTC_3

description: Gene expression of liver cancer cell lines untreated, replicate 3


title: ChIPseq-SET11-SDG2(H1866K)cd-H3K4me3-rep3


title: ChIPseq-SET11-Col0-input-rep1


title: ChIPseq-SET11-Col0-H3K4me3-rep1


title: HepG2_UTC_2

description: Gene expression of liver cancer cell lines untreated, replicate 2


title: WGBS-SET2-rdd-Rep3

data_processing:
The raw paired-end sequencing reads from each sample were mapped to Arabidopsis reference genome TAIR10 using  BSMAP (v2.90)
The methylation level for each cytosine was determined by calculating the ratio of methylated cytosines (C) to the sum of methylated cytosines and unmethylated cytosines
Assembly: Tair10
Supplementary files format and content: bigwig
Supplementary files format and content: wig
Supplementary files format and content: txt

extract_protocol:
Genomic DNA was extracted by using the CTAB-based DNA extraction.
500 ng DNA of each sample was sheared at 4°C for 2 min by using Covaris, and the WGBS library construction used Kapa DNA Hyper Kit (Roche) and TruSeq DNA UD indexes for Illumina (Illumina)


title: ChIPseq-SET11-Col0-input-rep2


title: WGBS-SET2-rdd-Rep2


title: ChIPseq-SET11-Col0-H3K4me3-rep2


title: ChIPseq-SET11-SDG2(H1866K)cd-H3K4me3-rep1


title: WGBS-SET2-SDG2ZF-rdd-Rep1


title: WGBS-SET2-rdd-Rep1


title: WGBS-SET2-SDG2ZF-rdd-Rep3


title: WGBS-SET1-SDG2-ZF-Rep3


title: WGBS-SET2-SDG2ZF-rdd-Rep2


title: WGBS-SET1-Col0-Rep2


title: WGBS-SET1-SDG2-ZF-Rep1


title: ChIPseq-SET9-H3K4me3-TRBIP1-ZF-Rep2

extract_protocol:
Three grams of Arabidopsis leaf tissue (4-5 week old) of each sample were used for ChIP experiment. 10 minutes cross-link with 1% formaldehyde. The chromatin was sheared with Biorupter with 26 cycles.
ChIP-seq libraries were prepared by using the Ovation Ultra Low System V2 kit (NuGEN).


title: ChIPseq-SET9-H3K4me3-fwa-Rep2-R2


title: ChIPseq-SET9-input-TRBIP1-ZF-Rep2


title: ChIPseq-SET11-SDG2(H1866K)cd-H3K4me3-rep2


title: ChIPseq-SET8-H3K4me3-fwa-Rep1


title: ChIPseq-SET9-input-fwa-Rep2


title: ChIPseq-SET8-H3-TRBIP1-ZF-Rep1


title: ChIPseq-SET8-H3-fwa-Rep1


title: ChIPseq-SET11-SDG2(H1866K)cd-input-rep4


title: ChIPseq-SET7-myc-JMJ14xTRBIP1-ZF-Rep2

value: Anti-Myc


title: ChIPseq-SET7-myc-Col0-Rep2


title: ChIPseq-SET7-myc-ROS1xSDG2-ZF-Rep2


title: ChIPseq-SET7-myc-ROS1-Rep2


title: ChIPseq-SET8-H3K4me3-TRBIP1-ZF-Rep1


title: ChIPseq-SET7-H3K4me3-rdd-Rep2


title: ChIPseq-SET7-H3K4me3-SDG2-ZF_rdd-Rep2


title: ChIPseq-SET7-H3K14ac-SDG2-ZF_rdd-Rep2


title: ChIPseq-SET6-myc-JMJ14


title: ChIPseq-SET6-myc-JMJ14xTRBIP1-ZF-Rep1


title: ChIPseq-SET6-myc-Col0


title: ChIPseq-SET6-input-SDG2-ZF_rdd-Rep1


title: ChIPseq-SET7-input-SDG2-ZF_rdd-Rep2


title: ChIPseq-SET6-input-JMJ14xTRBIP1-ZF-Rep1


title: WGBS-SET1-Col0-Rep1


title: ChIPseq-SET6-input-JMJ14


title: ChIPseq-SET7-H3K14ac-rdd-Rep2


title: ChIPseq-SET6-input-Col0


title: ChIPseq-SET6-input-rdd-Rep1


title: ChIPseq-SET6-H3K4me3-SDG2-ZF_rdd-Rep1


title: ChIPseq-SET6-H2AZ-SDG2-ZF_rdd-Rep1


title: ChIPseq-SET6-H2AZ-rdd-Rep1


title: ChIPseq-SET5-input-SDG2-ZF-Rep2


title: ChIPseq-SET5-input-Col0-Rep2


title: ChIPseq-SET7-input-rdd-Rep2


title: ChIPseq-SET4-myc-ROS1xSDG2-ZF-Rep1


title: ChIPseq-SET5-H2AZ-Col0-Rep2


title: ChIPseq-SET5-H2AZ-SDG2-ZF-Rep2


title: ChIPseq-SET4-myc-ROS1-Rep1


title: ChIPseq-SET4-myc-Col0-Rep1


title: ChIPseq-SET4-input-ROS1xSDG2-ZF-Rep1


title: ChIPseq-SET4-input-SDG2-ZF-Rep3


title: ChIPseq-SET4-input-ROS1-Rep1


title: ChIPseq-SET4-input-Col0-Rep2


title: ChIPseq-SET4-H2AZ-SDG2-ZF-Rep3


title: ChIPseq-SET4-input-Col0-Rep1


title: ChIPseq-SET4-H2AZ-SDG2-ZF-Rep1


title: ChIPseq-SET4-input-SDG2-ZF-Rep1


title: ChIPseq-SET4-H2AZ-Col0-Rep1


title: ChIPseq-SET3-input-SDG2-ZF-Rep2


title: ChIPseq-SET3-input-SDG2-ZF-Rep1


title: ChIPseq-SET3-H3K14ac-SDG2-ZF-Rep1


title: ChIPseq-SET3-input-Col0-Rep1


title: ChIPseq-SET3-input-Col0-Rep2


title: ChIPseq-SET3-H3K14ac-SDG2-ZF-Rep2


title: ChIPseq-SET6-H3K4me3-rdd-Rep1


title: ChIPseq-SET3-H3K14ac-Col0-Rep2


title: WGBS-SET1-SDG2-ZF-Rep2


title: ChIPseq-SET3-H3K14ac-Col0-Rep1


title: ChIPseq-SET2-input-rdr6-Rep2


title: ChIPseq-SET2-input-rdr6-Rep1


title: ChIPseq-SET2-input-noguideSDG2_rdr6


title: ChIPseq-SET2-input-SunTag-SDG2_rdr6-Rep2


title: ChIPseq-SET2-input-SunTag-SDG2_rdr6-Rep1


title: ChIPseq-SET2-H3K4me3-rdr6-Rep2


title: ChIPseq-SET2-H3K4me3-noguideSDG2_rdr6


title: ChIPseq-SET10-H3K4me3-fwaxrdr6-Rep2


title: ChIPseq-SET2-H3K4me3-SunTag-SDG2_rdr6-Rep1


title: ChIPseq-SET2-H3K4me3-rdr6-Rep1


title: ChIPseq-SET10-H3K4me3-fwaxrdr6-Rep1


title: ChIPseq-SET10-H3K4me3-dCAS9-MQ1v


title: ChIPseq-SET10-H3K4me3-TRBIP1-dCAS9-MQ1v-Rep2


title: ChIPseq-SET10-H3K4me3-TRBIP1-dCAS9-MQ1v-Rep1


title: ChIPseq-SET1-input-SDG2-ZF-Rep1


title: ChIPseq-SET1-input-Col0-Rep2


title: ChIPseq-SET1-input-SDG2-ZF-Rep2


title: ChIPseq-SET1-input-Col0-Rep1


title: ChIPseq-SET1-input-SDG2-ZF-Rep3


title: ChIPseq-SET1-H3K4me3-SDG2-ZF-Rep2


title: ChIPseq-SET1-H3K4me3-Col0-Rep2


title: ChIPseq-SET1-H3K4me3-Col0-Rep1


title: ChIPseq-SET1-H3K4me3-SDG2-ZF-Rep1


title: P0+18h ureter cultures, Cyclopamine treated vs control, repl. #2

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2100 ng (M8165) or 700 ng (M8166), repectively,  of each fluorescently labelled cRNA were used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values (for each channel independently) to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:  normalized PSArray i = PSArray i x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control 2

label_protocol: 200 ng of total RNA equivalents were used to synthesize AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Thermo Fisher Scientific) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1), reaction volumes were halved, and just one round of T7 amplification was conducted.

extract_protocol: Extraction of total RNA was performed using the QIAGEN RNAeasy micro kit according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from newborn pups (P0) and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 10% FCS) containing 10µM Cyclopamine or in medium containing DMF (1:1000, control).

tag: strain

value: NMRI

value: wildtype

tag: Sex

value: male

tag: developmental stage

tag: culture period

value: ureter

source_name: IWP-2 treated 2

value: 10 µM Cyclopamine


title: P0+18h ureter cultures, IWP-2 treated vs control, repl. #2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2100ng of each fluorescently labelled cRNA were used for hybridization.

treatment_protocol: Ureters were mechanically dissected from newborn pups (P0) and cultured on transwell membranes for 18h in culture medium (DMEM/F12 with 1x GlutaMAX, 1x Penicillin/Streptomycin, 1x NEAA, 10% FCS) containing 5 µM IWP-2 or in medium containing DMSO (1:1000, control).

