title: UOK109 cells, TFE3 rescue, Rep3

city: Baltimore

first: Wanlu

last: Chen

address: 615 N. Wolfe Street

institute: Johns Hopkins University

data_processing:
The RNA-seq data underwent initial processing with fastp for quality trimming of fastq files.
Subsequently, transcript quantification was performed using Salmon.
Read count extraction and normalization were performed using tximeta and DEseq2 package in R.
Assembly: hg38
Supplementary files format and content: comma separated values file includes normalized counts for each sample

source_name: UOK109 cells

growth_protocol: Cells were grown in Dulbecco's Modified Eagle's Medium (DMEM, 15-013-CV, Corning) supplemented with 10% v/v fetal bovine serum (FBS, 26140079, Gibco), 1% v/v Penicillin-Streptomycin (10,000 U/mL) (15140122, Thermo Fisher), 1% v/v GlutaMAX Supplement (35050061, Thermo Fisher), and 1% v/v Mem Non Essential Amino Acids Solution (100X) (11140050, Thermo Fisher). Cells were grown at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Cells were detached using accutase (A6964, Sigma-Aldrich), diluted in complete media and counted. One million cells were pelleted and the supernatant was aspirated. Cell pellets were snapfrozen and stored in -80 ºC freezer until RNA isolation. Total RNA was extracted using RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen) according to the manufacturer's instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Media was changed 6h before sample isolation.

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion

value: TFE3 rescue

value: baseline culturing conditions


title: UOK109 cells, TFE3 rescue, Rep2

status: Public on Apr 02 2025

type: SRA

state: MD

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: PA-1 wildtype replicate 2

city: Edinburgh

first: Silvia

last: Peluso

state: Midlothian

address: Western General Hospital, Crewe Road

country: United Kingdom

institute: MRC HGU at the University of Edinburgh

library_source: genomic

data_processing:
Quality of reads was verified using FASTQC 0.11.8 analysis.
50 bp paired-end reads. Resulting reads were trimmed using cutadapt paired-end trimming, and subsequently aligned to the hg38 human genome using bowtie2 version 2.2.6 paired-end alignment with options -N 1 -X 1000 -p 4.
Unmapped reads and those mapping to the mitochondrial genome were then removed and duplicate reads were filtered out using Picard 2.25.4 MarkDuplicates.
Reads were shifted by +4 bp for those mapping to the positive strand and −5 bp for those mapping to the negative strand.
Broad peaks were then called, to identify open chromatin regions, using MACS2. 2.1.1 callpeak with options –g hg, -f BEDPE, -B –broads and cutoff 0.01 options.
For visualization of normalised coverage bigwigs are generated using deepTools bamCoverage with options--normalizeUsing RPKM --minFragmentLength 30 --maxFragmentLength 1000.
Assembly: GRCh38
Supplementary files format and content: *.bed: Individual broad peaks from each replicate were merged using bedtools intersect; peaks were retained when present at least in two of the three replicates.
Supplementary files format and content: *.bw: For visualization purposes the bigwigs are obtained from merging the three replicates with samtools merge and processed as the data processing step indicated.

molecule: genomic DNA

source_name: PA-1 cells

growth_protocol: PA-1 cell lines were cultured in DMEM + Glutamax supplemented with 20% FBS, 1x non-essential amino acids and 1x penicillin/streptomycin.

extract_protocol:
ATAC-seq libraries were made as previously described (Buenrostro et al., 2015). Around 50000 for each replicate cells were pelleted (500g for 5 mins at 4°C), washed in cold PBS, then gently resuspended in 50 µL cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-360) and pelleted at 500g for 10 mins at 4°C. Supernatant was discarded and cell pellets placed on ice. Cells were gently resuspended in 50 µL transposition reaction mix as follows: 2X Tagment DNA buffer (Illumina 15027866), 20X Tagment DNA enzyme (Illumina 15027865) in ddH2O. Samples were incubated at 37°C for 30 mins. The transposed samples were then purified using the MinElute PCR purification kit (Qiagen 28204), according to the manufacturer’s instructions, with a final elution volume of 10 µL.
Transposed DNA samples were amplified by PCR by setting up a 50 µL reaction as follows: 10 µL transposed DNA, 9.7 µL ddH2O, 2.5 µL 25 µM customised Nextera PCR primer FW, 2.5 µL 25 µM customised Nextera PCR primer RV and 25 µL 2X NEBNext high-fidelity PCR master mix (New England Biosciences M0541). PCR amplification was performed on a thermal cycler.

value: Cultured cell line

value: wildtype


title: PA-1 wildtype replicate 3


title: HT1080−PPP1R3C−HA, Dox 0 µg/ml, rep2

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

description: Library name: HT_ctrl_2

data_processing:
The quality check and trimming of raw FASTQ data were performed using the fastp software.
Read mapping was conducted with HISAT2 (v2.0.5) using the Homo sapiens (human) genome assembly GRCh38 (hg38) as the reference.
The number of reads mapped to each gene was quantified using featureCounts (v1.5.0-p3).
TMM normalization and differential gene expression analysis were performed using the R packages edgeR (v4.2.2) and limma (v3.60.2), respectively.
Assembly: hg38
Supplementary files format and content: csv file includes the raw counts for each sample.

molecule: total RNA

source_name: Cell line

growth_protocol: High-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S). Cells were cultured at 37°C in a humidified incubator in an atmosphere of 95% air and 5% CO2.

extract_protocol:
Total RNA was isolated using Direct-zol RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer’s protocol.
The library was prepared for sequencing using standard Illumina protocols. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Dox inducible HT1080−PPP1R3C−HA cells and JJ012−PPP1R3C−HA cells were treated with Dox 1 µg/ml for 72 h.

tag: tissue

value: Cell line

value: Human Fibrosarcoma

value: Dox 0 µg/ml


title: JJ012−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep2

description: Library name: JJ012_Dox72_2

value: Human Chondrosarcoma

value: Dox 1 µg/ml for 72 h


title: PA-1 wildtype replicate 1


title: UOK109 cells, TFE3 rescue, Rep1


title: dialout_rep_8

city: Boston

first: Alexis

last: Caulier

state: Massachusetts

address: 1 Blackfan street

department: Oncology/Hematology

institute: Boston Children's Hospital

description: demultiplexed with BCL Convert

library_source: other

data_processing:
Files were demultiplexed with BCL convert then aligned with Cellranger with GRCh38 genome
Assembly: GRCh38
Supplementary files format and content: h5 matrix, gene expression counts stored in $`Gene Expression`
Supplementary files format and content: h5 matrix, peak counts stored in $`Peaks`
Supplementary files format and content: h5 matrix, CROPseq counts
Library strategy: 10x ATAC + GEX Multiome

molecule: other

source_name: Hematopoietic cells

growth_protocol: Erythroid media

extract_protocol: Chromium Single Cell Multiome ATAC + Gene Expression

value: Hematopoietic cells

value: erythroid cells


title: A-1 DGCR8 heterozygote replicate 3

value: DGCR8 heterozygote


title: A-1 DGCR8 heterozygote replicate 2


title: HT1080−PPP1R3C−HA, Dox 1 µg/ml for 72 h, rep2

description: Library name: HT_Dox72_2


title: UOK109 cells, NONOmut::TFE3 rescue, Rep2

value: NONOmut::TFE3 rescue


title: A-1 DGCR8 heterozygote replicate 1


title: UOK109 cells, NONOmut::TFE3 rescue, Rep1


title: UOK109 cells, NONOmut::TFE3 rescue, Rep3


title: dialout_rep_2

description: demultiplexed with BCL Convert


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep2

value: SFPQ{delta}CCD::TFE3 rescue


title: dialout_rep_1

description: demultiplexed with BCL Convert


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep1


title: UOK109 cells, SFPQΔCCD::TFE3 rescue, Rep3


title: UOK109 cells, SFPQ::TFE3 rescue, Rep3

value: SFPQ::TFE3 rescue


title: Spink7 KO skin day 0 biological rep 03

type: RNA

city: Chong qing

last: Zhao

address: 30 Main Street, Gao Tanyan

country: China

institute: Army Medical University

description: Gene expression data from the normal resting skin of Spink7 KO mice on day 0

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Clariom S Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100

label: biotin

organism: Mus musculus

source_name: Normal dorsal skin from 6 to 8-week-old C57BL/6J mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: Spink7 knockout (KO) mice and C57BL/6J mice were housed under a 12 hours light/dark cycle in a SPF room with water and food provided ad libitum

extract_protocol: Total RNA was extracted using Trizol reagent and purified up by RNeasy Micro Kit. The integrity (18S/28S) of RNA was evaluated by agarose gel electrophoresis and the concentrations was determined using NanoDrop

treatment_protocol: the 6 to 8-week-old C57BL/6J mice were anesthetized with 1% pentobarbital sodium and two 6.0 mm-diameter circular full-thickness excisional wounds were made in the shaved dorsal. At day 7,mice were euthanized and wound tissues were harvested with an 8.0-mm biopsypunch for RNA isolation

value: dorsal skin

value: Spink7 KO


title: Spink7 KO skin day 7 biological rep 03

description: Gene expression data from the proliferative phase wound skin of Spink7 KO mice on day 7

source_name: wound skin by day 7 post-injury from 6 to 8-week-old C57BL/6J mice


title: Spink7 KO skin day 7 biological rep 02


title: UOK109 cells, SFPQ::TFE3 rescue, Rep1

value: UOK109 cells

value: Patient-derived cells harboring NONO::TFE3 fusion


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep1

value: NONO{delta}CCD::TFE3 rescue

value: baseline culturing conditions


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep3


title: Spink7 KO skin day 7 biological rep 01


title: UOK109 cells, NONOΔCCD::TFE3 rescue, Rep2


title: Spink7 KO skin day 0 biological rep 01


title: Spink7 KO skin day 0  biological rep 02


title: Normal skin WT day 0 biological rep 03

description: Gene expression data from the normal resting skin of wild-type mice on day 0

value: WT


title: UOK109 cells, NONO::TFE3 rescue, Rep3

value: NONO::TFE3 rescue


title: Normal skin WT day 0  biological rep 02


title: Wound skin WT day 7 biological rep 03

description: Gene expression data from the proliferative phase wound skin of wild-type mice on day 7


title: UOK109 cells, NONO::TFE3 rescue, Rep2


title: UOK109 cells, NONO::TFE3 rescue, Rep1


title: UOK109 cells, NONO::TFE3-KO, Rep3

value: NONO::TFE3 KO


title: Wound skin WT day 7  biological rep 01


title: Wound skin WT day 7 biological rep 02


title: Barnyard_MCF-7_MM087_HyDrop_v2_beads

city: Leuven

first: Gert

last: Hulselmans

address: Herestraat 49 PO Box 602

department: Center for Brain and Disease Research

country: Belgium

institute: VIB

description:
Library name: HYA__140a21__20230818_mcf7_mmel_2
no resequencing

library_source: genomic single cell

data_processing:
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed to exclude the intersub-barcode PCR adapters MAWK
In house generated data (prefix HYA and FDM):  Barcode reads (read 2) were trimmed using trimgalore, corrected to a whitelist allowing 1 mismatch (in PUMATAC pipeline, nextflow version: nextflow-21.04.3), and appended to the fastq sequence identifier of the paired-end ATAC-seq reads (read 1 and read 3)
For all samples (mouse (in house generated and commercial), fly and barnyard cell lines): Reads were mapped to reference genomes using bwa-mem2 and fragemnet files were created with create_fragments_file by the (in PUMATAC pipeline, nextflow version: nextflow-21.04.3)
For mouse samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing the Otsu threshold in PUMATAC (nextflow version: nextflow-21.04.3) were included.
For Drosophila samples a data matrix (cistopic_obj) was generated using  pycistopic version 2.0a0. Cells passing  the trhshold of TSS_enrichment >2 and number of unique fragments > 800 in PUMATAC (nextflow version: nextflow-21.04.3) were included.
Assembly: For mouse samples: mm10, for hybrid samples in the barnyard: GRCh38_GRCm10 hybrid genome, for fly samples: dm6
Supplementary files format and content: For mouse and Drosophila samples: standard tab-separated fragments files, count matrix and metadata inforamtion for cell data (barcode) and region data in tsv format
Supplementary files format and content: For barnyard: standard tab separated fragment file

source_name: human breast cancer cell line and mouse melanoma cell line

growth_protocol:
Barnyard cell culture: cultured in RPMI1640 (ThermoFisher 11875093) medium supplemented with 10% FBS (ThermoFisher 10270–106), 1% penicillin/streptomycin (Life Technologies 15140122), and 10 ug/mL insulin (Sigma Aldrich I9278) and passaged twice per week. Melanoma cell lines were derived by physical resection of primary cutaneous lesions. Mouse melanoma cells were cultured in DMEM (ThermoFisher 13345364) supplemented with 10% FBS and 1% penicillin/streptomycin and passaged once per week. All cell lines tested negative for mycoplasma prior to use.
Mouse: The mice were housed under standard housing conditions in a pathogen-free facility with a 14 hr light, 10 hr dark light cycle from 7 to 21 hr. Mice used in the study were 60 days old.
Drosophila: All flies were raised on a yeast-based medium and kept at 25 °C on a 12h/12h day/night light cycle. For embryo collection, flies were transferred to cages fixed to a plate with a normal yeast-based medium 24 hours before embryo collection. On the day of embryo collection, the plate was exchanged for a juice plate. The juice was prepped by adding 20 g agar and 22 g sucrose to 300 ml distilled water, boiling, and then mixing in 100 ml apple juice, 10 ml 95% ethanol, and 5 ml 100% glacial acetic acid. The flies laid eggs for four hours. Sixteen hours later, the embryos aged between 16 to 20 hours were collected from the juice plate with a small brush and transferred to a 70 µm nylon mesh filter.

