title: Saline_4


title: GC080713_A03

status: Public on May 06 2022

type: SRA

city: Leuven

first: Maarten

last: Naesens

address: Herestraat 49

department: Department of Microbiology, Immunology and Transplantation

country: Belgium

institute: KU Leuven

library_source: transcriptomic

data_processing:
Single-end sequencing was performed using an Illumina HiSeq 4000 device
After adapter removal, 50bp-long raw reads were aligned to the reference genome hg38 using splice-aware aligner HISAT2
Absolute gene counts were generated using HTSeq based on the Ensemble83 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood

extract_protocol:
After collection, the blood samples were stored in PAXgene tubes at ambient temperature for at least 24 hours, and then stored at -80°C until extraction. Total RNA was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH).
Library preparation was done using the Lexogen QuantSeq mRNA kit according to the manufacturer’s instructions

tag: ar

tag: abmrh

tag: tcmr

tag: polyoma (no

tag: dsa


title: GC080712_B04


title: Saline_2

city: Singapore

first: Eleonora

last: Adami

address: 8 College Road

department: CVMD

country: Singapore

institute: Duke-NUS Medical School

description:
Whole Lung 3wks Saline treatment (Mouse)
counts_mouse_ab

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 or mouse genome mm10 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 92 and Mus musculus mm10 Ensembl release 86
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

molecule: polyA RNA

organism: Mus musculus

source_name: Lung

growth_protocol: see above

extract_protocol:
Total RNA was extracted from either the snap-frozen liver tissues or HSCs lysate using Trizol (Invitrogen) followed by RNeasy column (Qiagen) purification.
Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol:
Whole lung tissue lysate of mice treated with vehicle
see above

tag: strain

tag: genotype

value: WT

tag: treatment

value: Saline

tag: rin


title: GC080712_B02


title: Saline_1


title: X203_2

description:
Whole Lung 3wks BLM_X203 treatment (Mouse)
counts_mouse_ab

treatment_protocol:
Whole lung tissue lysate of mice treated with bleomycin and injected with X203 antibody
see above


title: X203_3


title: GC080712_B01


title: GC080712_A02


title: IgG_4

description:
Whole Lung 3wks BLM_IgG treatment (Mouse)
counts_mouse_ab

treatment_protocol:
Whole lung tissue lysate of mice treated with bleomycin and injected with IgG control antibody
see above


title: X203_4


title: GC080712_A06


title: GC080712_A05


title: X203_1


title: GC080712_B06


title: GC080712_A03


title: IgG_2


title: IgG_1


title: GC080712_A01


title: GC080712_B03


title: GC080711_H06


title: GC080712_B05


title: GC080711_H04


title: GC080711_H03


title: Injured heart Hr26 - scar

city: Berlin

first: Bo

last: Hu

address: Robert-Rössle-Straße 10

department: Berlin Institute for Medical Systems Biology

country: Germany

institute: Max-Delbueck-Center Berlin

description: scar sequences for lineage tracing

data_processing:
Demultiplexing of the illumina sequencing results using cellranger 3.0.2
Mapping using cellranger 3.0.2
Filtering, Normalizing and Clustering using seurat 3.0
Scar processing steps see Spanjaard et al. (2018, Nature Biotechnology), Briefly, scar sequences were aligned using bwa mem3 to a reference of dTomato. Valid cell barcodes were identified based on the single-cell transcriptome data (see previous paragraph). We removed reads that were unmapped, had an incorrect barcode, or did not start with the exact PCR primer we used. We truncated all scar sequences to 75 nucleotides and removed shorter sequences. In further filtering steps, we consecutively filtered out scars in order to remove all scars that did not fulfill the following quality control conditions. As a first step, we required all molecules to be sequenced at least twice to remove straightforward sequencing errors; this also reduces complexity for the subsequent filtering steps. To remove molecules caused by incorrect annealing, we selected only the most prevalent scar for each combination of barcode and UMI, only the most prevalent UMI for each barcode and scar, and only the most prevalent barcode for each UMI and scar. We then assessed similar (Hamming distance of 2 or less) scar sequences in each cell, only keeping both if they obey criteria designed to test whether both sequences are verifiably correct (see Spanjaard et al. for details). Finally, we removed cells that look like doublets by comparing their number of different scars to the scar number distribution for that cell type.
scvelo (velocyto.py) for RNA velocity analysis
Genome_build: GRCz11
Supplementary_files_format_and_content: h5: HDF5 Feature Barcode Matrix Format, Single-cell transcript count table with list of cell barcodes and gene names
Supplementary_files_format_and_content: csv-format: List of scar transcripts with CIGAR, cell name, cell barcode and UMI sequence
Supplementary_files_format_and_content: csv: list of scars used for tree building with scar sequence, cell barcode, library, cell name, number of reads, CIGAR, UMI sequence, number of libraries where the scar is present in at least two cells, creation probability, number of embryo libraries (from LINNAEUS) in which this scar is observed, and scar name. Note that scars observed in multiple libraries will have the same name. Also note that for downstream tree building, only the columns “Cell”, “p” and “Scar” are necessary.
Supplementary_files_format_and_content: loom: output from velocyto.py (http://velocyto.org)

organism: Danio rerio

source_name: Heart tissue

growth_protocol: Zebrafish were bred, raised, and maintained in accordance with the guidelines of the Max-Delbrück Center for Molecular Medicine and the local authority for animal protection (Landesamt für Gesundheit und Soziales, Berlin, Germany) for the use of laboratory animals, and followed the ‘Principles of Laboratory Animal Care’ (NIH publication no. 86-23, revised 1985) as well as the current version of German Law on the Protection of Animals. Zebrafish strains AB were used for cryoinjury procedure and behavioral analysis.

extract_protocol:
The heart was dissected from the fish and transferred into cold HBSS. The dissection included the atrium, ventricle and bulbus arteriosus, except for samples in which only the atrium or the ventricle was isolated. A needle and a syringe filled with cold HBSS were used to pierce into the lumen of the heart and thoroughly wash away most of the erythrocytes in the tissue. Afterwards, the tissue was opened carefully with forceps, and the heart tissue was incubated at 37 °C for 30 min in 500µl HBSS containing Liberase enzyme mix (Sigma-Aldrich, 0.26 U/mL final concentration) and Pluronic F-68 (Thermo Fisher Scientific, 0.1%), while shaking at 750 r.p.m. with intermittent pipette mixing. After most of the tissue was dissociated, the reaction was stopped by adding 500µl cold HBSS supplemented with 1% BSA. The suspension was centrifuged at 250g at 4°C and washed two times with 500µl cold HBSS containing 0.05% BSA, then filtered through a cell strainer of 35µm diameter. The quality of the single cell suspension was then confirmed under the microscope, and cells were counted prior to scRNA-seq library preparation.
Library were constructed following the manufacturer's protocols (10X Genomics)

treatment_protocol:
Cryoinjury: First, fish were pre-sedated in water containing 0.03 mg/ml Tricaine (PHARMAQ, pH 7). Concentration was then increased to 0.168 mg/ml for anesthesia. Fish were placed with the ventral side facing up into a foam holder under a dissecting scope. To access the heart, a small incision was made through the body wall and the pericardium, using microdissection forceps and scissors. Once the pericardial sac was opened, the heart ventricle was exposed by gently compressing the abdomen. Excess water was carefully removed by blotting with tissue paper, not allowing fish skin to dry. Then, a stainless steel cryoprobe precooled in liquid nitrogen was applied to the ventricular wall for 20 seconds. Fish were then placed in a tank of fresh system water with 1.5mg/l morphine sulphate for 6h. Reanimation was enhanced by the gill oxygenation where water around gills was aerated by pipetting for a couple of minutes.
Wnt inhibition: IWR-1 was dissolved in DMSO to prepare a stock concentration of 10mM. Wild-type fish were injected intraperitoneally with 25μl of 10μM IWR-1 in PBS or DMSO (0.1% in PBS)10. The injection was performed at 1dpi, 2dpi for the 3dpi analysis and for later time points, once every two days from 2dpi until the day of sacrifice.