value: 5 µM IWP-2


title: P0+18h ureter cultures, Cyclopamine treated vs control, repl. #1

source_name: control 1

value: female

source_name: IWP-2 treated 1


title: ARM-seq Day 35 AlkB Positive c305 Organoid 2

city: Santa Cruz

first: Todd

middle: Michael

last: Lowe

state: CA

address: 1156 High Street / MS: SOE-2

department: Biomolecular Engineering

institute: University of California, Santa Cruz

description: ARM-seq

data_processing:
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with tRAX (https://github.com/UCSC-LoweLab/tRAX), tRAX maps reads using bowtie2 to a custom database containing mature tRNA transcripts and the genome sequence.
tRNAs were converted into genome space with tRAX and coverage tracks were created with bedGraphToBigWig and genomeCoverageBed from UCSC Genome Browser tools and BEDtools.
Assembly: hg38
Supplementary files format and content: BigWig files of the sequencing results aligned to hg38 tRNAs

growth_protocol: Samples were obtained from 3 c305-derived brain organoids at 0, 2, 5, and 10 weeks old timepoints. They were grown in conditions as described in Kadoshima, et al., 2013

extract_protocol:
Isolation of total RNA from cerebral cortical organoids and stem cells was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.). Since a single organoid would yield far less total RNA, approximately 3-8 organoids would be pooled in trizol depending on organoid size for each sample replicate. Manufacturer’s recommended volume of TRI Reagent was added to each sample (~1 mL). For RNA purification of stem cells Trizol was directly added to cell culture plates on ice, scraped, and homogenized via pipetting. Organoids in Trizol were broken down via pipetting inside a 1mL eppendorf tube on ice via a syringe. All total RNA was processed using a MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. This was followed by a RNA Clean and Concentrate-25 (Zymo Research). Samples were divided into plus-AlkB experimental treatment and minus-AlkB control as previously described in ARM-seq methods (Cozen, et al., 2015). This was followed by a phenol chloroform cleanup treatment. RNA samples were then used for library preparations.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB). PCR-amplified libraries were purified using DNA Clean and Concentrate-5 (Zymo Research) and then size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries were then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O. Libraries were then quantified using NanoDrop and Agilent DNA High Sensitivity kit. For DM-tRNA-seq, libraries were constructed as using the TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex, LLC), which utilizes Illumina-compatible adapters for amplification and sequencing purposes. Libraries were amplified using PCR primers supplied with the NEBNext Small RNA library Prep Set (NEB) and  purified using Agencourt AMPure XP beads (Beckman). Resulting purified sequencing libraries were quantified using NanoDrop and Agilent DNA High Sensitivity kit. Libraries were then pooled equimolarly, and concentrated using a DNA Clean and Concentrate-5 (Zymo Research).  Pooled PCR-amplified libraries were size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel to remove unwanted primer dimer products. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries wer then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O.

treatment_protocol: Samples were divided into plus-AlkB experimental treatment and minus-AlkB control as described in ARM-seq methods in Cozen et al. 2015

value: iPSC

tag: timepoint

value: day 35

tag: library type

value: total small RNA (≤ 250 nts)

value: plus AlkB


title: RNAseq-rdd-rep3

data_processing:
Mapped to the reference genome of Arabidopsis TAIR10 using Bowtie2 (v2.1.0).
RSEM (v1.3.1) was used to calculate the gene expression level.
Trinity (v2.8.5) was used to call DEGs.
The track files were generated by using Samtools (v1.9) and deeptools (v3.1.3).
Assembly: Tair10
Supplementary files format and content: bigwig file

extract_protocol:
Total RNA was extracted from 4-5 week old leaf tissue from each sample by using Zymo RNA extraction kit.
1 ug RNA was used to prepare the RNA-seq library by following Illumina kit


title: Hi-C_Ddiscoideum

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: GCF_000146045.2 for S.cerevisiae , J01347.1 for the 2µ plasmid , GCA_000011445 for mycoides /    GCF_000004695.1 for D.discoideum / GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

organism: Dictyostelium discoideum

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

tag: background

value: SW


title: P0+18h ureter cultures, IWP-2 treated vs control, repl. #1


title: RNAseq-rdd-rep2


title: ARM-seq Day 35 AlkB Positive c305 Organoid 4

description: ARM-seq

tag: cell line


title: ARM-seq Day 14 AlkB Positive c305 Organoid 2

description: ARM-seq

tag: cell type

value: day 14


title: ARM-seq Day 14 AlkB Positive c305 Organoid 1

description: ARM-seq

tag: treatment


title: RNAseq-fwa-rep6

tag: tissue


title: ARM-seq Day 0 AlkB Positive c305 Organoid 7

description: ARM-seq

value: day 0


title: ARM-seq Day 0 AlkB Positive c305 Organoid 8

description: ARM-seq


title: ARM-seq Day 0 AlkB Positive c305 Organoid 5

description: ARM-seq


title: RNAseq-fwa-Rep3

value: Leaf tissue


title: ARM-seq Day 0 AlkB Positive c305 Organoid 3

description: ARM-seq


title: RNAseq-fwa-Rep1

value: 4-5 week old


title: RNAseq-fwa-Rep2


title: RNAseq-TRBIP2-ZF-Rep3


title: RNAseq-fwa-rep5


title: ARM-seq Day 35 AlkB Negative c305 Organoid 6

description: ARM-seq

value: minus AlkB


title: ChIPseq-SET1-H3K4me3-SDG2-ZF-Rep3


title: RNAseq-TRBIP2-ZF-Rep2


title: RNAseq-rdd-rep1


title: RNAseq-rdd-rep4


title: ARM-seq Day 35 AlkB Negative c305 Organoid 4

description: ARM-seq


title: ChIPseq-SET2-H3K4me3-SunTag-SDG2_rdr6-Rep2


title: ARM-seq Day 0 AlkB Positive c305 Organoid 4

description: ARM-seq


title: ARM-seq Day 35 AlkB Negative c305 Organoid 2

description: ARM-seq


title: RNAseq-TRBIP2-ZF-Rep1


title: RNAseq-TRBIP1-ZF-Rep6


title: RNAseq-TRBIP1-ZF-Rep5


title: ARM-seq Day 14 AlkB Negative c305 Organoid 1

description: ARM-seq


title: RNAseq-fwa-rep4


title: RNAseq-TRBIP1-ZF-Rep3


title: ARM-seq Day 0 AlkB Negative c305 Organoid 3

description: ARM-seq


title: ARM-seq Day 0 AlkB Negative c305 Organoid 1

description: ARM-seq


title: RNAseq-TRBIP1-ZF-Rep1


title: RNAseq-TRBIP1-ZF-Rep2


title: RNAseq-SDG2-rdd-rep3


title: RNAseq-SDG2-rdd-rep2


title: ARM-seq Day 0 AlkB Positive c305 Organoid 2

description: ARM-seq


title: FX15992_mRNA1_liquid_culture

city: College Park

first: Antony

middle: Merlin

last: Jose

state: MD

address: Rm 2136, Bioscience Research Building

department: Cell Biology and Molecular Genetics

institute: University of Maryland College Park

data_processing:
FASTQ files were processed to remove adapter sequences, reads less than 20 nt and reads with quality scores under 20 using the command “cutadapt -j 0 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -m 20 -q 20 -o cutread.gz fasta1.gz”
Reads were assigned transcript IDs and counted using the command “salmon quant -i celegans.index -l A -r cutread.gz -p 8 –validateMappings -o quant_file”
Genome_build: ce11
Supplementary_files_format_and_content: tab-delimited file with counts per million per trancript

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: mixed-stage whole animals

growth_protocol: Mixed-stage animals were cultured without starvation in either liquid culture or on multiple plates.

extract_protocol:
After washing animals in M9 buffer to remove bacteria and freeze-cracking animals, total RNA was extracted using TRIzol or RNA greater than 200 nt was extracted using RNAzol.
Libraries were prepared from RNA samples using the TruSeq Library Preparation Kit or the TruSeq Stranded mRNA Library Preparation Kit following standard Illumina protocols.
PolyA+ RNAseq libraries were sequenced using single reads or paired-end reads.