extract_protocol:
Mouse: The nuclei were extracted from mouse cortex samples that were snap-frozen in liquid nitrogen and stored at -80 °C. We transferred ~1 cm3 of frozen mouse cortex to 500 μL of ice-cold homogenization buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 0.1% IGEPAL CA-630, 1× complete protease inhibitor, and 1 mM DTT) in a Dounce Homogenizer. The tissue was left to thaw for 2 min before the tissue was homogenized with 10 strokes of the loose pestle and 5 strokes of the tight pestle. Before the end of a 5-minute incubation, the homogenate was filtered through a 70 μm cell strainer (Corning), and the homogenizer and strainer were washed with homogenization buffer to obtain a final volume of 1 mL. The filtrate was transferred to a 1.5 mL DNA LoBind tube (Eppendorf) and centrifuged at 500 xg for 5 minutes. The supernatant was discarded, and the pellet was topped up to 520 μL with wash buffer 1 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 320 mM sucrose, 0.1 mM EDTA, 0.5% BSA, 1× complete protease inhibitor, and 1 mM DTT) and resuspended. Next, we added 520 μL gradient medium (50% Optiprep, 10 mM Tris-HCl pH 7.5, 1 mM CaCl2, 5 mM MgCl2, 75 mM sucrose, 1× complete protease inhibitor, and 1 mM DTT) and mixed the entire volume by gentle pipetting. In a 2 mL DNA LoBind tube we layered 790 μL Optiprep cushion (29% Optiprep, 31 mM Tris-HCl pH 8, 77.5 mM KCl, 15.5 mM MgCl2, 129.2 mM sucrose) at the bottom and 1040 μL of the sample on top, gently without disrupting the cushion. The tube was then centrifuged at 9000 xg for 20 minutes at 4 °C. After the centrifugation the debris on top was carefully removed with a 1 mL tip and the rest of the supernatant was also carefully removed until 50 μL was left in the tube. The pellet was gently resuspended before we mixed it with 50 μL 0.2× permeabilization buffer (20 mM Tris-HCl pH 7.5, 20 mM NaCl, 6 mM MgCl2, 0.2% Tween-20, 0.02% IGEPAL CA-630, 0.02% Digitonin, 2% BSA, and 2 mM DTT) and left the nuclei suspension for 2 minutes on ice before we stopped the permeabilization by mixing it with 1 mL of wash buffer 2 (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA). The nuclei were pelleted by centrifugation at 500 xg for 5 minutes at 4 °C. The nuclei were resuspended in PBS with 0.04% BSA. For Drosophila, the nuclei were isolated by using an adapted protocol based on the nuclei isolation protocol for single-cell ATAC sequencing (10x Chromium CG000169-RevE).  Similar to mouse, for the barnyard, the cell lines were mixed to equal parts and a pellet of one million dissociated cells or fewer was incubated on ice in 200 μL of ATAC lysis buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.1% Tween-20, 0.1% NP-40, 3 mM MgCl2, 70 μM Pitstop in DMSO, 0.01% digitonin) for 5 minutes. 1 mL of ATAC nuclei wash buffer (1% BSA, 10 mM Tris-HCl pH 7.5, 0.1% Tween-20, 10 mM NaCl, 3 mM MgCl2) was added and the nuclei were pelleted at 500 xg, 4 °C for 5 minutes. The resulting pellet was resuspended in 100 μL of ice-cold PBS and filtered with a 40 μm strainer (Flowmi).
Nuclei, resuspended in PBS (supplemented with 0.04% BSA), were tagmented for one hour at 37 °C in 15 μL ATAC reaction mix (10% DMF, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 ng/µL Tn5, 70 µM Pitstop in DMSO, 0.1% Tween-20, 0,01% Digitonin). Tagmented nuclei were placed on ice and 95 µL of PCR mix (1.25× Phusion HF buffer, 15% Optiprep, 1.25 mM dNTPs, 75 mM DTT, 0.0625 U/µL Phusion HF polymerase, 0.0625 U/μL Deep Vent polymerase, 0.0125 U/μL ET SSB) was added. Next, 110 μL of nuclei mixed in PCR mix was co-encapsulated with 45 μL of HyDrop-ATACv2 beads in HFE-7500 Novac oil with EA-008 surfactant (RAN Biotech) using the Onyx microfluidics platform (Droplet Genomics). The resulting emulsion was split over two PCR tubes and was placed in a thermocycler with the following program: 72 °C – 15 mins, 98 °C – 3 mins, 12 cycles of 98 °C – 10 s; 55 °C – 30 s; 72 °C – 1 min; 72 °C – 5 mins, and finally the amplification products were cooled to 4 °C. To break the emulsion and remove excess oil, 125 μL of recovery agent (20% PFO in HFE) was added and the PCR tubes were inverted 10 times to mix before the oily phase was removed. Next, we added 180 μL GITC mix (5M GITC, 25 mM EDTA, 50 mM Tris-HCl pH 7.4), 10 μL Dynabeads, and 10 μL 2.4 M DTT to each of the aliquots, and mixed everything by pipetting up and down 10 times and incubating for 10 minutes. Dynabeads were pelleted on a magnet and washed twice with 80% ethanol. Elution was done in 50 μL of EB-DTT-Tween (24 mM DTT, 0.1% Tween-20 in EB (10 mM Tris-HCl pH 8.5)). Next, a 1.2× Ampure bead purification was performed according to manufacturer’s recommendations. Elution was done with 40 μL of EB-DTT (10 mM DTT in EB). The library was completed by amplifying the eluate in a total volume of 100 μL PCR mix (1× KAPA HiFi, 1 μM index i7 primer, 1 μM Universal P5 primer) with the following program: 95 °C – 3 mins, 12 cycles of 98 °C – 10 s; 63°C – 30 s; 72 °C – 1 min; 72 °C – 1 min, and finally a hold stage at 4 °C. The final libraries were subjected to 0.4×–1.2× doublesided Ampure purification and eluted in 20 μL elution buffer.

value: MCF-7 and mouse melanoma

value: 50:50 mixture of MCF-7 and mouse melanoma

tag: Sex

value: female

tag: age

tag: batch


title: UOK109 cells, NONO::TFE3-KO, Rep2


title: UOK109 cells, NONO::TFE3-KO, Rep1


title: mouse_cortex_HyDrop_v2_B_beads_7

description:
Library name: HYA__fcb55f__20231013_HyDropATAC_MouseCortex_B
re-sequenced on Illumina NovaSeq2000

source_name: brain cortex

value: brain cortex

value: divers cells of brain cortex

tag: strain

value: C57B/6J background

value: 60 days


title: Normal skin WT day 0  biological rep 01


title: mouse_cortex_HyDrop_v2_F_beads_7

description:
Library name: HYA__cc24b7__20240304_Mouse_Cortex-c-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: UOK109 cells, SFPQ::TFE3 rescue, Rep2

value: SFPQ::TFE3 rescue


title: 3D_NT_3

city: Seongnam-si

first: Hye-Ryoung

last: Kim

state: Gyeonggi-do

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

data_processing:
Total RNA-seq
The files were processed using Fastp (v0.23.1) to remove low-quality reads and adapters.
Paired-end reads were then mapped to the human reference genome (GRCh38) using STAR (v2.7.10.b).
The number of reads that were mapped at the gene level was calculated using Salmon (v1.10.0).
Assembly: The human reference genome (GRCh38)
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes TPM values for each sample

source_name: mesenchymal stem cell

extract_protocol:
Total RNA was isolated using Trizol reagent according to the manufactures’ instructions (Invitrogen), and its quality was assessed using the TapeStation4000 System (Agilent Technologies, Amstelveen, The Netherlands).
Libraries were prepared from total RNA using the CORALL RNA-Seq V2 Library Prep Kit (LEXOGEN, Austria).

value: mesenchymal stem cell

value: 3D culture non-treat


title: mouse_cortex_HyDrop_v2_F_beads_5

description:
Library name: HYA__853a40__20240304_Mouse_Cortex-b1-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: 3D_NT_2


title: mouse_cortex_HyDrop_v2_F_beads_6

description:
Library name: HYA__955707__20240304_Mouse_Cortex-b2-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: 3D_NT_1


title: 3D_MG_3

value: 3D culture after delivery of isolated MG63 MT


title: mouse_cortex_HyDrop_v2_F_beads_4

description:
Library name: HYA__167ec9__20240304_Mouse_Cortex-a2-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: mouse_cortex_HyDrop_v2_F_beads_3

description:
Library name: HYA__c0d7e5__20240304_Mouse_Cortex-a1-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: mouse_cortex_HyDrop_v2_F_beads_2

description:
Library name: HYA__3eb2c7__20240221_Mouse_Cortex-b-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: 3D_MG_1


title: mouse_cortex_HyDrop_v2_F_beads_1

description:
Library name: HYA__6b44d3__20240221_Mouse_Cortex-a-ATAC
re-sequenced on Illumina NovaSeqX and Nextseq 2000


title: 2D_MtMSC_3

value: 2D culture after delivery of isolated MG63 MT


title: 3D_MG_2


title: mouse_cortex_HyDrop_v2_E_beads_2

description:
Library name: HYA__fd6250__20240105_Mouse_Cortex-b-ATAC
re-sequenced on Illumina NovaSeqX


title: 2D_MtMSC_2


title: 2D_MtMSC_1


title: mouse_cortex_HyDrop_v2_B_beads_8

description:
Library name: HYA__14fb45__20231013_HyDropATAC_MouseCortex_D
re-sequenced on Illumina NovaSeq2000


title: mouse_cortex_HyDrop_v2_E_beads_1

description:
Library name: HYA__9667aa__20231116_HyATAC_MouseCortex_C2
no resequencing


title: mouse_cortex_HyDrop_v2_E_beads_5

description:
Library name: HYA__831196__20240105_Mouse_Cortex-a-ATAC
re-sequenced on Illumina NovaSeqX


title: mouse_cortex_HyDrop_v2_C_beads_3

description:
Library name: HYA__8d1d23__20231116_HyATAC_MouseCortex_C1
no resequencing


title: mouse_cortex_HyDrop_v2_D_beads_4

description:
Library name: HYA__ba8433__20231116_HyATAC_MouseCortex_B2
no resequencing


title: mouse_cortex_HyDrop_v2_C_beads_2

description:
Library name: HYA__d4ff32__20231116_HyATAC_MouseCortex_A
no resequencing


title: 2D_MSC_1

value: 2D culture non-treat


title: 2D_MSC_2


title: mouse_cortex_HyDrop_v2_D_beads_3

description:
Library name: HYA__66fdea__20231116_HyATAC_MouseCortex_B1
no resequencing


title: 2D_MG63_2

value: osteoblast


title: 2D_MG63_1


title: mouse_cortex_HyDrop_v2_B_beads_6

description:
Library name: HYA__3e5c73__20231031_HyDropAtac_MouseCortex_D2
re-sequenced on Illumina NextSeq2000


