title: Gpx4 KO_Mist1+ organoids_ P10_1

description:
Library name: Sample 19
all.fpkm_anno_1.txt
G-2-10-1


title: 29422-MND50-2

status: Public on Jun 24 2025

type: SRA

city: Shanghai

first: Guoming

last: Ma

address: 100 Haike Road, Zhangjiang Hi-Tech Park

department: Interdisciplinary Research Center on Biology and Chemistry

country: China

institute: Chinese Academy of Science

description: Library name: R17029219LR01

library_source: transcriptomic

data_processing:
The reads were aligned to the GRCh37 reference genome with HISAT2 (v.2.2.1) after removing the adapter sequences and low-quality reads using Trimmomatic (v.0.39)45. Read counts were quantified using FeatureCounts in Rsubread (v.2.0.1)46 using GENCODE GTF annotation version 19.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
TRIzol (Invitrogen) was used to extract total RNA. DNA digestion and reverse transcription were performed using the Hifair™ III 1st Strand cDNA Synthesis SuperMix for qPCR (YEASEN) according to the manufacturer’s instructions. qPCR was performed on cDNA using qPCR SYBR Green Master Mix (UNIQ) with a QuantStudio 7 Flex Real-Time PCR System according to the manufacturer’s instructions. The relative expression levels of target genes were measured using the ddCt method normalizing to control gene expression. ACTIN was used as a reference in the ALS-SOD1, ALS-FUS, and ALS-TARDBP subgroups. TFRC was used as a reference in the ALS-C9orf72. The primers used for qPCR are listed in Table S2.
RNA purification, reverse transcription, and library construction were performed in Mingma Technologies Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions. RNA integrity were measured using an Agilent 2100 Bioanalyzer (Agilent). The mRNA-focused sequencing libraries from total RNA were prepared using the VAHTS mRNA-seq v3 Library Prep Kit (VAHTS, NR611). PolyA mRNA was purified from total RNA and then fragmented. The final cDNA libraries were sequenced on  an Illumina HiSeq PE150 sequencing system following Illumina protocols provided by Mingma Technologies Co., Ltd. in Shanghai.

tag: cell line


title: 29523-MND50-2

description: Library name: R18004477LR01


title: Mist1+ organoids_P10_3

first: Fan

last: Chen

address: Yueyang Road, No. 320

institute: Center for Excellence in Molecular Cell Science, CAS

description:
Library name: Sample 18
all.fpkm_anno_1.txt
M-2-10-3

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data. Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1). Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCm38.p5
Supplementary files format and content: xls file includes RPKM values for each Sample.

molecule: total RNA

organism: Mus musculus

source_name: Stomach

growth_protocol: Stomach tissues of adult Mist1CreERT2;RFPLSL mice were dissociated into single cells and isolated RFP+ cells via fluorescence-activated cell sorting (FACS). And organoids were suspended with 50 μl Matrigel and maintained in proliferating medium at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Stomach

value: Mist1+ derived organoid

tag: cell type

value: Gastric epithelia

tag: genotype

value: WT

tag: treatment

value: Organoid proliferative culture


title: HUDEP-2 Mock Rep3

city: Sydney

first: Merlin

last: Crossley

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description: Library name: HUDEP-2 Mock Rep3

data_processing:
For HUDEP-2 RNA-seq, sequencing data was processed using the nf-core RNAseq workflow (v3.14) with the Kallisto pseudoaligner. Kallisto parameters were set with 100 bootstrap samples, and fragment length set to 75 with a standard deviation of 2 where single end reads were used.
Assembly: hg38
Supplementary files format and content: tsv abundance file - output from kallisto

growth_protocol: Human umbilical cord blood derived 2 (HUDEP2) cells were grown in serum free expansion medium (SFEM, StemSpan) supplemented with 50 ng/µL stem cell factor (In Vitro Technologies), 3 IU/mL erythropoietin (Lonza), 10 µM dexamethasone (Sigma-Aldrich), 1 µg/mL doxycycline (Sigma-Aldrich), and 0.5 mg/mL PSG. All cell cultures were incubated at 37°C in a water jacketed incubator with 5% CO2. CD34+ cells cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
HUDEP2 cells were harvested and washed in 1× PBS before lysis and RNA was isolated using TRI™ reagent (Sigma-Aldrich) according to the manufacturer’s instructions. RNA was purified using the RNeasy® Mini Kit and RNase-free DNase set (Qiagen) according to the manufacturer’s instructions. For CD34 cells, RNA samples were extracted with QIAGEN RNeasy micro Plus kit.
Stranded mRNA prep (Illumina) sequencing libraries were generated and RNA sequencing was performed by the Ramaciotti Centre for Genomics using NextSeq 1×75bp high output or NovaSeq 2x100bp flow cells (Illumina). For CD34 cells, RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: CD34+ cell were electroporated with Cas9+ NT/UHRF1 gRNA1

value: erythroid progenitor cell line

value: transfected with no plasmid

tag: batch


title: 29422-MND50-1

description: Library name: R17029218LR01


title: 29422-MND28-2

description: Library name: R17029216LR01


title: 29422-MND28-3

description: Library name: R17029217LR01


title: Mist1+ organoids_P10_2

description:
Library name: Sample 17
all.fpkm_anno_1.txt
M-2-10-2


title: HUDEP-2 Mock Rep2

description: Library name: HUDEP-2 Mock Rep2


title: 29422-IPS-3

description: Library name: R17030717LR01


title: Mist1+ organoids_P15_2

description:
Library name: Sample 23
all.fpkm_anno_1.txt
M-2-15-2


title: HUDEP-2 Mock Rep1

description: Library name: HUDEP-2 Mock Rep1


title: 29422-MND28-1

description: Library name: R17029215LR01


title: EVTd8_PPARG_noDox_rep2

city: AUSTIN

first: Qingqing

last: Guo

state: TX

address: 2506 Speedway

country: USA

institute: The University of Texas at Austin

description: RNA-seq

data_processing:
All sequencing reads were trimmed using Trim Galore v0.6.10 and aligned to the human reference genome (hg38) with STAR (version 2.7.11b).
Alignments were then filtered using Samtools (version 1.17) with MAPQ score >= 10.
Raw counts were quantified using featureCounts from the Subread package (version 2.0.6).
Assembly: hg38
Supplementary files format and content: Raw counts quantified using featureCounts

source_name: Placenta

extract_protocol:
Total RNA was extracted from cells using the RNeasy Plus Mini Kit (Qiagen) (74136). The mRNA was enriched using the NEBNext® Poly(A) mRNA Magnetic Isolation Module kit (E7490L).
The RNAs-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (E7770L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol. RNA-seq was conducted as paired-end 150 bp sequencing on the NovaSeq 6000 (Illumina).

value: Placenta

value: Human trophoblast stem cells

value: Cells were under control conditions from EVT differentiation day 1 to day 8.


title: 29422-IPS-2

description: Library name: R17030716LR01


title: Mist1+ organoids_P10_1

description:
Library name: Sample 16
all.fpkm_anno_1.txt
M-2-10-1


title: 29422-IPS-1

description: Library name: R17030715LR01


title: Gpx4 KO_Mist1+ organoids_ P5_3

description:
Library name: Sample 15
all.fpkm_anno_1.txt
G-2-5-3

value: Gpx4 KO Mist1+ derived organoid

value: Gpx4 KO


title: 29422-NPC-3

description: Library name: R17030720LR01


title: 29415-NPC-2

description: Library name: R17030725LR01


title: 29415-NPC-3

description: Library name: R17030726LR01


title: Gpx4 KO_Mist1+ organoids_ P5_2

description:
Library name: Sample 14
all.fpkm_anno_1.txt
G-2-5-2


title: 29415-NPC-1

description: Library name: R17030724LR01


title: 29415-MND50-1

description: Library name: R17030573LR01


title: EVTd8_PPARG_d3Dox_rep1

description: RNA-seq

value: Cells were treated with 500 ng/mL Doxycycline from EVT differentiation day 3 to day 8 to induce PPARG overexpression.


title: 29415-MND50-2

description: Library name: R17029225LR01


title: 29415-MND50-3

description: Library name: R17030574LR01


title: EVTd8_PPARG_d1Dox_rep2

description: RNA-seq

value: Cells were treated with 500 ng/mL Doxycycline from EVT differentiation day 1 to day 8 to induce PPARG overexpression.


title: 29415-MND28-2

description: Library name: R17029222LR01


title: 29415-MND28-3

description: Library name: R17029223LR01


title: Gpx4 KO_Mist1+ organoids_ P5_1

description:
Library name: Sample 13
all.fpkm_anno_1.txt
G-2-5-1


title: 29415-IPS-3

description: Library name: R17030723LR01


title: EVTd8_PPARG_d1Dox_rep1

description: RNA-seq


title: 29415-IPS-2

description: Library name: R17030722LR01


title: 29415-IPS-1

description: Library name: R17030721LR01


title: Mist1+ organoids_P5_2

description:
Library name: Sample 11
all.fpkm_anno_1.txt
M-2-5-2


title: Mist1- organoids_P5_3

description:
Library name: Sample 9
all.fpkm_anno_1.txt
M-1-5-3

value: Mist1- derived organoid


title: EVTd8_PPARG_noDox_rep1

description: RNA-seq


title: Mist1+ organoids_P5_1

description:
Library name: Sample 10
all.fpkm_anno_1.txt
M-2-5-1


title: Mist1- organoids_P5_2

description:
Library name: Sample 8
all.fpkm_anno_1.txt
M-1-5-2


title: 29149-NPC-2

description: Library name: R17030713LR01


title: 29415-MND28-1

description: Library name: R17029221LR01


title: Mist1+ organoids_P5_3

description:
Library name: Sample 12
all.fpkm_anno_1.txt
M-2-5-3


title: EVTd8_Rosi_Ctrl_rep2

description: RNA-seq


title: 29149-MND50-3

description: Library name: R17029214LR01


title: 29149-NPC-3

description: Library name: R17030714LR01


title: 29149-NPC-1

description: Library name: R17030712LR01


title: Mist1- organoids_P5_1

description:
Library name: Sample 7
all.fpkm_anno_1.txt
M-1-5-1


title: EVTd8_Rosi_rep2

description: RNA-seq

value: Cells were treated with 1 μM Rosiglitazone from EVT differentiation day 1 to day 8.


title: 29149-MND50-2

description: Library name: R17029213LR01


title: EVTd8_Rosi_Ctrl_rep1

description: RNA-seq


title: EVTd8_PPARG_d3Dox_rep2

description: RNA-seq


title: 29149-MND50-1

description: Library name: R17029212LR01


title: HFD_Mist1+_3

description:
Library name: Sample 6
all.fpkm_anno.txt
HFD-pos-3

value: Mist1+ cells

value: HFD

value: high fat diet


title: 29149-MND28-3

description: Library name: R17029211LR01


title: 29149-MND28-2

description: Library name: R17029210LR01


title: HFD_Mist1+_2

description:
Library name: Sample 5
all.fpkm_anno.txt
HFD-pos-2

value: Stomach

value: Gastric epithelia


title: 29149-MND28-1

description: Library name: R17029209LR01


title: EVTd8_T007_rep1

description: RNA-seq

value: Cells were treated with 1 μM T0070907 from EVT differentiation day 1 to day 8.