value: whole animals

tag: Stage

value: mixed

tag: genotype

tag: culture method

value: liquid

tag: extraction method

value: TRIzol

tag: library preparation method

value: TruSeq

tag: read method

value: single


title: FX02700_mRNA2_liquid_culture

tag: strain


title: Retina from rd10 mouse sample 2

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

description: Library name: rd_10_2

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on an Illumina Novaseq 6000 sequencer. The Fastq files were processed using the cellranger pipeline (version 7.0.1, reference genome: cellranger reference dataset refdata-gex-mm10-2020-A) with default options; the filtered count matrices were then used for the analyses.
All datasets were integrated using the R package Seurat (v4 - Hao and Hao et al. Integrated analysis of multimodal single-cell data. Cell (2021) [Seurat V4]), following their vignettes. After the integration, the standard pipeline was used to filter (percent.mt < 10, nFeature_RNA > 200, nCount_RNA > 1000), cluster (resolution = 1) and create the UMAP/tSNE visualizations using the default values.
The resulting dataset was annotated with the one from Heng, J.S. et al (2019), the RGC dataset from Tran, N.M. et al (2019), the dataset from Ling, J.P. et al (2020), and the amacrine cells dataset from Yan, W. et al (2020) using the cell type classification method from the Seurat package.
The final dataset was then converted to an anndata file for visualization in cellxgene (Megill, C. et al (2021)) with the cellxgene_vip plugin (Li, K. et al (2020)) for further analyses. For wild-type cone transcriptomic data, we used a publicly available dataset (GSE132229) from Heng, J.S. et al (2019).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Following CO2 euthanasia and cervical dislocation, six eyes from three rd10 mice were enucleated and transferred to CO2-independent medium (Thermo Fisher Scientific, Ref. 18045088) for dissection. The retinas were isolated, chopped into small fragments, and washed twice in warm homemade Ringer solution without Ca2+. The fragments were then incubated in 1 ml of activated papain (4 units/ml, Worthington Biochemical Corp., Ref. LSO 3124) at 37°C for 20 minutes. Digestion was halted by adding 1 ml of Neurobasal-A medium supplemented with L-Glutamine (1%) and fetal bovine serum (5%). DNase I (0.02 mg/ml, Sigma-Aldrich, Ref. D4263) was then added, and the tissue was gently dissociated by trituration using a 1000 µl pipette tips. A brief centrifugation (30 seconds, 115 g) was performed to separate the dissociated cells (supernatant) from aggregates. This process was repeated 4 to 6 times until the retinas were fully dissociated. The total cell suspension was then centrifuged for 10 minutes at 115 g. The resulting pellet was resuspended in a small volume of 1X PBS (calcium and magnesium-free) containing non-acetylated bovine serum albumin (400 µg/ml), then viability and cell concentration was determined using a Malassez counting chamber.
The barcoded cDNAs were prepared from dissociated cells using a 10 × genomics chromium and were used to construct the indexed scRNA-sequencing libraries according to Chromium Next GEM Single Cell 3′ Library v3.1 and dual Index Kit TT according to manufacturer’s protocol.

value: Retina


title: RNAseq-SDG2-rdd-rep1

tag: age

tag: ecotype


title: RNAseq-SDG2-ZF-Rep3


title: FX02700_mRNA1_liquid_culture


title: HC196_mRNA2_liquid_culture


title: RNAseq-SDG2-ZF-Rep1


title: Retina from rd10 mouse sample 1

description: Library name: rd_10_1


title: Retina from rd1 mouse sample 3

description: Library name: rd1_3


title: ARM-seq Day 14 AlkB Negative c305 Organoid 2

description: ARM-seq

value: iPSC


title: RNAseq-Col-0-Rep3


title: RNAseq-Col-0-Rep2


title: HC196_mRNA1_liquid_culture


title: RNAseq-Col-0-Rep1


title: RNAseq-TRBIP1-ZF-Rep4


title: Retina from rd1 mouse sample 2

description: Library name: rd1_2


title: N2_mRNA2_liquid_culture

value: wild type


title: AMJ1324_mRNA2_deletion_plates

value: plate

value: RNAzol

value: TruSeq Stranded mRNA

value: paired-end


title: Retina from rd1 mouse sample 1

description: Library name: rd1_1


title: AMJ1324_mRNA3_deletion_plates


title: N2_mRNA1_liquid_culture


title: FX15992_mRNA2_liquid_culture


title: Nap1l1-knockdown-3

city: Beijing

first: Yibo

last: Wang

state: Beijing

address: 167 Beilishi Rd

country: China

institute: National Center for Cardiovascular Diseases

description: Library name: Nap-3

data_processing:
The raw reads were filtered by Seqtk before mapping to the genome using HISAT2 (version 2.0.4). The gene fragments were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Cardiomyocyte

extract_protocol:
For gene overexpression, plasmids for rat CMV-Nap1l1D349E-Flag-EGFP, CMV-Nap1l1-HA-EGFP and the CMV-Flag-EGFP vector were transfected using Lipofectamine 3000 (Invitrogen, #L3000-015). Seventy-two hours after transfection, the cells were collected for the experiments. For gene knockdown, Nap1l1 and control siRNA (Shanghai Jima Pharmaceutical Technology, China) oligonucleotides were transfected into the cells at a concentration of 0.5 nmol/L with Lipofectamine RNAiMAX (Thermo Fisher Scientific). Seventy-two hours after transfection, the cells were collected for the experiments.
VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina®

value: Cardiomyocyte


title: N2_mRNA3_deletion_plates


title: N2_mRNA2_deletion_plates


title: N2_mRNA1_deletion_plates


title: sup2-6 RNA-seq rep2

first: Jing

last: An

address: 630 Rue Noetzlin

institute: Universite Paris Saclay

description:
Bioreplicate 2
RNA_sup2-6_2_S8

data_processing:
Trimming:Adapters were trimmed using  trimmomatic v0.38, Parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:30
mapping: Reads were mapped against the TAIR10 version of the Arabidopsis genome using STAR with the parameter: sjdbOverhang=75, outFilterType=BySJout and outFilterIntronMotifs=RemoveNoncanonical
Raw read counts were then extracted using featureCounts based on the gene annotations in TAIR10
Differentially expressed genes were identified using R 3.5.1 (www.R-project.org) and the package DESeq2 (adj. p value < 0.05).
Genome_build: TAIR10

source_name: Plantlet

growth_protocol: Seeds were sown on half-strength MS medium and grown under long day conditions (16h/8h), a temperature of 20 °C during the day and 18°C during the night, and a relative humidity of 60%. Plantlets were harvested after 12 days

extract_protocol:
Total RNA were extracted from 100mg of plantlets using the Nucleospin RNA plus kit (Macherey–Nagel), according to the manufacturer’s instructions.  For RNA-seq analysis, libraries were synthetized using NEBNext UltraII Directional RNA library Preparation Kit (NEB) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using 2 μg of total RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to manufacturer’s recommendations. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent).

tag: cultivar

tag: genotypes

value: Col0, S2-6 :crl-2 oep80 double mutant carrying EMS mutations  for CRL (G92A, genomic position from ATG ) and OEP80 (G2983A, genomic position from ATG)


title: Nap1l1-knockdown-2

description: Library name: Nap-2


title: sup2-6 RNA-seq rep3

description:
Bioreplicate 3
RNA_sup2-6_3_S9


title: AMJ1217_mRNA3_nonsense_plates


title: RNAseq-SDG2-ZF-Rep2

value: Leaf tissue

value: 4-5 week old


title: Nap1l1-knockdown-1

description: Library name: Nap-1


title: sup2-6 RNA-seq rep1

description:
Bioreplicate 1
RNA_sup2-6_1_S7


title: AMJ1217_mRNA2_nonsense_plates

value: whole animals


title: AMJ1217_mRNA1_nonsense_plates

value: mixed


title: Control-3

description: Library name: K-3


title: crl2 RNA-seq rep3

description:
Bioreplicate 3
RNA_crl2_3_S6

value: Col0, crl-2 mutant carrying an EMS mutation  for CRL (G92A, genomic position from ATG )


title: AMJ1159_mRNA3_nonsense_plates


title: AMJ1159_mRNA2_nonsense_plates


title: AMJ1159_mRNA1_nonsense_plates


title: crl 2RNA-seq rep2

description:
Bioreplicate 2
RNA_crl2_2_S5


title: Control-1

description: Library name: K-1


title: AMJ1324_mRNA1_deletion_plates


title: N2_mRNA1_nonsense_plates


title: 3Months_mouseBORG_BMS961+BMS641

city: Evry

first: Marco Antonio

last: MENDOZA-PARRA

address: 2 rue Gaston Crémieux

institute: CNRS UMR8030

description: Library name: 3Months_mouseBORG_BMS961+BMS641_CMM_FY

data_processing:
Primary analysis has been performed with our in-house developped tool SysISTD (SysFate Illumina Spatial transcriptomics Demultiplexer: https://github.com/SysFate/SysISTD). SysISTD generates as outcome a matrix presenting read counts per gene IDs in rows and spatial coordinates in columns. To focus the downstream analysis to the physical positions corresponding to the analyzed tissue, we used an in-house R script taking as entry an image of the DNA array scanned with the TRICT filter, releaving the presence of the fiducial borders introduced during the manufacturing of the DNA arrays. The focused matrix was quantile normalized with our previously described tool MULTILAYER (Moehlin et al; Cell Systems 2021). Then, the normalized matrix was further processed for revealing cell/tissue density contrast information by integrating normalized counts with Gexel (gene expression element, in analogy to pixel) value levels retrieved in the TRITC tissue image. The obtained normalized and pixels intensity adjusted matrix was used for all downstream analysis.
Assembly: mm9
Supplementary files format and content: normalized spatial matrices
Library strategy: Spatial transcriptomics

source_name: Brain organoid

growth_protocol: Mouse brain organoid protocol has been derived from Lancaster et al, 2013. ESCs should be present in culture as EBs (embryoid bodies).

extract_protocol:
Organoids are fixed with 4% paraformaldehyde, 6% sucrose for 20 min, washed 3 x 5 min with PBS and suspended in 30% sucrose at 4°C overnight. Several organoids are placed in plastic molds and submerged in OCT compound and frozen before being cryo-sectioned using a cryo-star. Frozen brain organoid molds are cryosectioned and deposited on top of in-house manufactured DNA arrays as described previously (Lozachmeur et al. Cell reports Methods 2023). Briefly, in-house manufactured DNA arrays are composed by a double-barcoded part encoding their unique position within the array, and a poly-T extremity allowing to capture messanger RNA.
Deposited tissue sections were processed for library preparation as described in our in-house protocol (Lozachmeur et al; Cell Reports Methods 2023). At the end of the process, libraries were used for Illumina sequencing (150 nts paired-ends sequencing; NovaSeq; >200 million reads per library).

