title: Mutated_oligo_pool_dCP_input_rep2

first: Alexander

last: Stark

address: Campus-Vienna-Biocenter 1

institute: The Research Institute of Molecular Pathology (IMP)

data_processing:
STARR-Seq paired-end reads were aligned to custom indexes containing the corresponding oligonucleotide sequences, using the align function from the Rsubread R package (version 2.12.2) with the following parameters: type= “dna”, unique= TRUE, maxMismatches= 3 (or = 5 for the mutant library). Only the pairs for which both reads could be aligned with expected orientations and positions were considered. Then, UMI sequences were retrieved, reads were collapsed as previously described (DOI: https://doi.org/10.1038/s41588-022-01048-5), and only the pairs with at least 5 reads in each of the two input replicates were considered for downstream analyses.
To calculate the activity of all pairs, we added one pseudocount read to UMI-collapsed counts and computed the log2 fold-change over input using DESeq2 (with at least two replicates). To normalize the samples between them and facilitate comparisons between different screens, we used the negative control sequence pair counts as scaling factors, so that the activities of negative control pairs are centered on zero. Before computing the individual activity of each candidate sequence, we first aimed at removing potential outlier negative control sequence, that might eventually show some activity in our screens. To do so, we assessed the activity of each negative control sequence by averaging its activity across all its observed combinations with other control sequences. Resulting activities were scale in R and only the 5’ and 3’ control sequences with a z-score value located between -1 and 1 were considered as valid, robust control sequences. Finally, these robust control sequences were used to compute the individual activity of each individual candidate sequence (which we refer to as “enhancers” for simplicity), by averaging their activities across all its observed combinations with at least 10 robust control sequences (otherwise, the individual candidate sequence was discarded). To classify an enhancer as active, we compared the activities of all its observed combinations with robust control sequences to the activities of control/control pairs using one-tailed Fisher’s exact tests (alternative= “greater”) followed by false discovery rate (FDR) multiple testing correction. Only the enhancer sequences with a log2 activity bigger than 1 and a FDR<0.05 were considered as active.
Assembly: dm3
Supplementary files format and content: For each replicate per condition, "umi_counts.txt" file contains the total ("total_counts" column) umi-collapsed counts ("umi_counts" column) for each combination of 5' ("L" column) and 3' ("R" column) enhancer IDs. Correspondance between IDs and enhancer sequences are available in Supplementary Tables 2,9,11.
Supplementary files format and content: For each oligo pool, the "FC_table.txt" file contains the log2 activity ("log2FoldChange" column) and the corresponding adjusted p.values ("padj" column) for each combination of 5' ("L" column) and 3' ("R" column) enhancer IDs (see Supplementary Tables 2, 9 and 11). The "ctlL" and "ctlR" specify whether 5' and 3' sequences were considered as robust controls, respectively. 5' and 3' individual activities are reported in the "indL" and "indR" columns, respectively, with "padjL" and "padjR" columns containing FDR-corrected p.values (only the enhancers with an individual acitivity>1 and a FDR<0.05 are considered active).
Library strategy: STARR-Seq

growth_protocol: Drosophila cells were cultured at 27ºC and passaged every 2-3 days. S2 cells were cultured in Schneider’s Drosophila Medium (SM, Gibco, #21720-024) supplemented with 10% heat inactivated FBS (Sigma, #F7524) and 1% Penicillin/Streptomycin. OSC cells were cultured in M3 Insect Medium supplemented with 0.6 mg ml-1 glutathione, 10% FBS, 10 mU ml-1 insulin and 10% fly extract.

extract_protocol:
UMI-STARR-Seq was performed as previously described (DOI: https://doi.org/10.1002/cpmb.105)
UMI-STARR-Seq libraries were UMI-tagged and constructed as previously described (DOI: https://doi.org/10.1002/cpmb.105)

treatment_protocol: For each biological replicate, 10^8 cells were resuspended in 400µL of a 1:1 dilution of HyClone MaxCyte electroporation buffer and serum-free SM, and electroporated with 20µg of the input libraries (see previous section) using the MaxCyte-STX system (‘Optimization 1’ protocol). For the induction of hormone-inducible enhancers, S2 cells were treated after 1h of recovery following electroporation, by adding 50μL of 10mg/mL with 20-Hydroxyecysone to 25mL flasks (~42μM final concentration).

value: input


title: WT H3 0 ChIP rep1

status: Public on Sep 05 2024

type: SRA

city: Strasbourg

first: Jean

last: Molinier

address: 12 rue du General Zimmer

country: France

institute: IBMP-CNRS

library_source: genomic

data_processing:
ChIP-seq analysis has been performed using the community curated nf-core ChIP-seq pipeline (version 1.2.2) with default parameters
Reads have been mapped on the reference genome (TAIR10) and MACS2 was used to call H3K9me2 broad peaks using H3 as a reference, and an effective genome size of 119,481,543 bp
Replicates were handled using the stringent irreproducibility discovery rate (IDR) framework and only peaks containing an IDR value superior or equal to a scaled IDR value of 540 were considered real, corresponding to an IDR of 0.05
Assembly: TAIR10
Supplementary files format and content: BigWig

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Plants were cultivated in vitro on solid GM medium [MS salts (Duchefa), 1% sucrose, 0.8% Agar-agar ultrapure (Merck), pH 5.8] and in a culture chamber under a 16 h light (light intensity ∼150 μmol m−2 s−1; 21°C) and 8 h dark (19°C) photoperiod

extract_protocol:
ChIP was performed upon sonication with the Bioruptor (Diagenode) using the Universal Plant Chip-seq Kit (Diagenode: C01010152) according manufacturers’ instructions
Libraries were prepared with the MicroPlex Library Preparation Kit v3  (Diagenode: C05010001) and the 24 Dual indexes for MicroPlex Kit v3 (Diagenode-: C05010003)

tag: tissue

value: Leaves

tag: ecotype

value: Col

tag: chip antibody

tag: genotype

value: WT

tag: treatment

value: no UV-C

tag: time point


title: Mutated_oligo_pool_dCP_screen_S2_rep1

city: Vienna

country: Austria

description:
150bp
Mutated_oligo_pool_dCP_S2_FC_table.txt

library_source: transcriptomic

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: S2 cells

tag: cell line

value: S2 cells

value: screen


title: 3D D5, rep2

status: Public on Sep 06 2024

city: La Jolla

first: Alyssa

last: Holman

state: CALIFORNIA

address: 9500 Gilman Drive Leichtag Biomedical Research Building 485

country: USA

institute: University of California San Diego

data_processing:
sciATAC reads were aligned with snaptools bwa aligner and converted to fragment files using Sinto. The ArchR package was used for processing, analysis, and visualization of the data.
Assembly: hg38
Supplementary files format and content: Mtx files were generated from ArchR. PeakMatrix.mtx contains all peaks for all samples. Corresponding PeakMatrix rows and columns are provided as csv files.

organism: Homo sapiens

source_name: H9 hPSC

growth_protocol: H9 hPSCs were maintained in mTESR1 with 5% CO2 at 37C.

extract_protocol:
Cells from hPSC, mesoderm, cardiac mesoderm, cardiac progenitor, and CM stages were dissociated and processed fresh for droplet-based snATAC-seq. Dissociated cells were stained with DAPI (Thermo Fisher Scientific). In total, 500,000 (DAPI-negative) were sorted and collected using a Sony SH800 sorter.
MinElute PCR Purification Kit (Qiagen) and size selection was performed with SPRISelect reagent (Beckman Coulter; 0.55× and 1.5×). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter; 1.5×). barcoded Tn5 transposomes

treatment_protocol: H9 hPSCs were differentiated into 2D and 3D CMs based on previously published protocols. DOI: 10.1038/nprot.2012.150; DOI: 10.1016/j.stem.2010.12.008

value: H9 hPSC

tag: cell type

value: hPSC

value: 3D cardiomyocyte differentiation


title: Mutated_oligo_pool_dCP_screen_S2_rep2


title: Mutated_oligo_pool_dCP_input_rep1

library_source: other

molecule: other


title: WT_oligo_pool_dCP_screen_OSC_rep2

description:
36bp
WT_oligo_pool_dCP_OSC_FC_table.txt

source_name: OSC cells

value: OSC cells


title: RNA_seq_WT_D0_rep1

city: Guangzhou

first: Yingying

last: Zhao

address: Kaiyuan Avenue

department: Chinese Academy of Sciences Guangzhou Branch

country: China

institute: Guangzhou Institutes of Biomedicine and Health

description: RNA seq of HN4 cell-induced organoid  at D0

data_processing:
The gene expression level of RNA-seq data was calculated by using  RSEM.
CUT&Tag reads were aligned to the hg38 genome using Bowtie2. Duplicate reads were removed with the function MarkDuplicates from Picard. The .bw files were generated by deepTools.
The gene expression level of scRNA-seq data was calculated by using  STAR.
The fragment files of scATAC-seq data was generated by using  Cell Ranger ATAC.
Assembly: hg38
Supplementary files format and content: .genes.results files contain the gene expression level of RNA-seq data
Supplementary files format and content: .bw files contain the CUT&Tag data that will be displayed in the Genome Browser, a web-based tool used to display a requested portion of a genome at any scale.
Supplementary files format and content: _data.tar.tar files contain the gene expression level of scRNA-seq data
Supplementary files format and content: _fragments.tsv.gz files contain the fragments of scATAC-seq data

source_name: brain organoid

growth_protocol: Cerebral organoids were generated according to the previously published protocols with dual smad inhibitors (Lancaster and Knoblich, 2014).

extract_protocol:
RNA-seq: To extract the total RNAs, organoids were collected and lysed with 1 ml TRIzol reagent (MRC, TR118-200), followed by adding 200 μL chloroform. After centrifugation (14,000 ×g for 10 min at 4°C), the total RNAs in the supernatant were precipitated with isopropanol. 1ug RNAs were subjected to RNA-seq library construction.  CUT&Tag: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). CUT&Tag assay was performed according to the Hyperactive In-Situ ChIP Library Prep Kit for Illumina (TD901-TD902, Vazyme).  scRNA-seq: Brain organoids at D21 and D30 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153).  snATAC-seq: Brain organoids at D21 were dissociated into a single-cell suspension using the Worthington Papain Dissociation System kit (Worthington, LK003153). Nuclei were extracted from organoid-derived single cells following Demonstrated Protocol of Nuclei Isolation for Single Cell ATAC Sequencing (10X GENOMICS).
RNA-seq: RNA Sequencing libraries were prepared according to the VAHTS mRNA-seq V3 Library Prep Kit for Illumina (NR611, Vazyme).   CUT&Tag: Library amplification was prepared using TruePrep Amplify Enzyme (TAE, Vazyme) followed by PCR purification (Vazyme).  scRNA-seq: 3'-library was constructed using Chromium Single Cell Reagent Kits v2 (10X GENOMICS).  snATAC-seq:Isolated nuclei were preceded to Tn5-mediated transposition, single cell barcoding, and library construction using Chromium Single Cell ATAC Reagent Kits (10X GENOMICS).