title: mouse_cortex_HyDrop_v2_B_beads_5

description:
Library name: HYA__30fc7f__20231031_HyDropAtac_MouseCortex_D1
re-sequenced on Illumina NextSeq2000


title: B9-D109-Mim-Gut-R3_S66

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

institute: Texas A&M University

data_processing:
The gene count matrices were generated from single-end reads with four lanes per sample with ~75 base pairs (bp).
The raw sequencing reads for each pooled sample, which included 2 lanes of single-end sequencing reads of 75 base pairs in length, were combined to generate a single FASTQ file per sample. These FASTQ files were then processed using Fastp (version 0.21.0) (Chen, 2018), trimming the sequencing reads to 50 base pairs with default parameters.
The reads from the four lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Before conducting differential gene expression or other transcriptomic analyses, the raw count matrix data was aggregated to the gene level if a gene was associated with more than one probe in the TempO-seq library. Next, quality control steps were applied to the raw counts as follows: (i) samples were excluded from further analyses if the number of uniquely mapped reads was lower than 50%, (ii) samples were excluded from further analyses if they had less than 200,000 total mapped reads, (iii) any potential outliers were detected using principal component analysis (PCA) using R function prcomp, and (iv) genes were excluded from further analysis if they had fewer than 2 counts across more that 5% of all retained samples. The final dataset contained a total of 13 samples (n=3 for Caco-2 Transwell, Caco-2 OrganoPlate, and J2 OrganoPlate; n=2 for D109 Transwell and D109 OrganoPlate) and 2,537 genes. This dataset was then processed using the DESeq2 package in R (Love, 2014 #12366) for further data visualization and differential gene expression analysis.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

extract_protocol:
Cell lysates were prepared from OrganoPlate® 3-lane 40 microphysiological system with flow (MPS) or static 24-well Transwells™. Following 10 minutes of incubation at room temperature, the cell lysate was flushed out by addition lysis buffer. Following 10 min of incubation at room temperature, the cell lysate was flushed out by addition of 15 uL of Enhanced 2× Lysis Buffer (201250, BioSpyder Technologies, Carlsbad, California). For Transwells, media was aspirated and 90 uL of 1× lysis buffer was added directly onto cells. After 10 min at room temperature the lysates were collected from each insert and stored at -80C until further processing.  The Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies, Carlsbad, CA) was used as an RNA sequencing technology of choice. Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported  detailed elsewhere (House et al., 2017)
TempO-seq libraries were prepared using the S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,976 transcripts according to the manufacturer’s instructions.

value: media

tag: platform

value: Mima-Gut


title: B6-J2-Mim-Gut-R3_S42


title: mouse_cortex_HyDrop_v2_D_beads_2

description:
Library name: HYA__0f6aa5__20231031_HyDropAtac_MouseCortex_B2
no resequencing


title: mouse_cortex_HyDrop_v2_B_beads_4

description:
Library name: HYA__a7a748__20231031_HyDropAtac_MouseCortex_C2
re-sequenced on Illumina NextSeq2000


title: B5-J2-Mim-Gut-R2_S34


title: B8-D109-Mim-Gut-R2_S58


title: mouse_cortex_HyDrop_v2_B_beads_3

description:
Library name: HYA__a52ea6__20231031_HyDropAtac_MouseCortex_C1
re-sequenced on Illumina NextSeq2000


title: mouse_cortex_HyDrop_v2_D_beads_1

description:
Library name: HYA__7e2d51__20231031_HyDropAtac_MouseCortex_B1
no resequencing


title: B3-Caco-Mim-Gut-R3_S18


title: mouse_cortex_HyDrop_v2_C_beads_1

description:
Library name: HYA__7ad445__20231031_HyDropAtac_MouseCortex_A1
no resequencing


title: 2D_MSC_3


title: mouse_cortex_HyDrop_v2_B_beads_2

description:
Library name: HYA__247495__20231013_HyDropATAC_MouseCortex_C
no resequencing


title: B4-J2-Mim-Gut-R1_S26


title: mouse_cortex_HyDrop_v2_B_beads_1

description:
Library name: HYA__7a1cc3__20231013_HyDropATAC_MouseCortex_A
re-sequenced on Illumina NextSeq2000


title: B2-Caco-Mim-Gut-R2_S10


title: mouse_cortex_HyDrop_v2_A_beads_2

description:
Library name: HYA__e1bdab__20230829_mouse_cortex_2
re-sequenced on Illumina NextSeq2000


title: A9-D109-TW-Gut-R3_S65

value: TW-Gut


title: 2D_MG63_3


title: A3-Caco-TW-Gut-R3_S17


title: A2-Caco-TW-Gut-R2_S9


title: A8-D109-TW-Gut-R2_S57


title: mouse embryonic stem cell target library rep 2

city: San Diego

first: Norjin

last: Zolboot

state: CA

address: 10550 North Torrey Pines Rd, DNC-222

department: Neuroscience

institute: The Scripps Research Institute

description: Library name: E14-ESC-target-r2

data_processing:
The first 8 nt that encodes the UMI in each read was extracted by UMI-tools and appended to the original read name, which was used to distinguish duplicated reads produced at PCR amplification steps.
The 3′ adapter and bases with Phred quality score lower than 20 were trimmed from reads using cutadapt v2.10. Reads less than 15bp were discarded.
Processed target library reads were aligned to the UCSC mm10 mouse genome using STAR v2.5.2a. Reads mapped to the same locus with identical UMIs were considered PCR duplicates and therefore collapsed using the UMI-tools dedup function with default 1-mismatch allowed in the UMI region for error correction. Processed small RNA reads were aligned to a miRNA genome index built from 1,915 murine pre-miRNA sequences from miRbase version 22 using Bowtie v2.4.2.
Peaks were called using the unpublished package CLIPanalyze. The function findPeaks () was run with the following parameters: bandwidth = 30, count.exons.only = FALSE, nthreads = 4, min.width = 15, merge.dist = 20. Differential read count analysis was performed between target and input control read counts in putative peaks using DESeq2 v1.36.0, and FDR-corrected p-values (adjusted p-values) were assigned to each peak.
bigWig files for visualization of target and input control libraries were produced using deepTools bamCoverage v3.1.3 with parameter “--binSize 1 --normalizeUsing CPM”
Assembly: mm10
Supplementary files format and content: bigWig for target and input libraries, counts for miRNA libraries
Supplementary files format and content: bed for target libraries

source_name: mouse embryonic stem cell line

growth_protocol: mESCs were cultured in GMEM (Sigma, G5154) supplemented with 12.5% FBS, Antibiotic/Antimycotic (Gibco, 15240062), GlutaMax (1 mM, Gibco, 35050061), non-essential amino acids (Gibco, 11140050), sodium pyruvate (1mM, Gibco, 11360070), 2-mercaptoethanol (1:100000, Sigma, M7522) and LIF (added fresh 1:1000, Chemicon®, ESG1106). The culture plates were incubated with 0.1% gelatin solution at RT for at least 10 min and the solution was completely removed before plating the cells. The cells were passaged every other day ~1:10-20

extract_protocol:
For miRNA and target libraries, RNAs were isolated with Spy3-AGO2 using HaloTag-SpyCatcher3 conjugated to a HaloLink resin from the sample. The miRNA/target and input samples (whole lysate) were run on an SDS-PAGE gel and the gel was cut between 70 kDa and 150 kDa. RNAs were then extracted from the gel using phenol/chloroform and purified with the RNA Clean & Concentrator-5 kit. For input libraries, RNAs were purified from lysates using MyONE Silane beads.
RNAs were ligated to RNA adapters on both ends (5' RNA adapter 5biotin/rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrCrNrNrNrNrNrNrNrNrNrN and 3' RNA adapter /5Phos/r(N:25252525)r(N:25252525)r(N:25252525)rUrGrGrArArUrUrCrUrCrGrGrGrUrGrCrCrArArGrG/3SpC3). After reverse transcription with a DNA primer DP3 (CCTTGGCACCCGAGAATTCCA), the library was amplified with DNA primers DP3 and DP5 (GTTCAGAGTTCTACAGTCCGACGATC). To construct the libraries for high-throughput sequencing, DNA primers TS Primer-X ( CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA, N=standard Illumina barcodes) and TS Primer-1 (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC) containing Illumina barcodes, sequencing primer binding sites and Illumina TruSeq indexes for multiplexing were introduced using PCR. After quantification and quality control, libraries were pooled and run on a NextSeq 2000 in a 100 bp single end run.

value: mouse embryonic stem cell line


title: A1-Caco-TW-Gut-R1_S1


title: mouse embryonic stem cell input library rep 2

description: Library name: E14-ESC-input-r2


title: mouse embryonic stem cell target library rep 1

description: Library name: E14-ESC-target-r1


title: D6_Spheroid_DOX_Rep2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
The RNA-seq data were first subjected to adaptor trimming and low-quality read filtering with flexbar (version 2.5) with the following parameters: -u 6 -m 36 -ae RIGHT -at 2 -ao 2 -x 3 -y 1.
The trimmed paired-end reads were then aligned to the human reference genome (hg19) by STAR (version 2.7.10b) under the parameters: -outFilterMismatchNoverLmax 0.1 --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 6 --alignSJDBoverhangMin 1 --outFilterType BySJout --outFilterIntronMotifs RemoveNoncanonicalUnannotated.
HTSeq (v0.13.5) was employed for gene expression quantification.
Assembly: hg19
Supplementary files format and content: tsv, gene expression read counts

source_name: iWDR36 iPS cells

extract_protocol:
Each sample is lysed using a 2 µL lysis buffer with 0.2% TritonX-100 and 40 U/mL Recombinant RNase Inhibitor, which disrupts cell membranes to release RNA and other cellular contents while preventing RNA degradation.
Poly(A)-tailed RNA molecules in cells were processed using the Smart-seq2 protocol. The RNA-seq libraries were constructed using the SMART-seq2 protocol, involving lysis of each sample in a specialized buffer, followed by reverse transcription and cDNA amplification for 16 cycles. Tagmentation with Tn5 enzyme mix and PCR was employed to build sequencing libraries, which were then amplified and purified. Library quality was assessed using PerkinElmer LabChip GX Touch, and sequencing was carried out on the Illumina NovaSeq 6000 platform in PE150 mode.

value: iWDR36 iPS cells

value: 8CLC in 3D culture

value: Dox

tag: treatment time

tag: culture time

value: 6 days

tag: morphology

value: Spheroid


title: mouse embryonic stem cell miRNA library rep 2

description: Library name: E14-ESC-miRNA-r2


title: mouse embryonic stem cell input library rep 1

description: Library name: E14-ESC-input-r1


title: D6_Spheroid_Ctrl_Rep2


title: P14 pyramidal neuron input library rep 2

description: Library name: P14-PN-input-r2

source_name: cortex

growth_protocol: Mice were group-housed on a 12-hr light-dark cycle and fed a standard rodent chow diet in the Dorris Neuroscience Center vivarium. All experimental protocols were approved by the Scripps Research Institute Institutional Animal Care and Use Committee (IACUC) and were in accordance with the guidelines from the NIH.