treatment_protocol: On Day 0, the EBs are dissociated with accutase (A6964-100ML; Sigma) for 10 min. Cells are seeded in P96 (ultra low attachment) plate at 5000 cells/ well in 150µl medium/ well [DMEM (4,5 g/l glucose) w/GLUTAMAX-I, 10% FBS-ES, 1% penicillin–streptomycin, 1% MEM-NEAA, and 0.02% β-mercaptoethanol, SB 431542 (1/1000)] and incubated for 2 days at 37°C. On Day 2, same medium is refreshed by taking out 75µl and adding 150µl fresh medium per well. On Day 4, medium is refreshed by taking out 150µl medium and adding 170µl Neural induction medium/ well (DMEM/F12, 1% N2 supplement, 1% Glutamax supplement, 1% MEM-NEAA, 1% Penicilline –Streptomycine, 0.1% Heparin solution). On day 6, the EBs are embedded in Matrigel GF reduced (11523550; Fisher scientific) for 45 min before transferring to P6 (ultra low attachment) plates in maturation medium (DMEM/F12 medium, Neurobasal medium, 2% B27 without vitamin A supplement, 1% Glutamax supplement, 1% Penicilline –Streptomycine, 0.5% N2 supplement, 0.5% MEM-NEAA, 0.025% insulin (I9278-5ML; Sigma). On day 9, medium is changed completely to maturation medium and adding 2% B27 with vitamin A supplement (11530536; Thermo Fisher Scientific) or retinoid ligands for a final concentration of [(ATRA (1µM), BMS753 (1µM); BMS641, BMS961, BMS641+961 (0.1µM)] and placed on an orbital shaker at 75-80 rpm. Two-thirds of medium is changed twice a week.

value: Brain organoid

value: CARLIN/Cas9 mESCs

value: Mouse stem cells

value: BMS961+BMS641 (3 months)


title: Col0 WT RNA-seq rep3

description:
Bioreplicate 3
RNA_Col_3_S3

value: WT


title: N1p1l1-overexpression-3

description: Library name: OE-3

organism: Rattus norvegicus


title: N1p1l1-overexpression-2

description: Library name: OE-2


title: crl2 RNA-seq rep1

description:
Bioreplicate 1
RNA_crl2_1_S4


title: N1p1l1-MT-3

description: Library name: MT-3


title: 3Months_mouseBORG_ATRA

description: Library name: 3Months_mouseBORG_ATRA_CMM_FW

value: ATRA (3 months)


title: 3Months_mouseBORG_BMS753

description: Library name: 3Months_mouseBORG_BMS753_CMM_FX

value: BMS753 (3 months)


title: N1p1l1-MT-1

description: Library name: MT-1


title: N1p1l1-MT-2

description: Library name: MT-2


title: Col0 WT RNA-seq rep1

description:
Bioreplicate 1
RNA_Col_1_S1


title: 3Months_mouseBORG_VitaminA

description: Library name: 3Months_mouseBORG_VitaminA_CMM_EG

value: Vitamin A (3 months)


title: Control-6

description: Library name: ctr-3


title: Control-2

description: Library name: K-2


title: Control-5

description: Library name: ctr-2


title: N2_mRNA3_nonsense_plates

value: wild type

value: plate

value: RNAzol

value: TruSeq Stranded mRNA


title: Control-4

description: Library name: ctr-1

value: Cardiomyocyte


title: D16_BMS961+BMS641

description: Library name: D16_BMS961+BMS641

data_processing:
Data from 9 conditions has been processed using Cell Ranger 7.0.1 for primary analyses, aligned to the mouse reference genome mm10 2020A. Cells were filtered out on the grounds of doublets (DoubletFinder V.2)(McGinnis et al., 2019), more than 5% of mitochondrial counts content, novelty score higher than 0.8, and cells with less than 200 genes. These cells from different conditions were merged and integrated by a selected group of genes (200 features). Read counts were normalized by SCTransform method and processed downstream for Uniform Manifold Approximation and Projection (UMAP). Clusters were identified (KNN method) based on gene expression similarities. Differential expression analysis was performed and filtered out genes with a log2 fold change < 0.25 and a p value > 0.05 using the Wilcoxon test. All these steps were performed in R (R core team 2024) using the package “Seurat” (Version 5) (Hao et al., 2024) and customized scripts.
Assembly: mm10
Supplementary files format and content: barcodes, features, matrix

source_name: CARLIN/Cas9 mESCs

extract_protocol:
Differentiated cells after 4, 8 or 16 days of treatment were disociated (Worthington Papain Dissociation System) and resuspended to the required concentration based on the 10X Genomics protocol requirements.
The Chromium instrument and Single cell 3’ Reagent Kit v3 (PN-1000128; 10X Genomics) was used to prepare individually barcoded single-cell RNA-Seq whole transcriptome libraries following the manufacturer’s protocol. The target number of cells was 8000 per condition. Libraries were sequenced on Illumina Novaseq 6000 using paired-end 150 cycles v3 kits (Read 1: 28 cycles; Index Read 1 (i7): 10 cycles; Read 2: 90 cycles).

treatment_protocol: ESCs were seeded onto poly-D-lysine–coated culture plates (0.1%) at a concentration of 100,000 cells per well (for cells collected at 4 days of differentiation), 40,000 cells per well (for cells collected at 8 days treated with ATRA), 20,000 cells per well (for cells collected at 8 days treated with ethanol, BMS753, or BMS961+641; for cells collected at 16 days treated with ATRA), 10,000 cells per well (for cells collected at 16 days treated with ethanol, BMS753, or BMS961+641). The cells are seeded in DMEM (4,5 g/l glucose) w/GLUTAMAX-I, 10% FBS-ES, 1% penicillin–streptomycin, 1% MEM-NEAA, and 0.02% β-mercaptoethanol. Next day, same medium is refreshed and retinoid ligands are added. ATRA was added for a final concentration of 1 μM. For treatment with RAR subtype–specific agonists, cells were incubated with BMS753 (RARα-specific; 1 μM) or BMS641 + BMS961 (RARβ + RARγ-specific; 0.1 μM each). After 8 days of treatment with either of the aforementioned retinoids, the medium was replaced by Neurobasal medium (11570556; Thermo Fisher Scientific) and B27 without vitamin A (11500446; Thermo Fisher Scientific) and cultured for eight more days. Half medium was refreshed every other day.

tag: timepoint

value: 16 days


title: HepG2 EV-2

city: Columbus

first: David

last: Brigstock

state: Ohio

address: 700 Children's Drive

institute: Nationwide Children's Hospital

description: Library name: Sample-2

data_processing:
Quality of libraries was determined via Agilent 4200 Tapestation using a High Sensitivity D1000 ScreenTape Assay kit.
The library was then run on Illumina MiniSeq platform.
The Quality Control of the sequencing data was done by miRTrace software.
2x75 paired-end service was applied, but only R1 was used. Read-length distribution was between 1.74M and 2.52M.
The miRNA counts were normalized and subjected to target searching and functional prediction by miRWalk
Assembly: GRCh38
Supplementary files format and content: Excel spreadsheet containing normalized counts of HepG2 miRNAs

source_name: Liver

growth_protocol: HepG2 cells were cultured with DMEM+10%Fetal bovine serum+1% Antibiotic-Antimycotic in T175 flasks and, when 90% confluent, were washed with DPBS twice and switched to serum-free medium.

extract_protocol:
Three batches of HepG2 EVs were used to isolate total RNA with QIAGEN miRNeasy kit. DNA was removed by Dnase I digestion. Approximately 200 ng of RNA was subjected to small RNA-seq.
Multiplex Small RNA Library was prepared using NEBNext® Small RNA Library Prep Set according to the manufacturer’s instructions

treatment_protocol: Supernatants from 48hr culture were subjected to differential centrifugation. EV pellets were recovered after ultracentrifugation at 100,000xg for 70min. The EV pellets were washed and spun down again for resuspension.

value: Liver

value: hepatocytes

value: wildtype

value: serum-free medium culture


title: D16_BMS753

description: Library name: D16_BMS753

value: CARLIN/Cas9 mESCs


title: Shell; Ctx_Sal; Seq 24-F

city: New York

first: Molly

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

data_processing:
Raw sequencing reads were mapped to the mRatBN7.2 genome using the NGS-Data-Charmer pipeline.  In brief, reads were trimmed to remove adaptor and low-quality sequences, then the reads were aligned to the reference genome. Duplicate alignments were removed prior to gene counting and downstream analysis. Counts of mapped reads were obtained using featureCounts against the GCF_015227675.2_mRatBN7.2 annotation.
Assembly: mRatBN7.2
Supplementary files format and content: counts_matrix.txt: Tab-delimited text file containing the raw read counts for annotated genes, with individual samples present as columns. fpkm_matrix.txt: Tab-delimited text file containing the normalized read counts (in fragments per kilobase per million) for annotated genes, with individual samples present as columns.