treatment_protocol: For rescue experiments, 1μM CHIR99021 (ChemBest Research Laboratories Ltd.) or PBS equivalent was added during D10 and D14

value: brain organoid

tag: time

value: untreated

tag: library strategy

value: RNA-seq

tag: library source

value: TRANSCRIPTOMIC


title: WT_oligo_pool_dCP_screen_S2_ecdysone_rep2

description:
36bp
WT_oligo_pool_dCP_S2_ecdysone_FC_table.txt

source_name: S2 cells + ecdysone

value: S2 cells + ecdysone


title: WT_oligo_pool_dCP_screen_S2_ecdysone_rep1


title: WT H3 2h ChIP rep2

value: UV-C


title: Focused_oligo_pool_hkCP_input_rep2

value: input


title: Focused_oligo_pool_hkCP_screen_S2_rep2

description:
36bp
Focused_oligo_pool_hkCP_S2_FC_table.txt


title: Focused_oligo_pool_hkCP_screen_S2_rep1


title: Focused_oligo_pool_dCP_screen_S2_rep2

description:
36bp
Focused_oligo_pool_dCP_S2_FC_table.txt


title: Focused_oligo_pool_dCP_input_rep2


title: Focused_oligo_pool_dCP_screen_S2_rep1


title: Focused_oligo_pool_dCP_input_rep1


title: WT_2kb_spacer_dCP_screen_S2_rep2

description:
36bp
WT_2kb_spacer_dCP_S2_FC_table.txt


title: WT_2kb_spacer_dCP_screen_S2_rep1

description:
36bp
WT_2kb_spacer_dCP_S2_FC_table.txt


title: WT_2kb_spacer_dCP_input_rep2


title: WT_oligo_pool_dCP_input_rep2


title: WT_oligo_pool_dCP_screen_S2_rep1

description:
36bp
WT_oligo_pool_dCP_S2_FC_table.txt


title: WT_oligo_pool_dCP_input_rep1


title: WT_oligo_pool_dCP_screen_S2_rep2

description:
36bp
WT_oligo_pool_dCP_S2_FC_table.txt


title: WT_oligo_pool_dCP_screen_OSC_rep1

description:
36bp
WT_oligo_pool_dCP_OSC_FC_table.txt


title: Synovial fibroblast, siDLX4c

city: New York

first: Teresina

last: Laragione

state: NY

address: 1468 Madison Ave

department: Medicine

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. Inthis step, clean data (clean reads) were obtained by removing reads containing adapter, readscontaining ploy-N and low quality reads from raw data. At the same time, Q20, Q30andGCcontent the clean data were calculated. All the downstream analyses were based on thecleandata with high quality
Remove reads with adapter contamination.
Remove reads when uncertain nucleotides constitute more than 10 per cent of either read (N > 10%).
Remove reads when low-quality nucleotides (Base Quality less than 5) constitute more than 50 per cent of the read.
Raw image data file from high-throughput sequencing(like Illumina ) was transformed to Sequenced Reads(called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw Data is stored in FASTQ(fq) format files, which contain reads sequence and corresponding base quality
Assembly: Hg19
Supplementary files format and content: The abundance of transcript reflects gene expression level directly. In RNA-seq experiment, we estimate gene expression level by the abundance of transcripts(count of sequencing) that mapped to genome or exon. Reads count is proportional to be proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments.(Mortazavi et al. 2008)
Supplementary files format and content: Tab-delimited text file includes fpkm for each sample

molecule: total RNA

source_name: synovial fibroblast

growth_protocol: Primary FLS cell lines from patients with RA were generated as previously described (15). Briefly, freshly obtained synovial tissues were minced and incubated with a solution containing DNase (0.15mg/ml), hyaluronidase type I-S (0.15 mg/ml), and collagenase type IA (1 mg/ml) (Sigma, St.Louis, MO) in DMEM (Invitrogen, Carlsbad, CA) for 1 hour at 37°C. Cells were washed and re-suspended in complete media containing DMEM supplemented with 10% FBS (Invitrogen), glutamine (300 ng/ml), amphotericin B (500 ng/ml) (Sigma), and gentamicin (20 μg/ml) (Invitrogen). After overnight culture, non-adherent cells were removed and adherent cells kept in culture. All experiments were performed with FLS after passage four (>95% FLS purity).

extract_protocol:
Total RNAextracted by Qiagen RNAeasy kit, and quantified by Nanodrop. 400 ng per sample was sent to Novogene (Beijing, China) for sequencing and analyses
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional libraryor dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, amplification, and purificationFor the directional library, it was ready after end repair, A-tailing, adapter ligation, sizeselection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer forsize distribution detection. Quantified libraries will be pooled and sequenced on Illuminaplatforms, according to effective library concentration and data amount. The clustering of the index-coded samples was performed according to the manufacturer’sinstructions. After cluster generation, the library preparations were sequenced on an Illuminaplatform and paired-end reads were generated

treatment_protocol: Dharmacon SMARTpool siRNA targeting each gene or a non-coding control were transfected into RA FLS according to the manufacturer’s instructions. Cells were then incubated at 37°C for 24–48 hours prior to initiating any assay. Knockdown was confirmed with qPCR.

value: synovial fibroblast

value: DLX4 Knockdown


title: Synovial fibroblast, siDLX4b


title: Synovial fibroblast, siDLX4a


title: ChIP-seq RBM FLAG ERα Repeat 1

city: Bangalore

first: Dimple

last: Notani

address: National Centre for Biological Sciences Tata Institute of Fundamental Research Bellary Road

department: Cellular Organization and Signallinga

country: India

institute: National Centre for Biological Sciences

data_processing:
For ChIP-seq analysis the raw reads obtained from the sequencing were aligned to the hg19 reference genome using Bowtie2. Reads with a quality score less than 20 were filtered out using the Filter Sam or Bam tool. Peaks were called using MACS2  with default settings.
For the fRIP-seq analysis the adaptor sequences were removed from the reads using Cutadapt, followed by alignment to the hg19 reference genome using RNA STAR. Duplicate reads were removed using UMI-tools deduplicate. Regions of fRIP-seq IP enrichment were called using MACS2with the fRIP-seq input as the control file. The log2FC of fRIP-seq IP /fRIP-seq input was calculated using the aligned BAM file with bamcompare.
For EU-seq analysis, the raw reads were aligned to hg19 using Bowtie2. PCR duplicates were removed using MarkDuplicates from Picard Tools. Read coverage on known E2 upregulated genes was calculated using multiBamSummary.
Assembly: hg19
Supplementary files format and content: bigwig and narrow peaks

source_name: Breast, mammary gland

growth_protocol: MCF-7 cells were maintained in DMEM with 10% FBS. For experiemtns MCF-7 cells were grown in stripping media with 5% characol stripped FBS for 72 hours.

extract_protocol:
For ChIP-seq experiment, genomic DNA was isolated as per standard ChIP-seq protocol. For fRIP-seq, RNA crosslinked to ERα were pulldown using anti ERα followed by purification of the total RNA using trizol. For EU-seq cells were chased with EU for 45 mins and total RNA was isolated using trizol. Further EU labelled RNA was biotinylated using Click Chemistry reaction and pulldown using Streptavidin beads using standard protocol. The pulldown RNA was extracted using Trizol and used for library preparation.
ChIP-seq library preparation using the NEBNext® Ultra™II DNA Library Prep kit with Sample Purification Beads (Catalogue-E7103L) following the manufacturer's protocol. The fRIP-seq purified RNA was used for preparing RNA-seq libraries, using the NEBNext rRNA Depletion Kit v2 and NEBNext Ultra II Directional RNA Library Prep, following the manufacturer's protocol. For EU-seq the nasecent RNA was converted to cDNA using the SuperScript™ IV First-Strand Synthesis System (catalogue number: 18091050). The second strand of cDNA was synthesized using the NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads (Catalogue no-E7765L). The double-stranded DNA was further fragmented, and the library was prepared using the NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina (E7805L), following the manufacturer's protocol.

treatment_protocol: MCF-7 cells were treated with 100nm of 17β estradiol for 1 hour followed by the either ChIP-seq or fRIP-seq. For EU-seq MCF-7 cells were treated with 100nm of 17β estradiol and 45 mins of EU.

value: Breast, mammary gland

value: epithelial cell


title: Synovial fibroblast, siCTL71b

value: WT

value: sictl


title: Synovial fibroblast, siCTL71a


title: fRIP-seq Veh ERα IP Repeat 1

value: EtOH


title: W-0-1-Input

city: Shanghai

first: Minhang

last: Yuan

address: Fenglin

department: Shanghai Institute of Plant Physiology and Ecology

institute: Chinese Academy of Sciences

data_processing:
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to TAIR RefSeq v10 using BWA 0.7.5a-r405  for ChIP-seq, all with default settings.
For ChIP-seq, MACS1.3.7 was used to identify read-enriched regions (peaks) with combined criteria: P value < 1e–5 and fold-change >32.  ChIP-seq data Target genes were defined as genes with a peak within or nearby the gene body (±2 kb).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Peak files and bigwig files were provided.

source_name: Wildtype (Col-0)_Untreated

growth_protocol: Plants  were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with H3K27me3 antibody.
Libraries were prepared according to Novogene Corporation (Beijing, China) protocols.Subsequently, pair-end sequencing of samples was performed on Illumuna platform (Illumina, CA, USA)

treatment_protocol: Four-week-old Arabidopsis plant leaves were treated in growth chambers, with relative humidity about 95% and temperature at 22℃ with 12/12h day/night photoperiod.

value: Wildtype (Col-0)

value: Untreated


title: siCTL_PSS-1

city: Dublin

first: Oleksii

middle: S

last: Rukhlenko

address: Systems Biology Ireland, University College Dublin

department: Systems Biology Ireland

country: Ireland

institute: University College Dublin

data_processing:
Processing was performed in R using rsubread package
Differential expression analysis was done using DeSeq2
Assembly: hg38
Supplementary files format and content: csv file with raw counts
Supplementary files format and content: csv files with DeSeq2 output for differentially expressed genes

source_name: Primary cells

growth_protocol: HUVECs were maintained in EGM2 complete medium at 5% CO2 and 37 deg C humidified incubator

extract_protocol:
Qiagen RNeasy Plus mini kit
PolyA selection on oligodT beads by random priming

treatment_protocol: HUVECs were treated with silencing RNAs as described and treated with different FSS levels for 16h before collection of RNA

value: Primary cells

value: HUVEC

value: Endothelial

value: Control NT siRNA

value: PSS


title: siCTL_PSS-2


title: siCDK2_STAT-5

value: siRNA for CDK2

value: STAT, control for CDK2 KN


title: siCDK2_STAT-3


title: siCTL_STAT-1


title: siCTL_STAT-2


title: siCTL_PSS-3


title: siCTL_STAT-3


title: WT_2kb_spacer_dCP_input_rep1

value: input


title: siCDK2_STAT-1


title: siCDK2_PSS-2


title: siCDK2_PSS-3


title: STATIC-1

value: STAT, control for PSS and OSS


title: STATIC-3


title: STATIC-2


title: OSS-1

value: OSS


title: siCDK2_PSS-4


title: OSS-2


title: Synovial fibroblast, siCTL71c

value: synovial fibroblast


title: UCS-treated_3

first: Ruojing

last: Huang

address: Huangpu Street 613

department: Department of Ophthalmology

institute: The First Affiliated Hospital of Jinan University

data_processing:
Adaptor and/or low-quality bases were trimmed from the sequenced reads
The clean reads were then mapped to GRCm38 using HISAT and the counts were extracted
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Mus musculus

source_name: cornea

extract_protocol:
RNA was extracted using Qiagen RNeasy kit as per manufacturer's protocol. RNA quality was inspected using Agilent 2100 Fragment analyzer
RNA libraries was constructed using TruSeq Stranded Total RNA Library Prep kit following manufacturer's protocol

treatment_protocol: 5 ul of 0.2% BAK was administered to each eye of the mice daily for a consecutive 14-day period. For UCS and UCPRP treatment, 5 ul of 20% UCS and UCPRP was respectively administered to the mice cornea thrice daily for a consecutive 10-day period.