value: cortex

value: pyramidal neurons


title: D6_Spheroid_Ctrl_Rep1


title: P14 pyramidal neuron input library rep 1

description: Library name: P14-PN-input-r1


title: D6_Blastoid_DOX_Rep2

value: Blastoid


title: P14 pyramidal neuron target library rep 1

description: Library name: P14-PN-target-r1


title: D6_Blastoid_Ctrl_Rep2


title: D6_Blastoid_DOX_Rep1


title: mouse_cortex_HyDrop_v2_A_beads_1

description:
Library name: HYA__ac683b__20230829_mouse_cortex_1
re-sequenced on Illumina NextSeq2000

value: brain cortex

value: divers cells of brain cortex

value: C57B/6J background

value: female

value: 60 days


title: D6_Blastoid_Ctrl_Rep1


title: P14 pyramidal neuron target library rep 2

description: Library name: P14-PN-target-r2


title: D4_Spheroid_DOX_Rep1

value: 4 days


title: P14 pyramidal neuron miRNA library rep 1

description: Library name: P14-PN-miRNA-r1


title: D4_Spheroid_DOX_Rep2


title: B1-Caco-Mim-Gut-R1_S2

value: media

value: Mima-Gut


title: Rloop (S9.6) CUT&Tag ERCC1 KO mESC 2

city: Solna

first: Simon

middle: J

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

description: Library name: Rloop_ERCC1_KO-rep2

data_processing:
Libraries were sequenced on an Illumina Nextseq 2000
Raw paired-end CUT&Tag FASTQ files were processed through a Snakemake workflow (18) available on GitHub (https://github.com/elsasserlab/cutntag). Essentially, reads were aligned to the mm39 reference genome and drosophila dm6 genome for spike-in with bowtie2 (19) 2.5.1, deduplicated with Picard (https://github.com/broadinstitute/picard) 3.0.0 and reads were further filtered by mapping quality (MQ > 10) using samtools (20) 1.17
Peaks were called using MACS3 3.0.0b1 (https://doi.org/10.1186/gb-2008-9-9-r137) with default parameters (-q 0.05).
deepTools (21) 3.5.2 bamCoverage was used to produce  scaled bigWig files using a calculated spike-in factor.
Assembly: GRCm39 (mm39)
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: embryonic stem cell

growth_protocol: Mouse embryonic stem (mES) cell lines were maintained on 0.1% gelatin-coated dishes in Buffalo rat liver (BRL)-conditioned KnockOut DMEM (Gibco) supplemented with 100 U/mL penicillin (Gibco), 100 mg/mL streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Gibco), 13 non-essential amino acids (Gibco), 50 mM b-mercaptoethanol (Gibco), 10% fetal calf serum (Capricorn Scientific) and leukemia inhibitory factor at 37ºC and 5% CO2, fed and split every 2-3 days.

extract_protocol:
Quantitative CUT&Tag experiments were performed as described previously (17) with modifications. Briefly, 2 x 105 mouse embryonic stem cells were harvested, washed once with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine), and then incubated in 200 mL of antibody buffer (wash buffer with 1% BSA, 2 mM EDTA, 0.01% NP-40 and 0.05% digitonin) with 1:100 purified FLAG-tagged BG4 antibody or S9.6 (Sigma-Aldrich) antibody dilution at 4°C by rotating overnight. The next day, the primary antibody was removed by centrifugation at 600 xg for 4 minutes at 4ºC, and cells were washed with 200 mL of dig-wash buffer (wash buffer with 1% BSA, 0.01% NP-40 and 0.05% digitonin) three times. After washing, BG4 antibody-incubated cells were resuspended in 200 mL of dig-wash buffer with 1:100 dilution of mouse anti-FLAG antibody (Sigma-Aldrich) and incubated at room temperature for 1 hour with slow rotation. Cells were washed with 200 mL of dig-wash buffer briefly three times to remove unbound antibodies. S9.6-treated or anti-FLAG treated cells were incubated with 1:100 dilution of rabbit anti-mouse antibody (Sigma-Aldrich) in 200 mL of dig-wash buffer at room temperature for 1 hour with slow rotation. After a brief wash with dig-wash buffer as above, cells were resuspended in 200 mL of dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 0.05% digitonin, 0.01% NP-40, 0.5 mM spermidine, 1% BSA) with 1:100 dilution of assembled pA-Tn5 and incubated at room temperature for 1 hour with slow rotation. pA-Tn5-bound cells were washed with 1 mL of dig-300 buffer three times, followed by tagmentation in 200 mL of tagmentation buffer (dig-300 buffer with 10 mM MgCl2) at 37°C for 1 hour with shaking at 800 rpm. After tagmentation, 15 mM EDTA, 500 mg/mL proteinase K and 0.1% SDS were added and further incubated at 63°C for another 1 hour to stop tagmentation and digest protein. Genomic DNA was extracted and purified with DNA Clean & Concentrator-5 (Zymo research). A spike-in was used where indicated to provide an external scaling factor for quantitative comparison across conditions. Briefly, G4 CUT&Tag was performed on S2 cells in parallel with the mouse samples. After tagmentation and genomic DNA purification, the tagmented DNA was quantified using Qubit assay. The tagmented samples were normalized to the same DNA concentration, and a constant amount (5% of sample) of tagmented Drosophila DNA (‘spike-in’) was added to each sample, at a ratio of 1:20. Afterwards, library PCR was performed as described above. An alternative method, mixing 5% S2 cells into the harvested cells before CUT&Tag procedure was also evaluated but showed larger variation due to the error attached to cell counting.
To generate G4 or R-loop libraries, purified genomic DNA was amplified with the universal i5 primer and barcoded i7 primer using NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs). The library PCR products were cleaned up with Agencourt AMPure XP beads (Beckman Coulter) and sequenced on an Illumina Nextseq 2000 instrument (illumina).

treatment_protocol: There was no treatment

value: embryonic stem cell

value: ERCC1 KO

value: No treatment

tag: antibody


title: Rloop (S9.6) CUT&Tag ERCC1 KO mESC 1

description: Library name: Rloop_ERCC1_KO-rep1


title: D4_Spheroid_Ctrl_Rep2

value: iWDR36 iPS cells

value: 8CLC in 3D culture


title: Rloop (S9.6) CUT&Tag ERCC1 WT mESC 1

description: Library name: Rloop_ERCC1_WT-rep1

value: WT


title: Rloop (S9.6) CUT&Tag ERCC1 WT mESC 2

description: Library name: Rloop_ERCC1_WT-rep2


title: G4 (BG4) CUT&Tag ERCC1 KO mESC 2

description: Library name: G4_ERCC1_KO-rep2


title: D4_Spheroid_Ctrl_Rep1

value: Spheroid


title: D6_Spheroid_DOX_Rep1

value: Dox

value: 6 days


title: u87 cells_high-level androgen fetal bovine serum_ rep3

city: shanghai

first: Zhen

last: Yang

address: No. 6600, Nanfeng Road, Fengxian District

department: Department of central laboratory

institute: Shanghai University of Medicine & Health Science Affiliated Sixth People’s Hospital South Campus

data_processing:
Illumina Casava1.7 software used for basecalling.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

value: glioblastoma

value: DHT


title: G4 (BG4) CUT&Tag ERCC1 KO mESC 1

description: Library name: G4_ERCC1_KO-rep1


title: mouse embryonic stem cell miRNA library rep 1

description: Library name: E14-ESC-miRNA-r1

value: mouse embryonic stem cell line


title: G4 (BG4) CUT&Tag ERCC1 WT mESC 2

description: Library name: G4_ERCC1_WT-rep2


title: u87 cells_high-level androgen fetal bovine serum_ rep1


title: P14 pyramidal neuron miRNA library rep 2

description: Library name: P14-PN-miRNA-r2

value: cortex

value: pyramidal neurons


title: u87 cells_high-level androgen fetal bovine serum_ rep2


title: u87 cells_fetal bovine serum_rep3

value: Control


title: G4 (BG4) CUT&Tag ERCC1 WT mESC 1

description: Library name: G4_ERCC1_WT-rep1


title: P15 Purkinje cells input library rep 2

description: Library name: PC-p15-input-r2

source_name: cerebella

extract_protocol:
For miRNA and target libraries, RNAs were isolated along with Spy3-Ago2 using HaloTag-SpyCatcher3 conjugated to a HaloLink resin from the sample. The miRNA/target and input samples (whole lysate) were run on a SDS-PAGE gel, the gel was cut between 70 kDa and 150 kDa. RNAs were then extracted from the gel using phenol/chloroform and purified with the RNA Clean & Concentrator-5 kit. For input libraries, RNAs were purified from lysates using MyONE Silane beads
RNAs were ligated to RNA adapters on both ends (5' RNA adapter 5biotin/rGrUrUrCrArGrArGrUrUrCrUrArCrArGrUrCrCrGrArCrGrArUrCrNrNrNrNrNrNrNrNrNrN and 3' RNA adapter /5Phos/r(N:25252525)r(N:25252525)r(N:25252525)rUrGrGrArArUrUrCrUrCrGrGrGrUrGrCrCrArArGrG/3SpC3). After reverse transcription with a DNA primer DP3 (CCTTGGCACCCGAGAATTCCA), the library was amplified with DNA primers DP3 and DP5 (GTTCAGAGTTCTACAGTCCGACGATC). To construct the libraries for high-throughput sequencing, DNA primers TS Primer-X ( CAAGCAGAAGACGGCATACGAGATNNNNNNGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA, N=standard Illumina barcodes) and TS Primer-1 (AATGATACGGCGACCACCGAGATCTACACGTTCAGAGTTCTACAGTCCGACGATC) containing Illumina barcodes, sequencing primer binding sites and Illumina TruSeq indexes for multiplexing were introduced using PCR. After quantification and quality control, libraries were pooled and run on a NextSeq 2000 in a 100 bp single end run.

treatment_protocol: Homozygous conditional Spy3-Ago2 mice were injected with an AAV expressing Cre under the PC-specific promoter L7 via intracerebroventricular injection. Cerebella were harvested at P7 and P15

value: cerebella

value: Purkinje cells


title: u87 cells_fetal bovine serum_rep2


title: u87 cells_fetal bovine serum_rep1


title: Rloop (S9.6) CUT&Tag DHX36/FANCJ double knockout mESC 1

data_processing:
Libraries were sequenced on an Illumina Nextseq 2000
Raw paired-end CUT&Tag FASTQ files were processed through a Snakemake workflow (18) available on GitHub (https://github.com/elsasserlab/cutntag). Essentially, reads were aligned to the mm39 reference genome and drosophila dm6 genome for spike-in with bowtie2 (19) 2.5.1, deduplicated with Picard (https://github.com/broadinstitute/picard) 3.0.0 and reads were further filtered by mapping quality (MQ > 10) using samtools (20) 1.17
Peaks were called using MACS3 3.0.0b1 (https://doi.org/10.1186/gb-2008-9-9-r137) with default parameters (-q 0.05).
deepTools (21) 3.5.2 bamCoverage was used to produce  scaled bigWig files using a calculated spike-in factor.
Assembly: GRCm39 (mm39)
Supplementary files format and content: Demultiplexed gene count table (tsv)
Library strategy: CUT&Tag

source_name: 129/Ola-derived IB10 mouse embryonic stem cell

growth_protocol: 129/Ola-derived IB10 mouse embryonic stem (mES) cell lines were maintained on 0.1% gelatin-coated dishes in Buffalo rat liver (BRL)-conditioned KnockOut DMEM (Gibco) supplemented with 100 U/mL penicillin (Gibco), 100 mg/mL streptomycin (Gibco), 2 mM GlutaMAX (Gibco), 1 mM sodium pyruvate (Gibco), 13 non-essential amino acids (Gibco), 50 mM b-mercaptoethanol (Gibco), 10% fetal calf serum (Capricorn Scientific) and leukemia inhibitory factor at 37ºC and 5% CO2, fed and split every 2-3 days.

value: embryonic stem cell

value: DHX36/FANCJ KO


title: P15 Purkinje cells target library rep 2

description: Library name: PC-p15target-r2


title: u87 cells_charcoal-stripped fetal bovine serum_rep3

value: CFBS


title: Rloop (S9.6) CUT&Tag DHX36/FANCJ double knockout mESC 2

value: 129/Ola-derived IB10 mouse embryonic stem cell

value: No treatment


title: u87 cells_charcoal-stripped fetal bovine serum_rep2


title: u87 cells_charcoal-stripped fetal bovine serum_rep1


title: 293T cells, CUT-Tag

city: Beijing

first: Chunyu

last: Yu

address: Xueyuan Road 38#

institute: Peking University

data_processing:
For CUT&Tag, quality control was performed using FastQC, reads were aligned to the human reference genome (GRCh38) using Bowtie2, and enriched genomic regions (peaks) were identified using MACS2 with p=0.01 at BAMPE mode.
Assembly: hg38
Supplementary files format and content: bigwig and narrowpeak files
Library strategy: CUT&Tag

growth_protocol: 293T cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
For nuclei preparation in CUT&Tag, cells were harvested by trypsinization and washed twice with cold PBS. The cell pellet was resuspended in NE-PER Nuclear and Cytoplasmic Extraction Reagent, incubated on ice for 10 minutes, and then centrifuged. The supernatant was discarded, and the nuclear pellet was resuspended in nuclei buffer, incubated again on ice, and centrifuged to obtain the clean nuclei.
For CUT&Tag, tagmentation involved incubating nuclei with Tn5 transposase loaded with sequencing adapters at 37°C for 1 hour. DNA was extracted using phenol-chloroform or a commercial DNA extraction kit, amplified by PCR with indexed primers, and purified using AMPure XP beads.