source_name: Shell

extract_protocol:
Direct-zol RNA kit (Zymo Research, CA)
SMARTer Stranded Total RNA-seq kit v3-Pico Input Mammalian (Takara Bio, CA)

value: Shell

value: Long-Evans

value: wild-type


title: Core ; Ctx_Sal; Seq 23-F

source_name: Core

value: Core


title: N2_mRNA2_nonsense_plates

value: whole animals

value: mixed

value: paired-end


title: Shell; Ctx_Sal; Seq 22-F


title: HepG2 EV-1

description: Library name: Sample-1


title: Core ; Ctx_Sal; Seq 21-F


title: Shell; Ctx_Coc; Seq 20-F


title: N1p1l1-overexpression-1

description: Library name: OE-1


title: BS-PCRseq-fwa-rep2

data_processing:
The raw paired-end sequencing reads from each sample were mapped to Arabidopsis reference genome TAIR10 using  BSMAP (v2.90)
The methylation level for each cytosine was determined by calculating the ratio of methylated cytosines (C) to the sum of methylated cytosines and unmethylated cytosines
Assembly: Tair10
Supplementary files format and content: txt

value: Leaf tissue

value: 4-5 week old


title: D16_ATRA

description: Library name: D16_ATRA

value: Mouse stem cells

value: ATRA


title: Core ; Ctx_Coc; Seq 19-F


title: D8_BMS961+BMS641

description: Library name: D8_BMS961+BMS641

value: 8 days


title: Col0 WT RNA-seq rep2

description:
Bioreplicate 2
RNA_Col_2_S2

value: WT


title: BS-PCRseq-fwa-rep1


title: HepG2 EV-3

description: Library name: Sample-3

value: Liver

value: hepatocytes


title: Shell; HC_Sal; Seq 16-F


title: Core ; Ctx_Coc; Seq 17-F


title: D8_ATRA

description: Library name: D8_ATRA


title: Core ; HC_Sal; Seq 15-F


title: BS-PCRseq-SDG2cd(H1866K)-ZF-rep4


title: D8_BMS753

description: Library name: D8_BMS753


title: D4_BMS961+BMS641

description: Library name: D4_BMS961+BMS641

value: 4 days


title: Core ; HC_Coc; Seq 13-F


title: Shell; HC_Coc; Seq 14-F


title: Core ; Ext_Sal; Seq 11-F


title: D4_BMS753

description: Library name: D4_BMS753

value: CARLIN/Cas9 mESCs


title: BS-PCRseq-SDG2cd(H1866K)-ZF-rep3


title: Shell; Ext_Sal; Seq 12-F

value: Shell


title: BS-PCRseq-SDG2cd(H1866K)-ZF-rep2


title: D4_ATRA

description: Library name: D4_ATRA


title: Core ; Ext_Coc; Seq 9-F

value: Long-Evans


title: BS-PCRseq-Col0-rep2


title: Shell; Ext_Coc; Seq 10-F

value: wild-type


title: D16_BMS961+BMS641_RNAPol2

description: Library name: D16_BMS961+BMS641_RNAPol2_CMM_FL

data_processing:
Cut&tag histone modification sequencing data were aligned to the mouse genome (mm9) using Bowtie2 (v2.4.1) under the default parameters. Chromatin state analysis has been performed with ChromHMM (v1.14). Bedgraph files and peak annotations were obtained with MACS2 and visualized within the IGV genome browser (v.2.4.15).
Assembly: mm9
Supplementary files format and content: Bedgraph files
Library strategy: Cut&Tag

extract_protocol:
Cells differentiated during 16 days of treatment were collected as dry pellets and used for Cut&Tag experiments were carried out as previously described (Kaya-Okur et al; Li et al), with some modifications. Briefly, 250.000 cells were captured with BioMagPlus Concanavalin A (Polysciences, 86057-3) and incubated with the appropriate primary antibody overnight at 4°C (anti-Histone H3 (tri methyl K4) antibody (Abcam, ab8580; 1:50); anti-Histone H3(acetyl K27) antibody (Abcam, ab4729; 1:50); anti-Histone H3(tri methyl K27) antibody (Abcam, ab192985; 1:50); Anti- RNA Pol II monoclonal antibody: diagenode (C15100055) (1:20)). For the experiment in which the antibody RNA Pol II was used, the mixture cells-beads were fixed with 1% PFA in 1xPBS for 15 minutes before the addition of the primary antibody. A secondary antibody was incubated at room temperature for 1 hour (Donkey anti-rabbit IgG antibody: Sigma-Aldrich, SAB3700932; 1:100). Fusion protein ProteinA-Tn5 was prepared in-house (plasmid Addgene #124601) by following a previously described protocol (Li et al).
Purified PA-Tn5 was loaded with the following adapters compatible with Illumina sequencing (hybridized with the complementary Mosaic sequence [PHO]CTGTCTCTTATACACATCT): MOS-universal: TACACTCTTTCCCTACACGACGCTCTTCCGATCTAGATGTGTATAAGAGACAG MOS-index: GTTCAGACGTGT.GCTCTTCCGATCTAGATGTGTATAAGAGACAG Loaded PA-Tn5 complex (0.16 μM) was incubated for 1 hour at RT, followed by tagmentation step for 2 hours at 37°C. DNA was extracted by phenol/chloroform (Sigma-Aldrich 77617) followed by ethanol precipitation. Finally, the tagmented DNA was amplified using Illumina primers (NEBNext® Multiplex Oligos for Illumina, NEB #7335S) with the following cycling conditions: 98°C for 30s, 20 cycles of 98°C for 10s and 65°C for 75 s; then final extension at 65°C for 5 min and hold at 12°C. DNA libraries were cleaned using 1x volume of SPRI-select beads (Beckman Coulter, B23318) and Illumina sequenced (150-nt pair-end sequencing; Illumina NovaSeq 6000).

treatment_protocol: mouse ESCs (CARLIN/Cas9 mESCs; Bowling et al; Cell 2020) were seeded onto poly-D-lysine–coated culture plates (0.1%) at a concentration of 100,000 cells per well (for cells collected at 4 days of differentiation), 40,000 cells per well (for cells collected at 8 days treated with ATRA), 20,000 cells per well (for cells collected at 8 days treated with ethanol, BMS753, or BMS961+641; for cells collected at 16 days treated with ATRA), 10,000 cells per well (for cells collected at 16 days treated with ethanol, BMS753, or BMS961+641). The cells are seeded in DMEM (4,5 g/l glucose) w/GLUTAMAX-I, 10% FBS-ES, 1% penicillin–streptomycin, 1% MEM-NEAA, and 0.02% β-mercaptoethanol. Next day, same medium is refreshed and retinoid ligands are added. ATRA was added for a final concentration of 1 μM. For treatment with RAR subtype–specific agonists, cells were incubated with BMS753 (RARα-specific; 1 μM) or BMS641 + BMS961 (RARβ + RARγ-specific; 0.1 μM each). After 8 days of treatment with either of the aforementioned retinoids, the medium was replaced by Neurobasal medium (11570556; Thermo Fisher Scientific) and B27 without vitamin A (11500446; Thermo Fisher Scientific) and cultured for eight more days. Half medium was refreshed every other day.

tag: antibody

value: anti-Pol2 (diagenode,C15100055)


title: Shell; HC_Sal; Seq 8-F


title: BS-PCRseq-SDG2cd(H1866K)-ZF-rep1


title: Core ; HC_Sal; Seq 7-F

value: Core


title: Shell; HC_Coc; Seq 6-F


title: BS-PCRseq-Col0-rep1


title: D16_BMS961+BMS641_H3K27me3

description: Library name: D16_BMS961+BMS641_H3K27me3_CMM_FK

value: anti-H3K27me3 (Abcam, ab192985)

tag: cell line


title: Core ; HC_Coc; Seq 5-F


title: BS-PCRseq-rdd-Rep2


title: Shell; Ext_Sal; Seq 4-F


title: Shell; Ctx_Coc; Seq 18-F


title: D16_BMS961+BMS641_H3K27ac

description: Library name: D16_BMS961+BMS641_H3K27ac_CMM_FJ

value: anti-H3K27ac (Abcam, ab4729)

tag: cell type


title: Core; Ext_Sal; Seq 3-F

tag: treatment


title: D16_BMS961+BMS641_H3K4me3

description: Library name: D16_BMS961+BMS641_H3K4me3_CMM_FI

value: anti-H3K4me3 (Abcam, ab8580)


title: BS-PCRseq-rdd-Rep1

tag: tissue

value: Leaf tissue

value: 4-5 week old


title: Core; Ext_Coc; Seq 1-F


title: BS-PCRseq-fwa-Rep2


title: Shell; Ctx_Sal; Seq 4-18


title: D16_BMS753_RNAPol2

description: Library name: D16_BMS753_RNAPol2_CMM_FH

value: Mouse stem cells

value: BMS753 (16 days)


title: Shell; Ctx_Coc; Seq 4-15


title: Shell; HC_Sal; Seq 4-12


title: BS-PCRseq-SDG2-ZF_rdr6-4


title: BS-PCRseq-SDG2-ZF_rdr6-3


title: D16_BMS753_H3K27me3

description: Library name: D16_BMS753_H3K27me3_CMM_FG


title: Shell; Ext_Sal; Seq 4-6


title: D16_BMS753_H3K27ac

description: Library name: D16_BMS753_H3K27ac_CMM_FF


title: BS-PCRseq-SDG2-ZF_rdd-7


title: Shell; Ext_Coc; Seq 4-3


title: Shell; Ctx_Coc; Seq 4-14


title: D16_BMS753_H3K4me3

description: Library name: D16_BMS753_H3K4me3_CMM_FE


title: BS-PCRseq-SDG2-ZF_rdd-30


title: Shell; HC_Coc; Seq 4-8


title: Shell; Ctx_Sal; Seq 4-17


title: Shell; HC_Sal; Seq 4-11


title: D16_ATRA_RNAPol2

description: Library name: D16_ATRA_RNAPol2_CMM_FD

value: ATRA (16 days)


title: Shell; Ext_Coc; Seq 4-2


title: D16_ATRA_H3K27me3

description: Library name: D16_ATRA_H3K27me3_CMM_FC


title: Shell; Ctx_Sal; Seq 4-16


title: D16_ATRA_H3K27ac

description: Library name: D16_ATRA_H3K27ac_CMM_FB


title: Shell; Ctx_Coc; Seq 4-13


title: Shell; Ext_Sal; Seq 4-5


title: BS-PCRseq-SDG2-ZF_rdd-24


title: BS-PCRseq-SDG2-ZF_rdd-21


title: Shell; HC_Coc; Seq 4-9


title: BS-PCRseq-SDG2-ZF_rdd-19


title: D16_ATRA_H3K4me3

description: Library name: D16_ATRA_H3K4me3_CMM_FA


title: Shell; HC_Coc; Seq 4-7


title: Shell; Ext_Coc; Seq 2-F


title: Shell; Ext_Sal; Seq 4-4


title: mouse lung tissues, OVA+PM2.5, rep3

city: Hebei

first: Xin

address: 372 Shengli North Street

institute: Hebei Chest Hospital

description:
Library name: OVA+PM2.5-3
OVA+PM2.5-3

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed toshort reads (Raw data) by base calling and these short reads are recorded in FASTQ format. Fastp (version0.23.1) was used to perform basic statistics on the quality of the raw reads.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file incude RPKM values for each samples

source_name: lung tissues

growth_protocol: Six-week-old male BALB/c mice were housed at a temperature of 22 ± 1℃ and humidity 45-55%, with a 12 h light/dark cycle for one week to adapt to the environment.