value: cornea

value: BAK-injured (UCS treated)


title: PSS-3


title: PSS-2


title: PSS-1


title: COLI

city: Blacksburg

first: Maria

last: Sharakhova

state: VIRGINIA

address: 360 West Campus Drive

department: Entomology

institute: Virginia polytechnic institute and state university

data_processing:
The sequence quality assessment was performed using FastQC software v.0.12.1
Juicer Pipeline was used to build the contact matrices and Hi-C heatmaps
Assembly: AaegL5
Supplementary files format and content: hic files include contact meatices and Hi-C heatmaps
Supplementary files format and content: text files include experiment description for hic files

organism: Aedes aegypti

source_name: 2-5 day Adult

extract_protocol:
The proximally-ligated DNA is prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)
Libraries are prepared with Arima-HiC+ for High Coverage kit (Arima Genomics)

value: 2-5 day Adult

tag: strain

value: COLI

tag: Sex

value: pooled male and female


title: StaticLSS-3

value: STAT, control for LSS


title: StaticLSS-2

value: Primary cells


title: HSS-2

value: HUVEC

value: Control

value: HSS


title: HSS-1

value: Endothelial


title: LSS-3

value: Control NT siRNA

value: LSS


title: HSS-3


title: STA-1

value: STAT, control for HSS


title: LSS-1


title: StaticLSS-1


title: LSS-2


title: single cell ATAC seq library of human samples (day0 to 10)

city: Leiden

first: Max

last: Fernkorn

address: Einsteinweg 55

department: Leiden Academic Centre for Drug Research (LACDR)

country: Germany

institute: University Leiden

library_source: genomic single cell

data_processing:
For time course single-cell multiome sequencing experiments, CellRanger ARC (v2.0.0) provided by 10x Genomics was used to demultiplex binary Illumina base call (BCL) files into FASTQ files, align the data against the GRCh38 (human), GRCm39 (mouse), and Macaca_fascicularis_6.0 (cynomolgus) reference, filter reads, as well as count barcodes and scRNA and scATAC molecules to generate feature-barcode matrices.
To mitigate technical cross-species batch effects, we pooled an equal number of cells from the three species for each of the samples.
Assembly: human genome GRCh38 (GENCODE v32/Ensembl98) and mouse genome GRCm39 obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every species (containing RNA counts and ATAC counts for all timepoints): matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx; the numbers 1 to 8 in the cell barcodes do correspond to the timepoints 0 to 10 days (0d, 8h, 1d, 2d, 3d, 4d, 7d and 10d).

source_name: H9 human embryonic stem cells

growth_protocol: PSCs were singularized using Accutase (Sigma Aldrich) and counted on the Countess II FL Automated Cell Counter (Invitrogen). For human ESCs and cynomolgus iPSCs 1.25 x 105 cells/cm2 were seeded onto Matrigel coated plates in UPPS media supplemented with 10 µM Y-27632 (R&D Systems) and incubated overnight, resulting in confluent cultures the following day for each species. For neural induction, media was exchanged to NPC differentiation and maintenance media consisting of 1:1 DMEM/F12 and Neuropan (PAN Biotech) supplemented with 0.5x N2 and B27 supplements, 1x MEM-NEAA, 1x GlutaMAX, 0.1 mM 2-Mercaptoethanol, 5 µg/mL Insulin, human recombinant (all Thermo Fisher Scientific), 10 µM SB431542 and 100 nM LDN193189 (both Peprotech). Cells were washed with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific) before daily media exchange.

extract_protocol:
Time course scATAC and scRNA libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturer’s protocol. Samples were collected at 0h, 8h, 1d, 2d, 3d, 4d, 7d and 10d post neural induction and cells of all three species were combined in equal amounts prior to the library preparation. The aimed target recovery was 10,000 single nuclei for sequencing.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturers instructions
scRNAseq and scATACseq

treatment_protocol: Neural induction for up to 10 days

value: H9 human embryonic stem cells

value: UPPS (pluripotency, day0) and NPC differentiation and maintenance media

tag: library type

value: scATAC


title: OSS-3

value: OSS


title: single cell gene expression library of human samples (day0 to 10)

library_source: transcriptomic single cell

value: mRNA


title: NGN2_Glut-58

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

institute: NorthShore University HealthSystem

data_processing:
ATAC-seq data analysis and peaking calling All raw sequence reads generated by Illumina NextSeq were demultiplexed at the University of Minnesota Genomics Center and provided as 2×75 bp paired-end FASTQ files (targeting 60 M reads per sample). Adapter remnants, low-quality reads, and low QSEQ short sequences near either end of reads were processed by Trimmomatic v0.39 (ILLUMINACLIP:NexteraPE-PE.fa:2:30:7, SLIDINGWINDOW:3:18, MINLENGTH:26). Only paired-end reads that survived Trimmomatic processing were retained.
The FASTQ files were individually mapped against the human genome reference file including decoy sequences (GRCh38p7.13/hg38, 1000 Genome Project) using bowtie2 (-x 2000, -mm --qc-filter –met 1 –sensitive –no-mixed -t) and subsequently merged and sorted as BAM-formatted files using samtools v1.14, with only uniquely high-quality mapped reads (MAPQ > 30, SAM flags 0x1, 0x2) retained. Picard tools MarkDuplicate was then used to remove all PCR and optical duplicated reads from the BAM file.
The insert size distribution histograms of each sample were individually generated using deepTools computeMatrix. All analyzed ATAC-seq samples passed standard QC based on the characteristic nucleosomal periodicity of the insert fragment size distribution and high signal-to-noise ratio around transcription start sites (TSS).
Assembly: hg38
Supplementary files format and content: bigwig

source_name: iPS-derived NGN2-induced Glutamatergic neuron

growth_protocol: iMG was generated from hiPSC lines as we described using the Brownjohn’s method. hiPSC were cultured in mTeSR plus media (100-0276, StemCell) with 2 ml daily media changes. At least 2 days after passaging, when hiPSC reached confluency ~80% they were dissociated with Accutase (07920, StemCell) and plated at 10,000 cells per well in 96-well round bottom ultra-low attachment plates (7007, Corning) in 100 µL EB media, and plates were centrifuged at 300 g for 3 min. Astrocyte (iAst) differentiation from NPCs; iAst were generated from NPCs using TCW’s protocol (PMID: 28757165). NPCs were maintained in Neural Expansion Medium and split approximately 1:3 every week with Accutase (07920, StemCell). Neural Expansion Medium was prepared as 245 ml Neurobasal Medium (21103049, Thermofisher), 245 ml Advanced DMEM/F-12 media (12634010, Thermofisher) and 10 ml Neural Induction Supplement (A1647801, Thermofisher).

extract_protocol:
ATAC-seq sample preparation was performed consistent with our previous publications. Briefly, 75,000 viable cells were used per run. The cells were lysed in ATAC-Resuspension Buffer (RSB) containing 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin for 3 min on ice to release nuclei. Isolated nuclei were washed and resuspended in a transposition mixture. After which, samples were incubated at 37°C for 30 min on a thermomixer at 1,000 rpm. Transposed DNA was purified by the DNA Clean and Concentrator-5 Kit (Zymo).
Eluted DNA was shipped to the University of Minnesota Genomic Center for library preparation and ATAC-seq on an Illumina NovaSeq 6000.

treatment_protocol: (MG)EB media was prepared by adding to the complete mTeSR media 50 ng/ml BMP-4 (120-05, PeproTech), 20 ng/ml SCF (300-07, PeproTech), 50 ng/ml VEGF-121 (100-20A, PeproTech), and ROCK inhibitor (1254/1, R&D Systems). Cells were cultured for 4 days, with half media change after 2 days. On day 4, 16 EBs were plated on a 6-well plate and cultured in 3 ml hematopoietic media with 2 ml media exchanges every 5 days. Hematopoietic media was prepared by adding to the X-VIVO 15 (BE08-879H, Lonza), 1% GlutaMax (35050061, Thermofisher), 1% Pen/strep (10378016, Thermofisher), 55 µM β-mercaptoethanol (21985023, Thermofisher), 100 ng/ml M-CSF (300-25, PeproTech), and 25 ng/ml IL-3 (200-03, PeproTech). After 5 days culturing EBs in hematopoietic media, PMPs started to appear in the suspension and were produced continuously in suspension for 34 days. After 10 days of culturing EBs, PMPs could be harvested from suspension and plated in RPMI 1640 media (21870076, Thermofisher) at 180,000 cells/cm2 in 6- or 12-well plates. After 1 hr, PMPs adhered to surface and media was changed to complete iMG media. Full media changes were done every 2 days. Complete iMG media was prepared with RPMI 1640 by adding 10% FBS (S11150H, R&D Systems), 1% Pen/strep, 1% GlutaMax, 100 ng/ml IL-24 (200-34, PeptroTech), and 10 ng/ml GM-CSF (300-03, PeproTech). Final differentiation of PMPs into iMG occurred over 25 days and cells could be kept for at least 1 month in this format; (iAst) NPCs were differentiated to astrocytes by seeding dissociated single cells at 15,000 cells/cm2 density on matrigel-coated plates in Astrocyte medium (1801, ScienCell: astrocyte medium, 2% FBS (0010), astrocyte growth supplement (1852) and 10U/ml Pen/Strep solution (0503)). Initial NPC seeding density and single cell dissociation are critical, particularly during the first 30 days of differentiation, in order to efficiently generate a homogenous population of astrocytes. At day -1, after 5-10 min incubation with accutase at 37˚C, NPCs were pipetted with a p1000 pipette 3-5 times, in order to yield a single cell suspension but limit cell death. Additional NPC medium was added and cells were transferred to a 15ml tube, spun at 250g for 5min, and plated on a matrigel-coated plate in Neural Expansion Medium medium. At day 0, NPC medium was switched to Astrocyte medium. From day 2, cells were fed every 48 hr for 20-30 days. When the cells reached 90- 95% confluency (approximately every 6-7 days), they were split to the initial seeding density (15,000 cells/cm2) as single cells in Astrocyte medium, and cultured on matrigel, following 5-10 min incubation with accutase, pipetting, and washing with DMEM (35050061, Thermofisher). After 30 days of differentiation, astrocytes could be split 1:3 every week with accutase and expanded up to 120 days (15-17 passages) in Astrocyte medium. Final differentiation of iAstoccurred over 30 days.

value: NGN2-induced Glutamatergic neuron


title: NGN2_Glut-61

value: iPS-derived NGN2-induced Glutamatergic neuron


title: NGN2_Glut-55


title: NGN2_Glut-52


title: NGN2_Glut-49


title: brain organoid, hypoxia, batch 2

city: Chicago

first: Yoav

last: Gilad

department: Genetic Medicine

institute: University of Chicago

description: 10x Genomics

data_processing:
cellranger v7.0.0
Assembly: hg38
Supplementary files format and content: TSV files ending in features.tsv.gz contain gene names (row names of count matrices) output from cellranger.
Supplementary files format and content: TSV files ending in barcodes.tsv.gz contain cell barcodes (column names of count matrices) output from cellranger.
Supplementary files format and content: MTX files ending in mtx.gz contain UMI counts for each gene and cell output from cellranger.
Supplementary files format and content: VCF file contains genotype data used for assigning cells to parental cell lines.