value: Human embryonic kidney

value: WT


title: Rloop (S9.6) CUT&Tag FANCJ knockout mESC 1

value: FANCJ KO


title: Rloop (S9.6) CUT&Tag DHX36 knockout mESC 2

value: DHX36 KO


title: Rloop (S9.6) CUT&Tag DHX36 knockout mESC 1


title: MDA-MB-231, H2AS40-KD, Rep1

city: Imabari-shi

first: Koji

last: Hayakawa

state: Ehime

address: 1-3 Ikoino-oka, Bldg. A2, Room 630

country: Japan

institute: Okayama University of Science

data_processing:
RNA-seq data was processed by RaNA-seq software (https://ranaseq.eu/home).
Sequence reads of ChIP-seq were aligned to the human genome (hg38) using Bowtie2 and peaks were identified using MACS2 in the Galaxy browser (www.galaxy.psu.edu).
Assembly: hg38
Supplementary files format and content: bigWig files include signals of each ChIP sample.
Supplementary files format and content: Excel file include TPM values for each Sample.

source_name: Mammary gland

growth_protocol: MDA-MB-231 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibodies in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Enriched ChIP DNA was collected using the ChIP-IT Express Enzymatic Kit (Active Motif), and Total RNA was extracted using the Monarch Total RNA Miniprep Kit (New England Biolabs).
Libraries for RNA-seq were prepared using NEBNex Ultra II RNA Library Prep Kit for Illumina (New England Biolabs), and Libraries for ChIP-seq were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEW ENGLAND Biolabs).

value: Mammary gland

value: Breast cancer

value: S40-type H2A knckdown


title: MDA-MB-231, Control-KD, Rep2


title: MDA-MB-231, H2AS40-KD, Rep2


title: MDA-MB-231, Control-KD, Rep3


title: Rloop (S9.6) CUT&Tag WT mESC 1


title: Rloop (S9.6) CUT&Tag WT mESC 2


title: G4 (BG4) CUT&Tag DHX36/FANCJ double knockout mESC 3


title: MDA-MB-231, Control-KD, Rep1


title: G4 (BG4) CUT&Tag DHX36/FANCJ double knockout mESC 2


title: G4 (BG4) CUT&Tag FANCJ knockout mESC 3


title: G4 (BG4) CUT&Tag DHX36/FANCJ double knockout mESC 1


title: MDA-MB-231,Input


title: Cultured cortical neurons, T6B, replicate 3 (input)

description: Library name: T6B input r3

data_processing:
Reads were aligned to the mouse genome (mm10) using STAR (v2.7.7a)
Reads counts were obtained and annotated using transcript information from GENCODE Release M25 with featureCounts
Assembly: mm10
Supplementary files format and content: text files for counts

source_name: embryonic cortices

growth_protocol: Primary cultured neurons were maintained in Neurobasal medium supplemented with B27 Plus and GlutaMAX in a humidified incubator at 37 °C, 5% CO2. Half media changes were performed every 3 days

extract_protocol:
Cells were washed once with ice-cold DPBS and lysed with whole cell lysis buffer prior to IP. Total RNA (IP and input) was extracted with RNeasy® Mini Kit
Total RNA samples were prepared into RNAseq libraries using the NEBNext UltraExpress™ RNA Library Prep Kit for Illumina. Briefly, for each sample 200 ng total RNA was polyA selected, fragmented and converted to double stranded cDNA followed by ligation of sequencing adapters. The libraries were then PCR amplified 12 cycles using barcoded PCR primers, purified and size selected using AmpureXP beads from Beckman Coulter.

treatment_protocol: At DIV10, primary cortical neurons transduced with AAV expressing mutant T6B or T6B

value: embryonic cortices

value: primary cortical neurons

value: cortical cells


title: G4 (BG4) CUT&Tag FANCJ knockout mESC 2


title: Cultured cortical neurons, T6B, replicate 2 (input)

description: Library name: T6B input r2


title: MDA-MB-231, H3K36me3, ChIP

tag: chip antibody


title: Cultured cortical neurons, T6B, replicate 3 (TNRC6 RIP)

description: Library name: T6B IP r3


title: MDA-MB-231, H3K27me3, ChIP


title: Rloop (S9.6) CUT&Tag FANCJ knockout mESC 2


title: MDA-MB-231, H2AS40-KD, Rep3


title: G4 (BG4) CUT&Tag DHX36 knockout mESC 2


title: G4 (BG4) CUT&Tag DHX36 knockout mESC 3


title: G4 (BG4) CUT&Tag FANCJ knockout mESC 1


title: Cultured cortical neurons, T6B, replicate 2 (TNRC6 RIP)

description: Library name: T6B IP r2


title: G4 (BG4) CUT&Tag DHX36 knockout mESC 1


title: G4 (BG4) CUT&Tag WT mESC 3


title: Cultured cortical neurons, T6B, replicate 1 (input)

description: Library name: T6B input r1


title: P15 Purkinje cells input library rep 1

description: P15 Purkinje cells input library rep 1

value: cerebella

value: input library


title: G4 (BG4) CUT&Tag WT mESC 1

value: embryonic stem cell


title: MDA-MB-231, H2AS40Gc, ChIP

value: Made in house


title: 293T cells, control rep2

data_processing:
Raw sequencing reads were quality-checked using FastQC. Reads were quantified to the human reference genome (GRCh38) using Kallisto.
Assembly: hg38
Supplementary files format and content: Tab-delimited text files of counts and tpm generated by kallisto.

extract_protocol:
Total RNA was extracted from 293T cells using the TRIzol reagent following the manufacturer's instructions. The quality and integrity of RNA were assessed using an Agilent Bioanalyzer 2100 system.
Poly(A) RNA was isolated from total RNA using oligo(dT) beads. RNA-seq libraries were constructed using the Illumina TruSeq RNA Library Preparation Kit. Libraries were indexed, amplified, and purified for sequencing.

treatment_protocol: For knockdown experiments, 293T cells were transduced with lentiviruses carrying shRNA targeting MRG15 (shMRG) or control vectors. Cells were selected using appropriate antibiotics to establish stable knockdown lines.


title: Cultured cortical neurons, T6B, replicate 1 (TNRC6 RIP)

description: Library name: T6B IP r1


title: P15 Purkinje cells target library rep 1

description:
P15 Purkinje cells target library rep 1
p15-target-peaks.bed

value: Purkinje cells

value: target library


title: Cultured cortical neurons, control (mutant T6B), replicate 3 (input)

description: Library name: Control input r3

value: mutant T6B (control)


title: P15 Purkinje cells miRNA library rep 2

description: P15 Purkinje cells miRNA library rep 2

value: miRNA library


title: 293T cells, control rep1

value: Human embryonic kidney

value: WT


title: P15 Purkinje cells miRNA library rep 1

description: P15 Purkinje cells miRNA library rep 1


title: P7 Purkinje cells input library rep 2

description: P7 Purkinje cells input library rep 2


title: 293T cells, shMRG rep2

value: MRG15 KD


title: Cultured cortical neurons, control (mutant T6B), replicate 3 (TNRC6 RIP)

description: Library name: Control IP r3


title: P7 Purkinje cells target library rep 2

description:
P7 Purkinje cells target library rep 2
p7-target-peaks.bed


title: Cultured cortical neurons, control (mutant T6B), replicate 2 (input)

description: Library name: Control input r2


title: 293T cells, shMRG rep1


title: P7 Purkinje cells target library rep 1

description:
P7 Purkinje cells target library rep 1
p7-target-peaks.bed


title: P7 Purkinje cells miRNA library rep 2

description: P7 Purkinje cells miRNA library rep 2


title: Cultured cortical neurons, control (mutant T6B), replicate 1 (input)

description: Library name: Control input r1


title: P7 Purkinje cells input library rep 1

description: P7 Purkinje cells input library rep 1


title: Cultured cortical neurons, control (mutant T6B), replicate 2 (TNRC6 RIP)

description: Library name: Control IP r2


title: MDA-MB-231, H3K4me3, ChIP

value: Mammary gland


title: Cultured cortical neurons, control (mutant T6B), replicate 1 (TNRC6 RIP)

description: Library name: Control IP r1


title: CGR8, Halo-Sox2a, dox, Halo-ChIP, rep1

city: Lausanne

first: Sim

last: Sakong

state: Vaud

address: AI 1133, Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

description: Library name: SQ_SS_ChIP_6_S6_m_3_Sox2a_rep1

data_processing:
Sequencing libraries were aligned (in BAM format) to either the mm10 release of the Mus musculus genome or the BDGP6 release of the Drosophila melanogaster genome using STAR 96, with parameters set to --alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd --outFilterMultimapNmax 1. Duplicate reads and any reads not mapped to chromosomes 1–19, X, or Y were removed using SAMTools (Ramírez et al., 2014).
For normalization, we first determined the total read counts in each BAM file mapped to the BDGP6 genome. We then computed normalization factors to equalize read numbers across all Drosophila BAM files. These factors were used to downsample the corresponding mouse genome alignments via SAMTools (Ramírez et al., 2014). Additionally, for replicate comparisons (e.g., Sox2 vs. Sox2a), we calculated a normalization factor from their relative sequencing depths, applying the factor to downsample the mouse alignment files in SAMTools as well.
Peak calling was performed on the downsampled or merged BAM files using MACS2 v3.0.0a7, specifying -f BAMPE -g mm for BED-format outputs. Regions falling within the mm10 blacklist (ENCODE consortium) were excluded.
Scores were determined (bigWig format) from the downsampled or merged bam files using the bamCoverage function from DeepTools v 3.3.0 (Li et al., 2009) with setting -- normalizeUsing RPKM. For the score comparison between different samples, the bam files of replicates were merged using SAMTools (Ramírez et al., 2014). As a result, the '*_merged.bw' files were generated.
Assembly: mm10
Supplementary files format and content: bigWig files including RPKM normalized reads
Supplementary files format and content: bed files with peaks obtained using MACS3 (MACS2 v 3.0.0a7)

source_name: SES5.1 (CGR8 derived, Halo-Sox2a)

growth_protocol: CGR8-derived mouse embryonic stem cells were cultured on 100 mm Petri dishes coated with 0.1% gelatin (Sigma G9391) at 37 °C under 5% CO₂. The growth medium was GMEM (Sigma G5154-500ML), supplemented with 10% ESC-qualified fetal bovine serum (Gibco 16141-079), 1% nonessential amino acids (Gibco 11140-050), 2 mM L-glutamine (Gibco 25030-024), 2 mM sodium pyruvate (Sigma S8636-100ML), 100 µM 2-mercaptoethanol (Sigma 63689-25), and 1% penicillin-streptomycin (BioConcept 4-01 F00-H). Additional factors included in-house produced leukemia inhibitory factor (LIF), 3 µM CHIR99021 (Merck 361559-5MG), and 0.8 µM PD184352 (Sigma PZ0181-25MG).

extract_protocol:
Fixation was performed in a PBS-based buffer, initially using 2 mM disuccinimidyl glutarate (Thermo Fisher Scientific, 20593) for 50 minutes at room temperature, followed by 1% formaldehyde (ThermoFisher, 28908) for an additional 10 minutes. The reaction was quenched with 200 mM Tris-HCl (pH 8.0) for 10 minutes. Cells were then harvested by centrifugation (600 g, 4 minutes, 4 °C) and resuspended in 1% ESC-qualified fetal bovine serum (Gibco, 16141-079). Sorting was carried out by FACS at 4 °C, ensuring that Sox2-expressing and Sox2a-expressing cells, as well as Sox17-expressing and Sox17b-expressing cells, had the same mean fluorescence intensities. Nuclei were prepared by suspending FACS-sorted cells in LB1 buffer (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, supplemented with 1:100 Protease inhibitor cocktail from Sigma #P8340-1ML) and incubating on ice for 10 minutes. Pellets were collected by centrifugation (1,700 g, 5 minutes, 4 °C), and this step was repeated once more. The pellets were resuspended in LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, plus 1:100 Protease inhibitor cocktail) and incubated on ice for 10 minutes, followed by the same centrifugation protocol. The resulting pellets were rinsed twice (without disturbing them) with SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS, supplemented with 1:100 Protease inhibitor cocktail). Finally, the pellets were resuspended in SDS shearing buffer on ice and sonicated in a Covaris E220 (200 cycles, 5% duty cycle, 140 W, 20 minutes). After sonication, the samples were centrifuged (10,000 g, 5 minutes, 4 °C), and the supernatant was retained. Chromatin immunoprecipitation (ChIP) and DNA purification were performed using the ChIP-IT High Sensitivity kit (Active Motif, #53040), following the manufacturer’s guidelines. For input chromatin, 20 µg was used for Sox2 and Sox2a, and 30 µg for Sox17 and Sox17b. Drosophila spike-in chromatin (Active Motif, 53083) was added at 1 ng for every 1 µg of target chromatin. A spike-in antibody (anti-H2Av, 0.5 µg per 10 ng of spike-in chromatin; Active Motif, 61686) was processed alongside 40 µL of Halo-Trap agarose beads per reaction. Each ChIP reaction was incubated overnight at 4 °C on a rotating platform at 30 rpm.
ChIP-seq sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645). After size selection with AMPure XP beads (Beckman Coulter, A63880), the libraries were sequenced on an Illumina NextSeq 500 with 75-bp paired-end reads.