extract_protocol:
Total RNA was extracted from the mouse lung tissues of Naive, OVA and OVA+PM2.5 groups using Trizol.  mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations.

treatment_protocol: The mice were randomly divided into three groups: Naive, OVA and OVA+PM2.5. Seven days before the start of the experiment, the OVA+PM2.5 mice received an anterior nasal cavity drop of PM2.5 suspension once a day until the day before the end of the experiment. The mice were intraperitoneally injected with 50 μg OVA and 1 mg aluminum hydroxide in a total volume of 200 μL on days 0, 7 and 14. A daily intranasal instillation was administered to the mice with 400 μg OVA in a total volume of 40 μL from days 21 to 27. The Naive group mice were subjected to an equal volume of saline solution in the same manner as controls. The mice were sacrificed on day 28. The lungs were collected and used for mRNA-seq.

value: lung tissues

value: OVA and PM2.5


title: Shell; Ext_Coc; Seq 4-1


title: BS-PCRseq-SDG2-ZF_rdd-18


title: mouse lung tissues, OVA+PM2.5, rep2

description:
Library name: OVA+PM2.5-2
OVA+PM2.5-2


title: Shell; Ctx_Coc; Seq 3-15


title: Shell; Ctx_Sal; Seq 3-18


title: Shell; HC_Sal; Seq 3-12


title: BS-PCRseq-SDG2-ZF_rdd-15


title: mouse lung tissues, OVA+PM2.5, rep1

description:
Library name: OVA+PM2.5-1
OVA+PM2.5-1


title: BS-PCRseq-SDG2-ZF_Col0-9


title: Shell; HC_Coc; Seq 3-9


title: mouse lung tissues, OVA, rep3

description:
Library name: OVA-3
OVA-3

value: OVA only


title: Shell; Ext_Sal; Seq 3-6


title: BS-PCRseq-SDG2-ZF_Col0-7


title: Shell; Ext_Coc; Seq 3-3


title: BS-PCRseq-SDG2-ZF_rdd-1


title: mouse lung tissues, OVA, rep2

description:
Library name: OVA-2
OVA-2


title: Shell; Ctx_Coc; Seq 3-14


title: Shell; HC_Sal; Seq 3-11


title: Shell; HC_Sal; Seq 4-10


title: BS-PCRseq-SDG2-ZF_Col0-6


title: Shell; HC_Coc; Seq 3-8


title: Shell; Ext_Coc; Seq 3-2


title: BS-PCRseq-SDG2-ZF_Col0-5


title: BS-PCRseq-SDG2-ZF_Col0-15


title: Shell; Ext_Sal; Seq 3-5


title: mouse lung tissues, Naive, rep2

description:
Library name: Naive-2
Naive-2

value: physiological saline


title: Core; Ctx_Coc; Seq 2-15


title: BS-PCRseq-SDG2-ZF_Col0-14


title: Core; HC_Sal; Seq 2-12


title: mouse lung tissues, Naive, rep1

description:
Library name: Naive-1
Naive-1


title: Core; HC_Coc; Seq 2-9


title: BS-PCRseq-SDG2-ZF_Col0-13


title: miRNA_IR3

city: Zaozhuang

first: Ping

last: Xu

address: Beian road 1

institute: Zaozhuang University

description: Library name: sample6

data_processing:
The samples were clustered using index codes by following procedures outlined in the instructions of the cBot Cluster Generation System and a TruSeq SR Cluster Kit v3-cBot-HS (Illumina). Single-end sequencing at 50 bp (miRNAs) and paired-end sequencing at 125/150 bp (lncRNAs and mRNAs) were performed on the libraries after clustering.
To compare the gene expressions of the groups, the R DESeq2 (1.10.1) program was used, with two biological replicates per group. This software evaluates gene expression data statistically by analyzing DGEs using a model based on the negative binomial distribution. Genes with an adjusted p-value ≤ 0.05 were considered to be expressed differently after using the Benjamini-Hochberg method to control the false discovery rate (FDR).
To adjust any biases related to gene length, GO enrichment analyses were carried out by targeting mRNAs linked with dysregulated lncRNAs-miRNAs using a GO seq Wallenius non-central hyper-geometric distribution technique. To evaluate the high-level functional activities connected to these target mRNAs, KEGG enrichment analyses were also performed (http://www.genome.jp/kegg/). The enrichment of the KEGG pathway was examined using KOBAS software.
Assembly: Cytoscape 3.5.1 software was used to construct all ceRNA networks comprising respective lncRNAs, miRNAs, and mRNAs.
Supplementary files format and content: tab-delimited text files include FPKM for each Sample.

source_name: thymus tissue

extract_protocol:
Animals (C57BL wild-type) were acquired from Beijing Vital River Laboratory Animal Technology Co., Ltd. The mice (4 weeks) were housed (three mice/cage) in a controlled (22 ℃, 45±10% humidity, 12 h light/dark cycle) environment. All animal-related experiments were conducted as per the guidelines and regulations of the care and use of laboratory animals and received approval from the animal center of Zaozhuang University (Shandong, China). The control group (n=3) was not exposed to any irradiation. The irradiated group (n = 3) received X-ray irradiation at 25 ºC with a dose of 6 Gy (800 cGy/min, radiation distance 40 cm). Following a 24-hour period，all mice were euthanized by intraperitoneal (IP) injection of sodium pentobarbital with the dose of 50 mg/kg and their thymus tissues were collected, and rapidly frozen in liquid nitrogen. The tissues were processed for RNA isolation using the TRIzol method. These RNA samples were transported on dry ice to an external company (Genechem Experimental Department) for sequencing.
The library was constructed using the NEBNext® Multiplex Prep kit Illumina® and the UltraTM RNA Library Prep Kit (NEB, USA).

value: thymus tissue

value: 5 weeks old

value: irradiated


title: Shell; Ctx_Sal; Seq 3-17

value: Shell

value: Long-Evans

value: wild-type


title: Core; Ctx_Sal; Seq 2-17

value: Core


title: Core; Ext_Coc; Seq 2-3


title: Core; Ctx_Coc; Seq 2-14


title: mouse lung tissues, OVA, rep1

description:
Library name: OVA-1
OVA-1


title: BS-PCRseq-SDG2-ZF_Col0-12

data_processing:
The raw paired-end sequencing reads from each sample were mapped to Arabidopsis reference genome TAIR10 using  BSMAP (v2.90)
The methylation level for each cytosine was determined by calculating the ratio of methylated cytosines (C) to the sum of methylated cytosines and unmethylated cytosines
Assembly: Tair10
Supplementary files format and content: bigwig
Supplementary files format and content: wig
Supplementary files format and content: txt

extract_protocol:
Genomic DNA was extracted by using the CTAB-based DNA extraction.
500 ng DNA of each sample was sheared at 4°C for 2 min by using Covaris, and the WGBS library construction used Kapa DNA Hyper Kit (Roche) and TruSeq DNA UD indexes for Illumina (Illumina)


title: Core; HC_Sal; Seq 2-11


title: miRNA_IR1

description: Library name: sample4


title: BS-PCR-rdr6-Rep2


title: BS-PCRseq-Col-0-Rep2


title: Core; HC_Coc; Seq 2-8


title: mouse lung tissues, Naive, rep3

description:
Library name: Naive-3
Naive-3


title: Core; Ext_Sal; Seq 2-5


title: Core; Ctx_Sal; Seq 2-18


title: Core; Ext_Coc; Seq 2-2


title: miRNA_WT2

description: Library name: sample2

value: control


title: BS-PCR-fwardr6

value: Leaf tissue


title: Core; Ctx_Sal; Seq 2-16


title: BS-PCR-rdr6-Rep1

value: 4-5 week old


title: Core; Ctx_Coc; Seq 2-13


title: Core; HC_Sal; Seq 2-10


title: miRNA_WT1

description: Library name: sample1


title: Core; HC_Coc; Seq 2-7


title: Core; Ext_Sal; Seq 2-4


title: Core; Ext_Sal; Seq 2-6


title: IR3

description: Library name: sample6


title: miRNA_IR2

description: Library name: sample5


title: IR2

description: Library name: sample5


title: Core; Ctx_Coc; Seq 1-15


title: BS-PCR-dCAS9-MQ1-Rep3


title: miRNA_WT3

description: Library name: sample3


title: Core; Ctx_Sal; Seq 1-18


title: Core; HC_Sal; Seq 1-12


title: IR1

description: Library name: sample4


title: Core; HC_Coc; Seq 1-9


title: BS-PCR-dCAS9-MQ1-Rep2


title: WT3

description: Library name: sample3


title: Core; Ext_Sal; Seq 1-6


title: BS-PCR-TRBIP1-dCAS9-MQ1-Rep4


title: BS-PCR-dCAS9-MQ1-Rep1


title: Core; Ctx_Sal; Seq 1-17


title: WT2

description: Library name: sample2


title: Core; Ext_Coc; Seq 1-3


title: Core; Ctx_Coc; Seq 1-14


title: Core; HC_Coc; Seq 1-8


title: BS-PCR-TRBIP1-dCAS9-MQ1-Rep3


title: BS-PCR-TRBIP1-dCAS9-MQ1-Rep2


title: WT1

description: Library name: sample1


title: Core; HC_Sal; Seq 1-11


title: BS-PCR-dCAS9-MQ1-Rep4


title: Core; Ext_Coc; Seq 2-1


title: Core; Ext_Coc; Seq 1-2


title: 20210908-NMK92F2U1

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S Euclid Ave

institute: Washington University in St Louis

description:
Library name: 20210908-NMK92F2-Fc1U1Bs2
20210908-NMK92F2U1 (W92.Female.Single specimen)