extract_protocol:
Organoids were dissociated to single cells using papain in the presence of TTX, D-AP5, and actinomycin D.  Single-cell encapsulation, RNA extraction, and cDNA synthesis were performed according to manufacturer's instructions (10x Genomics)
Libraries were prepared according to the manufacturer's instructions (10x Genomics, HT kit v3.1)

value: brain organoid

value: hypoxia (1% oxygen), 24 hours


title: brain organoid, chronic hyperoxia, batch 2

description: 10x Genomics

value: hyperoxia (21% oxygen), chronic


title: brain organoid, hyperoxia, batch 1

description: 10x Genomics

value: hyperoxia (21% oxygen), 24 hours


title: brain organoid, hypoxia, batch 1

description: 10x Genomics


title: brain organoid, normoxia, batch 2

description: 10x Genomics

value: normoxia (10% oxygen)


title: brain organoid, normoxia, batch 1

description: 10x Genomics


title: brain organoid, hyperoxia, batch 2

description: 10x Genomics


title: STA-3

value: Primary cells

value: HUVEC

value: Control


title: NGN2_Glut-47


title: STA-2

value: Endothelial


title: NGN2_Glut-48


title: NGN2_Glut-34


title: NGN2_Glut-33


title: NGN2_Glut-32


title: NGN2_Glut-26


title: NGN2_Glut-39


title: NGN2_Glut-42


title: NGN2_Glut-43


title: GA-66

source_name: iPS-derived GABAergic neuron

value: iPS-derived GABAergic neuron

value: GABAergic neuron


title: GA-65


title: NGN2_Glut-38


title: GA-63


title: GA-60


title: GA-56


title: GA-55


title: GA-52


title: GA-49


title: GA-42


title: GA-39


title: GA-51


title: GA-20


title: GA-33


title: GA-17


title: GA-19


title: NGN2_Glut-57


title: GA-18


title: GA-16


title: GA-13


title: GA-09


title: GA-10


title: GA-08


title: GA-12


title: GA-05


title: GA-04


title: GA-03


title: GA-35


title: GA-21


title: GA-06


title: DN-54

source_name: iPS-derived dopaminergic neuron

value: iPS-derived dopaminergic neuron

value: dopaminergic neuron


title: GA-02


title: DN-48


title: GA-15


title: GA-14


title: DN-47


title: DN-46


title: DN-43


title: DN-45


title: DN-44


title: DN-40


title: GA-11


title: DN-42


title: DN-39


title: GA-07


title: DN-38


title: DN-37


title: DN-26


title: DN-36


title: DN-27


title: DN-25


title: DN-23


title: DN-22


title: DN-21


title: DN-49


title: DN-19


title: DN-20


title: DN-16


title: OSXCre Oregon

city: Provo

first: Jared

middle: J

last: Barrott

state: UT

address: 701 E University Pkwy, 4005 LSB

department: Cell Biology and Physiology

institute: Brigham Young University

data_processing:
Reference fasta files were generated by combining the chromosome sequences from mm10 with splice junction sequences generated by USeq (v8.8.8) MakeTranscriptome using Ensembl transcript models
Reads were aligned with Novoalign (v2.08.01), allowing up to 50 alignments per read. USeq’s SamTranscriptomeParser selected the best alignment for each and converted the coordinates of reads aligning to splices back to genomic space.
Differential gene expression was measured using USeq DefinedRegionDifferentialSeq, which counts the number of reads aligned to each gene and then calls DESeq2 (v1.26.0) using default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Osteosarcoma

growth_protocol: Mice were > 6 months of age and represented male and female

extract_protocol:
Total RNA was isolated with the RNeasy mini kit (QIAGEN) per manufactuer's recommendations.
RNA was prepared using the Illumina TruSeq RNA kit (Illumina), checked with the Bioanalyzer RNA 6000 chip (Agilent Technologies), captured using the RiboZero method (Illumina), and 50-cycle end-read sequenced on an Illumina HiSeq 2000.

treatment_protocol: Tamoxifen was administered at 1 month of age by injecting a solution of tamoxifen at a concentration of 20 mg/mL intraperitoneally at a dose of 400 μg of tamoxifen per gram of mouse.

value: Osteosarcoma


title: DN-17


title: DN-14


title: DN-12


title: DN-13


title: DN-15


title: DN-10


title: DN-08


title: DN-04


title: DN-11


title: DN-03


title: DN-06


title: Ast-66

source_name: iPS-derived astrocyte

value: iPS-derived astrocyte

value: astrocyte


title: DN-05


title: Ast-64


title: DN-02


title: Ast-61


title: Ast-60


title: Ast-58


title: Ast-56


title: Ast-51


title: Ast-52


title: Ast-50


title: Ast-53


title: Ast-55


title: Ast-35


title: Ast-34


title: Ast-33


title: Ast-32


title: MG-66

source_name: iPS-derived microglia

value: iPS-derived microglia

value: microglia


title: jmj27 H3K9me2 30 min ChIP rep2

source_name: Leaves

value: Leaves

value: Col

value: UV-C

value: 30 min


title: MG-65


title: MG-63


title: Ast-65


title: Ast-31


title: MG-61


title: MG-57


title: MG-58


title: Ast-63


title: MG-53


title: MG-52


title: MG-62


title: MG-51


title: MG-35


title: MG-34


title: MG-60


title: MG-55


title: MG-30


title: MG-32


title: MG-31


title: MG-29


title: MG-50


title: MG-28


title: MG-21


title: MG-64


title: MG-20


title: MG-19


title: Focused_oligo_pool_hkCP_input_rep1

value: input


title: MG-16


title: MG-17


title: MG-12


title: MG-13


title: MG-15


title: MG-14


title: MG-09


title: MG-08


title: MG-05


title: MG-04


title: MG-03


title: MG-33


title: BeWo_siTFEB_FRSK_2

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files including raw counts

source_name: BeWo

growth_protocol: BeWo cells were obtained from ATCC and cultured in F-12K medium (Kaighn's Modification of Ham's F-12 Medium) (cat. no. 30-2004, ATCC) supplemented with 10% FBS (cat. no. ECS0180L, Euroclone), penicillin (100 IU/ml) and streptomycin (100 μg/ml) (cat. no. ECB3001D, Euroclone).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen) and 250 ng of total RNA was used for the construction of sequencing libraries.
3'DGE mRNA-seq research grade sequencing service (Next Generation Diagnostics srl)
3'DGE mRNA-seq

treatment_protocol:
To stimulate BeWo trophoblast differentiation, cells were treated with 100uM of Forskolin (F6886, Sigma-Aldrich). 250nM of Torin-1 was used to promote TFEB nuclear translocation.
siRNA transfection was performed in suspension using Lipofectamine RNAiMAX Transfection Reagent for 72hrs. siRNA negative control and siTFEB were used at final concentration of 20nM. The day after transfection, to stimulate BeWo trophoblast differentiation, cells were treated with 100uM of Forskolin (F6886, Sigma-Aldrich) for 48 hours.

value: BeWo

value: choriocarcinoma

value: WT

value: siRNA transfection + FRSK


title: BeWo_siTFEB_FRSK_4


title: BeWo_siTFEB_FRSK_3


title: BeWo_siTFEB_DMSO_4

value: siRNA transfection


title: BeWo_siTFEB_FRSK_1


title: BeWo_siTFEB_DMSO_3


title: BeWo_siTFEB_DMSO_2


title: BeWo_siTFEB_DMSO_1


title: BeWo_SCR_FRSK_2


title: BeWo_SCR_FRSK_1


title: MG-02


title: BeWo_SCR_DMSO_4


title: MG-06


title: BeWo_SCR_DMSO_3


title: BeWo_SCR_DMSO_2


title: BeWo_SCR_FRSK_4


title: BeWo_SCR_FRSK_3


title: BeWo_SCR_DMSO_1


title: CL14_breast_biopsy_M2

type: RNA

city: Cluj-Napoca

first: Oana

last: Baldasici

state: Cluj

address: Republicii 34-36

country: Romania

institute: The Oncology Institute Cluj-Napoca

description: Gene expression between mammosphere formation groups

hyb_protocol: The probes were hybridized for 17 h at 65oC on Agilent SurePrint G3 custom GE 4x180k arrays

scan_protocol: The slides were scanned with Agilent G2505C Microarray Scanner at 3 µm resolution

data_processing: Microarray images were processed with Agilent Feature Extraction software v. 11.5.1.1.

source_name: CL14,breast biopsy,mammosphere formation M2

label_protocol: Microarray probes labeled with Cy3 were synthesized from 100 ng of total RNA with Low Input Quick Amp Labeling Kit and checked for quality and quantity with NanoDrop ND-1000 (Thermo Fischer Scientific)

extract_protocol: Frozen biopsies were homogenized in TRIzol Reagent (Ambion, Life Technologies, Carlsbad, CA, USA) using a Miccra D-1 (Miccra GmbH, Mullheim, Germany) polytron and processed for total RNA extraction according to manufacturer instructions.

treatment_protocol: Breast tissue biopsies were collected by core needle aspiration under ultrasound guidance before patients received any treatment. First biopsies were sent for pathologic analysis, while second biopsies were used for mammosphere functional assay. Whenever possible, third biopsies were collected in RNAlater (Invitrogen, Waltham, MA, USA) and stored in liquid nitrogen for phenotype-associated molecular profiling.

value: breast tissue biopsy

tag: mammosphere formation group


title: BeWo_TFEB_KO_TFEB-GFP_TORIN-1_4

value: TFEB-KO

value: 48 hours


title: CL60_breast_biopsy_M2

source_name: CL60,breast biopsy,mammosphere formation M2


title: BeWo_TFEB_KO_TFEB-GFP_TORIN-1_3


title: CL66_breast_biopsy_M2

source_name: CL66,breast biopsy,mammosphere formation M2


title: BeWo_TFEB_KO_TFEB-GFP_TORIN-1_2


title: CL40_breast_biopsy_M1

source_name: CL40,breast biopsy,mammosphere formation M1


title: CL62_breast_biopsy_M1

source_name: CL62,breast biopsy,mammosphere formation M1


title: CL74_breast_biopsy_M1

source_name: CL74,breast biopsy,mammosphere formation M1


title: CL77_breast_biopsy_M1

source_name: CL77,breast biopsy,mammosphere formation M1


title: BeWo_TFEB_KO_TFEB-GFP_TORIN-1_1


title: CL46_breast_biopsy_M2

source_name: CL46,breast biopsy,mammosphere formation M2


title: CL76_breast_biopsy_M0

source_name: CL76,breast biopsy,mammosphere formation M0


title: CL64_breast_biopsy_M2

source_name: CL64,breast biopsy,mammosphere formation M2


title: BeWo_TFEB_KO_TFEB-GFP_FRSK_4

value: FRSK


title: BeWo_TFEB_KO_TFEB-GFP_FRSK_3


title: CL36_breast_biopsy_M2

source_name: CL36,breast biopsy,mammosphere formation M2


title: CL63_breast_biopsy_M1

source_name: CL63,breast biopsy,mammosphere formation M1


title: BeWo_TFEB_KO_TFEB-GFP_FRSK_2


title: Gene expression library, day 4, Human

data_processing:
3’ Gene Expression libraries of each time point (days 0, 2 and 4) were mapped against the mouse genome mm10 (GENCODE vM23/Ensembl98), the human genome GRCh38 (GENCODE v32/Ensembl98), both obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0), obtained from Ensembl. Mapping was performed using CellRanger 7.2.0 (10x Genomics). Using the cellranger multi function, sample demultiplexing was done in parallel to read alignment.
Assembly: mouse genome mm10 (GENCODE vM23/Ensembl98), the human genome GRCh38 (GENCODE v32/Ensembl98), both obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every demultiplexed sample: matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx

source_name: H9 human embryonic stem cells

growth_protocol: PSCs were singularized using Accutase (Sigma Aldrich) and counted on the Countess II FL Automated Cell Counter (Invitrogen). For human ESCs and cynomolgus iPSCs 1.25 x 105 cells/cm2 and for mouse EpiSCs 6.25 x 104 cells/cm2 were seeded onto Matrigel coated plates in UPPS media supplemented with 10 µM Y-27632 (R&D Systems) and incubated overnight, resulting in confluent cultures the following day for each species. For neural induction, media was exchanged to NPC differentiation and maintenance media consisting of 1:1 DMEM/F12 and Neuropan (PAN Biotech) supplemented with 0.5x N2 and B27 supplements, 1x MEM-NEAA, 1x GlutaMAX, 0.1 mM 2-Mercaptoethanol, 5 µg/mL Insulin, human recombinant (all Thermo Fisher Scientific), 10 µM SB431542 and 100 nM LDN193189 (both Peprotech). Cells were washed with Dulbecco’s phosphate buffered saline (DPBS; Thermo Fisher Scientific) before daily media exchange.

extract_protocol:
Cell pellets were washed in PBS + 0.04% BSA and individual samples were labeled with a Cell Multiplexing Oligo (CMO) for sample demultiplexing in the analysis process. The labeling reaction was stopped by addition of PBS + 1% BSA. After washing, labeled samples from all species and conditions were pooled at equal ratios to obtain a suspension of 1.5 × 106 cells. Since neural differentiation sometimes leads to increased cell death and cell debris, the pooled samples were sorted with an FACS Aria Fusion (BD Biosciences) to remove small particles and cell clumps based on forward and side scatter (FSC and SSC) gating. Sorted cell pools were used at the appropriate volume for a target cell recovery of 12,000 for day 0 and 22,000 cells for days 2 and 4, and loaded onto a Chromium Next GEM Chip following the manufacturer’s instructions
cDNA was generated through a reverse transcription reaction inside GEMs. Two types of sequencing libraries were generated: A 3’ Gene Expression Library for transcriptome sequencing and a Multiplexing Library for CMO sequencing to demultiplex the pooled samples.