treatment_protocol: CGR8-derived mouse embryonic stem cells, engineered for doxycycline-inducible expression of Halo-tagged Sox2, Sox2a, Sox17, or Sox17b, were treated for 20 hours with 300, 70, 1000, and 1000 ng/mL doxycycline, respectively. The resulting Halo-Sox proteins were subsequently labeled with 50 nM Halo-SiR dye.

value: SES5.1 (CGR8 derived, Halo-Sox2a)

value: mESCs

value: Halo (Chromotech, ota-20)

value: Dox (20 h)


title: CGR8, Halo-Sox2, dox, Halo-ChIP, rep2

description: Library name: SQ_SS_ChIP_5_S5_m_3_Sox2_rep2

source_name: SES4.1 (CGR8 derived, Halo-Sox2)

value: SES4.1 (CGR8 derived, Halo-Sox2)


title: P7 Purkinje cells miRNA library rep 1

description: P7 Purkinje cells miRNA library rep 1

value: cerebella


title: G4 (BG4) CUT&Tag WT mESC 2

value: 129/Ola-derived IB10 mouse embryonic stem cell

value: No treatment


title: 20 kPa Viscoelastic, rep 3

city: Los Angeles

first: Song

last: Li

state: California

address: 404 Westwood Plaza, Eng VI

institute: UCLA

description:
Library name: 20 kPa Viscoelastic 3
20 kPa Viscoelastic 3

data_processing:
Raw files were trimmed with Trimmomatic using default settings and then aligned to mouse reference genome (mm10) using STAR with default parameters. Transcriptome alignments were quantified using featureCounts with the GENCODE annotation file.
Assembly: mm10
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Ear

growth_protocol: Cells were expanded in mouse embryonic fibroblast (MEF) medium after isolation: DMEM (Gibco) with the addition of 10% fetal bovine serum (FBS, from Gibco) and 1% penicillin/streptomycin (Gibco), and used at passage 2.

extract_protocol:
Upon isolating RNA from the samples, messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads.
After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: 500,000 fibroblasts were seeded on substrates with various stiffness and viscoelasticity for 48 hours and collected to isolate RNA and prepare the library.

value: Ear

value: Fibroblast


title: CGR8, Halo-Sox17b, dox, Halo-ChIP

description: Library name: SQ_SS_ChIP_4_S4_m_3_Sox17b

source_name: SES9.1 (CGR8 derived, Halo-Sox17b)

value: SES9.1 (CGR8 derived, Halo-Sox17b)


title: CGR8, Halo-Sox17, dox, Halo-ChIP

description: Library name: SQ_SS_ChIP_3_S3_m_3_Sox17

source_name: SES7.1 (CGR8 derived, Halo-Sox17)

value: SES7.1 (CGR8 derived, Halo-Sox17)


title: CGR8, Halo-Sox2a, dox, input

description: Library name: SQ_SS_ChIP_IC_6_S14_m_3_Sox2a

value: Input control


title: 20 kPa Viscoelastic, rep 2

description:
Library name: 20 kPa Viscoelastic 2
20 kPa Viscoelastic 2


title: CGR8, Halo-Sox17b, dox, input

description: Library name: SQ_SS_ChIP_IC_4_S12_m_3_Sox17b


title: CGR8, Halo-Sox17, dox, input

description: Library name: SQ_SS_ChIP_IC_3_S11_m_3_Sox17


title: CGR8, Halo-Sox2, dox, Halo-ChIP, rep1

description: Library name: SQ_SS_ChIP_5_S5_m_3_Sox2_rep1


title: CGR8, ATAC

description: Library name: SS_ATAC2_S3_m_3_Ctrl

data_processing:
Sequencing libraries were aligned (in BAM format) to either the mm10 release of the Mus musculus genome using STAR 96, with parameters set to --alignMatesGapMax 2000 --alignIntronMax 1 --alignEndsType EndtoEnd --outFilterMultimapNmax 1. Duplicate reads and any reads not mapped to chromosomes 1–19, X, or Y were removed using SAMTools (Ramírez et al., 2014).
Peak calling was performed on the filtered BAM files using MACS2 v3.0.0a7, specifying -f BAMPE -g mm for BED-format outputs. Regions falling within the mm10 blacklist (ENCODE consortium) were excluded.
Scores were determined (bigWig format) from the filtered bam files using the bamCoverage function from DeepTools v 3.3.0 (Li et al., 2009) with setting -- normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: bigWig files including RPKM normalized reads from the filtered bam files
Supplementary files format and content: bed files with peaks obtained using MACS3 (MACS2 v 3.0.0a7) from the filtered bam files

source_name: SES11 (CGR8 derived, control)

extract_protocol:
CGR8-derived mouse embryonic stem cells expressing Halo-Sox2 or Halo-Sox2a were sorted by FACS at 4 °C, using the same intensity gating between Halo-Sox2 and Halo-Sox2a expression levels. The ATAC-seq method followed the protocol established by Buenrostro et al. (2013). Around 50,000 cells were lysed in 50 µL of ATAC lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl₂, 0.1% NP-40, pH 7.4), and the nuclei were collected by centrifugation (800 g, 5 minutes). The transposition reaction was carried out by suspending the nuclei in 50 µL of TAPS-DMF buffer (10 mM TAPS-NaOH, 5 mM MgCl₂, 10% DMF) supplemented with 0.5 µM Tn5 transposase (prepared in-house according to Picelli et al., 2014), followed by incubation at 37 °C for 30 minutes. DNA was purified to 10 µL of nuclease-free water using the DNA Clean & Concentrator kit (Zymo Research, D4004) at a 5:1 ratio of binding buffer to sample.
The transposed DNA was PCR-amplified in a 65-µL reaction using NEBNext High-Fidelity 2× PCR Master Mix (NEB, M0541L) with 0.5 mM Ad1.1 universal primer, 0.5 mM Ad2.X indexing primer, and 0.6× SYBR Green I (Thermo Fisher Scientific, S7585). The thermocycling program included a 5-minute step at 72 °C and 30 seconds at 98 °C, followed by five cycles of 98 °C for 10 seconds, 63 °C for 30 seconds, and 72 °C for 60 seconds. Afterward, 10 µL of the amplified DNA was subjected to qPCR, and the optimal total cycle number was determined by monitoring the fluorescence signal up to one-third of saturation, ensuring the reaction did not approach amplification saturation. The remaining DNA was then amplified accordingly, purified by column (Zymo D4004), and size-selected with AMPure XP beads (Beckman Coulter, A63880). Libraries were sequenced on an Illumina NextSeq 500 using 75-bp paired-end reads.

treatment_protocol: CGR8-derived mouse embryonic stem cells, engineered for doxycycline-inducible expression of Halo-tagged Sox2 or Sox2a, were treated for 20 hours with 300 and 70 ng/mL doxycycline, respectively. The resulting Halo-Sox proteins were subsequently labeled with 50 nM Halo-SiR dye.

value: SES11 (CGR8 derived, control)

value: Control


title: 2 kPa Viscoelastic, rep 2

description:
Library name: 2 kPa Viscoelastic 2
2 kPa Viscoelastic 2


title: combined_samples

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

description:
Library name: 12samples_combined
Parse Biosciences

library_source: transcriptomic single cell

data_processing:
The reads were mapped to the mouse genome mm10, and raw gene read counts were generated using the Mayo Clinic RNA-sequencing analytic pipeline, MAP-RSeq
The demultiplexing, barcoded processing, gene counting and aggregation were made using Parse pipeline (https://www.parsebiosciences.com/support-suite/)
Assembly: mm10
Supplementary files format and content: .csv file of gene annotation
Supplementary files format and content: .h5ad file with additional structure specifying how to store AnnData objects
Supplementary files format and content: .csv file of cell metadata
Supplementary files format and content: .mtx file of count matrices

molecule: nuclear RNA

source_name: mouse hemisphere

growth_protocol: The Abca7-floxed mice (Abca7floxp/floxp) were crossed with 5×FAD+/− mice [29] or Camk2a-Cre+/− mice to generate the founders: 5×FAD+/−; Abca7floxp/floxp mice and Abca7floxp/floxp; Camk2a-Cre+/− mice (nAbca7−/−). By breeding the mice, 5×FAD+/-; Abca7floxp/floxp; Camk2a-Cre+/- mice (5×FAD; nAbca7-/-) were generated. The 5×FAD+/−; Abca7floxp/floxp; Camk2a-Cre-/- littermates were used as controls (5×FAD; control).

extract_protocol:
The isolated nuclei were  fixed using a nuclei fixation kit from Parse Biosciences. Then the fixed single nuclei were barcoded with the Evercode WT mini v2 kit  and libraries were prepared from Parse Biosciences.
cDNA libraries were  sequenced with Illumina NextseqP2 at the Mayo Clinic Center for Individualized Medicine’s Medical Genome Facility.

value: mouse hemisphere


title: CGR8, Halo-Sox2a, dox, ATAC

description: Library name: SS_ATAC2_S2_m_3_Sox2a


title: CGR8, Halo-Sox2a, dox, Halo-ChIP, rep2

description: Library name: SQ_SS_ChIP_6_S6_m_3_Sox2a_rep2


title: CGR8, Halo-Sox2, dox, ATAC

description: Library name: SS_ATAC2_S1_m_3_Sox2


title: 2 kPa Viscoelastic, rep 1

description:
Library name: 2 kPa Viscoelastic 1
2 kPa Viscoelastic 1


title: CGR8, Halo-Sox2, dox, input

description: Library name: SQ_SS_ChIP_IC_5_S13_m_3_Sox2


title: RNA-seq DHX36/FANCJ double knockout mESC 2

data_processing:
Libraries were sequenced on an Illumina Nextseq 500, high output, with a 1 × 75 bp Illumina kit
Read 1 was used to identify the Illumina library index and CEL-Seq sample barcode and read 2 was aligned to the GRCm38 reference using Burrow-Wheeler aligner (BWA-MEM)
Reads that mapped equally well to multiple locations were discarded. Mapping and generation of count tables was done using the MapAndGo script (https://github.com/anna829 alemany/transcriptomics/tree/master/mapandgo).
Assembly: GRCm38 (hg38)
Supplementary files format and content: Demultiplexed gene count table (tsv)

extract_protocol:
1 x 10^5 mESCs were lysed in 120 µL TRIzol (Thermo Fisher Scientific), snap-frozen with liquid nitrogen, and further processed by Single Cell Discoveries (Utrecht, The Netherlands) following the manufacturer's protocol
Protocol similar to CEL-Seq2 was used to multiplex the bulk RNA-seq samples  (T. Hashimshony et al., 2016)