title: HFD_Mist1+_1

description:
Library name: Sample 4
all.fpkm_anno.txt
HFD-pos-1


title: EVTd8_Rosi_rep1

description: RNA-seq


title: 29149-IPS-2

description: Library name: R17030710LR01


title: 29149-IPS-3

description: Library name: R17030711LR01


title: EVTd8_T007_LGD_rep2

description: RNA-seq

value: Cells were treated with 1 μM T0070907 and 1 μM LGD1069 from EVT differentiation day 1 to day 8.


title: 1079-NPC-3

description: Library name: R17030756LR01


title: EVTd8_T007_LGD_rep1

description: RNA-seq


title: 29149-IPS-1

description: Library name: R18001290LR01


title: normal diet_Mist1+_3

description:
Library name: Sample 3
all.fpkm_anno.txt
Ctrl-pos-3

value: WT

value: normal diet


title: normal diet_Mist1+_2

description:
Library name: Sample 2
all.fpkm_anno.txt
Ctrl-pos-2


title: EVTd8_T007_Ctrl_rep2

description: RNA-seq

value: Placenta

value: Human trophoblast stem cells


title: 1079-MND50-2

description: Library name: R17029195LR01


title: Tac,D30,rep3

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description:
Library name: Tac_3_d30_R2
column name in raw_count_d30.txt:Tac_d30_3
raw_count_d30.txt

data_processing:
reads passed QC  are aligned to mouse  reference mm10 using aligner STAR v.2.5.2a
read counts were estimated using htseq (1.0.0)
Differential expression analysis is done using DESeq2 (V 1.30.1)
Assembly: mm10
Supplementary files format and content: tab-delimited files included the raw counts for each sample.

source_name: Jejum

extract_protocol:
The jejum tissues of the mice were dissected according to their anatomic features and stored immediately in RNAlater solution (QIAGEN) in RNAse-free 1.7-ml tubes (Denville Scientific, Holliston, MA) at -80°C to stabilize and protect the integrity of RNA. For each sample, total RNA was extracted from ~1 cm of ileum. Prior to the extraction, 500 µl of ice-cold RNase free PBS was added to the sample. To remove the RNAlater, the mixture was centrifuged at 8,000xg for 10 min and the resulting pellet resuspended in 500 µl ice-cold RNase-free PBS with 10 µl of β-mercaptoethanol.
Ribosomal RNA depletion and library construction were performed using the RiboZero Plus kit and TruSeq stranded mRNA library preparation kit Ribosomal RNA depletion and library construction were performed using the RiboZero Plus kit and TruSeq stranded mRNA library preparation kit (Illumina) according to the manufacturer’s recommendations and sequenced using Illumina NovaSeq 6000 S2 flow cell

treatment_protocol: C57BL/6 Mice received daily  immunosuppressant classes including tacrolimus, prednisone, mycophenolate mofetil (MMF), and Fingolimod (FTY)

value: Jejum

tag: strain

value: Tacrolimus

tag: time


title: 1079-NPC-1

description: Library name: R17030754LR01


title: 1079-MND50-1

description: Library name: R17029194LR01


title: 1079-MND28-3

description: Library name: R17029193LR01


title: 1079-MND50-3

description: Library name: R17029196LR01


title: normal diet_Mist1+_1

description:
Library name: Sample 1
all.fpkm_anno.txt
Ctrl-pos-1


title: EVTd8_T007_Ctrl_rep1

description: RNA-seq

value: Cells were under control conditions from EVT differentiation day 1 to day 8.


title: EVTd8_Ctrl_KD_rep2

description: RNA-seq

value: Cells were infected with non-targeting shRNA lentivirus from EVT differentiation day 1 to day 8.


title: 1079-MND28-2

description: Library name: R17029192LR01


title: Tac,D30,rep2

description:
Library name: Tac_2_d30_R2
column name in raw_count_d30.txt:Tac_d30_2
raw_count_d30.txt


title: EVTd8_T007_rep2

description: RNA-seq


title: EVTd8_Ctrl_KD_rep1

description: RNA-seq


title: 1079-MND28-1

description: Library name: R17029191LR01


title: Tac,D30,rep1

description:
Library name: Tac_1_d30_R2
column name in raw_count_d30.txt:Tac_d30_1
raw_count_d30.txt


title: EVTd3_T007_rep2

description: RNA-seq

value: Cells were treated with 1 μM T0070907 from EVT differentiation day 1 to day 3.


title: 1079-IPS-2

description: Library name: R17030752LR01


title: 1079-IPS-3

description: Library name: R17030753LR01


title: 1079-IPS-1

description: Library name: R17030751LR01


title: Pred,D30,rep3

description:
Library name: Pred_3_d30_R2
column name in raw_count_d30.txt:Pred_d30_3
raw_count_d30.txt

value: Prednisone


title: 1079-NPC-2

description: Library name: R17030755LR01


title: YY1_KD_rep3_RNA_seq

city: Qingdao

first: Luyang

last: Sun

address: 189 Songling Road

institute: QIBEBT

data_processing:
Low quality reads and sequencing adaptors were filtered using fastp version 0.12
Clean reads were aligned to the reference genome (hg19) using HISAT2 version 2.2.1
Gene-based read counting was performed using featureCounts version 2.0.3
Differentially expressed genes were identified using DESeq2 version 1.34
GO analysis was performed using clusterProfiler version 4.0
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw gene read counts for each sample

source_name: umbilical cord-derived mesenchymal stem cells

growth_protocol: Human cord blood mesenchymal stem cells (hMSCs) were purchased from ATCC (PCS-500-010, lot #63216949). Cells were grown in low glucose DMEM (Life Technologies 11885-084) supplemented with 10% FBS (Life Technologies 16000-044, lot #1314735) and 1× penicillin/streptomycin (Life Technologies 15140-122) at 37ºC with 5% CO2 and 3% O2. Medium was replaced every 4 days in the absence of passaging. Cells were grown to ~70% confluence and split 1:4 as needed. Cell density was below the concentration needed for reliable detection with a hemocytometer (105 cells/mL), so the growth curve was estimated as 2 population doublings per passage.

extract_protocol:
For RNA-seq, total RNA extraction and RNA-seq library preparation were performed as described in McCauley, B.S. et al. 2021. Ribosomal RNAs were depleted from 100ng of DNase-treated total RNA by NEBNext rRNA depletion kit (NEB, E6310).
For RNA-seq, the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB, E7760) was used for RNA-seq library construction.

treatment_protocol: human MSCs were cultured to PD12, PD14, and PD32. For YY1 knock-down experiments, shRNA-encoding lentiviral particles were used to knock down expression of YY1 in MSCs as previously described 46. MISSION shRNA #TRCN0000019898 was used to knock down YY1 expression; the non-targeting shRNA #SHC002 (NT) was used as a control. Lentiviruses were produced in HEK 293T cells by co-transfecting the shRNA plasmids and plasmids encoding VSVG and ΔR8.9 (gifts from Xhixun Dou) using TransIT-VirusGen transfection reagent (Mirus Bio, MIR 6703) following standard protocols. Supernatants were collected 48 hours after transfection, centrifuged at 1,500×g for 10 min at 4°C, and filtered through 0.45m filters. Lentiviruses were stored at -80ºC. PD 10 MSCs were infected with YY1 or NT shRNAs at 3 MOI in MSC growth medium with 6µg/mL polybrene for 6 hours and cultured in fresh MSC growth medium for 2 days under standard culture conditions. Successfully infected cells were selected for in MSC growth medium with 1µg/mL puromycin for 6 days.

tag: cell passage

value: YY1 KD


title: Pred,D30,rep2

description:
Library name: Pred_2_d30_R2
column name in raw_count_d30.txt:Pred_d30_2
raw_count_d30.txt


title: YY1_KD_rep2_RNA_seq

value: umbilical cord-derived mesenchymal stem cells


title: EVTd3_T007_LGD_rep2

description: RNA-seq

value: Cells were treated with 1 μM T0070907 and 1 μM LGD1069 from EVT differentiation day 1 to day 3.


title: YY1_KD_rep1_RNA_seq


title: EVTd3_T007_rep1

description: RNA-seq


title: YY1_NT_rep3_RNA_seq

value: control


title: YY1_NT_rep2_RNA_seq


title: Pred,D30,rep1

description:
Library name: Pred_1_d30_R2
column name in raw_count_d30.txt:Pred_d30_1
raw_count_d30.txt


title: YY1_NT_rep1_RNA_seq


title: MMF,D30,rep2

description:
Library name: MMF_2_d30_R2
column name in raw_count_d30.txt:MMF_d30_2
raw_count_d30.txt

value: MMF


title: EVTd3_T007_Ctrl_rep1

description: RNA-seq

value: Cells were under control conditions from EVT differentiation day 1 to day 3.


title: EVTd3_T007_Ctrl_rep2

description: RNA-seq


title: ucMSC_Old_YY1_ChIP

library_source: genomic

data_processing:
Raw reads were trimmed using fastp with default parameters.
Clean reads were aligned to human reference genome hg19 using Bowtie2 version 2.4.2.
Duplicated reads were removed using samtools markdup.
Peaks were called with MACS2 using input as the control.
Peak annotation was performed using the ChIPseeker R package according to human reference genome hg19.
Assembly: hg19
Supplementary files format and content: bigwig
Supplementary files format and content: peak

molecule: genomic DNA

extract_protocol:
PD 12 and PD 32 MSCs were fixed with 1% formaldehyde. As described in McCauley, B.S. et al. 2021, fixed cells were lysed and chromatin was sonicated to approximately 400 bp. A total of 10μL of cell lysate (equivalent to 100,000 cells) was used as initial input for both CTCF and YY1 ChIP. The True MicroChIP Kit (Diagenode, C01010130) was used for the target molecule extraction with the antibody of CTCF (AbCam #ab190237, lot GR3206274-4) and YY1 (Active Motif #61311, lot 34614003), respectively.
Sequencing libraries were prepared using the MicroPlex Library Preparation Kit v2 (Diagenode, C05010014) following manufacturer’s instructions

treatment_protocol: human MSCs were cultured to PD12 and PD32.