value: H9 human embryonic stem cells

value: NPC differentiation

tag: cell number_(cellranger)

tag: day


title: BeWo_TFEB_KO_TFEB-GFP_FRSK_1


title: CL75_breast_biopsy_M0

source_name: CL75,breast biopsy,mammosphere formation M0

tag: tissue


title: CL73_breast_biopsy_M0

source_name: CL73,breast biopsy,mammosphere formation M0


title: CL49_breast_biopsy_M2

source_name: CL49,breast biopsy,mammosphere formation M2


title: CL72_breast_biopsy_M0

source_name: CL72,breast biopsy,mammosphere formation M0


title: CL43_breast_biopsy_M2

source_name: CL43,breast biopsy,mammosphere formation M2


title: CL78_breast_biopsy_M1

source_name: CL78,breast biopsy,mammosphere formation M1


title: CL59_breast_biopsy_M1

source_name: CL59,breast biopsy,mammosphere formation M1


title: Gene expression library, day 0, Human

value: UPPS

value: pluripotent


title: Gene expression library, day 2, Human

value: NPC differentiation and maintenance media


title: BeWo_TFEB_KO_TFEB-GFP_DMSO_4

source_name: BeWo

value: DMSO


title: CL69_breast_biopsy_M0

source_name: CL69,breast biopsy,mammosphere formation M0


title: Gene expression library, day 4, with INK, Human

value: NPC differentiation and maintenance media + INK128


title: BeWo_TFEB_KO_TFEB-GFP_DMSO_3


title: BeWo_TFEB_KO_TFEB-GFP_DMSO_2


title: MA30, naïve_3_bulk RNA

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

institute: Tulane University

data_processing:
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203 UV Santa Cruz)
Cuffdiff were used for differential expression analysis (Slug Genomics, 203 UV Santa Cruz)
The Cuffdiff output was used to generate volcano plots (EnhancedVolcano) and ggplot (enrichplot)  using  R package 4.2.1
Assembly: mm10
Supplementary files format and content: Comma-delimited CSV files include differentially expressed genes for each comparisons

source_name: lung

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (QIAGEN, 74106) in accordance with the RNeasy Reagent manufacturer’s protocol. The concentration of RNA was determined by NanoDrop 2000. RNA quality was determined on an Agilent TapeStation 4150 using an Agilent RNA ScreenTape (Agilent, 5067-5576).
Total RNA libraries for RNA-seq were prepared using TruSeq total RNA Library Prep Kit following manufacturer's protocols.

value: lung

value: non infected


title: Gene expression library, day 2, with INK, Human


title: CL67_breast_biopsy_M0

source_name: CL67,breast biopsy,mammosphere formation M0


title: CL65_breast_biopsy_M0

source_name: CL65,breast biopsy,mammosphere formation M0


title: BeWo_TFEB_KO_CTRL_TORIN-1_4

value: BeWo

value: choriocarcinoma


title: BeWo_TFEB_KO_TFEB-GFP_DMSO_1


title: MA30, Irf7KO_Day2_3_bulk RNA

value: Irf7 KO


title: MA30, naïve_1_bulk RNA


title: CL54_breast_biopsy_M1

source_name: CL54,breast biopsy,mammosphere formation M1


title: MA30, Irf7KO_Day2_2_bulk RNA


title: BeWo_TFEB_KO_CTRL_TORIN-1_3


title: BeWo_TFEB_KO_CTRL_TORIN-1_2


title: MA30, Irf7KO_Day2_1_bulk RNA


title: BeWo_TFEB_KO_CTRL_FRSK_2


title: Input morula Spike-in

city: Yokohama

first: Azusa

last: Inoue

state: Kanagawa

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by fastp (version 0.21.0) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CATCH-seq and CUT&RUN, mm10 for general CATCH-seq and CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -t -N 1" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.5.1) with the parameters "--binSize 50 --scaleFactor 1 --normalizeUsing RPKM --numberOfProcessors 28 --extendReads 200 --ignoreDuplicates --smoothLength 100".
For allele-specific analysis of CATCH-seq and CUT&RUN in the B6 or BDF1 x PWK F1 hybrid embryos, BDF1 and PWK SNPs were masked as "N" in the reference genome. MACS2 (version 2.2.7.1) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H3K27me2 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Preimplantation embryo

extract_protocol:
For superovulation, 4- to 10-week-old B6N females were injected with 7.5 IU pregnant mare serum gonadotropin (ASKA Pharmaceutical) or 0.15 ml CARD HyperOva (Kyudo Co., Ltd) followed by 7.5 IU human chorionic gonadotropin (hCG) (ASKA Pharmaceutical) at a 48-h interval. Cumulus-oocyte complexes (COCs) were harvested 15–17 h after human chorionic gonadotropin injection. For in vitro fertilization, COCs were inseminated with activated spermatozoa in Human Tubal Fluid medium supplemented with 10 mg/ml BSA (Merck Millipore; 12657). Spermatozoa were obtained from the caudal epididymis of adult PWK/PhJ mice [RBRC00213 (RIKEN BioResource Research Center) originated from 003715 (The Jackson Laboratory)] and B6D2F1 (BDF1) males (Jackson Laboratory). Spermatozoa were capacitated by 1 h incubation in CARD FERTIUP (Kyudo) for PWK sperm or in Human Tubal Fluid medium for BDF1 sperm. At 6–8 h postinsemination, zygotes with two pronuclei were transferred to KSOM and cultured under a humidified atmosphere with 5% CO2/95% air at 37.8°C. For CATCH-seq and CUT&RUN sample collection, polar bodies were removed as described previously (Hayashi and Inoue 2023). Four-cell, eight-cell, morula and blastocyst embryos, were collected at 46–52, 60, 72 and 120 h post-insemination with 500-1,000 blastomeres for each CATCH-seq experiment.
CATCH-seq is an improved method of the ultra low-input native ChIP-seq (ULI-NChIP) (Brind’Amour et al. 2015), and the original protocol of CATCH-seq was described in (Zhu et al. 2021). We have made some changes in CATCH-seq to improve the usability. Cells were collected to 9 µL of Nuclei EZ lysis buffer (Sigma, NUC-101) supplemented with complete EDTA-free protease inhibitor cocktail and 1 mM phenylmethanesulfonyl fluoride. The samples were snap frozen in liquid nitrogen and stored at -80°C  until use. At the day of library construction, the samples were thawed on ice, and added with 1 µL of the lysis buffer containing a constant number of Drosophila melanogaster S2 cells (Thermo Fisher Scientific, R69007) for spike-in normalization purpose. Then, 1 µL of 1% Triton X-100 (Merck 93443) and 1% deoxycholate (Nacalai, 10712-54) mixture solution was added to the samples, and sit on ice for 5 min. The chromatin was fragmented by 2 U/µl MNase (M0247S, NEB) in 1xMNase buffer supplemented with 1% PEG6000 (HAMPTON RESEARCH, HR2-533) and 2 mM DTT (Nacalai) at 21 or 37°C  for 7.5 min. The digestion temperature was dependent on the experimental condition, including the lot of MNase and the freshness of PEG6000, which had been determined by fragment sizes of input libraries in a preliminary test. The MNase reaction was stopped by adding 1/10 volume of 100 mM EDTA and 1/12 volume of the 1% Triton X-100 and 1% deoxycholate mixture, and the samples were rest on ice for 15 min. The chromatin lysates were then added with freshly prepared immunoprecipitation buffer (Brind’Amour et al. 2015), and 5% volume was kept for input library construction. To the rest of the lysate, 30 ng of annealed I-SceI carrier DNA was added (Zhu et al. 2021). The forward and reverse strands of the carrier DNA were as follows: /5AmMC6/Gtagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggataacagggtaattagggat aacagggtaat*c/3AmMO/ and /5AmMC6/Gattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatccctaattaccctgttatcc cta*c/3AmMO/, respectively, where asterisks represent phosphorothioate bonds. The oligos were synthesized by Integrated DNA Technologies. For each immunoprecipitation reaction, 0.5 µL of rabbit anti-H3K27me2 (Cell Signaling Technologies, 9728), 500 ng of rabbit anti-H3K27me3 (Millipore 07449), or 250 ng of rabbit anti-H3K27ac (Diagenode C15410196) conjugated to precleared Dynabeads Protein A (Thermo Fisher Scientific, 10006D) and G (Thermo Fisher Scientific, 10007D) mixture was used. The quality of these antibodies was validated in previous studies [H3K27me2 (Ferrari et al. 2014a; Juan et al. 2016; Hojfeldt et al. 2018b; Lavarone et al. 2019; Meng et al. 2020), H3K27me3 (Adli et al. 2010; Kelly et al. 2019; Ren et al. 2019), H3K27ac (Zenk et al. 2021)]. After immunoprecipitation at 4°C overnight, the chromatin-Dynabeads were washed twice each by the low and high salt wash buffers, and the chromatin was eluted in the freshly prepared ChIP elution buffer at 65°C for 1 hr (Brind’Amour et al. 2015). DNA was recovered by phenol-chloroform extraction followed by ethanol precipitation. Adaptor ligation was performed by NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645, NEB) in a half scale of the manufacturer’s instruction, and the libraries were purified by 1.8x SPRIselect beads (B23318, Beckman Coulter). The DNA was amplified by KAPA Hifi 2X mater PCR mix (KK2605) for 13-15 PCR cycles with dual indexing primers (NEBNext Multiplex Oligos for Illumina, E6440). After purification with 0.9x SPRIselect beads, the samples were digested by I-SceI (5 U/µl, NEB, R0694) 37°C for 2 hrs followed by heat inactivation at 65°C for 20 min and purified by 0.9x SPRIselect beads. The second amplification was not performed. The libraries were sequenced on Nextseq500 (single-end reads) or Nextseq2000 (paired-end reads) (Illumina). CUT&RUN libraries were prepared as previously described (Hayashi and Inoue 2023). For each CUT&RUN library, 100-180 morula embryos were used per replicate, and the same number of embryos were used to compare between control and mutant embryos. The antibodies used in this study were rabbit anti-JARID2 (1/50; Cell Signaling Technologies, 13594), rabbit anti-SUZ12 (1/50; Cell Signaling Technologies, 3737), and rabbit anti-H3K36me3 (1/500; Abcam 9050) antibodies. The specificity of these antibodies was proven in previous studies (Hojfeldt et al. 2018; Healy et al. 2019; Hojfeldt et al. 2019; Glancy et al. 2023). Protein A-MNase was provided by S. Henikoff ’s laboratory (Skene and Henikoff 2017). For quantitative CUT&RUN, 20 pg of yeast DNA was added to each sample. CUT&RUN libraries were sequenced on a NextSeq 500 with single-end reads (Illumina).