value: embryonic stem cell

value: DHX36/FANCJ KO


title: 20 kPa Elastic, rep 3

description:
Library name: 20 kPa Elastic 3
20 kPa Elastic 3


title: RNA-seq DHX36/FANCJ double knockout mESC 1


title: RNA-seq FANCJ knockout mESC 3

value: FANCJ KO


title: RNA-seq DHX36/FANCJ double knockout mESC 3


title: RNA-seq FANCJ knockout mESC 1


title: RNA-seq FANCJ knockout mESC 2


title: RNA-seq DHX36 knockout mESC 3

value: DHX36 KO


title: 20 kPa Elastic, rep 1

description:
Library name: 20 kPa Elastic 1
20 kPa Elastic 1


title: 20 kPa Viscoelastic, rep 1

description:
Library name: 20 kPa Viscoelastic 1
20 kPa Viscoelastic 1


title: RNA-seq DHX36 knockout mESC 2


title: 2 kPa Elastic, rep 3

description:
Library name: 2 kPa Elastic 3
2 kPa Elastic 3


title: RNA-seq DHX36 knockout mESC 1


title: 2 kPa Viscoelastic, rep 3

description:
Library name: 2 kPa Viscoelastic 3
2 kPa Viscoelastic 3


title: RNA-seq WT mESC 3

value: WT


title: RNA-seq WT mESC 2


title: 2 kPa Elastic, rep 1

description:
Library name: 2 kPa Elastic 1
2 kPa Elastic 1


title: RNA-seq WT mESC 1


title: 2 kPa Elastic, rep 2

description:
Library name: 2 kPa Elastic 2
2 kPa Elastic 2


title: Single gastruloid from pre-culture condition 6, biological replicate 5

city: Utrecht

first: Peter

last: Zeller

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate15-con6-H2

data_processing:
Raw fastq files were processed according to the VASA-seq Snakemake workflow of the SingleCellMultiOmics (SCMO) package (version 0.1.30). In brief, reads were demultiplexed for CELseq barcodes with a hamming distance of 0 and trimmed for default adapters with CutAdapt (version 4.1). Read 2 was mapped to the mouse GRCm38 genome (Ensembl 97) using STAR (version 2.5.3a). Mapped reads were tagged, filtered for a mapping quality > 50, and deduplicated using samtools (version 1.15.1). Transcript counts files were saved as .csv
Assembly: GRCm38 genome (Ensembl 97)
Supplementary files format and content: pickle.gz

source_name: single gastruloid

growth_protocol: 129S1/SvImJ / C57BL/6 mESCs were cultured in a humidified incubator (5 % CO2, 37 °C) on 0.1 % gelatin-coated cell culture dishes in ESLIF medium (GMEM (Gibco) containing 10 % fetal bovine serum (FBS), 1 % Sodium Pyruvate, 1 % non- essential amino acids, 1 % GlutaMAX, 1 % penicillin-streptomycin, 0.2 % b-mercaptoethanol, and 1000 units/mL mouse leukaemia inhibitory factor (mLIF, ESGRO)). Cells were split every second day by washing with PBS0, dissociating with TrypLE for ~5 mins, centrifuging at 300 g for 3 mins, and replating the pellet 1:5 on gelatinised plates. Pre-culture conditions consisted of different pulse timings and lengths with 2i medium (48.1 % DMEM/F12 (Gibco) and 48.1 % Neurobasal (Gibco) containing 0.5 % N-2 supplement (Gibco, # 17502048), 1 % B-27 supplement (Gibco, # 17504044), 1 % GlutaMAX, 1.1 % penicillin-streptomycin, 0.2 % b-mercaptoethanol, 1000 units/mL mouse leukaemia inhibitory factor (mLIF, ESGRO), 0.03 % chiron (CHIR99021, Tocris # 4423) and 0.01 % PD032509 (Sigma, # PZ0162). During pre-culture conditions, cells were split at day 2 and 3; medium was refreshed at day 2 and 4.

extract_protocol:
mESCs gastruloids were dissociated by washing with PBS0, dissociating with TrypLE for ~5 mins. Single gastruloids were washed with PBS0, followed by incubation with 50 μL trypsin without phenol red (Gibco) for ~5 mins at 37 °C. Gastruloids were mechanically broken up into a single-cell suspension by pipetting with a P200. Cells were centrifuged at 300 g for 3 mins, re-suspended in PBS0 supplemented with 5 % FBS, and filtered through a 35 μm filter (Falcon, 352235). Prior to fluorescence-activated cell sorting (FACS), DAPI was added to the cell suspension to assess cell viability.
Libraries were prepared following the CEL-seq2 protocol (Hashimshony. et al., 2012). The libraries were sequenced with the Illumina NextSeq 500. Paired end sequencing (26 bp at read 1 and 61 bp at read 2) was performed. Transcriptome was sequenced on the Illumina NextSeq 500 with 2 x 75 bp reads or 1 x 75 bp reads (26 bp at read 1 and 61 bp at read 2).

value: 129S1/SvImJ / C57BL/6 mESCs

value: single gastruloid


title: Single gastruloid from pre-culture condition 6, biological replicate 4

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate14-con6-G2


title: MII oocyte from post-hCG vitrified follicle, biol rep 12

city: Pitscataway

first: Shuo

last: Xiao

state: NJ

address: 170 Frelinghuysen Rd, Room 404

department: Pharmacology & Toxicology

institute: Rutgers University

description: Library name: V24

data_processing:
Galaxy version 24.2.rc1
RNA-seq reads were aligned to the whole mouse genome assembly-mm10 by HISAT2, quantified by featureCounts in Galaxy
Assembly: mm10
Supplementary files format and content: csv files includes raw counts for each sample

source_name: germ cell

extract_protocol:
RNA extraction and library preparation was done using SMART-Seq2 v4 Ultra Low Input RNA kit according to manufacture's instruction
RNA extraction and library preparation was done using SMART-Seq2 v4 Ultra Low Input RNA kit according to manufacture's instruction

value: germ cell

value: MII oocyte

value: Vitrified and hCG


title: Single gastruloid from pre-culture condition 1, biological replicate 2

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate10-con1-B2


title: Single gastruloid from pre-culture condition 1, biological replicate 3

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate11-con1-C1


title: Single gastruloid from pre-culture condition 1, biological replicate 5

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate13-con1-F4


title: 20 kPa Elastic, rep 2

description:
Library name: 20 kPa Elastic 2
20 kPa Elastic 2

value: Ear

value: Fibroblast


title: MII oocyte from post-hCG vitrified follicle, biol rep 10

description: Library name: V22


title: Single gastruloid from pre-culture condition 1, biological replicate 1

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate9-con1-A1


title: Single gastruloid from pre-culture condition 5, biological replicate 5

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate8-con5-C2


title: MII oocyte from post-hCG vitrified follicle, biol rep 11

description: Library name: V23


title: Single gastruloid from pre-culture condition 5, biological replicate 4

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate7-con5-F1


title: Single gastruloid from pre-culture condition 5, biological replicate 1

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate4-con5-B3


title: MII oocyte from post-hCG vitrified follicle, biol rep 9

description: Library name: V21


title: Single gastruloid from pre-culture condition 5, biological replicate 3

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate6-con5-D2


title: Single gastruloid from pre-culture condition 5, biological replicate 2

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate5-con5-C3


title: MII oocyte from post-hCG vitrified follicle, biol rep 7

description: Library name: V13


title: MII oocyte from post-hCG vitrified follicle, biol rep 8

description: Library name: V20


title: Single gastruloid from pre-culture condition 6, biological replicate 3

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate3-con6-F2


title: Single gastruloid from pre-culture condition 6, biological replicate 2

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate2-con6-C1


title: mESCs, condition 6, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate12-con6

source_name: mESCs

value: mESCs


title: MII oocyte from post-hCG vitrified follicle, biol rep 5

description: Library name: V11


title: mESCs, condition 6, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate11-con6


title: MII oocyte from post-hCG vitrified follicle, biol rep 4

description: Library name: V10


title: Single gastruloid from pre-culture condition 1, biological replicate 4

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate12-con1-H3


title: mESCs, condition 5, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate9-con5


title: mESCs, condition 4, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate8-con4


title: MII oocyte from post-hCG vitrified follicle, biol rep 3

description: Library name: V9


title: mESCs, condition 4, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate7-con4


title: mESCs, condition 2, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate3-con2


title: MII oocyte from post-hCG vitrified follicle, biol rep 1

description: Library name: V2


title: mESCs, condition 3, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate5-con3


title: mESCs, condition 1, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate2-con1


title: mESCs, condition 2, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate4-con2


title: mESCs, condition 1, technical replicate 1

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate1-con1


title: Low-N treated roots of PuHox52-OE rep3

city: Harbin City

first: Chenghao

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
RNA-seq reads were mapped to the P. trichocarpa genome v.3.1 using TopHat.
Differentially expressed genes (DEGs) were identified using the DESeq2 package in R. Fold change ≥ 2 and FDR < 0.05 were required for DEGs to be considered significant.
Gene Ontology (GO) enrichment analysis was carried out using the AmiGO Term Enrichment Tool (http://bioinfo.cau.edu.cn/agriGO/index.php) with a Fisher’s exact test result with corrected P < 0.05 considered significantly enriched.
Assembly: Ptrichocarpa_533_v4.0.fa
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Populus ussuriensis

source_name: root

growth_protocol: Clonally propagated in vitro Populus ussuriensis plants were maintain in woody plant medium (WPM) with 25 g/L sucrose and 6 g L-1 agar with 16 h/8 h day/night photoperiod at 24-26 ℃.

extract_protocol:
Roots were  harvested before total RNA extraction using the method of CTAB. Library construction and sequencing were performed by Biomarker Technologies (Beijing, China) and Bioacme Technologies (Wuhan, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Selected top one internodes of in vitro propagated WT and PuHox52-OE plants, which were grown on WPM for 6 d to develop consistently, and then choose consistently developed plants for the subsequent normal-N and low-N for 3 wks.

value: root

value: tissue seedling

tag: time

value: Low-N


title: MII oocyte from post-hCG fresh follicle, biol rep 12

description: Library name: F25

value: Fresh and hCG


title: MII oocyte from post-hCG fresh follicle, biol rep 10

description: Library name: F22


title: Low-N treated roots of PuHox52-OE rep1


title: MII oocyte from post-hCG fresh follicle, biol rep 11

description: Library name: F23


title: Low-N treated roots of WT rep3


title: MII oocyte from post-hCG vitrified follicle, biol rep 6

description: Library name: V12


title: C20 P21 D3

city: Omaha

first: Howard

middle: S

last: Fox

state: Nebraska

address: 42nd and Emile

institute: University of Nebraska Medical Center

data_processing:
We use nf-core RNAseq pipeline version 3.10.1 to process the raw data. STAR aligner is used to align the raw reads to a combination of hg38 and NC_001802.1 reference genome.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes TPM values for each sample

growth_protocol: C20 cells were maintained in 150-cm2 tissue culture flasks (Falcon) in DMEM supplemented with 5% FBS, 10 mM HEPES, 1% P/S, and 1% sodium pyruvate at 37°C in a humidified incubator under 5% CO2.

extract_protocol:
Total RNA was extracted from cells using Trizol, and RNA quantity and purity were determined by a NanoDropOne spectrophotometer (Nanodrop Technologies).
RNA-seq library preparation was performed as described elsewhere and as follows (Link, Duttke et al. 2018). RNA isolation from C20 cells was carried out as described above and total RNA was enriched in poly-A tailed RNA transcripts by double incubation with Oligo d(T) Magnetic Beads (NEB, S1419S) and fragmented for 9 minutes at 94°C in 2X Superscript III first-strand buffer containing 10 mM DTT (Invitrogen, #P2325). The 10 μL of fragmented RNA was added to 0.5 μL of Random primers (Invitrogen, #48190011), 0.5 μL of Oligo d(T) primer (Invitrogen, #18418020), 0.5 μL of SUPERase inhibitor (Ambion, #AM2696), 1 μL of 10 mM dNTPs and incubated at 50°C for 3 minutes. Then, 5.8 μL of water, 1 μL of 10 mM DTT, 0.1 μL of 2 μg/μL Actinomycin D (Sigma, #A1410), 0.2 μL of 1% Tween-20 (Sigma) and 0.5 μL of SuperScript III (Invitrogen, #ThermoFisher 18080044) was added to the mix. Reverse-transcription (RT) reaction was performed at 25°C for 10 minutes followed by 50°C for 50 minutes. RT product was purified with RNAClean XP (Beckman Coulter, #A63987) and eluted in 10 μL in 0.01% Tween 20. The RNA-cDNA complex was then added to 1.5 μL of 10X Blue Buffer (Enzymatics, #B0110-L), 1.1 μL of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 μL of 5 μ/mL RNAseH (Enzymatics, #Y9220L), 1 μL of 10 U/μl DNA polymerase I (Enzymatics, #P7050L), 0.15 μL of 1% Tween 20 and 1.05 μL of nuclease free water; and incubated at 16°C for 2.5 hours or overnight. The resulting dsDNA product was purified using 28 μL of Sera-Mag SpeedBeads Magnetic Carboxylate (ThermoFisher, #65152105050250) diluted in 20% PEG8000, 2.5 M NaCl to a final 13% PEG concentration, washed twice with 80% EtOH, air dry and eluted in 40 μL of 0.05% Tween 20. The purified 40 μL of dsDNA was end-repaired by blunting followed by A-tailing and adapter ligation as described elsewhere (Heinz, Benner et al. 2010) using BIOO Barcodes (BIOO Scientific, #514104), 0.33 μL 1% Tween 20 and 0.5 μL T4 DNA ligase HC (Enzymatics, #L6030-HC-L). Libraries were amplified by PCR for 11–15 cycles using Solexa IGA and Solexa IGB primers (AATGATACGGCGACCACCGA and CAAGCAGAAGACGGCATACGA, respectively), and size selected for fragments (200-500 bp) by gel extraction (10% TBE gels, Life Technologies EC62752BOX). Eluted libraries were quantified using a Qubit dsDNA HS Assay Kit and sequenced on a NovaSeq 6000 (Illumina, San Diego, California).