tag: chip antibody


title: MMF,D30,rep1

description:
Library name: MMF_1_d30_R2
column name in raw_count_d30.txt:MMF_d30_1
raw_count_d30.txt


title: ucMSC_Young_Hic

data_processing:
Hi-C data analysis was performed using ICE.An iterative multistep mapping strategy was used to map each end of the two paired-end reads independently. Each read was first truncated to 25 bp and mapped to the genome.
Reads that did not map successfully were extended by 5 bp and re-mapped iteratively until the original read length was reached (100 bp). Aligned reads were then filtered based on the orientation, length, and concordance of the DNA restriction fragment.
Filtered clean reads were binned along the genome at 40kb resolution and then normalized with the ICE method.
The correlation between contact probability and genomic distance was done by first defining all possible genomic separations into logarithmical bins, then calculating the mean of Hi-C contact frequencies in each bin.
Each chromosomal arm was analyzed separately, with interchromosomal reads excluded.
Assembly: hg19
Supplementary files format and content: hic matrix

extract_protocol:
About 1 million MSCs from both PD 12 and PD 32 were fixed with 1% formaldehyde and incubated at room temperature for 10 minutes, then quenched with 2.5M glycine for 5 minutes. The cells were washed with PBS twice followed by brief centrifugation. MSCs were then lysed with Hi-C lysis buffer 93 and digested with MboI (NEB R0147S) overnight. After DNA labeling, proximity ligation, crosslink reversal, and biotin pull-down, target DNA were extracted.
Sequencing library of extracted DNA were performed as described in Lieberman-Aiden, E. et al., 2009


title: ucMSC_Old_INPUT_ChIP


title: TSC_PPARG_KD2

description: RNA-seq

value: TSCs were infected with PPARG shRNA_2 lentivirus and maintained for 72 hours.


title: EVTd3_T007_LGD_rep1

description: RNA-seq


title: ucMSC_Young_INPUT_ChIP


title: TSC_PPARG_KD1

description: RNA-seq

value: TSCs were infected with PPARG shRNA_1 lentivirus and maintained for 72 hours.


title: ucMSC_Young_YY1_ChIP


title: FTY,D30,rep3

description:
Library name: FTY_3_d30_R2
column name in raw_count_d30.txt:FTY_d30_3
raw_count_d30.txt


title: Input_A375_hs_i90

city: South San Francisco

first: Rohit

last: Reja

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Raw reads were aligned to the mouse reference (GRCh38) using GSNAP (with parameters -M 2 -n 10 -B 2 -i 1 --pairmax-dna=1000 --terminal-threshold=1000 --gmap-mode=none --clip-overlap). Reads were filtered to include only uniquely mapped reads. MACS2 was used to call peaks.
Assembly: GRCh38
Supplementary files format and content: Peak calls in excel format relative to the input per sample

source_name: Skin

extract_protocol:
A375 cells  were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine. Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantification of the total chromatin yield. An aliquot of chromatin (25 μg) was precleared with protein Agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 μl of antibody against ETV5 (Abcam, catalog number ab102010), H3K27Ac (Active Motif, catalog number 39133) or H3K4me3 (Active Motif, catalog number 39159). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65°C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (qPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad). The resulting signals were normalized for primer efficiency by carrying out qPCR for each primer pair using Input DNA.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).

treatment_protocol: A375 cells were treated with ERK inhibitor Vertex11e for 1 h.


title: Input_SNP_hs_i91


title: H3K4me3_ChIP_COP1WT+ERKi_2

value: Active Motif, catalog number 39159

value: Skin

value: ERK inhibitor


title: Control,D30,rep3

description:
Library name: control_3_d30_R2
column name in raw_count_d30.txt:control_d30_3
raw_count_d30.txt

value: Jejum

value: Control


title: FTY,D30,rep1

description:
Library name: FTY_1_d30_R2
column name in raw_count_d30.txt:FTY_d30_1
raw_count_d30.txt


title: TSC_Ctrl_KD_rep2

description: RNA-seq

value: Placenta

value: Human trophoblast stem cells

value: TSCs were infected with non-targeting shRNA lentivirus and maintained for 72 hours.


title: H3K4me3_ChIP_COP1WT+ERKi_1


title: TSC_Ctrl_KD_rep1

description: RNA-seq


title: MMF,D30,rep3

description:
Library name: MMF_3_d30_R2
column name in raw_count_d30.txt:MMF_d30_3
raw_count_d30.txt


title: ucMSC_Old_Hic


title: TSC_RXRA_rep2

description: Chromatin IP against RXRA under control conditions in TSCs.

data_processing:
All data reads were trimmed with Trim Galore (version 0.6.10) and mapped to the hg38 human reference genome using Bowtie2 (version 2.5.1) with default parameters.
The alignments were further filtered with Samtools (version 1.17) with MAPQ >= 10.
PCR duplicates were subsequently eliminated with Picard Tools (version 2.27.2).
Peaks were detected utilizing MACS3 (version 3.0.0b3) with a false discovery rate (FDR) < 0.05.
RPGC-normalized bigwig files were produced using the deepTools bamCoverage (version 3.5.2).
Assembly: hg38
Supplementary files format and content: RPGC-normalized bigwig files

extract_protocol:
ChIP were performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNAs were applied for the generation of sequencing libraries using the NEBNext Ultra II DNA Library Prep Kit (E7103L) and NEBNext Multiplex Oligos for Illumina (E7600S) following the manufacturer’s protocol.

value: TSCs under control conditions.


title: H3K27ac_ChIP_COP1WT+ERKi_2

value: Active Motif, catalog number 39133


title: H3K27ac_ChIP_COP1WT+ERKi_1


title: TSC_RXRA_rep1


title: Control,D30,rep2

description:
Library name: control_2_d30_R2
column name in raw_count_d30.txt:control_d30_2
raw_count_d30.txt


title: ucMSC_Old_CTCF_ChIP

value: umbilical cord-derived mesenchymal stem cells


title: Control,D30,rep1

description:
Library name: control_1_d30_R2
column name in raw_count_d30.txt:control_d30_1
raw_count_d30.txt


title: ETV5_ChIP_COP1WT+ERKi_rep1

value: Abcam, catalog number ab102010


title: ETV5_ChIP_COP1WT+ERKi_rep2


title: H3K4me3_ChIP_COP1SNP+ERKi_2


title: ucMSC_Young_CTCF_ChIP


title: TSC_PPARG_rep2

description: Chromatin IP against PPARG under control conditions in TSCs.


title: FTY,D30,rep2

description:
Library name: FTY_2_d30_R2
column name in raw_count_d30.txt:FTY_d30_2
raw_count_d30.txt


title: H3K4me3_ChIP_COP1SNP+ERKi_1


title: H3K27ac_ChIP_COP1SNP+ERKi_1


title: TSC_PPARG_rep1


title: H3K27ac_ChIP_COP1SNP+ERKi_2


title: Tac,D7,rep2

description:
Library name: Tac_2_d7
column name in raw_count_d7.txt:FTY_d7_2
raw_count_d7.txt

value: Tacrolimus


title: ETV5_ChIP_COP1SNP+ERKi_rep2


title: ETV5_ChIP_COP1SNP+ERKi_rep1


title: Input_EVTd8

description: Input control for chromatin IP under control conditions at EVT day 8.

value: Cells under control conditions on EVT day 8.


title: H3K27ac_ChIP_COP1WT_2

value: No treatment


title: H3K4me3_ChIP_COP1WT_1


title: Input_EVTd3_T007

description: Input control for chromatin IP under treatment with 1 µM T0070907 from EVT day 1 to day 3.

value: Cells treated with 1 µM T0070907 from EVT day 1 to day 3.


title: Pred,D7,rep3

description:
Library name: Pred_3_d7
column name in raw_count_d7.txt:MMF_d7_3
raw_count_d7.txt

value: Prednisone


title: H3K27ac_ChIP_COP1WT_1


title: Pred,D7,rep2

description:
Library name: Pred_2_d7
column name in raw_count_d7.txt:MMF_d7_2
raw_count_d7.txt


title: Pred,D7,rep1

description:
Library name: Pred_1_d7
column name in raw_count_d7.txt:MMF_d7_1
raw_count_d7.txt


title: H3K4me3_ChIP_COP1SNP_2

value: Active Motif, catalog number 39159


title: H3K27ac_ChIP_COP1SNP_1

value: Skin


title: Tac,D7,rep3

description:
Library name: Tac_3_d7
column name in raw_count_d7.txt:FTY_d7_3
raw_count_d7.txt


title: ETV5_ChIP_COP1SNP_rep2


title: ETV5_ChIP_COP1WT_rep1


title: H3K27ac_ChIP_COP1SNP_2


title: EVTd8_PPARG_rep2

description: Chromatin IP against PPARG under control conditions at EVT day 8.


title: Input_EVTd3_Ctrl

description: Input control for chromatin IP under control conditions at EVT day 3.

value: Cells under control conditions on EVT day 3.


title: EVTd8_RXRA_rep1

description: Chromatin IP against RXRA under control conditions at EVT day 8.


title: MMF,D7,rep2

description:
Library name: MMF_2_d7
column name in raw_count_d7.txt:Pred_d7_2
raw_count_d7.txt

value: Jejum

value: MMF


title: ETV5_ChIP_COP1WT_rep2


title: JQ1_9_p58

city: Milwaukee

first: Joshua

last: Nord

state: WI

address: 8701 W Watertown Plank Rd

institute: Medical College of Wisconsin

description: Library name: Sample 24

data_processing:
Raw sequences (FASTQ files) were aligned to rat reference genome rn7.2 using STAR (73), differential expression was performed using DE-seq (74), and gene level absolute expression was quantified using CuffLinks (75). Analysis was done using default parameters through Basepair (www.basepairtech.com).
Assembly: rn7.2
Supplementary files format and content: CSV files include: ID, symbol, count, FPKM, and TPM

organism: Rattus norvegicus

growth_protocol: INS 832/13 rat insulinoma cells were cultured in RPMI 1640 supplemented with 10% v/v fetal bovine serum (FBS, Gemini Bio), 2 mM L-glutamine, 1 mM sodium pyruvate, 10 mM HEPES, 50 µM 2-mercaptoethanol, 100 units/mL penicillin, and 100 μg streptomycin.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 1 ug of total RNA was used for library preparation
Libraries were prepared according to the manufacturer's specifications using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs).

treatment_protocol: BET bromodomain inhibitor (+)-JQ1 (dissolved in DMSO) was administered at 500nM for 1 hour prior to the addition of IL-1B for 1, 3, or 9 hours. An equal volume of DMSO was used as a control.

value: Rat insulinoma cell line

value: WT

value: 6-hr IL-1


title: EVTd8_PPARG_rep1

value: Placenta

value: Human trophoblast stem cells


title: Input_TSC

description: Input control for chromatin IP under control conditions in TSCs.

value: TSCs under control conditions.


title: Tac,D7,rep1

description:
Library name: Tac_1_d7
column name in raw_count_d7.txt:FTY_d7_1
raw_count_d7.txt


title: JQ1_9_p57

description: Library name: Sample 23


title: H3K4me3_ChIP_COP1WT_2


title: FTY,D7,rep3

description:
Library name: FTY_3_d7
column name in raw_count_d7.txt:Tac_d7_3
raw_count_d7.txt


title: EVTd3_RXRA_T007_rep2

description: Chromatin IP against RXRA under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: JQ1_3_p58

description: Library name: Sample 21

value: 3-hr IL-1


title: JQ1_3_p57

description: Library name: Sample 20


title: MMF,D7,rep3

description:
Library name: MMF_3_d7
column name in raw_count_d7.txt:Pred_d7_3
raw_count_d7.txt


title: EVTd8_RXRA_rep2


title: H3K4me3_ChIP_COP1SNP_1


title: MMF,D7,rep1

description:
Library name: MMF_1_d7
column name in raw_count_d7.txt:Pred_d7_1
raw_count_d7.txt


title: ETV5_ChIP_COP1SNP_rep1

value: Abcam, catalog number ab102010


title: EVTd3_RXRA_T007_rep1


title: FTY,D7,rep1

description:
Library name: FTY_1_d7
column name in raw_count_d7.txt:Tac_d7_1
raw_count_d7.txt


title: JQ1_1_p58

description: Library name: Sample 18

value: 1-hr IL-1


title: JQ1_3_p55

description: Library name: Sample 19


title: EVTd3_RXRA_Ctrl_rep2

description: Chromatin IP against RXRA under control conditions at EVT day 3.