tag: developmental stage

value: morula

value: Preimplantation embryo

value: BDF1 x PWK

value: wild-type


title: MA30, naïve_2_bulk RNA


title: H3K27me2 morula Spike-in

tag: chip antibody


title: BeWo_TFEB_KO_CTRL_FRSK_4

tag: genotype

value: TFEB-KO

value: FRSK

value: 48 hours


title: BeWo_TFEB_KO_CTRL_FRSK_1

tag: treatment


title: BeWo_TFEB_KO_CTRL_DMSO_4


title: H3K27me2 8cell Spike-in


title: H3K27me2_8cell_rep1-2_additional_reads

value: C57BL/6 (B6) x PWK


title: BeWo_TFEB_KO_CTRL_DMSO_3


title: BeWo_TFEB_KO_CTRL_DMSO_2


title: H3K27ac morula Jarid2 KO rep2

value: H3K27ac(Diagenode, C15410196)

value: Jarid2 knockout


title: H3K27ac morula CTR rep2

value: control


title: BeWo_TFEB_KO_FRSK_4


title: Input blastocyst Aebp2/Jarid2 dKO

value: blastocyst

value: Aebp2/Jarid2 double knockout


title: BeWo_TFEB_KO_CTRL_FRSK_3


title: Input blastocyst Jarid2 KO


title: BeWo_TFEB_KO_CTRL_DMSO_1

value: DMSO


title: BeWo_TFEB_KO_CTRL_TORIN-1_1

value: BeWo


title: Input 8cell Spike-in


title: BeWo_TFEB_KO_FRSK_1

value: choriocarcinoma


title: Input blastocyst Aebp2 KO

value: Aebp2 knockout


title: BeWo_TFEB_KO_FRSK_2


title: H3K27me3 blastocyst Aebp2/Jarid2 dKO rep1

value: H3K27me3(Miilipore, #07449)


title: H3K27me3 blastocyst Aebp2/Jarid2 dKO rep2

value: Preimplantation embryo


title: Input blastocyst CTR

value: BDF1 x PWK


title: H3K27me3 blastocyst Jarid2 KO rep2


title: BeWo_TFEB_KO_DMSO_3


title: BeWo_TFEB_KO_DMSO_4


title: H3K27me3 blastocyst Aebp2 KO rep1


title: BeWo_TFEB_KO_FRSK_3


title: H3K27me3 blastocyst Jarid2 KO rep1


title: H3K27me3 blastocyst Aebp2 KO rep2


title: BeWo_FRSK_3

value: WT


title: BeWo_TFEB_KO_DMSO_2

value: TFEB-KO


title: BeWo_TFEB_KO_DMSO_1


title: BeWo_FRSK_4

value: FRSK


title: H3K27me3 blastocyst CTR rep2


title: BeWo_FRSK_2

value: 48 hours


title: BeWo_FRSK_1


title: BeWo_DMSO_4


title: Input morula Jarid2 KO rep1

value: morula


title: BeWo_DMSO_2


title: Input morula CTR rep1


title: BeWo_DMSO_3


title: H3K27me2 morula Jarid2 KO rep2


title: Input morula  CTR rep2


title: BeWo_DMSO_1


title: BeWo_TFEB_FRSK_WCE_2

description:
BEWO_TFEB_FRSK_IP.fc.signal.bw
BEWO_TFEB_FRSK_IP_union_I0.01_named.bed

data_processing:
Basecalls performed using bcl2fastq v2.20.0.422
Paired sequencing reads were aligned on human hg38 reference genome using BWA
Reads were filtered with samtools to remove unmapped read pairs, not primary alignment, reads failing platform quality, with mapping quality score below 30 and duplicate reads were then removed using picard MarkDuplicates
Each sample was equally split in two pseudoreplicates and peaks were called with MACS2 with p < 0.1 on both samples and pseudoreplicates and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.01
Each pair of replicated sample was combined and and filtered after Irreproducible Discovery Rate analysis with a threshold of 0.01;  coordinates from each replicate and from the combined peak lists were merged using bedtools and peaks supported by at least two out of the three were selected
bigWig IP vs input fold change signal profiles were produced using macs2 bdgcmp and then converted with UCSC bedGraphToBigWig tool
Assembly: hg38
Supplementary files format and content: bigWig, bed

growth_protocol: HeLa cells were maintained in DMEM High Glucose supplemented with 10% fetal bovine serum (FBS) heat-inactivated and antibiotics in humidified atmosphere with 5% CO2 at 37C. BeWo cells were obtained from ATCC and cultured in F-12K medium (Kaighn's Modification of Ham's F-12 Medium) (cat. no. 30-2004, ATCC) supplemented with 10% FBS (cat. no. ECS0180L, Euroclone), penicillin (100 IU/ml) and streptomycin (100 μg/ml) (cat. no. ECB3001D, Euroclone).

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at room temperature. Samples for ChIP-seq were prepped as previously described (Cesana et al. 2018)
Libraries were prepared from 10 ng of DNA using the NEBNext® Ultra™ II DNA Library Prep Kit following the manufacturer protocol

treatment_protocol: To stimulate BeWo trophoblast differentiation, cells were treated with 100uM of Forskolin (F6886, Sigma-Aldrich)


title: BeWo_TFEB_FRSK_2

value: TFEB antibody


title: BeWo_TFEB_FRSK_WCE_1


title: BeWo_TFEB_FRSK_1


title: H3K27me2 morula CTR rep1


title: Input 8-cell

value: C57BL/6 (B6) x PWK

value: wild-type


title: HeLa_TFEB_HBSS_WCE_2

description:
HeLa_TFEB_STV_IP.fc.signal.bw
HeLa_TFEB_STV_IP_union_I0.01_named.sorted.bed

source_name: HeLa

value: HeLa

value: epithelial cell

value: HBSS


title: H3K27me2 morula Jarid2 KO rep1

value: Jarid2 knockout


title: H3K27me2 morula CTR rep2

value: control


title: HeLa_TFEB_HBSS_WCE_1


title: HeLa_TFEB_HBSS_2


title: HeLa_TFEB_HBSS_1


title: RNA-seq, morula, CTR, rep2

description: RNA-seq morula embryo Jarid2 CTR rep2

data_processing:
For RNA-seq, all reads after trimming by fastp (version 0.21.0) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.6a) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted". The RPKM values of each gene were generated by RSEM (version 1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file include raw counts for each sample

extract_protocol:
About 20 or single mourla embryo(s) per sample were pooled to generate each RNA-seq library. The zona pellucida was removed by brief incubation in acidic Tyrode's solution. All samples for RNA-seq were washed three times in 0.2% BSA/PBS before being transferred into a 0.2-ml tube with ~0.5μl carryover.
RNA-seq libraries were prepared as previously described (Mei et al. 2021). Briefly, complementary DNA was prepared using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara; 634890) according to the manufacturer’s instructions. Library construction was performed on a Nextera XT DNA Library Prep Kit (Illumina; FC-131-1024) with 200 pg complementary DNA, according to the manufacturer’s instructions. All RNA-seq libraries were sequenced on a NextSeq 500 (bcl2fastq version 2.17 and RTA version 2.4.11) with single-end 75-bp reads (Illumina).


title: RNA-seq, morula, Jarid2 KO, rep2

description: RNA-seq morula embryo Jarid2 KO rep2


title: RNA-seq, morula, CTR, rep1

description: RNA-seq morula embryo Jarid2 CTR rep1


title: T98G 2D Day9

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

data_processing:
The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a hg38 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
The resulting expression matrix was used as input to the Seurat library v4.3.0
Assembly: hg38
Supplementary files format and content: 10x Gene Expression matrix

source_name: Brain tumor

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS.

value: Brain tumor

value: Brain tumor cell line T98G

value: Glioblastoma

value: Cells were transduced with PU.1, IRF8, BATF3 (PIB) and EGFP

value: Cells were collected 9 days after viral transduction

tag: facs-sorted cell_type

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR

tag: organoid formation


title: Input morula Jarid2 KO rep2

tag: cell type

value: Preimplantation embryo

value: BDF1 x PWK


title: low_mg_rep2_rnaseq

city: Piscataway

first: Srujana

middle: Samhita

last: Yadavalli

state: NJ

address: 190 Frelinghuysen Rd

department: Genetics

institute: RUTGERS UNIVERSITY

data_processing:
For Ribo-RET, the raw sequencing data are already demultiplexed, and the adaptors have been removed using cutadapt (Martin 2011).
For Ribo-RET, the reads were then depleted of rRNA and tRNA and deduplicated using umi_tools dedup. The Ribo-RET reads were aligned to the E. coli MG1655 genome NC_000913.3 (RefSeq assembly accession: GCF_000005845.2) using hisat2 (Kim et al. 2019), and the ribosome density was assigned to the 3’ end of the reads. Initiation peak density was calculated for the annotated translation start sites by summing up the normalized reads (reads per million, RPM) within four to twenty nucleotides downstream of the first nucleotide in the start codon.
For RNA-Seq, the raw reads are demultiplexed.
For transcript quantification of RNA-Seq reads, Kallisto (Bray et al. 2016) was used.
Assembly: E. coli MG1655 genome NC_000913.3 (RefSeq assembly accession: GCF_000005845.2)
Supplementary files format and content: For Ribo-RET, the csv file has the reads mapped to the translation start sites of annotated proteins. the reads are normalized to reads per million by tallying reads per position by annotated start sites, and adjusting for sequencing depth
Supplementary files format and content: For RNA-Seq, the csv file contains reads mapped to E. coli using kallisto. The reads are normalized tpm read counts provided by kallisto

organism: Escherichia coli

source_name: Bacterial cell

growth_protocol: Overnight cultures of wild-type E. coli grown in supplemented minimal A medium (0.2% glucose, 0.1% casamino acids) and 1 mM MgSO4 were diluted 1:500 in 100 ml of fresh medium and the specified concentrations of MgSO4. For low Mg2+ stress, no Mg2+ was added when overnight cultures were diluted into fresh medium. Media containing 10 mM Mg2+ was used as the no-stress condition.

extract_protocol:
Once the cultures reached an OD600 of ~0.4, they were split into two 50 ml conical tubes. Cells from one tube were pelleted and submitted to Genewiz for RNA-Seq, while the cells from the second tube were used for Ribo-RET. For Ribo-RET, cells were treated with retapamulin at a final concentration of 100 µg ml-1 for 5 minutes at 37°C with continuous shaking. After retapamulin treatment, cells were filtered through a nitrocellulose membrane with a pore size of 0.45 µm, quickly scraped off the surface, and flash-frozen in liquid nitrogen. The resulting samples were processed, and libraries were prepared as described previously (Cope et al. 2022)
Libraries for RNA-Seq were prepared by Genewiz. Ribo-RET libraries were prepared as described previously (Cope et al. 2022) with the following modifications. Specifically, RNA fragments of 15-30 nucleotides (nt) in length were isolated by performing a tight gel size selection, and rRNA depletion was performed using the RiboCop for Gram-negative bacteria kit (Lexogen).
The resulting RNA fragments were then pooled, and libraries were prepared, with a final library structure consisting of a 5' adapter – 4 random bases – insert – 5 random bases – sample barcode – 3' adapter. The randomized bases serve as Unique Molecular Identifiers (UMIs) for deduplication. The multiplexed library was sequenced on an Illumina HiSeq 4000 with a paired-end reading of 150 bases (PE150 runs) at a sequencing depth of 40-60 million raw reads per sample

value: Bacterial cell

value: Wild type

value: low magnesium


title: H3K27me3 blastocyst CTR rep1

value: H3K27me3(Miilipore, #07449)

value: blastocyst


title: low_mg_rep1_rnaseq

treatment_protocol: For low Mg2+ stress, no Mg2+ was added when overnight cultures were diluted into fresh medium. Media containing 10 mM Mg2+ was used as the no-stress condition.


title: T98G 3D Day9

tag: cell line

tag: time


title: T98G 3D Day7

value: Cells were collected 7 days after viral transduction


title: no_stress_riboseq

data_processing:
For Ribo-RET, the raw sequencing data are already demultiplexed, and the adaptors have been removed using cutadapt (Martin 2011).
For Ribo-RET, the reads were then depleted of rRNA and tRNA and deduplicated using umi_tools dedup. The Ribo-RET reads were aligned to the E. coli MG1655 genome NC_000913.3 (RefSeq assembly accession: GCF_000005845.2) using hisat2 (Kim et al. 2019), and the ribosome density was assigned to the 3’ end of the reads. Initiation peak density was calculated for the annotated translation start sites by summing up the normalized reads (reads per million, RPM) within four to twenty nucleotides downstream of the first nucleotide in the start codon.
For RNA-Seq, the raw reads are demultiplexed.
For transcript quantification of RNA-Seq reads, Kallisto (Bray et al. 2016) was used.
Assembly: E. coli MG1655 genome NC_000913.3 (RefSeq assembly accession: GCF_000005845.2)
Supplementary files format and content: For Ribo-RET, the csv file has the reads mapped to the translation start sites of annotated proteins. the reads are normalized to reads per million by tallying reads per position by annotated start sites, and adjusting for sequencing depth
Supplementary files format and content: For RNA-Seq, the csv file contains reads mapped to E. coli using kallisto. The reads are normalized tpm read counts provided by kallisto
Library strategy: Ribo-Seq

value: No stress


title: SUM159_RSL3_b

city: Rehovot

first: Sima

last: Lev

address: 234 Herzl St.