tag: tissue

value: heart

tag: condition

value: Injured

tag: days post injury (dpi)

value: non-treated

value: Zebrabow M

tag: 10x chemistry version


title: GC080711_H05


title: GC080712_A04


title: Injured heart Hr25 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr24 - scar

description: scar sequences for lineage tracing


title: IgG_3


title: GC080711_G06


title: Injured heart Hr22 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr23 - scar

description: scar sequences for lineage tracing


title: GC080711_H01


title: GC080711_G05


title: Injured heart Hr11 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr7 - scar

description: scar sequences for lineage tracing


title: GC080711_G04


title: Injured heart Hr6  - scar

description: scar sequences for lineage tracing


title: GC080711_G03


title: GC080711_G02


title: Injured heart Hr27 - scar

description: scar sequences for lineage tracing


title: GC080711_H02


title: GC080711_F06


title: GC080711_G01


title: Injured heart Hr1 - scar

description: scar sequences for lineage tracing


title: Healthy heart H8  - scar_ventricle

description: scar sequences for lineage tracing

value: Healthy


title: Injured heart Hr2 - scar

description: scar sequences for lineage tracing


title: Healthy heart H8  - scar_atrium

description: scar sequences for lineage tracing


title: Healthy heart H6 - scar

description: scar sequences for lineage tracing


title: GC080711_F05


title: GC080711_F04


title: Healthy heart H7 - scar

description: scar sequences for lineage tracing


title: GC080711_F03


title: Healthy heart H5 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr35

value: IWR-treated


title: GC080711_F02


title: Injured heart Hr10 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr34


title: GC080711_E06


title: GC080711_E05


title: GC080711_F01


title: GC080711_E04


title: Injured heart Hr32


title: GC080711_E03


title: Injured heart Hr29


title: Injured heart Hr30

value: DMSO-control


title: Injured heart Hr33


title: GC080711_E02


title: GC080711_E01


title: Injured heart Hr27


title: Injured heart Hr26


title: Injured heart Hr28


title: GC080711_D04


title: Injured heart Hr31


title: GC080711_D06


title: GC080711_D03


title: Injured heart Hr25


title: GC080711_D01


title: GC080711_D02


title: GC080711_C06


title: Injured heart Hr22


title: GC080711_C04


title: GC080711_C05


title: Injured heart Hr10


title: Injured heart Hr9


title: Injured heart Hr6 - Ventricle


title: Injured heart Hr7 - Atrium


title: GC080711_C02


title: GC080711_D05


title: GC080711_C03


title: Injured heart Hr19 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr6 - Atrium


title: Injured heart Hr20 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr15 - scar

description: scar sequences for lineage tracing


title: GC080711_C01


title: Injured heart Hr2


title: Injured heart Hr7 - Ventricle


title: Injured heart Hr24


title: GC080711_B05


title: Injured heart Hr4 - scar

description: scar sequences for lineage tracing


title: Healthy heart H8 - Ventricle


title: Injured heart Hr13 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr14 - scar

description: scar sequences for lineage tracing


title: GC080711_B04


title: Injured heart Hr21 - scar

description: scar sequences for lineage tracing


title: Injured heart Hr1


title: Injured heart Hr21


title: Injured heart Hr12 - scar

description: scar sequences for lineage tracing


title: GC080711_B03


title: Injured heart Hr20


title: Healthy heart H7


title: Injured heart Hr19


title: Healthy heart H6


title: GC080711_B02


title: Injured heart Hr14


title: GC080711_B06


title: Injured heart Hr13


title: Injured heart Hr12


title: GC080711_B01


title: Healthy heart H5


title: Injured heart Hr2 - 2nd sample for more cells


title: Injured heart Hr4


title: Injured heart Hr23

data_processing:
Demultiplexing of the illumina sequencing results using cellranger 3.0.2
Mapping using cellranger 3.0.2
Genome_build: GRCz11
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format, Single-cell transcript count table with list of cell barcodes and gene names

source_name: Zebrafish heart

extract_protocol:
Single cell suspension were made using Liberase(TM) in HBSS buffer
Library were constructed following the manufacturer's protocols (10X Genomics)

treatment_protocol: Fish were either untreated or treated with 1.5mg/l morphine sulphate dissolved in system water. Fish were hold in tanks individually for the period of treatment of 6 hours.

value: AB

tag: morphine treatment

value: yes


title: Injured heart Hr3 - scar

description: scar sequences for lineage tracing


title: GC080711_A06


title: Injured heart Hr18


title: Injured heart Hr8

value: no


title: Injured heart Hr16


title: Healthy heart H8 - Atrium


title: GC080711_A05


title: Injured heart Hr15


title: GC080711_A03


title: siNCOA3_Input

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

country: China

institute: Fudan University

library_source: genomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters.
PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis.
Bam files were converted to BigWig files using deepTools.
Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using deepTools.

molecule: genomic DNA

source_name: Huh 7

growth_protocol: Huh 7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Invitrogen, Carlsbad, CA, USA) containing 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) and antibiotics (penicillin and streptomycin, Invitrogen) at 37 °C in 5% CO2.

extract_protocol:
ChIP-seq was performed as described previously (Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. Methods.2009;48:240-8).
DNA-seq library preparation

treatment_protocol: Before siRNA transfection, around 0.4 million Huh 7 cells  were seeded in to 6 well plate per well. Next day, cells in each well were transfected with 9μl of siRNA or NC (10μM) using Lipofectamine RNAiMAX. To set up HK2 knocking down stable cell lines, Huh 7 cells were transfected with shHK2 lentivirus, renew the medium after 8 hours later, for another 24 hours, sorting the positive cells which stable expressing GFP with FACS.

tag: cell type

value: HCC

tag: chip antibody

value: Huh 7 cells were transfected with siNCOA3 using Lipofectamine RNAiMAX.


title: Injured heart Hr11


title: SG_1LM

city: Chongqing

first: Hanfu

last: Xu

address: 2 Tiansheng Road, Beibei District

institute: State Key Laboratory of Silkworm Genome Biology Southwest University

data_processing:
The Cell Ranger software pipeline (version 3.1.0) provided by 10× Genomics was applied to demultiplex the cellular barcodes, map reads to the reference genome and transcriptome by using the STAR aligner, and downsample reads as required to generate normalized aggregate data across samples, generating a matrix of gene counts versus cells.
Genome_build: GCF_000151625.1_ASM15162v1
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

organism: Bombyx mori

source_name: silk gland cells

growth_protocol: B. mori (Nistari strain) embryos developed to E8D, 1L1D larvae, and 1LM larvae were maintained under standard laboratory conditions and collected to obtain SG samples.

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
After the cell viability test, single-cell separation, complementary DNA amplification and library construction were performed according to the manufacturer’s protocol for Chromium Single-cell 3’ Kits (10× Genomics).

treatment_protocol: SG samples from each developmental stage were composed of a mixture of ~2000 intact SGs to ensure sufficient materials for subsequent cell dissociation. Tissues were dissociated and then resuspended in 1 mL PBS containing 0.04% BSA.Wash the tissue with medium (1640). Cut the tissue into pieces in the culture medium, add an appropriate amount of enzyme and digest it in a constant temperature incubator for 30-60min. Over 40 after digestion μ M cell sieve.Wash the culture medium for more than two times (centrifugation for 5min at 300g at 4 ℃). Wash the culture medium for more than two times (centrifugation for 5min at 300g at 4 ℃).

value: B. mori (Nistari strain)

value: Eukaryotic cell

tag: in vivo &in vitro

value: In vitro expansion

tag: developmental stage

value: first larval molting, 1LM


title: SG_E8D

value: 8 days post-egg laying, E8D


title: GC080711_A02

tag: ar

tag: abmrh


title: siNCOA3_H3K27ac

value: H3K27ac, Active motif, 39133


title: SG_1L1D

value: day 1 of first-instar larvae, 1L1D


title: GC080711_A01

tag: tcmr

tag: polyoma (no


title: Injured heart Hr3

value: heart

value: Injured

value: non-treated

tag: strain


title: siEP300_Input

value: Huh 7 cells were transfected with siEP300 using Lipofectamine RNAiMAX.


title: siNC_Input

value: Huh 7 cells were transfected with siNC using Lipofectamine RNAiMAX.


title: GC080710_H06

tag: dsa


title: GC080710_H05


title: GC080711_A04


title: siNC_H3K27ac

tag: treatment


title: siEP300_H3K27ac


title: H7_NCOA3

value: NCOA3, Active motif, 39797

value: untreated


title: GC080710_H04


title: GC080710_H03


title: H7_SP1

value: SP1, Proteintech, 21962-1-AP


title: GC080710_H02


title: H7_P300

value: HCC

value: EP300, Active motif, 61903


title: GC080710_H01


title: Huh7NaAc_Input

value: Huh7 cells were treatment with acetate (5 mM).


title: GC080710_G06


title: si-DYRK1A-input

first: Cong

last: Lan

state: Chognqing

address: 10 Changjiangzhilu Road

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University

data_processing:
ChIP-seq peak calling was carried out using MACS 1.4.2 (Model based analysis of ChIP-seq) with default setting to profile binding regions.
ChIP-seq reads were mapped to rat genome assembly rn6.
Assembly: rn6

organism: Rattus norvegicus

source_name: input DNA

growth_protocol: We isolated  cardiomyocytes using 1-day-old SD rats and  cultured in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum at 37℃ in atmosphere with 5% CO2.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
The ChIP-seq libraries were constructed using the NEBNext ChIP-seq Library Prep Master Mix Set for the Illumina system and sequencing was performed with the Hiseq 3000 sequencer by the Guangzhou Epibiotek (Guangzhou, China).

treatment_protocol: Neonatal cardiomyocytes in primary culture were transfected with siRNA against DYRK1A (si-DYRK1A) or scramble siRNA (si-NC) and cultured for 48 h to prepare sample (three biological replicates for each group)

value: Neonatal rat cardiomyocytes


title: Huh7NaAc_H3K27ac


title: GC080710_G05


title: Huh7CTL_Input

value: Huh7 cells were treatment with PBS.