title: JQ1_1_p57

description: Library name: Sample 17


title: EVTd3_RXRA_Ctrl_rep1


title: Control,D7,rep2

description:
Library name: control_2_d7
column name in raw_count_d7.txt:control_d7_2
raw_count_d7.txt

value: Control


title: Control,D7,rep3

description:
Library name: control_3_d7
column name in raw_count_d7.txt:control_d7_3
raw_count_d7.txt


title: JQ1_9_p55

description: Library name: Sample 22


title: Control,D7,rep1

description:
Library name: control_1_d7
column name in raw_count_d7.txt:control_d7_1
raw_count_d7.txt


title: FTY,D7,rep2

description:
Library name: FTY_2_d7
column name in raw_count_d7.txt:Tac_d7_2
raw_count_d7.txt


title: JQ1_0_p57

description: Library name: Sample 14

value: 0-hr IL-1


title: JQ1_0_p55

description: Library name: Sample 13


title: DMSO_9_p57

description: Library name: Sample 11

value: Vehicle


title: EVTd3_PPARG_T007_rep1

description: Chromatin IP against PPARG under treatment with 1 µM T0070907 from EVT day 1 to day 3.

value: Cells treated with 1 µM T0070907 from EVT day 1 to day 3.


title: DMSO_9_p55

description: Library name: Sample 10


title: DMSO_9_p58

description: Library name: Sample 12


title: 12wk, R62, Rep 2 Spatial Transcriptomics

city: Irvine

first: Ricardo

last: Miramontes

address: 845 Health Sciences Rd

institute: UC Irvine

description:
Library name: 1b-5_A1_12wk_R62
Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing data were processeed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv.gz
Library strategy: Spatial Transcriptomics

source_name: Brain, male, 12-week

extract_protocol:
Fresh frozen brain tissue were OCT embedded, snap frozen over isopentane bath immersed in liquid nitrogen, and 10uM frozen sections were sectioned with cryostat and mounted to 10x Visium slides in capture area
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides and Reagent kit according to manufacturer's construction (Rev E)

value: Brain, male, 12-week

value: Transgenic (R62)


title: EVTd3_PPARG_Ctrl_rep2

description: Chromatin IP against PPARG under control conditions at EVT day 3.

value: Cells under control conditions on EVT day 3.


title: DMSO_3_p58

description: Library name: Sample 9


title: 12wk, R62, Rep 3 Spatial Transcriptomics

description:
Library name: 2-2_A1_12wk_R62
Fresh frozen spatial transcriptome sequencing


title: DMSO_3_p57

description: Library name: Sample 8


title: EVTd3_PPARG_Ctrl_rep1


title: DMSO_3_p55

description: Library name: Sample 7


title: JQ1_0_p58

description: Library name: Sample 15


title: JQ1_1_p55

description: Library name: Sample 16


title: EVTd3_NCOA3_T007_rep2

description: Chromatin IP against NCOA3 under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: DMSO_1_p57

description: Library name: Sample 5


title: DMSO_1_p58

description: Library name: Sample 6


title: 12wk, R62, Rep 1 Spatial Transcriptomics

description:
Library name: 1b-7_D1_12wk_R62
Fresh frozen spatial transcriptome sequencing


title: EVTd3_NCOA3_T007_rep1


title: DMSO_0_p58

description: Library name: Sample 3


title: DMSO_1_p55

description: Library name: Sample 4


title: EVTd3_PPARG_T007_rep2


title: DMSO_0_p57

description: Library name: Sample 2


title: 12wk, NT, Rep 2 Spatial Transcriptomics

description:
Library name: 3b-1_B1_12wk_NT
Fresh frozen spatial transcriptome sequencing

value: Non-transgenic (NT)


title: 12wk, NT, Rep 3 Spatial Transcriptomics

description:
Library name: 4-4_B1_12wk_NT
Fresh frozen spatial transcriptome sequencing


title: RecovRB4

city: Toledo

first: Montaña

last: Mena

state: Toledo

address: Avda. Carlos III s/n

department: Environmental Sciences

country: Spain

institute: UCLM

data_processing:
Quality control of the raw sequencing data was performed with FastQC Screen v0.11.7. Low quality reads and artifacts were removed using Trimmomatic. cDNA fragments were aligned to the reference Arabidopsis genome (Araport11) using Salmon and Tximport was used to quantify gene counts. Differential gene expression was analyzed with EdgeR TMM normalization algorithm to generate fold-change values and adjusted p-values using the Benjamini-Hochberg method. Genes with counts<5 in at least 3 biological replicates were filtered.
Assembly: Araport11
Supplementary files format and content: tab-delimited raw counts for each sample

organism: Arabidopsis thaliana

source_name: Plantlet

growth_protocol: Seeds were sterilized with chlorine gas and stratified for 4 days at 4ºC prior to light exposure. Seedlings were grown in ½ strength MS and 1% (w/v) agar. Growth chambers were set at 70% RH, 70 µmol·m-2·s-1 and long day (16-h-light/8-h-dark). Control temperature was 21ºC and warm temperature 28ºC.

extract_protocol:
RNAseq was harvested with ReliaPrep™ RNA Tissue Miniprep System (Promega).
Library was constructed using "TruSeq Stranded mRNA Library Prep Kit" following the TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 (Macrogen, Inc.; Geumcheon‐gu, Seoul, South Corea).

treatment_protocol: Short warm-temperature pulses began with Col-0 seedlings grown for 3 days at 21ºC (T0). Control treatments: 16 h at 21ºC (T1, 21ºC) and 24 h at 21ºC (T2, 21ºC). Warm-temperature treatments: 16 h at 28ºC (T1, 28ºC) and 24 h at 28ºC (T2, 28ºC). Recovery treatment: 16 h at 28ºC plus 8h at 21ºC (Recov).

value: Plantlet

value: 3 days at 21ºC+16 h at 28ºC+8h at 21ºC (Recov)


title: DMSO_0_p55

description: Library name: Sample 1

value: Rat insulinoma cell line

value: WT


title: RecovRB6


title: EVTd3_NCOA3_Ctrl_rep1

description: Chromatin IP against NCOA3 under control conditions at EVT day 3.

value: Placenta

value: Human trophoblast stem cells


title: EVTd3_MED1_T007_rep2

description: Chromatin IP against MED1 under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: 4dpl21RB3

value: 3 days at 21ºC+24h at 21ºC (T2, 21ºC)


title: 4wk, R62, Rep 3 Spatial Transcriptomics

description:
Library name: 1-6_D1_4wk_R62
Fresh frozen spatial transcriptome sequencing

source_name: Brain, male, 4-week

value: Brain, male, 4-week


title: RecovRB3


title: 4dpl21RB2


title: EVTd3_MED1_T007_rep1


title: 4wk, R62, Rep 2 Spatial Transcriptomics

description:
Library name: 1-1_A1_4wk_R62
Fresh frozen spatial transcriptome sequencing


title: 4dpl21RB1


title: 4wk, R62, Rep 1 Spatial Transcriptomics

description:
Library name: 2-7_B1_4wk_R62
Fresh frozen spatial transcriptome sequencing


title: 3dpLRB3

value: 3 days at 21ºC (T0)


title: EVTd3_MED1_Ctrl_rep2

description: Chromatin IP against MED1 under control conditions at EVT day 3.


title: EVTd3_NCOA3_Ctrl_rep2


title: 3dpLRB2


title: 3dpl24h28CRB2

value: 3 days at 21ºC+24h at 28ºC (T2, 28ºC)


title: EVTd3_MED1_Ctrl_rep1


title: 4wk, NT, Rep 3 Spatial Transcriptomics

description:
Library name: 3-5_C1_4wk_NT
Fresh frozen spatial transcriptome sequencing


title: 4wk, NT, Rep 2 Spatial Transcriptomics

description:
Library name: 3-1_D1_4wk_NT
Fresh frozen spatial transcriptome sequencing


title: 3dpl24h28CRB1


title: 3dpl24h28CRB3


title: EVTd3_MED15_T007_rep2

description: Chromatin IP against MED15 under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: 16h28RB3

value: 3 days at 21ºC+16 h at 28ºC (T1, 28ºC)


title: 16h28RB1


title: 16h21RB3

value: 3 days at 21ºC+16 h at 21ºC (T1, 21ºC)


title: EVTd3_MED15_T007_rep1

value: Cells treated with 1 µM T0070907 from EVT day 1 to day 3.


title: 16h21RB2


title: EVTd3_MED15_Ctrl_rep2

description: Chromatin IP against MED15 under control conditions at EVT day 3.


title: 4wk, NT, Rep 1 Spatial Transcriptomics

description:
Library name: 1-2_C1_4wk_NT
Fresh frozen spatial transcriptome sequencing


title: P0, R62, Rep 2 Spatial Transcriptomics

description:
Library name: 6-p0-3_B1_R62
Fresh frozen spatial transcriptome sequencing

source_name: Brain, male, postnatal day 0

value: Brain, male, postnatal day 0


title: 12wk, NT, Rep 1 Spatial Transcriptomics

description:
Library name: 4-1_B1_12wk_NT
Fresh frozen spatial transcriptome sequencing

value: Brain, male, 12-week


title: P0, R62, Rep 1 Spatial Transcriptomics

description:
Library name: 3-p0-3_D1_R62
Fresh frozen spatial transcriptome sequencing

value: Transgenic (R62)


title: EVTd3_MED15_Ctrl_rep1

value: Cells under control conditions on EVT day 3.


title: 16h28RB2

value: Plantlet


title: 16h21RB1


title: MUTEPPP#3_rep3

description:
AthMUTEPPP.3.3
S12_G3
G3rep3bis

data_processing:
Quality control of the raw sequencing data was performed with FastQC Screen v0.11.7. Reads with Phred scores higher than 20 and 30 were identified, and artifacts were removed using Trimmomatic 0.38. cDNA fragments were aligned to the reference Arabidopsis genome (TAIR10.1) using HISAT2 v2.1.0 and Bowtie2 v2.3.4.1. StringTie v2.1.3b was used to assemble alignments into transcripts and determine their abundance, quantified and normalized. Differential gene expression was analyzed with DESeq2, using the nbinomWaldTest to generate fold-change (FC) values and adjusted p-values using the Benjamini-Hochberg method.
Assembly: TAIR10.1
Supplementary files format and content: tab-delimited text file includes read counts for each sample

source_name: whole seedlings

growth_protocol: Seeds were sown in vitro on Petri dishes containing solid MS medium supplemented with 1% sucrose. After stratification, they were grown at 21 degrees Celsius under a 16h light/8h dark photoperiod and a light intensity of 70 μmol m‐2 s‐1 PAR. Whole seedlings were harvested 2 days post-germination and frozen in liquid nitrogen.