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute of Science

description: Count matrix - SUM159.csv

data_processing:
Libraries were sequenced by the Illumina Novaseq 6000 using SP mode 100 cycles kit (Illumina)
Mapping of sequences to the genome was performed by the UTAP pipeline (UTAP: User-friendly Transcriptome Analysis Pipeline, Kohen et al. BMC Bioinformatics 2019, 20(1):154)
Reads were trimmed using cutadapt (DOI:10.14806/ej.17.1.200) (parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a “A{10}” –times 2 -u 3 -u -3 -q 20 -m 25).
The remaining reads were mapped to the genome (hg38) using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No).
Assembly: hg38
Supplementary files format and content: Matrix table with gene counts for every gene and every sample

growth_protocol: Cells were maintained in RPMI medium supplemented with 10% FBS, 1% Penicillin-Streptomycin solution.

extract_protocol:
RNA was extracted using TRI reagent (Sigma), following standard extraction protocol.
RNAseq libraries were constructed by applying a bulk adaptation of the MARS‐seq protocol (Jaitin et al. 2014 Science.343:776-9).

treatment_protocol: Cells were treated with the IC50 doses of Erastin, RSL3 or equal concentrations of DMSO, for 9h (Erastin) or 4h (RSL3).

value: triple negative breast cancer line

tag: concentration


title: low_mg_riboseq

tag: strain


title: RNA-seq, morula, Jarid2 KO, rep1

description: RNA-seq morula embryo Jarid2 KO rep1

value: morula

value: Jarid2 knockout


title: T98G 3D GFP

value: Brain tumor

value: Brain tumor cell line T98G

value: Cells were transduced with EGFP

value: sorted live(DAPI-) and EGFP+


title: SUM159_RSL3_a

description: Count matrix - SUM159.csv


title: ectopic neuroblast, replicate 3

city: Merced

first: Michael

last: Cleary

state: CA

address: 5200 N. Lake Rd.

department: School of Natural Sciences

institute: University of California, Merced

data_processing:
as described in Gogakos et al., Cell Reports, 2017
Assembly: UCSC genome release 6.40
Supplementary files format and content: csv file containing normalized tRNA read counts and differential expression statistics for nuclear and mitochondrial isodecoders

source_name: brain

growth_protocol: larvae were cultured on standard growth medium at 25C.

extract_protocol:
Total RNA was extracted using Trizol
Hydro-tRNAseq according to method of Gogakos et al., Cell Reports, 2017

value: brain

value: L3 larval stage

value: neuroblast-biased


title: wildtype, replicate 2

value: neuron-biased

value: Oregon R


title: no_stress_rep1_rnaseq

value: Bacterial cell

value: Wild type


title: ectopic neuroblast, replicate 2


title: wildtype, replicate 3


title: SUM159_Erastin_b

description: Count matrix - SUM159.csv

value: Erastin


title: SUM159_DMSO_a

description: Count matrix - SUM159.csv

value: DMSO


title: SUM159_Erastin_a

description: Count matrix - SUM159.csv


title: wildtype, replicate 1


title: T98G 2D Day7

value: Glioblastoma

value: Cells were transduced with PU.1, IRF8, BATF3 (PIB) and EGFP

value: Cells were collected 7 days after viral transduction

value: sorted live(DAPI-), EGFP+, and expressing at least one of CD45 and HLA-DR


title: HS578_RSL3_b

description: Count matrix - BT549 and HS578.csv

value: triple negative breast cancer line


title: Adult Midgut, dHNF4 RNAi, sample#4

city: Cologne

first: Gilles

last: Storelli

address: Joseph Stelzmannstrasse 26

department: CECAD Research Center

institute: University of Cologne

description: mex>dHNF4 RNAi biol rep 4

data_processing:
The quality of the sequencing reads was checked using FastQC. Sequencing reads were trimmed using Trim Galore! Software.
D. melanogaster annotated transcripts (BDGP6.32) were downloaded from Ensembl.
Transcript abundance was estimated using Kallisto-Quant.
Read counts were normalised to ERCC spike-in controls and differential gene expression analysis was performed using RUVSeq and edgeR Bioconductor R packages.
Assembly: D. melanogaster annotated transcripts (BDGP6.32)
Supplementary files format and content: The excel file contains several spreadsheets. The “TPM” spreadsheet contains Transcripts Per Million (TPM) read counts for each transcript detected by sequencing in each sample.The “results” spreadsheet contains log2 fold change (logFC) and p-value for transcripts in dHNF4 RNAi intestines compared to control intestines. The “significant” spreadsheet contains transcripts whose levels are significantly altered in dHNF4 RNAi midguts compared to control midguts. The “gene-info” spreadsheet contains information about the transcripts (Gene stable ID, Transcript stable ID, Gene Synonym, Gene name, Gene description and Gene type).

source_name: Midgut

growth_protocol: Animals were fed a yeast only diet until 7 days post ecolsion. Animals were maintained at 25°C with a 12h light/12h dark cycle.

extract_protocol:
Total RNA was extracted using the Promega Reliaprep RNA Tissue Miniprep System (#Z6112)
Libraries were prepared using the Illumina Stranded Truseq RNA sample Prepearation Kit

value: Midgut

tag: Sex

value: Male

tag: Stage

value: Adult

value: mex-GAL4/+; UAS-dHNF4 RNAi NIG9310-R2/+

value: Yeast only diet


title: HS578_Erastin_b

description: Count matrix - BT549 and HS578.csv


title: HS578_RSL3_a

description: Count matrix - BT549 and HS578.csv


title: Adult Midgut, dHNF4 RNAi, sample#3

description: mex>dHNF4 RNAi biol rep 3


title: Adult Midgut, dHNF4 RNAi, sample#2

description: mex>dHNF4 RNAi biol rep 2


title: HS578_Erastin_a

description: Count matrix - BT549 and HS578.csv


title: no_stress_rep2_rnaseq

value: No stress


title: Adult Midgut, dHNF4 RNAi, sample#5

description: mex>dHNF4 RNAi biol rep 5


title: HS578_DMSO_b

description: Count matrix - BT549 and HS578.csv


title: ectopic neuroblast, replicate 1

value: brain

value: L3 larval stage

value: neuroblast-biased


title: Adult Midgut, dHNF4 RNAi, sample#1

description: mex>dHNF4 RNAi biol rep 1


title: T98G 3D Day3

value: Brain tumor

value: Brain tumor cell line T98G

value: Cells were collected 3 days after viral transduction


title: Adult Midgut, Control, sample#5

description: w1118; dHNF4 RNAi biol rep 5

value: w1118/Y ; ; UAS-dHNF4 RNAi NIG9310-R2/+


title: PEDOT:PSS no electrical stimulation, rep 2

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Reads were aligned to GRCh38.p13/hg38 using STAR (Dobin et al., 2013). Release 43 (GRCh38.p13) of the Gencode gene annotation was used. Reads were assigned to genes and count.txts generated using Htseq (Anders, et al., 2015).
Differential gene expression was analyzed via EBSeq in R (Leng et al., 2013).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene count.txts for every gene and sample

growth_protocol: SH-SY5Y cells were seeded on poly-L-lysine and laminin-coated P(rGO), PEDOT:PSS, or ITO films in normal growth media and maintained for 2 d, then differentiated. For differentiation, serum was reduced to 5% FBS on day 2, 2.5% on day 3 and 1% on day 5. 100 U/mL penicillin/streptomycin (Gibco, 15140-122) was added on day 2. With the reduction of FBS, 10 μM retinoic acid (Sigma-Aldrich, R2625) was added to the culture on day 3 and maintained until day 6. On day 6, media was replaced with DMEM/F12 supplemented with 50 ng/mL brain-derived neurotrophic factor (BDNF) (Sigma-Aldrich, B3795) and maintained for 4 d.

extract_protocol:
RNA was extracted and purified using RNeasy Mini Kit (Qiagen, 74106) with on-column DNase digestion using RNase-Free DNase Set (Qiagen, 79254)
RNA libraries were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490S) along with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S) and NEBNext Multiplex Oligos for Illumina (NEB, E6440S)

treatment_protocol: Cells were differentiated in cell culture plates (controls) or P(rGO), PEDOT:PSS, or ITO films. For ES samples, cells were stimulated with a periodic, 0.1 VP-P (from 0 to +0.1 V), 1 Hz, square wave potential for 8 h/d for the final 4 days of differentiation

value: Neuroblastoma

value: Differentiated on PEDOT:PSS, no electrical stimulation


title: Adult Midgut, Control, sample#4

description: w1118; dHNF4 RNAi biol rep 4


title: Gene expression library, day 4, Cynomolgus

organism: Macaca fascicularis

source_name: 56A1 cynomolgus induced pluripotent stem cells

value: NPC differentiation and maintenance media

value: NPC differentiation


title: Gene expression library, day 2, Cynomolgus

value: 56A1 cynomolgus induced pluripotent stem cells


title: Gene expression library, day 4, with INK, Cynomolgus

value: NPC differentiation and maintenance media + INK128


title: Gene expression library, day 2, with INK, Cynomolgus


title: ITO no electrical stimulation, rep 2

value: Differentiated on ITO, no electrical stimulation


title: SUM159_DMSO_b

description: Count matrix - SUM159.csv

value: triple negative breast cancer line

value: DMSO


title: ITO no electrical stimulation, rep 1


title: BT549_RSL3_b

description: Count matrix - BT549 and HS578.csv


title: BT549_Erastin_a

description: Count matrix - BT549 and HS578.csv

value: Erastin


title: HS578_DMSO_a

description: Count matrix - BT549 and HS578.csv


title: ITO with electrical stimulation, rep 1

value: Differentiated on ITO, with electrical stimulation


title: ITO with electrical stimulation, rep 2


title: PEDOT:PSS no electrical stimulation, rep 1


title: Gene expression library, day 0, Mouse

source_name: 129S2C1a mouse epiblast stem cells

value: 129S2C1a mouse epiblast stem cells

value: UPPS

value: pluripotent


title: Adult Midgut, Control, sample#3

description: w1118; dHNF4 RNAi biol rep 3

value: Midgut

value: Male

value: Adult

value: Yeast only diet


title: BT549_Erastin_b

description: Count matrix - BT549 and HS578.csv


title: BT549_DMSO_a

description: Count matrix - BT549 and HS578.csv


title: P(rGO) no electrical stimulation, rep 2

value: Neuroblastoma

value: Differentiated on P(rGO), no electrical stimulation


title: PEDOT:PSS with electrical stimulation, rep 2

value: Differentiated on PEDOT:PSS, with electrical stimulation


title: PEDOT:PSS with electrical stimulation, rep 1


title: Gene expression library, day 0, Cynomolgus

value: 56A1 cynomolgus induced pluripotent stem cells


title: Adult Midgut, Control, sample#2

description: w1118; dHNF4 RNAi biol rep 2

value: w1118/Y ; ; UAS-dHNF4 RNAi NIG9310-R2/+


title: BT549_RSL3_a

description: Count matrix - BT549 and HS578.csv


title: Gene expression library, day 4, Mouse

value: NPC differentiation and maintenance media

value: NPC differentiation


title: BT549_DMSO_b

description: Count matrix - BT549 and HS578.csv

value: triple negative breast cancer line

value: DMSO


title: HepG2_mock_rep2_Nuclear_RNA_seq

first: Jingyi

last: Fei

address: GCIS W142, 929 E 57th Street

institute: The University of Chicago

data_processing:
The adaptor sequences were trimmed with Cutadapt using the parameter cutadapt -a CCCAGATCGGAAGAGCACACGTC
The reads were first mapped to the corresponding rRNA sequences to remove rRNA contamination.
The remaining unmapped reads were mapped to the human genome hg38.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file included raw counts on gene level.