title: GC080710_G04


title: si-NC-input

value: si-NC


title: si-DYRK1A-H3K4Me3


title: si-DYRK1A-H3K27ac


title: si-NC-H3K4Me3


title: Huh7CTL_H3K27ac


title: GC080710_G03


title: si-NC-H3K27ac


title: H3K27ac_shHK2_Input

value: Huh7 cells were transfected with shHK2 lentivirus, renew the medium after 8 hours later, for another 24 hours, sorting the positive cells which stable expressing GFP with FACS.


title: GC080710_G02


title: H3K27ac_shHK2

value: H3K27ac, Active motif, 39133


title: H3K27ac_shNC_Input

value: Huh7 cells were transfected with shNC lentivirus, renew the medium after 8 hours later, for another 24 hours, sorting the positive cells which stable expressing GFP with FACS.


title: GC080710_G01


title: GC080710_F06


title: H3K27ac_shNC


title: GC080710_F05


title: MTP group Replicate 3

city: Zhengzhou

first: Min

last: Yan

state: Henan

address: East Jinshui Road No.156

institute: Henan University of Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm10
Supplementary files format and content: counts, FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: liver

value: 300μg/kg Moderate-dose TP (MTP)

tag: treatment method

value: oral gavage for 7 days


title: MTP+CR group Replicate 1

tag: tissue

value: 300μg/kg Moderate-dose TP + 100 mg/kg CR (MTP+CR)


title: MTP+CR group Replicate 3


title: MTP+CR group Replicate 4


title: NC group Replicate 4

value: Normal saline (NC)


title: MTP group Replicate 4


title: MTP group Replicate 1


title: MTP group Replicate 2


title: NC group Replicate 3


title: MTP+CR group Replicate 2


title: NC group Replicate 2


title: PARP1_IP-1

city: Wu Han

first: Jing

last: Ke

address: No. 17 High-tech 6th Road, East Lake High-tech Development Zone, Wuhan, Hubei 430200, China.

institute: Renmin Hospital of Wuhan University

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniquely mapped reads were remained. One more reads with the same start and end position, only one is considered.
After reads were aligned onto the genome, we analysed the unique reads binding regions of PARP1 on genome using “ABLIRC” strategy.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include peak information for each group.

source_name: HK-2 cell

growth_protocol: HK-2 cells were first lysed in ice-cold lysis buffer (10 mM HEPES, pH 7.0, 100 mM KCl, 5 mM MgCl2, 0.5% NP-40, 10 mM DTT) with 200 U/ml RNase inhibitor (Promega) and a protease inhibitor (Roche) on ice for 5 min

extract_protocol:
The beads were washed 6 times with lysis buffer and then divided into two groups, one for RNA isolation from PARP1-RNA complexes and another for the western blotting assay for PARP1. immunoprecipitation.The PARP1-bound RNAs were isolated from the immunoprecipitate of monoclonal Flag antibody (Sigma), followed by the preparation of the Illumina Truseq pair-end libraries.
The reverse transcription was performed with RT primers harboring 3′ adaptor sequence and random hexamer. The generated cDNAs were PCR-amplified and the 200–500 bp products were purified.

treatment_protocol: The supernatant was pre-cleared with 100 μl of DynaBeads protein G (Life Technologies) at 4 °C for 30 min. The pre-cleared supernatant was incubated with DynaBeads protein G conjugated with monoclonal Flag antibody (Sigma) or Input at 4℃ for 30 min.

tag: cell line

value: HK-2 cell

tag: condition

value: PARP1 IP


title: GC080710_F04


title: PARP1_IP-2


title: GC080710_F03


title: DuodenumChip, EED, ND, rep2

type: RNA

city: Boston

first: Don

last: Ingber

state: Massachusetts

address: 3 Blackfan Circle, CLSB 5th Floor

country: USA

institute: Wyss Institute for Biologically Inspired Engineering at Harvard University

description: Duodenum chip seeded with EED patient epithelium grown in organoid media depleted of nicotinamide and tryptophan

hyb_protocol: Fragmented, biotinylated cDNA was added to a hybridization cocktail, denatured, loaded on Clariom D GeneChips and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, GeneChips were washed and stained using the FS450_0001 protocol.

scan_protocol: The stained GeneChips were scanned at 532 nm on a GeneChip Scanner 3000.

data_processing: Robust multichip average (RMA) was used to generate normalized expression intensity dataa for subsequent analysis (R package: oligo; function: rma).

label: biotin

label_protocol: Using a random primer incorporating a T7 promoter, double-stranded cDNA was synthesized from 100 ng total RNA. cRNA was generated from the double-stranded cDNA template though a 16 hr in-vitro transcription reaction, followed by purification using magnetic beads. Single stranded cDNA was regenerated from the cRNA through a random primed reverse transcription using a dNTP mix containing dUTP. The RNA was hydrolyzed with RNase H and the cDNA purified using magnetic beads. The cDNA was fragmented by incubation with a mixture of UDG and APE 1 restriction endonucleases. The fragmented cDNA was then end-labeled via a terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: Organoids were kept in complete growth medium, and passaged every 7 days in a 1:4 ratio. Before cell seeding, S-1 Chips (Emulate) were activated using ER1/2 (Emulate) and UV exposure for 20 minutes. Chips were then coated with 200 μg ml−1 collagen I (BD Corning) and 100 μg ml−1 Matrigel (BD Corning) in serum-free DMEM-F12 (Gibco) for 2 hours at 37 °C. After wash, organoids were broken into smaller fragments using enzymatic activity (TryplE, Gibco) and seeded in the luminal upper channel of the chips. They were then allowed to adhere for 24h before introduction of flow and mechanical deformation as described before. For the -N/-T treatment, niacinamide and tryptophan were removed from the basal medium (DMEM-F12, Gibco) used to prepare the expansion culture medium (used for the luminal and lower channels) and no additional niacinamide was added.

extract_protocol: Total RNA was performed using the Qiagen RNeasy kit per manufacturer instructions.

treatment_protocol: After 16-18 days in culture with continuous flow (60 µl/h) and mechanical deformation (10%, 0.15 Hz), medium was changed to differentiation medium (serum and Wnt-3A free, and -N/-T free for the respective group), in the luminal top channel and expansion culture medium in the lower channel for 4 additional days.

value: Duodenum

tag: gender

value: male

tag: age

tag: disease state

value: Environmental Enteric Dysfunction (EED)

value: nutritionally depleted medium


title: NC group Replicate 1


title: PARP1_input-2

value: input


title: GC080710_F02


title: GC080710_E06


title: DuodenumChip, Healthy, ND, rep1

description: Duodenum chip seeded with healthy patient epithelium grown in organoid media depleted of nicotinamide and tryptophan

value: healthy


title: GC080710_F01


title: PARP1_input-1


title: shCtrl_3rd

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1 AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2  Qvalue < =0.05
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

growth_protocol: The human HK-2 cell line was purchased from the Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. Cells were seeded into a petridish (100 mm) at a density of 1 × 105 cells/mL per well, and cultured at 37 ℃with 5% CO2 in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS) (Hyclone), penicillin (100 U/ml) and streptomycin (100 g/ml). PARP1 shRNA and shCtrl plasmids transfection of HK-2 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's instructions. Transfected cells were harvested after 48 h.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion). The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using Smartspec Plus (BioRad). The integrity of RNA was further verified by 1.5% agarose gel electrophoresis.
For each sample, 1μg of total RNA was used for RNA-seq library preparation by VAHTS Stranded mRNA-seq Library Prep Kit (Vazyme). Polyadenylated mRNAs were purified and fragmented, and then converted into double strand cDNA. After the step of end repair and A tailing, the DNAs were ligated to VAHTS RNA Adapters (Vazyme). Purified ligation products corresponding to 200-500 bps were digested with heat-labile UDG, and the single strand cDNA was amplified, purified, quantified and stored at -80℃ before sequencing.
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina HiSeq X Ten system for 150 nt paired-end sequencing.

treatment_protocol: shRNA against human PARP1 transfection of HK-2 cells was performed using lipofectAMINE 2000

tag: genotype

value: control


title: Spinal cord, sham group, 3 day, rep1, input

city: guangzhou

first: Fanning

last: Zeng

state: Guangdong

address: Jingxi Street, Baiyun District

department: Department of Anesthesiology

institute: Nanfang hospital, Southern Medical University

description:
genes_fpkm_expression.txt
SHAM_1_input

data_processing:
Illumina Novaseq™ 6000 the 2×150bp was used for paired-end sequencing (PE150).
Fastp software  were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
HISAT2 was used to map reads to the reference genome Mus musculus (Version: v101).
Mapped reads of IP and input libraries were provided for R package exomePeak.Called peaks were annotated by intersection with gene architecture using R package ChIPseeker.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR.
Assembly: Mus musculus (Version: v101)
Supplementary files format and content: tdf or bigwig format include m6A peaks for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: spinal cord

extract_protocol:
The spinal cord of mice at 3rd, 7th, 14th day after spared nerve injury and sham group was isolated for RIP-Seq and RNA-Seq.Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.    Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.   e6150, USA) under 86℃ 7min.    Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630).    Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat.    1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.   m0209, USA), RNase H (NEB, cat.   m0297, USA) and dUTP Solution (Thermo Fisher, cat.   R0133, USA）.    Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads.    After the heat-labile UDG enzyme (NEB, cat.   m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR. The average insert size for the final cDNA library was 300±50 bp.
Then we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: After the mice were anesthesia under sevoflurane (3-5%), being carefully separate the common peroneal nerve and the tibial nerve, tightly ligate the common peroneal nerve and tibial nerve with 6-0 silk, cut off the distal end of the ligated nerve, and remove 2-4 mm of the distal nerve stump. In the sham group, only the sciatic nerve and its three peripheral branches were exposed and then the muscles and skin are sutured.