extract_protocol:
RNA extraction was performed using the "High Pure RNA Tissue Kit" (Roche; 12033674001) with modifications.
The library was constructed using the "TruSeq Stranded mRNA Library Prep Kit" following the TruSeq Stranded mRNA Reference Guide # 1000000040498 v00 (Macrogen, Inc.; Geumcheon‐gu, Seoul, South Corea).

treatment_protocol: No additional treatments were applied to the plates.

value: whole seedlings


title: 3dpLRB1


title: MUTEPPP#3_rep2

description:
AthMUTEPPP.3.2
S11_G3
G3rep2bis


title: EVTd3_MED12_T007_rep2

description: Chromatin IP against MED12 under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: P0, NT, Rep 2 Spatial Transcriptomics

description:
Library name: 1-p0-3_A1_NT
Fresh frozen spatial transcriptome sequencing

value: Non-transgenic (NT)


title: P0, NT, Rep 1 Spatial Transcriptomics

description:
Library name: 1-p0-1_A1_NT
Fresh frozen spatial transcriptome sequencing


title: MUTEPPP#3_rep1

description:
AthMUTEPPP.3.1
S10_G3
G3rep1bis


title: MUTEv5#5_rep3

description:
AthMUTEv5.5.3
S9_G2
G2rep3bis


title: MUTEv5#5_rep2

description:
AthMUTEv5.5.2
S8_G2
G2rep2bis


title: MUTEv5#5_rep1

description:
AthMUTEv5.5.1
S7_G2
G2rep1bis


title: 12wk R62 Rep 3, 4wk R62 Rep 3, 4wk NT Rep 2, 4wk NT Rep 3, Mixed FLEX single nuclei-RNA-seq

description:
Library name: 1b-7_12wk_R62_2-7_4wk_R62_1-2_4wk_NT_3-1_4wk_NT
10x Genomics FLEX BC001, 1b-7, 12-week-HD BC002, 2-7, 4-week-HD BC003, 1-2, 4-week-NT BC004, 3-1, 4-week-NT

library_source: transcriptomic single cell

data_processing:
Raw reads and cell barcode demultiplexed to generate count matrix using CellRanger software (v7.1.0) using a value of 9000 for the force_cells parameter.
The obtained count matrices for each sample were merged and filtered for based on number of features expressed and number of mitochondrial genes.
Downstream analyses with Seurat (v3.1.5) include normalization, dimension reduction by principal component analysis (‘RunPCA’) using the top 3000 variable features, uniform manifold approximation and projection (‘RunUMAP’), Shared Nearest Neighbor (SNN) Graph construction (‘FindNeighbors’), and finally Louvain clustering (‘FindClusters’) using the first 20 principal components and a resolution of 0.20 to determine cluster assignment.
To identify cell type markers and differentially expressed genes between different conditions, Wilcoxon rank sum test was used (‘FindMarkers’)
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain, male, mixed (4wk, 12-week)

extract_protocol:
Fresh frozen tissue were OCT embedded, snap frozen over isopentane bath immersed in liquid nitrogen and ~700uM of 30uM sections of tissue were collected. Sections were fixed for 21 hours with 4% PFA and dissociated using Liberase TL (postnatal day 0) or Liberse TH (4-week and 12-week) and processed with the 10x Genomics Chromium Fixed RNA Profiling kit according to manufacter's instructions. Tissue was then dissoaciated with a gentleMACS OctoDissociator and cell quality and number evaluated.
Probe hybiridization and library construction were performed with the 10x Genomics Single Cell Gene Expression FLEX according to the manufacter's instructions. 4 samples were multiplexed and 2 samples singleplex. After probe hybridization, nuclei were pooled (if multiplexed), partitioned into GEMs and ligation and extension was in GEMs  Samples were sequenced with the Illumina NovaSeq system with a target sequenciong depth of at least 30,000/nuclei.

value: Brain, male, mixed (4wk, 12-week)

value: Mixed Sample (Non-transgenic (NT), Transgenic (R62))


title: EVTd3_MED12_T007_rep1

value: Placenta

value: Human trophoblast stem cells


title: MUTEv5#2_rep3

description:
AthMUTEv5.2.3
S6_G1
G1rep3bis


title: EVTd3_MED12_Ctrl_rep2

description: Chromatin IP against MED12 under control conditions at EVT day 3.


title: EVTd3_MED12_Ctrl_rep1


title: MUTEv5#2_rep2

description:
AthMUTEv5.2.2
S5_G1
G1rep2bis


title: P0 NT Rep 1, P0 R62 Rep 1, P0 NT Rep 2, P0, R62, Rep 2, Mixed FLEX single nuclei-RNA-seq

description:
Library name: 1-p0-3_NT_3-p0-3_R62_1-p0-1_NT_6-p0-3_R62
10x Genomics FLEX BC001, 1-P0_3, P0-NT BC002, 3-P0_3, P0-HD BC003, 1-P0_1, P0-NT BC004, 6-P0_3, P0-HD


title: MUTE_rep2

description:
AthMUTE.1.2
S2_CT
CTrep2bis


title: EVTd3_H3K27ac_T007_rep2

description: Chromatin IP against H3K27ac under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: MUTE_rep3

description:
AthMUTE.1.3
S3_CT
CTrep3bis


title: MUTE_rep1

description:
AthMUTE.1.1
S1_CT
CTrep1bis


title: EVTd3_H3K27ac_T007_rep1


title: RPE_iCut_ABCB1_cr6_ATRi_10h_LaminB2_R1-gatc.counts.txt.gz

city: Amsterdam

first: Xabier

last: Vergara

state: North Holland

address: Plesmalaan 121

department: Molecular Genetics

country: Netherlands

institute: Netherlands Cancer Institute

description:
Library name: 6604_17_pA-DamID_ABCB1_cr6_ATRi_10h_R1_AGTACAAG_S43_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

data_processing:
We processed the DNA sequencing data using the previously published computational pipeline (https://github.com/vansteensellab/pADamID_ABCB1_Novaseq)
Assembly: hg38
Supplementary files format and content: There are two processed data formats: (1) -gatc.counts.txt.gz, read counts per gatc sequence in the genome used for domainograms and (2) -20kb.bw, bigwig file at 20kb resolution
Library strategy: DamID-Seq

growth_protocol: Culturing methods per cell line are described in the manuscript

extract_protocol:
genomic DNA was extracted using the Bioline kit (details in methods section)
We followed pA-DamID library preparation protocol used for NOVAseq (details in methods section)

treatment_protocol: Trearment per sample are described in the manuscript

value: hTERT-immortalized retinal pigment epithelial

value: wildtype

tag: antibody

tag: transfection

tag: timepoint


title: EVTd3_H3K27ac_Ctrl_rep2

description: Chromatin IP against H3K27ac under control conditions at EVT day 3.


title: 4wk NT Rep 1 FLEX single nuclei-RNA-seq

description:
Library name: 3-5_4wk_NT
10x Genomics FLEX BC001,1-6,4-week-HD

value: Brain, male, 4-week


title: P0 R62 Rep 3, P0 NT Rep 3, 12wk R62 Rep 3, 12wk NT Rep 3, Mixed FLEX single nuclei-RNA-seq

description:
Library name: 4-p0-1_R62_7-p0-3_NT_2-2_12wk_R62_4-1_12wk_NT
10x Genomics FLEX BC001, 4-P0_1, P0-HD BC002, 7-P0_3, P0-NT BC003, 2-2, 12-week-HD BC004, 4-1, 12-week-NT

source_name: Brain, male, mixed (postnatal day 0, 12-week)


title: MUTEv5#2_rep1

description:
AthMUTEv5.2.1
S4_G1
G1rep1bis


title: EVTd3_H3K27ac_Ctrl_rep1


title: RPE_iCut_ABCB1_cr6_ATRi_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_43_pA-DamID_ABCB1_cr6_ATRi_10h_R2_CCGAAGTA_S53_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: WT3_MuSCs_IgG_CutRun

city: Montreal

first: Vahab

middle: D.

last: Soleimani

state: Quebec

address: 3755 Chem. de la Côte-Sainte-Catherine

department: Lady Davis Institute for Medical Research

country: Canada

institute: Jewish General Hospital

description: Library name: MuSCsWT3IgG_SOL2381A4-1

data_processing:
Illumina BaseSpace software was used for basecalling.
Data was analysed using the GenPipes pipeline v.3.1.5 (https://academic.oup.com/gigascience/article/8/6/giz037/5513895)
Peaks were called using MACS2(v2.1.1)
Assembly: mm10
Supplementary files format and content: The bigWig files are normalized genome-wide signal coverage tracks used for visual inspection of the peaks and comparison between conditions
Library strategy: Cut&Run

source_name: skeletal muscle/ muscle stem cells

extract_protocol:
45 000 Muscle stem cells (ITGA7+/VCAM1+/CD11b-/CD45-/CD31-/Ly6a-) were isolated by Fluorescence Activated Cell Sorting (FACS) into 2%FBS in PBS for the Cut&Run on freshly isolated cells. For the Cut&Run of REST, cells were first  isolated by FACS and cultured in growth media for 1 week and then 100 000K cells were obtained to perform Cut&Run.
Cut&Run of H3K27me3 on MuSCS and Cut&Run of REST  on myoblasts were performed using the commercially available Cut&Run Kit (Epicypher, 14-1048) according to the manufacturer’s guidelines. Libraries were prepared using the Cut&Run Library Prep Kit (Epicypher, 14-1001) according to the manufacturer’s guidelines.

value: skeletal muscle/ muscle stem cells


title: RPE_iCut_ABCB1_cr6_ATRi_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_18_pA-DamID_ABCB1_cr6_ATRi_10h_R1_Dam_ACTATGCA_S44_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: 4wk R62 Rep 1 FLEX single nuclei-RNA-seq

description:
Library name: 1-6_4wk_R62
10x Genomics FLEX BC001, 3-5, 4-week-NT


title: RPE_iCut_ABCB1_cr6_ATRi_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_44_pA-DamID_ABCB1_cr6_ATRi_10h_R2_Dam_GCCACATA_S65_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ABCB1_cr6_M3814_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_19_pA-DamID_ABCB1_cr6_M3814_10h_R1_CATCAAGT_S45_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: 12wk NT Rep 1, 12wk R62 Rep 1, 12wk NT Rep 2, 4wk R62 Rep 2 Mixed FLEX single nuclei-RNA-seq

description:
Library name: 4-4_12wk_NT_1b-5_12wk_R62_3b-1_12wk_NT_1-1_4wk_R62
10x Genomics FLEX BC001, 4-4, 12week-NT BC002, 1b-5, 12week-HD BC003, 3b-1, 12week-NT BC004, 1-1, 4week-HD


title: EVTd3_EP300_T007_rep2

description: Chromatin IP against EP300 under treatment with 1 µM T0070907 from EVT day 1 to day 3.