data_processing:
For Visium: After cDNA library construction and sequencing, the read alignment algorithm ‘count’ method in Space Ranger (v1.3.0) from the 10X Genomics was used to align reads to the mouse reference genome (mm10, 2020A). The resulting count matrix and associated H&E physiological images were then used by the R package Seurat (v.4.0.4) for subsequent analysis. The filtered gene-count matrices of all samples were normalized using SCTransform before being merged into one object for joint processing and analysis using the FindNeighbors and FindClusters function in Seurat using standard processing parameters (30 PCs, original Louvain algorithm).
Assembly: mm10
Supplementary files format and content: for Visium data, for each library, a Seurat object in rds format was provided.
Library strategy: Spatial Transcriptomics

source_name: kidney

growth_protocol: To get E16.5 kidneys, 4 female mice and 1 male mouse were grouped for mating on day 1 at 5 pm. Then the male was removed from the females on day 2 at 10 am. Day 2 was designated as E0.5 for any pregnant females. For kidneys collected from other ages, mice were purchased from the Jackson Laboratory.

extract_protocol:
Mice at E16.5 and P0 were euthanized by decapitation. Older mice were euthanized by carbon dioxide asphyxiation. For each mouse, one kidney was embedded in optimal cutting temperature compound (OCT) and the other one was fixed in 10% neutral buffered formalin (Epredia, 5725) and then embedded in paraffin.
For Visium: Fresh mouse kidneys were embedded with OCT on dry ice. OCT-embedded tissues sectioned at 10 μm thickness were then placed on Visium Spatial Gene Expression Slide following Visium Spatial Protocols-Tissue Preparation Guide (10X Genomics, CG000240 Rev A). Visium ST libraries were constructed following Visium Spatial Gene Expression Reagent Kits User Guide CG000239 Rev A (10X Genomics).

value: kidney

tag: Sex

value: Female

value: WT


title: p38α-ELK1D_Replicate3_Timepoint 2

city: New Haven

first: Jaylissa

middle: Marie

last: Torres Robles

state: CT

address: 333 Cedar St. Department of Pharmacology, Yale School of Medicine

department: Chemistry and Pharmacology

institute: Yale University

description: Library name: Sample_19

data_processing:
Sequences were aligned using an internal barcode, incorporated by forward PCR amplifying primer, allowing for one base mismatch and trimmed. Barcode-matched sequences were mapped to the ELK1 D-site library and unique sequences were counted using the FASTX toolkit, Perl and the Yale Center for Genome Analysis shRNA Analysis Pipeline through Yale Center for Research Computing, Ruddle cluster.
Starting Library raw sequencing data files were concatenated into a single file before proceeding with trimming and barcode alignments -/+1 mismatch.
Assembly: A custom sequence library was used.
Supplementary files format and content: Table of raw counts is in .xslx format, containing the total number of counts of each sequence within our library under indicated conditions, timepoints, and replicates

growth_protocol: Yeast two-hybrid strain PJ694-A was cultured in yeast synthetic complete media supplemented with 2% glucose

extract_protocol:
Extracted DNA was PCR-amplified with Illumina indexing primers and a second internal primer for sequence alignment.
An oligonuclotide pool encoding short linear motifs from the human proteome  with common flanking sequence was amplified by PCR, restriction digested and ligated into the yeast two-hybrid prey plasmid encoding ELK1 between the SpeI and AgeI sites, replacing the native ELK1 D-site. MAX Efficiency DH10B electrocompetent E. coli (ThermoFisher) were transformed with the ligation reaction product. Transformed cells were spread on 15 cm Luria-Bertani Broth (LB) agar plates supplemented with 0.1 mg/ml ampicillin and grown overnight at 37°C. Plasmid DNA was isolated from pooled colonies (Qiagen Maxi prep kit). Colony counts from serial dilution plates confirmed the presence of at least 50 transformants per library sequence. The variable sequence was PCR-amplified and sequenced (Illumina HiSeq 4000) to verify clone representation of all library components. Yeast two hybrid stran PJ694A harboring ERK2 or p38 bait plasmids was transformed with the library plasmid pool for competitive growth Y2H screens.

treatment_protocol: For library screens, yeast harboring bait plasmids were transformed with the ELK1 D-site library plasmid pool and selected on agar plates containing SD-Leu-Trp media. Transformants were suspended in SD-Leu-Trp liquid media and grown at 30 °C. When the culture reached an OD600 of 1.0, it was used to inoculate 50 mL of selective media (SD-Leu-Trp-His + 50 μM 3-AT) and 50 mL of non-selective media (SD-Leu-Trp) at an OD600 of 0.1. Yeast cultures were subjected to two growth and dilution cycles, with 25 mL aliquots reserved for DNA extraction each time.

value: Yeast


title: 20210907-NMK92M1U1

description:
Library name: 20210907-NMK92M1-Fc1U1Bs2
20210907-NMK92M1U1 (W92.Male.Single specimen)

value: Male

tag: genotype


title: BS-PCR-TRBIP1-dCAS9-MQ1-Rep1

source_name: Arabidopsis leaf tissue


title: p38α-ELK1D_Replicate3_Timepoint 1

description: Library name: Sample_18


title: BS-PCR-SunTag-SDG2-rdr6-Rep2


title: BS-PCR-SunTag-SDG2-rdr6-Rep1


title: p38α-ELK1D_Replicate2_Timepoint 1

description: Library name: Sample_15


title: p38α-ELK1D_Replicate2_Timepoint 2

description: Library name: Sample_16


title: 20210205-NMKE16_5M1RU2, 20210205-NMKE16_5M1LU2, 20210205-NMKE16_5M2RU2, 20210205-NMKE16_5M2LU2

description:
Library name: 20210205-NMKE16.5-Fc1U2Z1Bs1
20210205-NMKE16_5M1RU2 (E16.5.Male.Top Right); 20210205-NMKE16_5M1LU2 (E16.5.Male.Top left); 20210205-NMKE16_5M2RU2 (E16.5.Male.Bottom Right); 20210205-NMKE16_5M2LU2 (E16.5.Male.Bottom Left)


title: p38α-ELK1D_Replicate3_Timepoint 0

description: Library name: Sample_17


title: p38α-ELK1D_Replicate2_Timepoint 0

description: Library name: Sample_14


title: 20210318-NMKE16_5F1RU1, 20210318-NMKE16_5F1LU1, 20210318-NMKE16_5F2RU1, 20210318-NMKE16_5F2LU1

description:
Library name: 20210318-NMKE16.5F-Fc1U1Z1Bs1
20210318-NMKE16_5F1RU1 (E16.5.Female.Top Right); 20210318-NMKE16_5F1LU1 (E16.5.Female.Top left); 20210318-NMKE16_5F2RU1 (E16.5.Female.Bottom Right); 20210318-NMKE16_5F2LU1 (E16.5.Female.Bottom Left)


title: p38α-ELK1D_Replicate1_Timepoint 2

description: Library name: Sample_13


title: BS-PCR-SunTag-SDG2-WT-Rep2


title: p38α-ELK1D_Replicate1_Timepoint 1

description: Library name: Sample_12


title: BS-PCR-SunTag-SDG2-WT-Rep1


title: p38α-ELK1D_Replicate1_Timepoint 0

description: Library name: Sample_11


title: Core; Ext_Sal; Seq 1-5


title: 20210205-NMKE16_5M1RU1, 20210205-NMKE16_5M1LU1, 20210205-NMKE16_5M2RU1, 20210205-NMKE16_5M2LU1

description:
Library name: 20210205-NMKE16.5-Fc1U1Z1Bs1
20210205-NMKE16_5M1RU1 (E16.5.Male.Top Right); 20210205-NMKE16_5M1LU1 (E16.5.Male.Top left); 20210205-NMKE16_5M2RU1 (E16.5.Male.Bottom Right); 20210205-NMKE16_5M2LU1 (E16.5.Male.Bottom Left)


title: 20210129-AKICT3MU1

description:
Library name: 20210129-AKICT3M-Fc1U1Z1Bs1
20210129-AKICT3MU1 (W12.Male.Single specimen)


title: ERK2-ELK1-D_Replicate3_Timepoint 1

description: Library name: Sample_9


title: ERK2-ELK1-D_Replicate2_Timepoint 2

description: Library name: Sample_7


title: BS-PCR-SunTag-SDG2-Rep2


title: BS-PCR-SunTag-SDG2-Rep1


title: ERK2-ELK1-D_Replicate3_Timepoint 2

description: Library name: Sample_10


title: ERK2-ELK1-D_Replicate3_Timepoint 0

description: Library name: Sample_8


title: 20210129-AKICT3FU1

description:
Library name: 20210129-AKICT3F-Fc1U1Z1Bs1
20210129-AKICT3FU1 (W12.Female.Single specimen)