value: spinal cord

tag: rip antibody

value: sham

tag: time

value: 3 day


title: Spinal cord, spared nerve injury, 14 day, rep3, input

description:
genes_fpkm_expression.txt
D14_3_input

value: spared nerve injury

value: 14 day


title: Spinal cord, sham group, 3 day, rep3, input

description:
genes_fpkm_expression.txt
SHAM_3_input


title: GC080710_E04

tag: ar


title: shPARP1_3rd

value: PARP1 knockdown


title: shCtrl_1st


title: DuodenumChip, EED, Control, rep3

description: Duodenum chip seeded with EED patient epithelium grown in complete organoid media

value: complete medium


title: GC080710_E03

tag: abmrh


title: DuodenumChip, EED, ND, rep1

source_name: Duodenum chip seeded with EED patient epithelium grown in organoid media depleted of nicotinamide and tryptophan


title: DuodenumChip, Healthy, ND, rep3

source_name: Duodenum chip seeded with healthy patient epithelium grown in organoid media depleted of nicotinamide and tryptophan


title: GC080710_E05

tag: tcmr


title: Spinal cord, sham group, 3 day, rep2, input

description:
genes_fpkm_expression.txt
SHAM_2_input


title: shCtrl_2nd


title: Spinal cord, spared nerve injury, 14 day, rep1, input

description:
genes_fpkm_expression.txt
D14_1_input


title: Spinal cord, spared nerve injury, 14 day, rep2, input

description:
genes_fpkm_expression.txt
D14_2_input


title: GC080710_E02

tag: polyoma (no


title: DuodenumChip, Healthy, Control, rep3

description: Duodenum chip seeded with healthy patient epithelium grown in complete organoid media


title: Spinal cord, spared nerve injury, 7 day, rep3, input

description:
genes_fpkm_expression.txt
D7_3_input

value: 7 day


title: shPARP1_1st

value: HK-2 cell


title: DuodenumChip, Healthy, Control, rep1

source_name: Duodenum chip seeded with healthy patient epithelium grown in complete organoid media


title: shPARP1_2nd


title: GC080710_D06


title: GC080710_E01


title: DuodenumChip, EED, Control, rep2

source_name: Duodenum chip seeded with EED patient epithelium grown in complete organoid media


title: Spinal cord, spared nerve injury, 7 day, rep2, input

description:
genes_fpkm_expression.txt
D7_2_input


title: Spinal cord, spared nerve injury, 7 day, rep1, input

description:
genes_fpkm_expression.txt
D7_1_input


title: DuodenumChip, Healthy, ND, rep2


title: Spinal cord, spared nerve injury, 3 day, rep3, input

description:
genes_fpkm_expression.txt
D3_3_input


title: MEF cells - input DNA_rep3

city: Lyon

first: Fabrice

last: Lavial

address: 28 rue Laennec

country: France

institute: CRCL

data_processing:
Atoh8 and Bcl11b ChIP-sequencing datasets were aligned to the mouse reference genome assembly mm10 using Bowtie 2.1.0 under by default parameters
Peak calling was performed using MACS 2.1.1. Atoh8-specific sites were obtained by subtracting binding sites observed within the AM-tag processed control dataset (BEDTools 2.29.2).
Enrichment heat maps and mean density plots were obtained with seqMINER.  De novo motif analysis has been performed with MEME-ChIP
Read counts enrichment signals were visualized with IGV genome browser.  Genome_build: mm10
Supplementary_files_format_and_content: Peak calling was performed using MACS 2.1.1. In addition, bedgraphs were also generated at this stage for genome browser visualization (IGV).
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph files (MACS 2.1.1.)
Supplementary_files_format_and_content: Peak list files (MACS 2.1.1.)

source_name: MEF cells

growth_protocol: MEFs were isolated from E13.5 embryos after removal of the head and internal organs. The remaining tissues were physically dissociated and incubated in trypsin at 37°C for 10 min after which cells were resuspended in MEF medium.

extract_protocol:
After 3 days, DNA was extracted, precipitated and purified using the Tag-ChIP-IT kit (53022, Actif Motif).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: MEFs were infected with lentiviral particles carrying AM-tagged Atoh8.

tag: chip antibody

value: whole cell extract

value: untreated

tag: cell line/type

value: Mouse embryonic fibroblast (MEF)


title: GC080710_D03

tag: dsa


title: Spinal cord, spared nerve injury, 3 day, rep1, input

description:
genes_fpkm_expression.txt
D3_1_input

tag: treatment


title: DuodenumChip, EED, ND, rep3

tag: tissue

value: Duodenum

value: male

value: Environmental Enteric Dysfunction (EED)


title: DuodenumChip, EED, Control, rep1


title: DuodenumChip, Healthy, Control, rep2

value: healthy


title: MEF cells - AM-empty_rep2

value: mouse AM-Tag (active motif 9111)


title: Spinal cord, spared nerve injury, 14 day, rep3

description:
D14_IP_peak.txt
D14_3_IP

value: spinal cord

value: m6A (No. 202003, Synaptic Systems, Germany)


title: Spinal cord, sham group, 3 day, rep1

description:
SHAM_IP_peak.txt
SHAM_1_IP

value: sham

value: 3 day


title: MEF cells - input DNA

data_processing:
Atoh8 ChIP-sequencing datasets were aligned to the mouse reference genome assembly mm10 using Bowtie 2.1.0 under by default parameters
Peak calling was performed using MACS 2.1.1. Atoh8-specific sites were obtained by subtracting binding sites observed within the AM-tag processed control dataset (BEDTools 2.29.2).
Enrichment heat maps and mean density plots were obtained with seqMINER.
De novo motif analysis has been performed with MEME-ChIP
Read counts enrichment signals were visualized with IGV genome browser.
Genome_build: mm10
Supplementary_files_format_and_content: Peak calling was performed using MACS 2.1.1. In addition, bedgraphs were also generated at this stage for genome browser visualization (IGV).


title: GC080710_C06


title: MEF cells - Bcl11b_rep1

value: ab18465 (abcam) and A300-385A (Bethyl Laboratories)


title: MEF cells - AM-Atoh8_rep1


title: Spinal cord, spared nerve injury, 3 day, rep2, input

description:
genes_fpkm_expression.txt
D3_2_input

value: spared nerve injury


title: GC080710_D05


title: GC080710_C04


title: MEF cells - input DNA_rep2


title: MEF cells - AM-Atoh8_rep2


title: Spinal cord, spared nerve injury, 14 day, rep1

description:
D14_IP_peak.txt
D14_1_IP

value: 14 day


title: Spinal cord, spared nerve injury, 7 day, rep3

description:
D7_IP_peak.txt
D7_3_IP

value: 7 day


title: GC080710_C03


title: TC sh#Atoh8 rep3

description:
processed data file: raw_count_TC.txt
processed data file: normalized_count_TC.txt
processed data file: model_fc_TC.txt

data_processing:
Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DESeq2 package.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: raw_count_TC.txt: Tab-delimited text file including raw counts for each sample.
Supplementary_files_format_and_content: normalized_count_TC.txt: Tab-delimited text file including normalized counts for the each sample.
Supplementary_files_format_and_content: model_fc_TC.txt: Tab-delimited text file including FC, p-value and adjusted p-value.

source_name: mouse embryonic fibroblasts

growth_protocol: TCs were cultivated in DMEM medium supplemented with 5% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS)

extract_protocol:
RNAs were extracted with Macherey-Nagel NucleoSpin RNA kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: mouse embryonic fibroblasts

tag: strain

tag: shRNA

value: Malignant transformation induction


title: GC080710_D01


title: TC sh#Atoh8 rep2


title: Spinal cord, sham group, 3 day, rep2

description:
SHAM_IP_peak.txt
SHAM_2_IP


title: CapC_D13_rep3

city: Oxford

first: Mohsin

last: Badat

address: Headley Way

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: DpnII digested 3C library, enriched for fragments of interest by oligonucleotide pulldown

data_processing:
Library Strategy: NG Capture-C
Adaptor Removal: Trim Galore
Fragment reconstruction into a single read: Flash
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment: Bowtie 2
Processing: Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Processing: Combining data from multiple replicates (custom scripts)
Processing: Removal of ploidy regions and off target capture (custom scripts)
Genome_build: hg19
Supplementary_files_format_and_content: custom format (chr start stop interactions viewpoint)

source_name: CD34 Culture

growth_protocol: 50ml of fresh blood was venesected from the patient and stored in EDTA Vacuettes (Becton Dickson. Blood was diluted with PBS and overlaid onto Histopaque-1077 (Sigma) and centrifuged for 30 min at 630 rcf (no brake). Peripheral Blood Mononuclear Cells (PBMCs) were washed in PBS and MACS buffer (PBS, 2 µM EDTA, 0.5% BSA) and stained with Human CD34 Microbead kit (Miltenyi Biotec) following the manufacturer’s instruction for 30 minutes (4 ºC) before being passed successively through one LS Column (Miltenyi Biotec) with three MACs buffer washes. CD34+ cells were resuspended in Phase I medium for a three-phase differentiation adapted from that used for the BEL-A cell line (Trakarnsanga, Nat Comms 2017). Briefly, for differentiation 3x105 cells were resuspended on day 0 in Phase I media at 2x105 cells ml-1. Cell counts were performed on days 3 and 5 with additional Phase I media added to return the concentration to 105 cells ml-1. On day 7, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase II media at 2x105 cells ml-1. Cells were counted on day 9 and diluted to 2x105 cells ml-1 Phase II media. On day 11, cells were counted and pelleted (300 rcf, 5 min, RT) and resuspended in Phase III media at 106 cells ml-1. Cells were harvested on day 13.