title: RPE_iCut_ABCB1_cr6_M3814_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_45_pA-DamID_ABCB1_cr6_M3814_10h_R2_CCGTGAGA_S57_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: WT7_myob_REST_IgG_CutRun

description: Library name: MyoblastsWT7IgG_SOL2381A12-1

treatment_protocol: Cut&Run of H3K27me3 on MuSCS and Cut&Run of REST  on myoblasts were performed using the commercially available Cut&Run Kit (Epicypher, 14-1048) according to the manufacturer’s guidelines. Libraries were prepared using the Cut&Run Library Prep Kit (Epicypher, 14-1001) according to the manufacturer’s guidelines.


title: EVTd3_EP300_T007_rep1


title: RPE_iCut_ABCB1_cr6_M3814_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_46_pA-DamID_ABCB1_cr6_M3814_10h_R2_Dam_GCGAGTAA_S66_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: WT6_myob_REST_CutRun

description: Library name: MyoblastsWT6REST_SOL2381A11-1


title: RPE_iCut_ABCB1_cr6_M3814_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_20_pA-DamID_ABCB1_cr6_M3814_10h_R1_Dam_AGAGTCAA_S46_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: EVTd3_EP300_Ctrl_rep2

description: Chromatin IP against EP300 under control conditions at EVT day 3.


title: RPE_iCut_ABCB1_cr6_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_5_pA-DamID_ABCB1_cr6_10h_R1_ACCACTGT_S28_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: DMSO


title: RPE_iCut_ABCB1_cr6_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_31_pA-DamID_ABCB1_cr6_10h_R2_CAACCACA_S29_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: WT5_myob_REST_CutRun

description: Library name: MyoblastsWT5REST_SOL2381A10-1


title: RPE_iCut_ABCB1_cr6_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_32_pA-DamID_ABCB1_cr6_10h_R2_Dam_CTGAGCCA_S56_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: EVTd3_EP300_Ctrl_rep1


title: RPE_iCut_ABCB1_cr6_ATMi_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_41_pA-DamID_ABCB1_cr6_ATMi_10h_R2_CCAGTTCA_S63_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ABCB1_cr6_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_6_pA-DamID_ABCB1_cr6_10h_R1_Dam_AAGGTACA_S26_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X253,Resistant_Vehicle

city: San Francisco

first: Alex

middle: G

last: Lee

address: 1550 4th Street

institute: UCSF

data_processing:
Processed reads were mapped to the human reference genome (hg38) using the STAR aligner (v2.5.1b). Gene-level expression was quantified using STAR's 'quantMode' feature with GENCODE p5 annotations.  Aligned reads were normalized using the trimmed mean of M-values (TMM) method (EdgeR v3.24.3), and counts were log2(cpm + 1) transformed
Assembly: hg38
Supplementary files format and content: tab delimited

growth_protocol: Cells were grown in the flanks of NSG mice.

extract_protocol:
RNA was extracted using RNRasy spin columns (Qiagen).
Libraries were created using stranded mRNA Prep kits (Illumina), validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen,Carlsbad, CA).

treatment_protocol: CB-5083 or vehicle were administered by oral gavage 24 hours prior to euthanasia and extraction of xenograft tissue.

value: fusion positive rhabdomyosarcoma

value: PAX7-FOXO1 positive

value: 0.5% methylcellulose by oral gavage


title: WT4_MuSCs-K27me3

description: Library name: MuSCsWT4H3K27me3_SOL2381A3-1


title: RPE_iCut_ABCB1_cr6_ATMi_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_15_pA-DamID_ABCB1_cr6_ATMi_10h_R1_CTGTAGCC_S35_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ABCB1_cr6_ATMi_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_16_pA-DamID_ABCB1_cr6_ATMi_10h_R1_Dam_ACGTATCA_S42_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X234,Resistant_CB_5083

value: CB-5083 50 mg/kg in 0.5% methylcellulose by oral gavage


title: WT2_MuSCs-K27me3

description: Library name: MuSCsWT2H3K27me3_SOL2381A2-1


title: X233,Resistant_CB_5083


title: X232,Resistant_CB_5083


title: RPE_iCut_ABCB1_cr6_24h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_34_pA-DamID_ABCB1_cr6_24h_R2_Dam_CTGGCATA_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ABCB1_cr6_24h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_7_pA-DamID_ABCB1_cr6_24h_R1_AACGTGAT_S31_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: Gpx4 KO-Mist1+ organoids, P5

description: GM

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed
properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: GRCm38.p5
Supplementary files format and content: xls file includes RPKM values for each Sample.

growth_protocol: Organoids were suspended with 50 μl Matrigel and maintained in proliferating medium at 37 °C with 5% CO2 in a humidified incubator.

extract_protocol:
Total mRNA was extracted using TRIZOL Reagent following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Stomach

value: Gpx4 KO Mist1+ derived organoid

value: Gastric epithelia

value: Gpx4 KO

value: Organoid proliferative culture


title: RPE_iCut_pool9tracr_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6642_33_pA-DamID_tracr_10h_R2_AGTCACTA_S34_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X231,Resistant_Vehicle


title: Mist1+ organoids, P5

description: M-plus

value: Mist1+ derived organoid

value: WT


title: RPE_iCut_pool9tracr_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6642_34_pA-DamID_tracr_10h_R2_Dam_CCAGTTCA_S35_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X230,Resistant_Vehicle


title: RPE_iCut_pool9tracr_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6642_15_pA-DamID_tracr_10h_R1_CTGTAGCC_S17_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_pool9tracr_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6642_16_pA-DamID_tracr_10h_R1_Dam_ACACAGAA_S25_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: Mist1- organoids, P5

description: M-minus

value: Mist1- derived organoid


title: WT4_myob_REST_CutRun

description: Library name: MyoblastsWT4REST_SOL2381A9-1


title: RPE_iCut_ABCB1_cr6_ATMi_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_42_pA-DamID_ABCB1_cr6_ATMi_10h_R2_Dam_GATAGACA_S62_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: hTERT-immortalized retinal pigment epithelial


title: RPE_iCut_pool9_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_40_pA-DamID_pool9_10h_R2_Dam_GAGCTGAA_S47_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: wildtype


title: X218,Sensitive_CB_5083

value: PAX3-FOXO1 positive


title: RPE_iCut_pool9_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_14_pA-DamID_pool9_10h_R1_Dam_ACGCTCGA_S39_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_pool9_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_13_pA-DamID_pool9_10h_R1_ATGCCTAA_S38_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X217,Sensitive_CB_5083


title: Forebrain MR Knockout3

city: Research Triangle Park

first: Serena

middle: M

last: Dudek

state: NC

address: 111 TW Alexander Dr.

department: Neurobiology

institute: NIEHS

data_processing:
Raw reads were processed by SpaceRanger with default setting.
Assembly: mm10
Supplementary files format and content: The filtered feature count matrix was generated from SpaceRanger.
Library strategy: Spatial transcriptome

source_name: mouse brain with forebrain Nr3c2 conditional deletion

extract_protocol:
The frozen sections of mouse mouse brain were placed on 10X genomics Visium spatial transcriptomics slides
RNA libraries were prepared according to the Visium spatial transcriptomic slide manual

value: brain

value: Emx1-Cre positive:MR fl/fl


title: Forebrain MR Knockout2


title: X216,Sensitive_CB_5083

value: fusion positive rhabdomyosarcoma


title: RPE_iCut_tracr_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_28_pA-DamID_tracr_10h_R2_Dam_CGCATACA_S22_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X215,Sensitive_Vehicle


title: RPE_iCut_tracr_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_2_pA-DamID_tracr_10h_R1_Dam_AACGCTTA_S24_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: Forebrain MR Knockout1


title: Forebrain MR Wildtype3

source_name: control mouse brain


title: RPE_iCut_ADAM22_cr3_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_35_pA-DamID_ADAM22_cr3_10h_R2_CACTTCGA_S60_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X214,Sensitive_Vehicle


title: RPE_iCut_pool9_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_39_pA-DamID_pool9_10h_R2_CATACCAA_S64_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ADAM22_cr3_10h_LaminB2_R1-gatc.counts.txt.gz

description:
Library name: 6604_9_pA-DamID_ADAM22_cr3_10h_R1_CGCTGATC_S33_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: X213,Sensitive_Vehicle


title: RPE_iCut_tracr_10h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_27_pA-DamID_tracr_10h_R2_ATCCTGTA_S20_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: Translating RNA-seq, rep4,read1

city: Austin

first: Can

last: Cenik

state: Texas

address: 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas

description: Library name: AR_4_POLY_RNA

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy
We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboFlow
Assembly: Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: Ribo file

molecule: cytoplasmic RNA

growth_protocol: HEK293T cell lines were obtained from ATCC. HEK293T cell lines were maintained in Dulbecco's modified Eagle's media (DMEM, GIBCO) supplemented with 10% Fetal Bovine Serum (FBS, GeminiBio) and 1% Penicillin and Streptomycin (GIBCO, Life Technologies) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Four replicates of ~8 X10^6 HEK293T cells were plated in 150 cm2 plates. After ~18 h, cells were washed and then scraped with ice cold PBS, followed by centrifugation at 300 g for 5 min. 600 ul Lysis buffer (20 mM Tris, 150 mM NaCl, 5 mM MgCl2, 1mM DTT, Triton and 100 ug/ml of cycloheximide) was added to the cell pellet followed by incubation on ice for 10 min and the lysate was clarified by centrifugation at 1300g for 10 min at 4Â°C. The cleared lysate (50 ul) was directly used for total RNA extraction by adding 700 ul of Trizol (Zymo). 200 ul of the lysate along with 20 ul of the Ribonucleoside Vanadyl Complex was layered on the 1M sucrose cushion and subjected to ultracentrifugation at 38000 rpm for 2.5 h at 4°C. The remaining 350 ul was used for ribosome profiling. The pellet was dislodged in 700 ul of Qiazol and stored -80 °C until use the next day.
Total RNA and translating RNA was extracted using Zymo RNA miniprep kit as per manufacturer's protocol (Zymo). The concentration was estimated using nanodrop and the integrity of the extracted RNA was determined by 2100 Bioanalyzer (RNA 6000 Pico Kit, Agilent). 1μg of the extracted RNA was used for Poly A selection using NEBNext poly(A) mRNA magnetic isolation kit (NEB, E7490S). This was followed by library preparation using NEBNext Ultra II RNA library prep kit for Illumina (NEB, E7770S) as per the manufacturer's protocol using 7 PCR cycles. The quality and concentration of the libraries formed were determined by Bioanlyzer (High sensitivity DNA assay kit, Agilent). Equimolar amounts of the libraries were pooled and sequencing was done using NovaSeqx Plus (2X150 paired end).
For ribosome profiling, RNA was isolated using miRNeasy Mini kit and size-selected by running 1 µg of each sample in a 15% polyacrylamide TBE-UREA gel. 26–34 nt RNA fragments were excised, RNA fragments were extracted and precipitated. Ribosome profiling libraries were prepared using the D-Plex Small RNA-Seq Kit (Diagenode) as previously described. The cDNA was amplified for eleven cycles. Each library was cleaned with AMPure XP beads and eluted with 30 μL of RNase-free water. To completely remove the primer-dimers, size-selection was done using a 12 % polyacrylamide gel followed by excision of the fragment (~200bp). The DNA was extracted by overnight incubation in a buffer (10 mM magnesium acetate tetrahydrate, 0.5 M ammonium acetate, 1 mM EDTA (pH 8.0) at room temperature followed by ethanol precipitation (-20 °C, overnight) to recover the size selected libraries. The resulting libraries were analyzed with the Agilent High Sensitivity DNA Kit (Agilent). Each library was mixed in equimolar proportion for sequencing with the NovaSeqx Plus (2X150 paired end).