title: ERK2-ELK1-D_Replicate2_Timepoint 1

description: Library name: Sample_6


title: 20210117-NMK0F2U1, 20210117-NMK0M2U1

description:
Library name: 20210117-NMK0-FM2-Fc1U1Z1Bs1
20210117-NMK0F2U1 (P0.Female.Left); 20210117-NMK0M2U1 (P0.Male.Right)


title: ERK2-ELK1-D_Replicate1_Timepoint 2

description: Library name: Sample_4


title: 20210117-NMK0F1U1, 20210117-NMK0M1U1

description:
Library name: 20210117-NMK0-FM1-Fc1U1Z1Bs1
20210117-NMK0F1U1 (P0.Female.Left); 20210117-NMK0M1U1 (P0.Male.Right)


title: ERK2-ELK1-D_Replicate2_Timepoint 0

description: Library name: Sample_5


title: DQGD129

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

institute: CNRS

description:
Library name: Sample24
total RNA-seq

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Reads have been mapped against the TAIR10 genome using hisat2 (v.2.2.1), with the following options: -p 4 -k 20 --max-intronlen 2000 --rna-strandness R.
Read counts were then extracted for each representative transcript using FeatureCounts (v.2.0.6) and the Araport11 annotation (“Araport11_GTF_genes_transposons.Jul2023.gtf”) by specifying “gene” as feature type (-t option) and “gene_id” as attribute type (-g option).
Differential expression analysis was performed in R (v.4.2.2) using the DESeq2 package (Love et al. 2014) (v1.38.3).
Assembly: TAIR10
Supplementary files format and content: Gene count matrices from FeatureCount are given (1 file for seeds, 1 file for flowers)

source_name: Flower

growth_protocol: Arabidopsis plants were grown on soil in long-day conditions with a 16 h light/8 h darkness photoperiod in a greenhouse (at 21/18 °C). The Arabidopsis thaliana plants used in this work are of Columbia accession (Col-0). Arabidopsis mutants analyzed in this study are T-DNA insertion lines described previously: urt1-1 (SALK_087647C) (Sement et al. 2013) and heso1-4 (GK-369H06-017072) (Joly et al. 2023; Vigh et al. 2024). Flowers (unopened flower buds) and dry mature seeds were harvested from a minimum of five plants each for three biological replicates. Samples were harvested two weeks after the onset of flowering for flowers and eight weeks after the onset of flowering for dry mature seeds, when all siliques of the plants were dry.

extract_protocol:
Total RNA from seeds was extracted according to the protocol (Meng and Feldman 2010) except for the last precipitation performed at -80 °C for 1 hour. RNA from flowers was extracted with TRI Reagent (EUROMEDEX, TR118-100) following the manufacturer's protocol. Total RNA was then purified using the RNeasy MinElute Cleanup kit (Qiagen, 74204).
Total RNA was treated with DNase I (Thermo Fisher Scientific, EN0521) and purified using the RNeasy MinElute Clean-up (Qiagen, 74204). RNA-seq libraries were then produced from 500 ng of DNase-treated RNAs using the TruSeq Stranded Total RNA Library Prep Plant (Illumina, 20020610) according to manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 2000 system by the GenomEast platform (paired-end sequencing, 2 × 50 bases).

value: Flower

tag: replicate

value: Biological replicate 3

value: heso1-4 urt1-1


title: DQGD128

description:
Library name: Sample23
total RNA-seq


title: ERK2-ELK1-D_Replicate1_Timepoint 1

description: Library name: Sample_3


title: ELK1-D Starting Library 5

description: Library name: Sample_1e


title: DQGD127

description:
Library name: Sample22
total RNA-seq


title: ERK2-ELK1-D_Replicate1_Timepoint 0

description: Library name: Sample_2


title: 20210108-NMK0FU1, 20210108-NMK0MU1

description:
Library name: 20210108-NMK0-FM-Fc1U1Z1Bs1
20210108-NMK0FU1 (P0.Female.Left); 20210108-NMK0MU1 (P0.Male.Right)


title: DQGD126

description:
Library name: Sample21
total RNA-seq

value: WT (Col-0)


title: ELK1-D Starting Library 4

description: Library name: Sample_1d


title: 20210108-NMK0FU2, 20210108-NMK0MU2

description:
Library name: 20210108-NMK0-FM-Fc1U2Z1Bs1
20210108-NMK0FU2 (P0.Female.Left); 20210108-NMK0MU2 (P0.Male.Right)


title: 20201228-NMK3MU2

description:
Library name: 20201228-NMK3-M-Fc1U2Z1Bs1
20201228-NMK3MU2 (W3.Male.Single specimen)


title: ELK1-D Starting Library 3

description: Library name: Sample_1c


title: 20201228-NMK3FU1

description:
Library name: 20201228-NMK3-F-Fc1U1Z1Bs1
20201228-NMK3FU1 (W3.Female.Single specimen)


title: ELK1-D Starting Library 2

description: Library name: Sample_1b


title: DQGD125

description:
Library name: Sample20
total RNA-seq

value: Biological replicate 2


title: ELK1-D Starting Library 1

description: Library name: Sample_1a


title: DQGD124

description:
Library name: Sample19
total RNA-seq


title: ChIP_rep1_input

description:
FG129
FG129

data_processing:
For standard ChIP-seq, bowtie2 was used to align paired-end RNA-seq data on the appropriate genome reference. For calibrated Scc1 ChIP-seq, bowtie2 was used in two rounds of alignments, first on C. glabrata (CBS138) and then on the appropriate S. cerevisiae genome reference, allowing the generation of IP and input (WCE) alignments that exclusively mapped on S. cerevisiae (and vice-versa for C. glabrata).
Only fragments with an insert size shorter than 1kb were retained. Only concordant pairs were retained, and fragments with a mapping quality lower than 10 were discarded. PCR duplicates were removed using samtools. When available, the input was similarly processed.
Fragment coverage was normalized by library depth (CPM) and converted into a genomic track (bigwig) using deepTools. Input-normalized fragment coverage was also generated, when possible, using bamCompare from deepTools with “--scaleFactorsMethod readCount”.
Assembly: GCF_000146045.2
Supplementary files format and content: Bigwig files for ChIP-seq coverage (IP, IP/Input and calibrated) are provided. Peaks are provided as .narrowPeak files.

organism: Saccharomyces cerevisiae

extract_protocol:
Cells were fixed using 4mL of fixative solution (50 mM Tris-HCl, pH 8.0; 100 mM NaCl; 0.5 mM EGTA; 1 mM EDTA; 30% (v/v) formaldehyde) for 30 min at room temperature (RT) with rotation. The fixative was quenched with 2mL of 2.5M glycine (RT, 5 min with rotation). The cells were then harvested by centrifugation at 3,500 rpm for 3 min and washed with ice-cold PBS. The cells were then resuspended in 300 mL of ChIP lysis buffer (50 mM HEPES KOH, pH 8.0; 140 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate; 1 mM PMSF; 2X Complete protease inhibitor cocktail (Roche)) and transferred in 2mL tubes containing glass beads (ozyme, P000913-LYSK0-A.0) before mechanical cells lysis. The soluble fraction was isolated by centrifugation at 2,000 rpm for 3min then transferred to sonication tubes (Covaris milliTUBE 1ml, 520135) and samples were sonicated to produce sheared chromatin with a size range of 200-1,000bp using a Covaris sonicator. After sonication the samples were centrifuged at 13,200 rpm at 4°C for 20min and the supernatant was transferred into 700µL of ChIP lysis buffer. 80µL (27µl of each sample) of the supernatant was removed (termed ‘whole cell extract [WCE] sample’) and store at -80°C. 5ug of antibody was added to the remaining supernatant which is then incubated overnight at 4°C (wheel cold room). 50µL of protein G Dynabeads or protein A Dynabeads was then added and incubated at 4°C for 2h. Beads were washed 2 times with ChIP lysis buffer, 3 times with high salt ChIP lysis buffer (50mMHEPES-KOH, pH 8.0; 500 mM NaCl; 1 mM EDTA; 1% (v/v) Triton X-100; 0.1% (w/v) sodium deoxycholate;1 mM PMSF), 2 times with ChIP wash buffer (10 mM Tris-HCl, pH 8.0; 0.25MLiCl; 0.5% NP-40; 0.5% sodium deoxycholate; 1mM EDTA;1 mMPMSF) and 1 time with TE pH7.5. The immunoprecipitated chromatin was then eluted by incubation in 120µL TES buffer (50 mMTris-HCl, pH 8.0; 10 mM EDTA; 1% SDS) for 15min at 65°C and the supernatant is collected termed ‘IP sample’. The WCE samples were mixed with 40µL of TES3 buffer (50 mM Tris-HCl, pH 8.0; 10 mM EDTA; 3% SDS). ALL (IP and WCE) samples were de-cross-linked by incubation at 65°C overnight. RNA was degraded by incubation with 2µL RNase A (10 mg/mL) for 1h at 37°C. Proteins were removed by incubation with 10µL of proteinase K (18 mg/mL) for 2h at 65°C. DNA was purified by a phenol/Chloroform extraction.
The triplicate IP samples were mixed in 1 tube and libraries for IP and WCE samples were prepared using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions. Paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed.

tag: background


title: ChIP_rep1_IP

description:
FG130
FG130


title: 20201228-NMK0FU1, 20201228-NMK0MU1

description:
Library name: 20201228-NMK0-FM-Fc1U1Z1Bs1
20201228-NMK0FU1 (P0.Female.Left); 20201228-NMK0MU1 (P0.Male.Right)