treatment_protocol: After plating 250k cells per well of a 6 well, 48 hours later, C20 cells were treated with vehicle (H20) or 1uM dopamine (Sigma) for three hours.

value: microglia

value: dopamine (1uM)

tag: timepoint

value: 3 hours


title: C20 P22 D3

tag: cell line


title: Single gastruloid from pre-culture condition 6, biological replicate 1

description:
CELSEQ2
20201019_gastruloids_allPlates.pickle.gz
LS-gastruloids-plate1-con6-D2

tag: cell type


title: MII oocyte from post-hCG fresh follicle, biol rep 9

description: Library name: F21

tag: genotype


title: Low-N treated roots of WT rep2

tag: treatment


title: mESCs, condition 5, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate10-con5


title: HUDEP-2 insA ko clone3

city: Guangzhou

first: xiuqin

last: bao

address: 1838 Guangzhou

institute: Southern Medical University

description: Library name: HUDEP-2 insA ko3

data_processing:
All clean reads passed quality control with FASTQC and were mapped onto hg19 with bowtie2.
After removal of duplicates with picard, the bam data were ranked, and an index was created with samtools.
We used MACS2 to generate peak calls
Using bamCoverage for base depth statistics for visualization.
Assembly: hg19
Supplementary files format and content: bigwig files were generated using the MACS

extract_protocol:
we used Tn5 to digest the accessible chromosme region and ligest the NGS adaptor to the accessible chromosome region.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

value: Human umbilical cord blood-derived erythroid progenitor


title: MII oocyte from post-hCG fresh follicle, biol rep 8

description: Library name: F20

value: WT


title: Low-N treated roots of WT rep1

tag: tissue


title: MII oocyte from post-hCG vitrified follicle, biol rep 2

description: Library name: V7


title: HUDEP-2 insA ko clone2

description: Library name: HUDEP-2 insA ko2


title: mESCs, condition 3, technical replicate 2

description:
CELSEQ2
20220217_all_mESCs.pickle.gz
MB-mESCs-plate6-con3

value: 129S1/SvImJ / C57BL/6 mESCs


title: HUDEP-2 insA ko clone1

description: Library name: HUDEP-2 insA ko1


title: C20 P18 D3


title: HUDEP-2 insA clone3

description: Library name: HUDEP-2 insA3


title: C20 P23 D3


title: MII oocyte from post-hCG fresh follicle, biol rep 6

description: Library name: F10


title: MII oocyte from post-hCG fresh follicle, biol rep 7

description: Library name: F11


title: Low-N treated roots of PuHox52-OE rep2


title: C20 P22 Veh

value: vehicle (H20) control


title: HUDEP-2 insA clone1

description: Library name: HUDEP-2 insA1


title: HUDEP-2 cells,WT3

description: Library name: HUDEP-2 WT3


title: MII oocyte from post-hCG fresh follicle, biol rep 4

description: Library name: F7

value: germ cell


title: HUDEP-2 cells,WT1

description: Library name: HUDEP-2 WT1


title: HUDEP-2 cells,WT2

description: Library name: HUDEP-2 WT2


title: C20 P19 Veh


title: GC_SRBC7d_M30

city: Nijmegen

first: Franka

last: Buytenhuijs

state: Please select your county

address: Toernooiveld 200

institute: Radboud University

description: Library name: GC_SRBC7d_M30_v5372

data_processing:
CDR3β identification, clonotype clustering and correction of sequencing errors were performed using MiTCR software.
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Spleen Germinal Center

extract_protocol:
Total RNA was extracted as described above and TCRβ-chain transcripts were amplified independently in a two-step reaction according to the manufacturer’s protocol (iRepertoire; patent no. 7,999,092).
The obtained TCRβ libraries were quantified using the PerfeCTa-NGS-Quantification Kit according to manufacturer’s protocol (Quantabio) and sequenced using the Illumina MiSeq Reagent Kit v2 300-cycle (150 paired-end read; Illumina), gaining an average of $\approx$1.8 × 10^6 reads per sample.

value: Spleen Germinal Center

value: T cell

value: 7 days after antigen challenge with SRBC


title: BCZ_SRBC7d_M30

description: Library name: BCZ_SRBC7d_M30_v5372

source_name: Spleen B cell zone

value: Spleen B cell zone


title: C20 P19 D3


title: TCZ_SRBC7d_M30

description: Library name: TCZ_SRBC7d_M30_v5372

source_name: Spleen T cell zone

value: Spleen T cell zone


title: C20 P18 Veh


title: C20 P23 Veh


title: MII oocyte from post-hCG fresh follicle, biol rep 2

description: Library name: F3

value: MII oocyte


title: BCZ_SRBC7d_M29

description: Library name: BCZ_SRBC7d_M29_v5370


title: GC_SRBC7d_M28

description: Library name: GC_SRBC7d_M28_v5380


title: MII oocyte from post-hCG fresh follicle, biol rep 1

description: Library name: F2


title: HUDEP-2 insA clone2

description: Library name: HUDEP-2 insA2


title: GC_SRBC7d_M29

description: Library name: GC_SRBC7d_M29_v5370


title: TCZ_SRBC7d_M28

description: Library name: TCZ_SRBC7d_M28_v5380


title: HT1080, input

city: Durham

first: Makoto

last: Nakagawa

address: 308 Research Drive

institute: Duke University

data_processing:
ChIP-Seq reads were trimmed by Skewer (v0.1.126) and aligned to reference human genome (GRCh38/hg38 assembly) using BWA (v0.7.12).
The bigwig file creation and the peak calling procedure were performed with HOMER (v4.11)
Each peak was annotated by the annotatePeaks command of HOMER, and the total number of mapped reads in each sample was normalized to ten million mapped reads.
Differential peaks were identified by the getDifferentialPeaks command of HOMER, setting thresholds for log fold change and p-value as 1.5 and 0.05, respectively.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Cell line

growth_protocol: High-glucose DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S). Cells were cultured at 37°C in a humidified incubator in an atmosphere of 95% air and 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 30 minutes. After quenching and cell lysis, chromatin was sonicated using an M220 focused-ultrasonicator (Covaris).
Libraries were prepared for sequencing using standard Illumina protocols. The final DNA library was obtained by size selection and PCR amplification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: Dox inducible HT1080−HA−SREBF2 cells and parental control cells were treated with Dox 1 µg/ml for 72 h.

value: Cell line

value: Human Fibrosarcoma

value: Dox 1 ug/ml for 72 h


title: GC_SRBC7d_M27

description: Library name: GC_SRBC7d_M27_v5374


title: BCZ_SRBC7d_M28

description: Library name: BCZ_SRBC7d_M28_v5380


title: GV oocyte from day 8 vitrfied follicle, biol rep 4

description: Library name: V85

value: GV oocyte

value: Vitrified


title: MII oocyte from post-hCG fresh follicle, biol rep 5

description: Library name: F9

value: Fresh and hCG


title: GV oocyte from day 8 vitrfied follicle, biol rep 3

description: Library name: V84


title: BCZ_SRBC7d_M27

description: Library name: BCZ_SRBC7d_M27_v5374


title: C20 P21 Veh

value: microglia

value: 3 hours


title: GC_SRBC7d_M26

description: Library name: GC_SRBC7d_M26_v5362

value: WT


title: TCZ_SRBC7d_M27

description: Library name: TCZ_SRBC7d_M27_v5374


title: HT1080, HA, ChIP, rep 1

value: HA (ab9110; Abcam)


title: HT1080, HA, ChIP, rep 2


title: GV oocyte from day 8 vitrfied follicle, biol rep 1

description: Library name: V82

value: germ cell


title: GV oocyte from day 8 vitrfied follicle, biol rep 2

description: Library name: V83


title: MII oocyte from post-hCG fresh follicle, biol rep 3

description: Library name: F6


title: BCZ_SRBC7d_M26

description: Library name: BCZ_SRBC7d_M26_v5362


title: TCZ_SRBC7d_M26

description: Library name: TCZ_SRBC7d_M26_v5362


title: TCZ_SRBC7d_M29

description: Library name: TCZ_SRBC7d_M29_v5370


title: HT1080−HA−SREBF2, input


title: HT1080−HA−SREBF2, HA, ChIP, rep 2


title: GV oocyte from day 8 fresh follicle, biol rep 4

description: Library name: F84

value: Fresh


title: scRNAseq, GEX library 1

city: Seoul

first: Sowon

last: Choi

state: Seoul

address: 329, Daehak-ro 103, Jongno-gu

institute: Seoul National University

description: 10x Genomics

data_processing:
Raw sequencing reads were aligned to GRCh38 (human) using the Cell Ranger (version 7.1.0, 10x Genomics)
Assembly: GRCh38 (human)
Supplementary files format and content: Comma-separated values files and matrix files

source_name: kidney biopsy specimen

extract_protocol:
The kidney tissue biopsy was was chopped and dissociated with Liberase™ TL in a 37°C water bath for 30 minutes. The tissue was then mechanically dissociated using a wide-bore pipette tip. Afterwards, the cells isolated from the tissue were filtered through a strainer with a mesh size of 70µm,  followed by centrifugation
Libraries were generated using the Chromium Single Cell 3′ Library & Gel Bead Kit V3.1 and Chromium Single Cell 3′ Chips according to the manufacturer’s instructions. Briefly, scRNA-seq analysis were performed following the manufacturer's guidelines (10x Genomics, Chromium Next Gem Single Cell 3' Reagent Kits v3.1, CG000204). In short, single-cell samples and reagents were loaded on a 10X Chromium controller for droplet generation, followed by reverse transcription in the droplets, cDNA amplification and fragmentation. Then, fragments were ligated with adapters and dual-indices to mitigate index-hopping. The 4150 TapeStation system was used to evaluate the quality of the barcoded single-cell transcriptome libraries.

value: kidney biopsy specimen

tag: subject status

value: 5-year-old boy diagnosed with a COQ10 nephropathy caused by compound heterozygous COQ2 mutation


title: GV oocyte from day 8 fresh follicle, biol rep 3

description: Library name: F83


title: SMAD2+/R114C*(RA10)_R1, ATACseq

city: Boston

first: Jon

last: Seidman

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Libraries were sequenced (Illumina HiSeq 2000 or Illumina HiSeq 2500, paired end)  to a depth of 100 million reads per sample
All data was combined into a single fastq file
Reads were aligned to the hg38 reference genome using BWA-MEM.
Mitochondrial and duplicate reads were discarded using Samtools and Picard’s MarkDuplicates, respectively
Tagdirectories were created and combined for each genotype, and peaks were called using HOMER (v4.11), Heinz et al. 2008
Assembly: hg38
Supplementary files format and content: ATACseq combined peaks for each genotype

growth_protocol: Induced pluripotent stem cells (iPSCs) were routinely generated by re-plating 6 non-adherent cell line cultures (typically 5 x 106 cells) on a matrigel coated plate in MTESR medium (Stemcell Technologies)

extract_protocol:
ATAC-seq was performed as previously described (Buenrostro et al., 2015; Corces et al., 2017).
ATACseq libraries were prepared for sequencing using standard Illumina protocols

value: Induced pluripotent stem cells

value: missense

value: untreated


title: GC_SRBC7d_M25

description: Library name: GC_SRBC7d_M25_v5364

value: Spleen Germinal Center

value: T cell

value: 7 days after antigen challenge with SRBC


title: BCZ_SRBC7d_M25

description: Library name: BCZ_SRBC7d_M25_v5364

value: Spleen B cell zone