treatment_protocol: To validate translational buffering, we attempted to generate a series of knockdowns of buffered genes using the MultiCas12a approach. Briefly, we synthesized a three 10-plex cRNA array targeting 8 buffered and 2 non-buffered genes as double stranded gene fragments (Twist Biosciences). The arrays differed in the gRNA efficiency of their target. A fourth crRNA array targeted the intergenic region to be used as a negative control. Overall, four 10-plex crRNA were cloned in pCH67 into the Bsmb1 cloning site (Addgene, 217667) using NEBuilder HiFi DNA Assembly Master Mix (NEB, E2621). Lentivirus was generated with the cloned pCH67 or pCH45 (multiAsCas12a-KRAB, Agdgene, 217330) along with psPAX2 (Addgene, 12260)and pMD2.G (Addgene ,2259) using lipofectamine 3000 (Invitrogen) as per manufacturer's protocol.The lentivirus was used to infect HEK293T cells followed by selection using puromycin. Following selection, BFP positive cells were sorted using FACS to select for cells that express MultiCas12a. HEK293T cells were then continued to grow for 24 hours followed by plating in 150 cm2 plates to perform ribosome profiling, with matched total and translating RNA sequencing. However the knockdown efficiency was low with this approach,

value: Human embryonic kidney

value: Control

value: CRISPR KD


title: parental_cells_EB_snRNA-seq

city: Chicago

first: De

last: Xing

state: IL

address: 264 E Huron St., Suite: 4-121

department: Feinberg School of Medicine, Obstetrics and Gynecology

institute: Northwestern University

description:
Library name: iPSC_EB_snRNA-seq
10X Genomics

data_processing:
FASTQ files were demultiplexed using 10X Genomics' Cellranger
FASTQ files were aligned to GRCh38 using 10X Genomics' Cellranger-arc v. 2.0.2 using default settings
Assembly: GRCh38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

molecule: nuclear RNA

source_name: iPSC

growth_protocol: EBs were formatted and maintained with the STEMCELL Aggrewell400 protocol with modification. The Aggrewell 400 24-well plate (Fisher Scientific, 34450) was coated with anti-adherence rinsing solution (STEMCELL Technologies, 07010). Then the CAG-OsTIR1, EF1a-OsTIR1 and EF1α-ATAFB2 parental cell lines were dissociated with Accutase, mixed equally and seeded into the coated Aggrewell 400 24-well plate at 1.2 x 10^6 per well (1000 cells per microwell) in Aggrewell EB Formation Medium (STEMCELL Technologies, 05893). Half of the media was replaced with fresh Aggrewell EB Formation Medium after 24 h. At 48 h after seeding, EBs were harvested and moved to ultra-low attachment six-well plates in Essential 6™ (E6) Medium (Thermo Scientific, A1516401). EBs were maintained in culture for 19 days by replenishing with fresh E6 media every other day. EBs were collected and dissociated at day 21.

extract_protocol:
The collected EBS were washed with DPBS once, then treated with Accutase and incubated at 37 °C. After 10 min, EBs in Accutase were dissociated by pipetting with P1000 tip for 30 s every 5 min until EBs were completely dissociated. E6 media was added to terminate the dissociation, and cells were filtered through a 40 μM strainer (Fisher Scientific, 08-771-1) before counting. Dissociated cells from the EBs were used for scRNA-seq library preparation with a targeted collection of 1 x 10^4 cells.
Single-cell 3' RNA-seq libraries were generated with 10x Genomics Chromium Next GEM Single Cell 3' Reagent Kit v.3 following the manufacturer's guidelines. Briefly, cells were resuspended in the master mix and loaded together with partitiioning oil and gel beads to generate GEM. The poly-A RNA in every single GEM was retrotranscripted to cDNA, followed by  barcoding, cleanup and library pre-amplification PCR.

value: iPSC


title: Forebrain MR Wildtype1

value: Emx1-Cre negative:MR fl/fl


title: RPE_iCut_ADAM22_cr3_10h_Dam_R2-gatc.counts.txt.gz

description:
Library name: 6604_36_pA-DamID_ADAM22_cr3_10h_R2_Dam_GAATCTGA_S59_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: RPE_iCut_ADAM22_cr3_10h_Dam_R1-gatc.counts.txt.gz

description:
Library name: 6604_10_pA-DamID_ADAM22_cr3_10h_R1_Dam_ACAGCAGA_S30_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"


title: Translating RNA-seq, rep2,read1

description: Library name: AR_2_POLY_RNA

value: knowkdown


title: 1063_2

city: Boston

first: Jiekun

last: Yang

address: 32 Vassar Street

institute: MIT

description:
Mucosal Sample 2
10x Genomics

data_processing:
We received the sequences, mapped the reads against the GRCh38 human reference genome, and quantified the read counts using Cell Ranger pipeline version 3.1.0 (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Metastatic melanoma

extract_protocol:
We enzymatically digested and dissociated fresh tumor samples according to tissue dissociation kit protocols using the gentleMACS™ Dissociator (Miltenyi). Dissociated tissues were filtered, centrifuged, and the isolated cells were resuspended in 0.1% BSA in PBS.
Briefly, 5000-6000 cells were profiled per sample using the Chromium Single Cell 3’ RNA reagent kit v3 according to the 10X Genomics protocol. The generated cDNA libraries were indexed, pooled, and sequenced in batches.

value: Metastatic melanoma


title: 1063_3

description:
Mucosal Sample 3
10x Genomics


title: Translating RNA-seq, rep1,read1

description: Library name: AR_1_POLY_RNA


title: UT IGG Rep2

city: New York City

first: Justin

last: Perry

state: New York

address: 1275 York Avenue

department: Immunology Program

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Samples were processed using a nextflow-based pipeline available athttps://github.com/michaelbale/jlabflow.
Reads were trimmed using the Cutadapt wrapper trim-galore and mapped to mm10 with bowtie2 using --very-sensitive-localwith a maximum insert size of 1000bp. Theinitial bam file was then filtered for a minimum MAPQ of 30. Mitochondrial mapped reads, PCR duplicates, reads mapped within regions of a unified forbidden list from encode
TMM-normalized signal tracks were visualized using deep tools bamCoverage with a calculated scaleFactor derived from the edgeR packagecalcNormFactors.
Assembly: mm39
Supplementary files format and content: bigwig
Library strategy: CuT&Run

source_name: Bone Marrow Derived Macrophage

extract_protocol:
CUT&RUN was performed using the EpiCypher CUTANTA ChIC/CUT&RUN kit according to the manufacturer’s protocol. 5x10^6 cells per replicate were harvested for untreated and butyrate treated bone marrow derived macrophages, washed with 1X PBS, and resuspended in wash buffer. After an incubation for 10 minutes with activated Concanavalin A beads, cells were permeabilized and incubated overnight with rabbit IgG (Antibodies Online ABIN101961), or H3K27ac (Cell Signaling Technology 8173S). Cells were then washed with permeabilization buffer and incubated with pA/G-MNase (EpiCypher) followed by addition of 2mM CaCl2 and incubation for 2 hours at 4C. Stop buffer was added, and fragments were purified using the CUTANA DNA Purification Kit (Epicypher). Library preparation was done utilizing Kapa Hyperprep Kit (Roche KK8504). Libraries were sequenced on Illumina NovaSeq6000 (50 bp paired end) at Weill Cornell Medicine.
Library preparation was done utilizing Kapa Hyperprep Kit (Roche KK8504).

value: Bone Marrow Derived Macrophage


title: Total RNA-seq, rep4,read1

description: Library name: AR_4_T_RNA


title: UT IGG Rep1


title: H3K4me1-H2WT-Rep2__PXU008

city: Suzhou

first: Peng

last: Xu

state: Jiangsu

address: Office3625 Building703, RENAI ROAD No.199, INDUSTRIAL PARK DISTRICT

department: Suzhou Medical College

institute: Soochow University

description: Library name: sample 10

data_processing:
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files. We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Assembly: hg19
Supplementary files format and content: bigwig

source_name: Human bone marrow

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: Human bone marrow

value: erythroblast cells

value: WILD TYPE

value: H3K4me1(Abcam, ab8895)


title: H3K4me1-H2WT-Rep1__RFC944

description: Library name: sample 9


title: H3K4me1-H2F11KO7-Rep2__PXU010

description: Library name: sample 8

value: FBXO11 knockout


title: But IGG Rep3

value: Butyrate


title: 1098_2

description:
Sample 37
10x Genomics


title: Total RNA-seq, rep3,read1

description: Library name: AR_3_T_RNA


title: 406_2

description:
Sample 36
10x Genomics


title: UT IGG Rep3


title: H3K4me1-H2F11KO7-Rep1__RFC945

description: Library name: sample 7


title: But IGG Rep2


title: 1224_2

description:
Sample 35
10x Genomics


title: Total RNA-seq, rep2,read1

description: Library name: AR_2_T_RNA


title: But IGG Rep1


title: RPE_iCut_ABCB1_cr6_24h_LaminB2_R2-gatc.counts.txt.gz

description:
Library name: 6604_33_pA-DamID_ABCB1_cr6_24h_R2_CAAGACTA_S54_R1_001_library
pA-DamID sample from manuscript "Megabase-scale detachment of genome-nuclear lamina interactions is required for efficient repair of double stranded breaks"

value: hTERT-immortalized retinal pigment epithelial

value: wildtype


title: 620_2

description:
Sample 39
10x Genomics


title: UT K27ac Rep3


title: 1224_1

description:
Sample 34
10x Genomics


title: Ribosome profiling, rep4,read1

description: Library name: AR_4_RPF

data_processing:
Ribosome profiling data were processed using RiboFlow. We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step. We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”. For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboPy
We extracted the first 12 nucleotides from the 5’ end of the reads using UMI-tools with the following parameters: 'umi_tools extract -p "^(?P<umi_1>.{12})(?P<discard_1>.{4}).+$" --extract-method=regex'. The four nucleotides downstream of the UMIs are discarded as they are incorporated during the reverse transcription step.
We clipped the 3’ adapter AAAAAAAAAACAAAAAAAAAA using cutadapt with the parameters “-a AAAAAAAAAACAAAAAAAAAA --overlap=4 --trimmed-only --maximum-length=56 --minimum-length=31 --quality-cutoff=28”.
For RNA-seq  we clipped the 3’ adapter AGATCGGAAGAGCACACGTCTGAACTCCAGTCA using the  cutadapt with the parameters “-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA --quality-cutoff=28' After UMI extraction and adapter trimming, reads were aligned to ribosomal and transfer RNAs using Bowtie2 with the parameters "-L 15 --no-unal --norc". The unaligned reads were mapped to a manually-curated transcriptome with the parameters "-L 15 --norc --no-unal". We retained alignments with mapping quality greater than 2 followed by deduplication using UMI-tools. As the last step, .ribo files are created using RiboFlow
Assembly: Assembly: A curated transcriptome of primary transcripts was used for alignment. Reference files for use with RiboFlow are located at https://github.com/ribosomeprofiling/references_for_riboflow
Supplementary files format and content: Ribo file
Library strategy: Ribo-Seq