molecule: nuclear RNA

source_name: Liver cancer cells

growth_protocol: HeLa or HepG2 cells were cultured with DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using TRIzol reagent (ThermoFisher). Poly A RNA was isolated using Dynabeads mRNA DIRECT Purification Kit (ThermoFisher). Ribosome RNA was depleted by RiboMinus Eukaryote Kit (ThermoFisher).
Libraries were prepared with SMARTer Stranded Total RNA-Seq Kit v2 (Takara) following the manufacturer's instructions.

treatment_protocol: For heat shock treatment, HeLa cells were stressed at 43°C for 2 h. For plab B treatment, cells were treated with Plad B (100 nM) at 37°C for 4 h.

value: Liver cancer cells

value: WT

value: Mock


title: Adult Midgut, Control, sample#1

description: w1118; dHNF4 RNAi biol rep 1


title: P(rGO) with electrical stimulation, rep 1

value: Differentiated on P(rGO), with electrical stimulation


title: P(rGO) with electrical stimulation, rep 2


title: Gene expression library, day 4, with INK, Mouse

value: 129S2C1a mouse epiblast stem cells

value: NPC differentiation and maintenance media + INK128


title: Differentiated control, rep 2

value: Differentiated on cell culture plates


title: HepG2_mock_rep1_Nuclear_RNA_seq


title: P(rGO) no electrical stimulation, rep 1


title: Gene expression library, day 2, Mouse


title: Gene expression library, day 2, with INK, Mouse


title: U2OS, RNA-seq, exposed to a 5 Gy X-Ray irradiation

city: Seville

first: Patrick

last: Toolan-Kerr

address: Calle Américo Vespucio 24 Edificio

country: Spain

institute: University of Seville

data_processing:
Kallisto (version 0.44.0) was used to pseudoalign paired-end sequencing reads to the transcriptome
GENCODE was used as the reference transcriptome annotation.
Transcript abundance was generated using the iCLIP Nextflow analysis pipeline (https://app.flow.bio/)
Assembly: Hg38
Supplementary files format and content: summary count data for reads at gene level produced by the iCLIP nextflow Flow analysis pipeline

source_name: Bone

growth_protocol: U2OS cells were in DMEM  supplemented with  10% FBS and antibiotics

extract_protocol:
Total RNAs were extracted using Rneasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Bone

value: Osteosarcoma

value: 5 Gy X-Ray, Recovery 4h


title: single cell ATAC seq library of mouse samples (day0 to 10)

data_processing:
For time course single-cell multiome sequencing experiments, CellRanger ARC (v2.0.0) provided by 10x Genomics was used to demultiplex binary Illumina base call (BCL) files into FASTQ files, align the data against the GRCh38 (human), GRCm39 (mouse), and Macaca_fascicularis_6.0 (cynomolgus) reference, filter reads, as well as count barcodes and scRNA and scATAC molecules to generate feature-barcode matrices.
To mitigate technical cross-species batch effects, we pooled an equal number of cells from the three species for each of the samples.
Assembly: human genome GRCh38 (GENCODE v32/Ensembl98) and mouse genome GRCm39 obtained from 10x Genomics, and the cynomolgus genome GCA_011100615.1 (Genome assembly 6.0)
Supplementary files format and content: For every species (containing RNA counts and ATAC counts for all timepoints): matrix.mtx: count matrix of genes and barcodes in Market Exchange Format (MEX); features.tsv: table of corresponding Ensemble Ids (first column) and Gene Ids (second column), corresponding to rows in matrix.mtx; barcodes.tsv: table of cell barcodes, corresponding to columns in matrix.mtx; the numbers 1 to 8 in the cell barcodes do correspond to the timepoints 0 to 10 days (0d, 8h, 1d, 2d, 3d, 4d, 7d and 10d).

extract_protocol:
Time course scATAC and scRNA libraries were prepared using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturer’s protocol. Samples were collected at 0h, 8h, 1d, 2d, 3d, 4d, 7d and 10d post neural induction and cells of all three species were combined in equal amounts prior to the library preparation. The aimed target recovery was 10,000 single nuclei for sequencing.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (10x Genomics) according to the manufacturers instructions
scRNAseq and scATACseq

value: UPPS (pluripotency, day0) and NPC differentiation and maintenance media

tag: library type

value: scATAC


title: HeLa_pladB_rep2_Nuclear_RNA_seq

source_name: Cervical cancer cells

value: HeLa

value: Cervical cancer cells

value: Pladienolide B treated


title: HeLa_mock_rep2_Nuclear_RNA_seq


title: HeLa_HeatShock_rep2_Nuclear_RNA_seq

value: Heat shock


title: Capture Hi-C in wild type mouse bone marrow derived macrophages

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Custom-designed selection probes (SureSelect- Agilent) against BACH1-bound genomic sites

data_processing:
Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Assembly: mm10
Supplementary files format and content: Bigwig file that contain the chromatin interaction frequencies.

source_name: bone marrow-derived macrophages

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using formaldehyde-based cross-linking method and processed to Hi-C using the Arima Hi-C kit. A capture enrichment step was applied to the generated Hi-C libraries using sustom-designed probes (SureSelect, Agilent Tier 2 -2,9Mb ). Our design has two components combined in the same probe set : a. The Hmox1 genomic locus (tiled probescovering a 500kb area). The coordinates of this area arechr8:74850001-75350000. b.9127 sites covering the top BACH1’s ChIP-seqsites (in untreated BMDMs) sorted based on the RPKM.
Hi-C and cHi-C libraries were prepared with the Arima Hi-C kit and Agilent SureSelect library systems according to the manufacturer protocol.

treatment_protocol: Treatments of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.

tag: duration of_treatment_(hours)

value: bone marrow-derived macrophages

value: Bach1 fl/fl (control)

value: vehicle


title: U2OS, RNA-seq, control

value: WT

value: No treatment


title: Untreated control, rep 1

value: Neuroblastoma

value: Untreated on cell culture plates


title: HeLa_HeatShock_rep1_Nuclear_RNA_seq


title: Differentiated control, rep 1

value: Differentiated on cell culture plates


title: H3K27ac morula Jarid2 KO rep1

value: H3K27ac(Diagenode, C15410196)

value: morula

value: Preimplantation embryo

value: BDF1 x PWK

value: Jarid2 knockout


title: H3K27me3 no-injection Morula

value: H3K27me3(Miilipore, #07449)

value: no-injection


title: Untreated control, rep 2


title: HeLa_mock_rep1_Nuclear_RNA_seq

value: HeLa

value: Cervical cancer cells

value: Mock


title: HeLa_pladB_rep1_Nuclear_RNA_seq

value: Pladienolide B treated


title: H3K27me3 Jarid2OE Morula

value: Jarid2 overexpression


title: H3K27ac morula CTR rep1

value: control


title: CUT&RUN H3K36me3 morula rep1

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
For CUT&RUN, all sequencing reads after trimming by fastp (version 0.21.0) were aligned to the mouse and D.melanogaster genome sequences (mm10 + dm6 for spike-in CATCH-seq and CUT&RUN, mm10 for general CATCH-seq and CUT&RUN) using Bowtie2 (version 2.3.5) with the "-q -t -N 1" options. Genome coverage tracks were generated using the bamCoverage from deepTools (version 3.5.1) with the parameters "--binSize 50 --scaleFactor 1 --normalizeUsing RPKM --numberOfProcessors 28 --extendReads 200 --ignoreDuplicates --smoothLength 100".
For allele-specific analysis of CATCH-seq and CUT&RUN in the B6 or BDF1 x PWK F1 hybrid embryos, BDF1 and PWK SNPs were masked as "N" in the reference genome. MACS2 (version 2.2.7.1) was used for peak calling with the parameters "-g mm --nomodel --nolambda --broad". H3K27me2 peaks with distance shorter than 5 kb were merged using the merge function from BEDtools (version 2.26.0) for downstream analysis.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&RUN

value: H3K36me3(Abcam, ab9050)

value: wild-type


title: single cell gene expression library of mouse samples (day0 to 10)

first: Max

last: Fernkorn

institute: University Leiden

value: 129S2C1a mouse epiblast stem cells

value: UPPS (pluripotency, day0) and NPC differentiation and maintenance media

value: mRNA


title: K27_OE_A2

city: Hangzhou

first: Xingnan

last: Huang

address: No.18 Shilongshan Road

institute: Westlake University

data_processing:
bcl2fastq conversion software used for basecalling.
TrimGalore was used to clean adapters.
Reads were aligned to mm10 by using Bowtie2.
MACS2 software was used for peak calling. bamCoverage fo deepTools was used for generating bigwig files
Assembly: mm10
Library strategy: CUT&Tag

source_name: Mouse Embryo

extract_protocol:
Tagmentation was performed for 1 hr in Dig-300 buffer and then fragmentated with 300µL tagmentation buffer incubated for 1 hr at TM. Extracted nucleic acid with phenolic chloroform and dissolved in 1xTE solution.
The nucleic acid samples suspension was amplificated 13 cycles with 50µL amplification mix (TAE, TAB and P5, P7 primer) (TD901, Vazyme), and purified using VAHTS DNA Clean Beads (N411, Vazyme)

value: Mouse Embryo

value: Stem Cell

value: Transient

value: Cpt1a Overexpression

value: anti-H3K27ac (Abcam, no. ab4729, 1:50)


title: HepG2_mock_rep2_polyA_RNA_seq

value: Liver cancer cells

value: WT


title: CUT&RUN SUZ12 morula Jarid2 KO rep1

value: morula

value: Preimplantation embryo

value: BDF1 x PWK

value: Jarid2 knockout


title: CUT&RUN SUZ12 morula Jarid2 CTR rep2

value: control


title: H3K27me3 Jarid2OE L2C

value: BDF1 x BDF1

value: Jarid2 overexpression


title: H3K27me3 no-injection L2C

value: no-injection


title: CUT&RUN SUZ12 morula Jarid2 KO rep2


title: K27_OE_A1


title: CUT&RUN SUZ12 morula Jarid2 CTR rep1


title: HeLa_HeatShock_rep2_polyA_RNA_seq

value: HeLa

value: Cervical cancer cells

value: Heat shock


title: CUT&RUN JARID2 morula rep2

value: C57BL/6 (B6) x PWK

value: wild-type


title: Atf3-ChIP-1

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
RNA-seq reads were aligned to the mouse genome available in Ensembl (release 95) with HISAT2 (v2.1.0)
StringTie (v1.3.3b) for transcript assembly
The quantitative gene expression (FPKM) was obtained with Ballgown
Deeptools bamCoverage (CPM normalized and extended reads) was used to generate bigwig files from bam files
MACS2 was used for peak calling and to generate bed files from aligned reads
HOMER annotatePeaks.pl was used to annotate the peaks.
Assembly: mm10
Supplementary files format and content: csv
Supplementary files format and content: bigwig

source_name: intestine

extract_protocol:
organoids were harvested and collected by centrifugation. Total RNA was extracted with RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions.
The RNA-seq library were prepared for sequecing using NEBNext Ultra RNA library Prep Kit for Illumina. For ChIP-seq library, Alive lentivirus-infected organoids overexpressing Atf3 were sorted and collected into 500 uL PBS, cells conducted ChIP-seq following the NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein, H259-YH01) and the lysates were incubated with anti-ATF3 antibody (1:100, Abcam, ab207434) at 4 ℃ overnight. DNA extracted using Tagment DNA Extract Beads was used as a templet, and amplification was performed with 2X KAPA HIFI HotStart polymerase (KAPA, KK2601).The library was purified with 1.4X AMPure beads and sequenced with the Illumina Novaseq 6000.

value: intestine

value: cells from intestnial organoids


title: HeLa_HeatShock_rep1_polyA_RNA_seq