extract_protocol:
3C Libraries were generated according to the NG Capture-C protocol (Davies et al. 2016). Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80. Cells were thawed on ice, washed in dH2O and homogenised with repeated pipetting using a P1000 tip (20 times). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer. The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencies were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 70%. DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies).
5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Ultra DNA sample preparation reagent kit using the standard protocol. Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments. Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using the Nimblegen SeqCap reagents and an adapted protocol. The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Miseq (150 bp paired-end reads)

treatment_protocol: Not applicable

value: Erythroid

tag: gender

value: Female

tag: differantiation day

value: Day 14


title: Spinal cord, sham group, 3 day, rep3

description:
SHAM_IP_peak.txt
SHAM_3_IP


title: GC080710_D02

source_name: Blood


title: GC080710_D04


title: GC080710_C05


title: GC080710_C01


title: MEF cells - AM-empty_rep1

value: untreated

value: Mouse embryonic fibroblast (MEF)


title: CapC_D13_rep2

value: Day 13


title: GC080710_B05


title: GC080710_C02


title: TC sh#Control rep1

value: sh#Control


title: MEF cells - Bcl11b_rep2


title: Spinal cord, spared nerve injury, 7 day, rep1

description:
D7_IP_peak.txt
D7_1_IP

value: spinal cord


title: Spinal cord, spared nerve injury, 7 day, rep2

description:
D7_IP_peak.txt
D7_2_IP

value: m6A (No. 202003, Synaptic Systems, Germany)


title: MEF sh#Atoh8 rep2

description:
processed data file: raw_count_MEF.txt
processed data file: normalized_count_MEF.txt
processed data file: model_fc_MEF.txt

data_processing:
Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DESeq2 package.
Genome_build: mm8 (MGSCv36)
Supplementary_files_format_and_content: raw_count_MEF.txt: Tab-delimited text file including raw counts for each sample.
Supplementary_files_format_and_content: normalized_count_MEF.txt: Tab-delimited text file including normalized counts for the each sample.
Supplementary_files_format_and_content: model_fc_MEF.txt: Tab-delimited text file including FC, p-value and adjusted p-value.

growth_protocol: MEF were generated from E13.5 mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol.


title: GC080710_B02

data_processing:
Single-end sequencing was performed using an Illumina HiSeq 4000 device
After adapter removal, 50bp-long raw reads were aligned to the reference genome hg38 using splice-aware aligner HISAT2
Absolute gene counts were generated using HTSeq based on the Ensemble83 annotation
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample


title: TC sh#Atoh8 rep1


title: MEF sh#Control rep2


title: GC080710_A06


title: GC080710_B01


title: MEF sh#Control rep1


title: CapC_D13_rep1


title: Spinal cord, spared nerve injury, 3 day, rep3

description:
D3_IP_peak.txt
D3_3_IP


title: TC sh#Control rep3


title: T cells, DSF,  bio rep 2

first: Qinlan

last: Wang

address: Chongqingnan R.280

institute: Shanghai Jiaotong University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10

source_name: from mouse lymph nodes

growth_protocol: Primary OT-I T cells were maintained in complete RPMI 1640 media [10% fetal bovine serum( FBS), 0.05 mM 2-mercaptoethanol, 1 mM NEAA] in humidified atmosphere with 5% CO2

extract_protocol:
Cells were fed with complete RPMI 1640 media.
RNA was harvested, 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: T cells were treated with DMSO or DSF for 2h.

value: from mouse lymph nodes

tag: cell line

value: primary OT-I T cells

value: T cells

tag: genotype

value: wildtype

value: DSF


title: T cells, DMSO, biol rep 3

value: DMSO


title: Spinal cord, spared nerve injury, 3 day, rep2

description:
D3_IP_peak.txt
D3_2_IP

tag: rip antibody

value: spared nerve injury

tag: time

value: 3 day


title: Spinal cord, spared nerve injury, 14 day, rep2

description:
D14_IP_peak.txt
D14_2_IP

value: 14 day


title: GC080710_A05

tag: ar

tag: abmrh


title: T28_rep4

data_processing:
Demultiplexed using Geneious 7.0.
The designed barcode sequences from the library were assembled into a mapping reference sequence to align the processed reads to the library.
The reads were then aligned to the reference sequence using the "Map to Reference" function in Geneious 7.0.
After alignment, the number of uniquely aligned reads for each library sequence was calculated.
The sgRNA score was generated and ranked according to the depletion or enrichment of the normalized sgRNA counts.
Genome_build: not provided
Supplementary_files_format_and_content: sgRNAs_and_CRISPR-cas9_KO_Results.xlsx: Excel file

growth_protocol: 1×10^7 cells per mouse were subcutaneously injected into NOD/Scidil2Rγ−/− (NSG) mice for xenograft tumor formation.

extract_protocol:
Genomic DNA of day 0 samples and xenograft tumor were extracted from each sample with the Qiagen Blood & Cell Culture Midi Kit.
sgRNA cassettes were PCR-amplified from genomic DNA of each sample.
The amplicons resulting from the second PCR were extracted with beads (Beckman Coulter, USA), quantiﬁed, mixed, and sequenced using a NextSeq 500 instrument (Illumina, USA).

treatment_protocol: After 4 weeks, the xenograft tumor were collected and stored for further processing.

value: Huh 7

value: Hepatocellular carcinoma (HCC) cells

tag: time point

value: Day 28


title: Spinal cord, spared nerve injury, 3 day, rep1

description:
D3_IP_peak.txt
D3_1_IP


title: TC sh#Control rep2

value: mouse embryonic fibroblasts

value: Malignant transformation induction


title: GC080710_A04

extract_protocol:
After collection, the blood samples were stored in PAXgene tubes at ambient temperature for at least 24 hours, and then stored at -80°C until extraction. Total RNA was extracted using the PAXgene Blood miRNA Kit® (PreAnalytiX GmbH).
Library preparation was done using the Lexogen QuantSeq mRNA kit according to the manufacturer’s instructions

tag: tcmr

tag: polyoma (no


title: T cells, DMSO, biol rep 1


title: MEF sh#Atoh8 rep1


title: GC080710_A03

tag: dsa


title: GC080710_B03


title: T cells, DSF,  bio rep 1

tag: treatment


title: GC080710_A02


title: T28_rep1


title: INF-dpi-5-B

city: Winnipeg

first: Jessy

middle: Andrew

last: Slota

state: Manitoba

address: 1015 Arlington St.

department: One Health Division

country: Canada

institute: National Microbiology Laboratory; Public Health Agency of Canada

data_processing:
Low-quality sequences were trimmed using Trimmomatic
ribosomal RNA reads were removed with Bowtied
Cleaned reads were mapped to the hamster (golden syrian) genome using HISAT2
Transcripts mapping to genes in the host genome were counted using FeatureCounts
Reads that failed to map to the host genome were mapped to the SARS-CoV-2 genome using HISAT2
Reads that mapped to the viral genome were counted using FeatureCounts
Assembly: MesAur1.0
Supplementary files format and content: Raw read count matrix.csv is a matrix of raw read counts for the host genome
Supplementary files format and content: Viral Raw read counts.csv is a matrix of raw read counts for the viral genome

organism: Mesocricetus auratus

source_name: organotypic cerebellar slice culture

growth_protocol: Sagittal sections (300μm in thickness) were prepared from the cerebellar tissue using a vibratome (Microm HM650V) and transferred to Millicell CM transwell inserts within 6-well culture plates with medium for long-term culturing

extract_protocol:
Total RNA from organotypic slices were isolated using the RNeasy mini kit (Qiagen) and quantified using the nanodrop
Next generation sequencing libraries were prepared from 100ng of total RNA using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) with the TruSeq RNA Single Indexes Set B (Illumina)

treatment_protocol: Hamster cerebellar brain slices were treated with either 0 (Mock), 450 or 6850 PFU of SARS-CoV-2 by pipetting 2of diluted inoculum directly onto each slice