title: H3K27ac-H2WT-Rep2__PXU001

description: Library name: sample 5

value: H3K27ac(Abcam, ab4729)


title: 1098_1

description:
Sample 33
10x Genomics


title: UT K27ac Rep2


title: H3K27ac-H2WT-Rep1__PXU008

description: Library name: sample 4


title: Ribosome profiling, rep3,read1

description: Library name: AR_3_RPF

value: Human embryonic kidney


title: H3K27ac-H2F11KO7-Rep3__RFC960

description: Library name: sample 3


title: Ribosome profiling, rep2,read1

description: Library name: AR_2_RPF


title: 880_1

description:
Sample 31
10x Genomics


title: But K27ac Rep3


title: Ribosome profiling, rep1,read1

description: Library name: AR_1_RPF


title: H3K27ac-H2F11KO7-Rep2__PXU013

description: Library name: sample 2


title: H3K27ac-H2F11KO7-Rep1__PXU009

description: Library name: sample 1


title: 1122_1

description:
Sample 30
10x Genomics


title: T47D, PRB, 3D, R5020 treated, rep3

city: Minneapolis

first: Noelle

middle: E

last: Gillis

state: Minnesota

address: 2231 6th ST SE, CCRB

institute: University of Minnesota

description: Library name: PRB_3D_R50_rep3

data_processing:
Illumina adapters were removed using Trim-Galore.
For alignment and transcript assembly, the sequencing reads were mapped to hg38 using STAR.
Sorted reads were counted using HTSeq.
Normalization and differential expression analysis was performed using DESeq2
Assembly: hg38
Supplementary files format and content: tab delimited text files containing count data for each sample

source_name: ER+ breast cancer

growth_protocol: T47D cells were cultured in MEM 10 (Corning,) containing 5% FBS (Corning), 1% penicillin streptomycin (Gibco), nonessential amino acids (Gibco), and 6 ng/mL of insulin (Gibco). To make PR isoform-specific models, T47D (Y; naturally occurring PR-null variant) cells were transduced with lentiviral pLenti CMV Neo containing PR-A WT, PR-A S294A, PR-B WT, or PR-B S294A cDNA. Cells were selected and maintained with 0.5 mg/ml G418 (Corning).

extract_protocol:
1 ug of total RNA was extracted and purified using RNeasy Plus Kit (Qiagen) according to manufacturer’s protocol.
Libraries were built from individual samples with the TruSeq Stranded mRNA kit (Illumina). RNA-Seq libraries were pooled and sequenced on the Illumina NovaSeq X Plus with 50 bp paired-end reads

treatment_protocol: For experiments with R5020 (PerkinElmer) treatment, cells were hormone-starved in phenol red-free MEM (Gibco) containing 5% dextran-coated charcoal-stripped FBS (HyClone), 1% penicillin streptomycin (Gibco), nonessential amino acids (Gibco), and 6 ng/mL of insulin (Gibco) for 24 hours prior to addition of 10 nM R5020.

value: ER+ breast cancer

tag: pr isoform_expression

value: B

tag: growth condition


title: Total RNA-seq, rep1,read1

description: Library name: AR_1_T_RNA

value: CRISPR KD


title: 1098_3

description:
Sample 29
10x Genomics


title: sputum, asthma, rep 24

city: New Haven

first: Xiting

last: Yan

state: Connecticut

address: 300 Cedar Street, Ste S441D

department: Internal Medicine

institute: Yale School of Medicine

description:
genexSC-24
10x Genomics Chromium 3' V2

data_processing:
The demultiplexed, barcoded processing, gene counting and aggregation were made using the Cell Ranger pipeline V3.1.
Assembly: GRCh38
Supplementary files format and content: seurat object V5

source_name: sputum

extract_protocol:
Fresh sputum samples with viability >70% was prepared by suspending the cell pellet (~1 x 10^6) in 1ml PBS and processed using the Chromium V2 chips and protocol from 10X Genomics for RNA Seq. Some of the samples were preserved using DMSO and thawed before processing using the protocol.
Library was constructed according to the manufacter's instructions (single cell 3' V2 protocol, 10x Genomics).

value: sputum

value: primary cells

value: immune cells and bronchial epithelial cells

tag: condition

value: asthma


title: T47D, PRB, 3D, R5020 treated, rep2

description: Library name: PRB_3D_R50_rep2


title: 1138_1

description:
Sample 28
10x Genomics

value: Metastatic melanoma


title: 808_1

description:
Sample 32
10x Genomics


title: UT K27ac Rep1

value: Bone Marrow Derived Macrophage


title: sputum, asthma, rep 23

description:
genexSC-23
10x Genomics Chromium 3' V2


title: 620_1

description:
Sample 27
10x Genomics


title: T47D, PRB, 3D, R5020 treated, rep1

description: Library name: PRB_3D_R50_rep1


title: MB49 cells, WT, treat DMSO 2

city: chiayi

first: Michael

middle: W Y

last: Chan

state: chiayi

address: No. 168, Section 1, Daxue Road, Minxiong Township

department: Dept of Biomedical sciences

country: Taiwan

institute: National Chung Cheng University

data_processing:
bases with low quality and sequences from adapters in raw data were removed using program fastp (version 0.20.0)
The filtered reads were aligned to the reference genomes using HISAT2 (version 2.1.0)
The software FeatureCounts (v2.0.1) in Subread package was applied for the quantification of the gene abundance
Differentially expressed genes (DEGs) were identified by DESeq2 (version 1.28.0) [4] or EdgeR (version 3.36.0)
Assembly: Mus_musculus.GRCm38.99
Supplementary files format and content: Excel file format is in tsv format and includes TPM values and counts
Supplementary files format and content: Excel includes TPM values, fold change values, T test values for each sample

source_name: Bladder cancer cell

growth_protocol: MB49 cells were maintained in RPMI-1640 (GIBCO, Cat. no.31800) supplemented with 10% Fetal Bovine Serum(FBS), HEPES, L-glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was extracted using Rneasy mini kit (cat no.74104 and 74106) and 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA)
RNA Libraries were sequenced on an Illumina NovaSeq 6000 platform

treatment_protocol: MB49 cells were treated with cyproheptadine supplemented in RPMI media for 48hrs. 0.1% DMSO containing media was treated as control.

value: Bladder cancer cell

value: Urothelial carcinoma cell

value: WT

value: treat DMSO


title: sputum, asthma, rep 22

description:
genexSC-22
10x Genomics Chromium 3' V2


title: MB49 cells, WT, treat DMSO 1


title: 1063_1

description:
Sample 26 (Mucosal Sample 1)
10x Genomics


title: But K27ac Rep2

value: Butyrate


title: MB49 cells, WT, treat cyproheptadine 2

value: treat Cyproheptadine


title: But K27ac Rep1


title: sputum, asthma, rep 21

description:
genexSC-21
10x Genomics Chromium 3' V2


title: 406_4

description:
Sample 25
10x Genomics


title: MB49 cells, WT, treat cyproheptadine 1


title: T47D, PRB, 3D, vehicle treated, rep2

description: Library name: PRB_3D_veh_rep2

value: vehicle


title: T47D, PRB, 3D, vehicle treated, rep1

description: Library name: PRB_3D_veh_rep1


title: 964_1

description:
Sample 24
10x Genomics


title: sputum, asthma, rep 20

description:
genexSC-20
10x Genomics Chromium 3' V2


title: RAW264.7 cells, Sync-label Enrich, LPS, rep3

city: Beijing

first: Qidong

last: Deng

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_LPS_3

data_processing:
Raw reads were trimmed with Trim Galore!(v0.6.7) to remove low-quality bases and adapters and subsequently aligned to the Homo sapiens genome (Ensembl GRCh38.107) or Mus musculus (GRCm38.98) by HISAT2 (v2.2.1) with with ‘-rna-strandness RF’ parameters. After the low-quality reads were filtered out by SAMtools (v1.9), fragments mapped on the exons were processed using featureCounts (v2.0.2) to obtain the gene expression matrix. The R/Bioconductor package DESeq2 (v1.36.0) was used for data normalization and differential expression analysis.
Assembly: hg38, mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: wildtype RAW264.7 cells with Sync-label and LPS treatment

growth_protocol: HeLa and RAW264.7 cell lines were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum and 1% penicillin/ streptomycin at 37°C under 5% CO2.

extract_protocol:
Cells grown in cell culture dishes at ~90% confluency were incubated with 50 nM photocatalyst in fresh medium at 37°C under 5% CO2 for 30 min, washed with PBS for three times, incubated with 50 µM QMPAB-2 in culture medium for 30 min and washed twice with PBS. After washing, cells were maintained in fresh medium at 37°C under 5% CO2 for 5 min and illuminated with blue LED (4 mW cm-2; λmax ∼460 nm) for 15 min at room temperature. Cells were placed about 5 cm from the light source. After illumination, cells were immediately collected using cell scraper and lysed with TRIzol reagent. Cellular total RNA purification was operated following the manufacture protocol by isopropanol precipitation.Total RNA was extracted using TRIzol reagent(Invitrogen).
RNA libraries were prepared using SMARTer Stranded Total RNA-Seq Kit v2(Takara). Labeled RNA was captured using Dynabeads MyOne Streptavidin C1 (Invitrogen).

value: macrophage

value: Sync-label+,LPS+


title: sputum, asthma, rep 19

description:
genexSC-19
10x Genomics Chromium 3' V2


title: 98_1

description:
Sample 23
10x Genomics


title: T47D, PRA, 3D, R5020 treated, rep2

description: Library name: PRA_3D_R50_rep2

value: ER+ breast cancer

value: A


title: sputum, asthma, rep 18

description:
genexSC-18
10x Genomics Chromium 3' V2

value: sputum


title: RAW264.7 cells, Sync-label Enrich, LPS, rep2

description:
5_RAW_Sync_label_LPS_VS_Blank_DESeq2_DEG.csv
RAW264.7_Sync-label_LPS_and_Blank_Reads_Count.txt
RAW_Sync_LPS_2


title: 978_1

description:
Sample 22
10x Genomics


title: sputum, control, rep 17

description:
genexSC-17
10x Genomics Chromium 3' V2

value: primary cells

value: control


title: 479_1

description:
Sample 20
10x Genomics


title: T47D, PRA, 3D, R5020 treated, rep1

description: Library name: PRA_3D_R50_rep1


title: T47D, PRB, 3D, vehicle treated, rep3

description: Library name: PRB_3D_veh_rep3

value: B