value: hamster (golden syrian)

tag: tissue

value: organotypic cerebellar slice culture

tag: timepoint

value: 5 dpi


title: INF-dpi-5-C

tag: strain


title: T cells, DSF,  bio rep 3

value: from mouse lymph nodes

tag: cell type


title: GC080710_B06


title: GC080710_B04


title: INF-dpi-1-C

value: 1 dpi


title: T0_rep5

value: Day 0


title: T cells, DMSO, biol rep 2

value: primary OT-I T cells

value: T cells

value: wildtype


title: INF-dpi-5-A


title: Apo_fox

city: Nanjing

first: Jie

last: Dong

address: Hankou road 22

institute: Nanjing University

description: tsst

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: breast cancer

tag: chip antibody

value: Anti-FOXO3A antibody, Abcam, Cat.ab12162


title: INF-dpi-1-A


title: Epidermis, Chrm3KO, Replicate 2, scRNAseq

city: Irvine

first: Bogi

last: Andersen

address: Sprague Hall Rm 206

institute: University of California, Irvine

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: epidermis

extract_protocol:
In brief, skin samples were collected from postnatal day 0 Chrm3 KO C57BL/6J mice and incubated overnight in epidermal separation buffer. The epidermis was then separated from the dermis and the suspension of epidermal cells were passed through a 40 μM filter. Dead cells were removed using Dead Cell Removal kit.
University of California, Irvine, Genomic High Throughput Facility (UCI-GHTF) prepared the Chromium Single Cell 3‘ v1 (10x Genomics) libraries according to manufacter’s protocol. The libraries were sequenced with Illumina NovaSeq6000.

value: epidermis

value: skin cells

value: Chrm3 KO

tag: Sex

value: Male

tag: age

value: Postnatal day 0


title: T28_rep5

source_name: Huh 7

tag: cell line

value: Huh 7

value: Hepatocellular carcinoma (HCC) cells

value: Day 28


title: T28_rep3


title: INF-dpi-14-C

value: hamster (golden syrian)

value: organotypic cerebellar slice culture

value: 14 dpi


title: T0_rep4

value: Day 0


title: GC080710_A01


title: Apo_fox Input

description: Input

value: input


title: INF-dpi-1-B

value: 1 dpi


title: T28_rep2


title: T0_rep2


title: T0_rep3


title: T0_rep1


title: INF-dpi-14-B


title: Alg60 SMN+chABC Ribbons Day 32

city: Albany

first: Janet

middle: L

last: Paluh

state: NY

address: CNSE, Nanofab East, 257 Fuller Road

department: Nanobioscience

institute: SUNY Polytechnic Institute

description:
NMP differentiation protocol
Alg60_chABC_S10

data_processing:
Illumina RTA 2.2.68 Basecaller
Hisat2 Alignments 2-2.1.0 to UCSC HG38
FeatureCounts v1.6.2 Quantiication
DESeq Differential Expression
Genome_build: hg38

source_name: Human iPSC  line F3.5.2 passage 20

growth_protocol: hiPSC in 2D grown in mTeSR Plus medium were induced to Neuromesodermal Progenitors (NMPs) and neurons as described in text and 2D colonies dissociated

extract_protocol: TruSeq Stranded RNA (illumina)

value: African-American self designation

value: hiPSC derived

value: Alg60 SMN+chABC Ribbons

tag: developmental stage

value: Day 32


title: Alg60 SMN Ribbons Day 32

description:
NMP differentiation protocol
Alg60_S9

value: Alg60 SMN Ribbons


title: CTL-dpi-5-C

value: 5 dpi

value: Mock


title: CTL-dpi-5-B


title: CTL-dpi-5-A


title: ATAC_D13_rep1

description: Genome-wide library of tagmented fragments

data_processing:
Library Strategy: ATAC-seq
Mapping : bowtie -m 2 --maxIns 350, hg9
For un-mapping reads : trimming adaptors trim_galore -- length 10, combining overlapping R1-R2 reads : flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with  bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks
Genome_build: hg19
Supplementary_files_format_and_content: bigWig : (DEEPtools) bamCoverage converison of filtered fragments (reconstructed, duplicate-filtered fragments : see above) from bam to bigwig,  (--binSize 10 --normalizeUsingRPKM --minMappingQuality 30)

extract_protocol:
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013) on single cell suspensions. 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen).
Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). The libraries were quantified using the universal library quantification kit (KAPA Biosystems).

value: Erythroid

tag: gender

value: Female

tag: differantiation day

value: Day 13


title: ATAC_D13_rep2


title: CTL-dpi-1-C


title: Epidermis, Chrm3KO, Replicate 1, scRNAseq

value: epidermis

value: skin cells

tag: genotype

value: Chrm3 KO

value: Male

value: Postnatal day 0


title: NHLF_C018_BSL_S10

description:
Normal human Lung fibroblasts BSL
counts_human

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 or mouse genome mm10 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 92 and Mus musculus mm10 Ensembl release 86
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: Lung Fibroblasts

growth_protocol: see above

extract_protocol:
Total RNA was extracted from either the snap-frozen liver tissues or HSCs lysate using Trizol (Invitrogen) followed by RNeasy column (Qiagen) purification.
Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol:
Normal human lung fibroblasts (Passage 3) at baseline
see above

value: BSL

tag: rin


title: CTL-dpi-14-C

value: hamster (golden syrian)

value: organotypic cerebellar slice culture

value: 14 dpi


title: NHLF_C018-IL11_S12

description:
Normal human Lung fibroblasts IL11
counts_human

treatment_protocol:
Normal human lung fibroblasts (Passage 3) were stimulated with 5ng/ml of recombinant human IL-11 for 24h
see above


title: NHLF_C018-TGFB_S11

description:
Normal human Lung fibroblasts TGFB
counts_human

treatment_protocol:
Normal human lung fibroblasts (Passage 3) were stimulated with 5ng/ml of recombinant human TGFB1 for 24h
see above

value: TGFB


title: NHLF_014_BSL_S13


title: non-3d-8

city: Los Angeles

first: Yuyan

last: Cheng

state: CA

address: 695 Charles E Young Dr S Rm 2305

department: Neurology

institute: UCLA

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the HTSeq program with mouse mm10 refSeq (refFlat table) as a reference.
Differential expression analysis was conducted with the Bioconductor package edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: raw read count for each sample

source_name: Retinal Ganglion Cells

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For RNA-seq, RNA from 5,000 – 10,000 FACS-sorted RGCs were isolated with RNeasy Micro Kit (Qiagen), and RNA-seq libraries were prepared with SMART-Seq v4 Ultra Low Input RNA Kit (Clontech), following manufacturers’ protocols.
The cDNA was fragmented to 300 base pairs (bp) using the Covaris M220 (Covaris), and then the manufacturer’s instructions were followed for end repair, adaptor ligation, and library amplification. The libraries were quantified by the Qubit dsDNA HS Assay Kit (Molecular Probes); Library size distribution and molar concentration of cDNA molecules in each library were determined by the Agilent High Sensitivity DNA Assay on an Agilent 2200 TapeStation system.

value: Crush (Day 3)

value: WT Control

value: Retinal Ganglion Cells


title: NHLF_014-TGFB_S14

first: Eleonora

last: Adami

address: 8 College Road

institute: Duke-NUS Medical School


title: CTL-dpi-14-B

value: Mock


title: CTL-dpi-14-A


title: ChIP-seq_Input_BT549_rep2

city: Daejeon

first: Taemook

last: Kim

address: 291 Daehak-ro, Yuseong-gu

department: Biological sciences

country: South Korea

institute: Korea Advanced Institute of Science and Technology

data_processing:
(ChIP-seq) The ChIP-seq data were aligned to the human reference genome (hg19) using bowtie2.
CTCF and H3K27ac peaks were called using Macs2 with option (p < 0.001).
Super enhancer and enhancer was identified using Homer (findPeaks) with options (-style superhistone and -typical) from H3K27ac ChIP-seq data.
BigWig was generated by normalizing to total mapped read each sample. Briefly, bedGraph was generated using a Macs2 (pileup) and normalized by total mapped reads. The replicate sample was calculated as an average normalized bedGraph. Finally, normalized bedGraph was converted to bigWig using a bedGraphToBigWig.
The CTCF enrichment around the HMEC CTCF peak at the HMEC TAD boundaries was used meta value calculated using bwtool with meta-option (up:meta:down, 1:1:1). The enrichment difference of CTCF or H3K27ac between HMEC and BT549 cells was calculated as log2 (BT549/HMEC) value, respectively.
Genome_build: hg19

source_name: Triple negative breast cancer B cell

growth_protocol: All cell lines, which is a normal cell and breast cancer cell, used in this study were purchased from ATCC. Human mammary epithelial cell (HMEC, PCS-600-010, ATCC) was cultured in mammary epithelial cell basal medium (PCS-600-030, ATCC) supplemented with mammary epithelial cell growth kit (PCS-600-040) as ATCC suggested. T47D (HTB-133) was cultured in RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (ATCC, 30-2020) and 0.2 units/ml of human insulin (Life Technologies, 12585-014). BT549 (HTB-122) was cultured in RPMI-1640 supplemented with 10% FBS and 0.023 units/ml of human insulin. HCC1954, HCC70, and ZR-75-30 were cultured in RPMI-1640 supplemented with only 10% FBS. All cell lines were grown in the humidified incubator at 37°C containing 5% CO2.

extract_protocol:
(ChIP-seq) The cells were washed twice with PBS and incubated with 1% formaldehyde for 10 min at RT. The crosslinking was quenched with 125 mM glycine for 5min at RT, and the cells were harvested with cold PBS and suspended in SDS lysis buffer (50mM Tris-HCl, pH 8.0, 1% SDS, 10mM EDTA). Following the suspended chromatin was sheared using a ultrasonicator (Covaris S220) and incubated overnight with the relevant antibodies against anti-CTCF (Millipore; 07-729), anti-H3K27ac (Abcam; ab4729) and Protein A, G sepharose (GE Healthcare; 17-1279-03 and 17-0618-05) at 4°C with agitation. The Immune complex was washed in the order of low-salt wash buffer (20mM Tris-HCl, pH8.0, 150mM NaCl, 0.1% SDS, 1% Triton X-100, 2mM EDTA), high-salt wash buffer (20mM Tris-HCl, pH 8.0, 250mM LiCl, 1% NP-40, 1% sodium deoxycholate, 1mM EDTA), and LiCl wash buffer, and finally, washed twice with TE buffer. Following the washed immune complexes were eluted with elution buffer (1% SDS, 0.1M NaHCO3). Finally the immune complexes were eluted with elution buffer (1% SDS, 0.1M NaHCO3) and de-crosslinked overnight at 68°C. The immunoprecipitated DNA was treated with proteinase K and RNase A and phenol-chloroform-isoamyl alcohol precipitation.
(ChIP-seq) The ChIP-seq libraries were prepared using a Accel-NGS 2S Plus DNA Library Kit (SWIFT; 21024)

tag: subtype

value: Triple negative breast cancer B


title: ChIP-seq_Input_HCC70_rep2

source_name: Triple negative breast cancer A cell

value: Triple negative breast cancer A


title: ChIP-seq_Input_BT549_rep1


title: 24h after transfection CT mRNA

city: Seoul

first: Hyeon-Cheol

last: Lee

address: 136, Changgyeonggung-ro,Jongro-gu

department: Research center

institute: BPgene Co., Ltd.

description:
RNAseq for CT-transfected MDA-MB-468 cell at 24h incubation
468-CT-24h

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling and quality check using FastQC v0.11.7
Sequenced reads were trimmed for adaptor sequence using Trimmomatic 0.38, and mapped to hg38 whole genome using HISAT2 version 2.1.0 and Bowtie2 2.3.4.1
Transcript assembly and abundance estimation using StringTie v2.1.3b
Statistical significance of the differential expression data was determined using DESeq2
Gene-enrichment and functional annotation analysis and pathway analysis for significant gene list were performed based on gProfiler
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values
Supplementary files format and content: Matrix table with raw gene counts

source_name: Basal like cell (epithelial morphology)

growth_protocol: Human triple-negative breast cancer cell lines (MDA-MB-468)  were cultured in Plasmax™ cell culture medium (Xymbio) supplemented with 2.5% dialyzed FBS (Gibco) and 1X Penicillin-Streptomycin (Gibco). Cells were maintained at 37 °C under 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was isolated from cells using TRIzol solution. After RNA extraction, it was quantified at a concentration of 1 μg.
Libraries were prepared according to TruSeq Stranded mRNA Sample Preparation Guide, Part #  15031047 Rev. E accompanying the TruSeq Stranded mRNA LT Sample Prep Kit

treatment_protocol: Cells were plated 24 h before transfection in a 6-well plate at 5x105 cells/well. Cells were transfected 1.25 µg of mRNA complexed with Lipofectamine® MessengerMAX (Invitrogen) diluted in Opti-MEM medium (Gibco) to obtain a total volume of 200 µl. The transfection mix was added to the cells and cells were incubated at 37 °C, 5% of CO2 incubator during a time period depending on the experiment.

value: TNBC cells

value: Transfection of CT mRNA for 24h


title: non-3d-5


title: NHLF_014-IL11_S15

city: Singapore


title: non-3d-7


title: non-3d-4


title: LONZA_NHLF3_BSL_S7

description:
Normal human Lung fibroblasts BSL (Commercial)
counts_human

source_name: Lung Fibroblasts (Commercial)


title: ChIP-seq_Input_HCC1954_rep1

source_name: Her2+ cell

value: Her2 positive


title: ChIP-seq_Input_HCC70_rep1


title: LONZA_NHLF3-TGFB_S8

description:
Normal human Lung fibroblasts TGFB (Commercial)
counts_human


title: MEF rep2 (RNA-seq)

data_processing:
Sequenced reads were mapped to mm8 (release M19) whole genome and reads per gene were counted using STAR (ver. 2.5b).
Read counts were analyzed with R DeSeq2 package.
Genome_build: mm9
Supplementary_files_format_and_content: raw_count.csv: tab delimited csv file including raw counts for each sample
Supplementary_files_format_and_content: normalized_count.csv: tab delimited csv file including normalized counts for the each sample
Supplementary_files_format_and_content: model_fc.csv: tab delimited csv file including FC, p-value and adjusted p-value

growth_protocol: MEF were generated from E13.5 Bcl11b-tdTomato mice embryos and cultivated in DMEM medium supplemented with 10% foetal bovine serum (FBS), 100U/ml penicillin / streptomycin (PS), 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM Non Essential Amino Acids (NEAA) and 0.1mM b-mercaptoethanol. iPS cells were grown in DMEM containing 15% KnockOut™ Serum Replacement, 1,000 U/ml leukemia inhibitory factor, 100U/ml PS, 1mM sodium pyruvate, 2mM L-glutamine, 0.1mM NEAA and 0.1mM b-mercaptoethanol. Malignant cells were cultivated in the same medium than MEF.

extract_protocol:
RNAs were extracted with Qiagen RNeasy kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEF are infected by OSKM retroviruses to induce Repro or by K-Ras G12V, shp53 lentiviruses combined with cMyc retroviral infection to induce Transfo and FACS-cell sorted after 5 days.

value: mouse embryonic fibroblast (MEF)

value: control mouse embryonic fibrobalsts


title: non-3d-10

value: CHOP Knockout


title: 12h after transfection CT mRNA

description:
RNAseq for CT-transfected MDA-MB-468 cell at 12h incubation
468-CT-12h

value: Transfection of CT mRNA for 12h


title: CTL-dpi-1-B

value: hamster (golden syrian)

value: 1 dpi


title: ChIP-seq_Input_ZR7530_rep2

source_name: Luminal B cell

value: Luminal B


title: CHOP-3d-5


title: CTL-dpi-1-A

value: organotypic cerebellar slice culture


title: MEF rep1 (RNA-seq)


title: 24h after transfection NT5M mRNA

description:
RNAseq for NT5M-transfected MDA-MB-468 cell at 24h incubation
468-NT5M-24h

value: Transfection of NT5M mRNA for 24h


title: LONZA_NHLF3-IL11_S9

description:
Normal human Lung fibroblasts IL11 (Commercial)
counts_human


title: ChIP-seq_Input_HCC1954_rep2


title: ChIP-seq_Input_ZR7530_rep1


title: LONZA_NHLF2_BSL_S4

value: BSL


title: ChIP-seq_Input_T47D_rep2

source_name: Luminal A cell

value: Luminal A


title: 12h after transfection NT5M mRNA

description:
RNAseq for NT5M-transfected MDA-MB-468 cell at 12h incubation
468-NT5M-12h

value: Transfection of NT5M mRNA for 12h


title: 6h after transfection NT5M mRNA

description:
RNAseq for NT5M-transfected MDA-MB-468 cell at 6h incubation
468-NT5M-6h

value: Transfection of NT5M mRNA for 6h


title: LONZA_NHLF2-TGFB_S5

value: TGFB


title: CHOP-3d-2

value: Crush (Day 3)

value: Retinal Ganglion Cells


title: ChIP-seq_Input_T47D_rep1


title: CHOP-3d-3


title: ChIP-seq_Input_HMEC_rep2

source_name: human mammary epithelial cell

value: Primary Mammary Epithelial Cell


title: CHOP-3d-1


title: LONZA_NHLF2-IL11_S6


title: LONZA_NHLF1_BSL_S1


title: 6h after transfection CT mRNA

description:
RNAseq for CT-transfected MDA-MB-468 cell at 6h incubation
468-CT-6h

value: TNBC cells

value: Transfection of CT mRNA for 6h


title: 6h after transfection cdN mRNA

description:
RNAseq for CdN-transfected MDA-MB-468 cell at 6h incubation
468-cdN-6h

value: Transfection of CdN mRNA for 6h


title: ChIP-seq_Input_HMEC_rep1


title: 12h after transfection cdN mRNA

description:
RNAseq for CdN-transfected MDA-MB-468 cell at 12h incubation
468-cdN-12h

value: Transfection of CdN mRNA for 12h


title: CEBPG-3d-9

value: CEBPG Knockout


title: LONZA_NHLF1-TGFB_S2


title: CEBPG-3d-8


title: ATAC-seq_BT549_rep2

data_processing:
(ATAC-seq) ATAC-seq data were aligned to the human reference genome (hg19) using bowtie2 with option (-X 100) to extract a nucleosome-free region less than 100bp.
The duplicated reads were discarded using Picard.
Macs2 was used to call an open chromatin region with option (--shift 100, --extsize 200, p-value < 0.001).
The chromatin accessibility around the HMEC CTCF peak at the HMEC TAD boundaries was used meta value calculated using bwtool with meta-option (up:meta:down, 1:1:1).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol: (ATAC-seq) Nuclei were incubated in fresh 25ul TD Buffer (10mM Tris-HCl, 5mM MgCl2, 10% dimethylformamide, pH8.0) with 2.5ul Tn5 Transposase for 30min at 37°C. QIAquick PCR purification kit(Qiagen; cat. no. 28106) was used to purify DNA fragments. We used HiFi HotStart ReadyMix (KAPA; KK2601) for library amplification following provided manual except number of PCR cycle. The amplified library was purified with a QIAquick PCR purification kit (Qiagen; cat. no. 28106)

value: Triple negative breast cancer B


title: ATAC-seq_BT549_rep1


title: LONZA_NHLF1-IL11_S3


title: CEBPG-3d-6


title: 6h control

description:
RNAseq for MDA-MB-468 cell at 6h incubation
468-CON-6h

value: No transfection


title: 24h control

description:
RNAseq for MDA-MB-468 cell at 24h incubation
468-CON-24h


title: CHOP-3d-4

value: CHOP Knockout


title: ATAC-seq_HMEC_rep2

value: HMEC


title: BMSCs, miR130b-3p_rep2, Day 3

first: Qiancheng

last: Xiao

address: Building 25, No. 1188, LIANHANG Road, Pujiang Town, Minhang District, Shanghai

institute: Shanghai OE Biotech Co., Ltd

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences using fastqc v0.11.5
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v 0.36
Using hisat2 v 2.2.1.0  to align clean reads to the GRCh38.p12
Using the estimateSizeFactors function of the DESeq v1.18.0 （pvalue<0.05, |log2FoldChange|>1）   R package to normalize the counts
Assembly: Hg38

source_name: Primary isolated cells

growth_protocol: Mesenchymal stem cells were maintained in Human Bone Marrow Mesenchymal Stem Cell Medium (Cyagen, HUXMA-90011) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
miR-130a-3p or miR-130b-3p minics  were transfected using Lipofectamine RNAiMAX according to the manufacturer’s instructions
About 3 days after transfection, cells were harvested and lysised using Trizol.

value: Primary isolated cells

value: mesenchymal stem cells

value: miR-130b-3p overexpression

value: miRNA mimic transfection

tag: time

value: Day 3


title: 24h after transfection cdN mRNA

description:
RNAseq for CdN-transfected MDA-MB-468 cell at 24h incubation
468-cdN-24h

value: Transfection of CdN mRNA for 24h


title: ATF3-3d-8

value: Crush (Day 3)

value: ATF3 Knockout

value: Retinal Ganglion Cells


title: ATAC-seq_HMEC_rep1

value: Primary Mammary Epithelial Cell


title: BMSCs, miR130b-3p_rep1, Day 3


title: RNA-seq_TNBC_Tissue13

data_processing:
(RNA-seq) The sequenced short reads were aligned to the human reference genome (hg19) using STAR.
The aligned read was used to generate read count and fragment per kilobase of transcript per million (FPKM) of genes using Cufflinks (Cuffnorm and Cuffdiff).
Differentially expressed genes (DEG) between normal (HMEC and normal tissue) and breast cancer (cell or tissue) was classified by statistically significant criteria (q-value<0.01, abs(log2FC) > 1) using Cuffdiff.
Gene ontology (GO) analysis of DEGs was performed using a ConsensusPathDB-human (KEGG pathway and gene ontology).
Gene expression and DEG were visualized by heatmap and boxplot using the R package (pheatmap and ggplot2). The vocano plot and venn diagram was drawn using a R package (ggplot2)
Genome_build: hg19
Supplementary_files_format_and_content: diff.txt.gz

source_name: Triple negative breast cancer tissue, patient13

growth_protocol:
All cell lines, which is a normal cell and breast cancer cell, used in this study were purchased from ATCC. Human mammary epithelial cell (HMEC, PCS-600-010, ATCC) was cultured in mammary epithelial cell basal medium (PCS-600-030, ATCC) supplemented with mammary epithelial cell growth kit (PCS-600-040) as ATCC suggested. T47D (HTB-133) was cultured in RPMI-1640 (ATCC, 30-2001) supplemented with 10% FBS (ATCC, 30-2020) and 0.2 units/ml of human insulin (Life Technologies, 12585-014). BT549 (HTB-122) was cultured in RPMI-1640 supplemented with 10% FBS and 0.023 units/ml of human insulin. HCC1954, HCC70, and ZR-75-30 were cultured in RPMI-1640 supplemented with only 10% FBS. All cell lines were grown in the humidified incubator at 37°C containing 5% CO2.
The frozen fresh tumor samples were collected from resected breast tumors from patients at the Seoul National University Hospital (SNUH) in South Korea with informed consent and institutional IRB approval. The frozen tissues provided are as follows: Contralateral breast normal tissue and triple negative breast cancer tissue. These frozen samples were snap-frozen in liquid nitrogen and stored at -80°C.

extract_protocol:
(RNA-seq) Total RNAs were purified using TRIzol reagent (Invitrogen, cat # 15596-026) according to the manufacturer’s protocol. mRNA isolation were performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; E7490L)
(RNA-seq) The RNA-seq libraries were generated using a NEBNext Ultra II Directional RNA Library Prep Kit (NEB; E7760S).

tag: tissue/cell type

tag: histological subtype

value: Triple negative breast cancer IDC


title: 12h control

description:
RNAseq for MDA-MB-468 cell at 12h incubation
468-CON-12h

value: TNBC cells

tag: treatment


title: ATF4-3d-1

value: ATF4 Knockout


title: ATF3-3d-9


title: ATF4-3d-3


title: RNA-seq_TNBC_Tissue14

source_name: Triple negative breast cancer tissue, patient14


title: BMSCs, miR130a-3p_rep2, Day 3

value: miR-130a-3p overexpression


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-SMC2]

city: Magdeburg

first: Constanze

last: Nossol

address: Leipziger Str. 44

department: Medical Faculty

institute: Otto-von-Guericke University

description: Gene expression data from liver sample of offspring

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42C on Affymetrix GeneChip Porcine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

organism: Sus scrofa

source_name: Jejunum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

treatment_protocol: Air-liquid interface culture (Ali) and submerged membrane culture (SMC) were applied to porcine enterocytes.

tag: agen

value: SMC

tag: passage rate


title: ATF3-3d-6

tag: strain

tag: cell type


title: BMSCs, miR130a-3p_rep3, Day 3

city: Shanghai


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-SMC3]


title: RNA-seq_TNBC_Tissue11

source_name: Triple negative breast cancer tissue, patient11


title: BMSCs, miR130a-3p_rep1, Day 3


title: ATF3-3d-7


title: RNA-seq_TNBC_Tissue10

source_name: Triple negative breast cancer tissue, patient10


title: RNA-seq_TNBC_Tissue12

source_name: Triple negative breast cancer tissue, patient12


title: ATF3-3d-5


title: RNA-seq_TNBC_Tissue2

source_name: Triple negative breast cancer tissue, patient2


title: RNA-seq_TNBC_Tissue3

source_name: Triple negative breast cancer tissue, patient3


title: BMSCs, miR130b-3p_rep3, Day 3


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-SMC1]


title: CEBPG-3d-10

source_name: Retinal Ganglion Cells

value: CEBPG Knockout


title: rna-no-crush-rep1

description: rawEx.tsv.gz

data_processing:
For RNA-seq, raw sequenced reads were mapped to the reference genome Mus musculus (mm10) refSeq (refFlat) using STAR with default parameter.
Data quality was assessed on base-quality calls, nucleotide composition of sequences, insert sizes, per cent of uniquely aligned reads and transcript coverage using custom scripts and Picard Tools.
Total counts of read fragments aligned to candidate gene regions were derived using the HTSeq program with mouse mm10 refSeq (refFlat table) as a reference.
Differential expression analysis was conducted with the Bioconductor package edgeR.
mm10

value: No Crush (Day0)


title: RNA-seq_TNBC_Tissue7

source_name: Triple negative breast cancer tissue, patient7


title: rna-4dpc-rep3

description: rawEx.tsv.gz

value: Crush (Day 4)


title: CORL47dCas9VP64_sgZFP36L1#2_biolrep2

first: Matthew

last: Oser

state: MA

address: 450 Brookline Avenue, Mayer 457

institute: Dana-Farber Cancer Institute

data_processing:
The abundance of transcripts reflects gene expression level directly. In RNA-seq experiments, gene expression level is estimated by the abundance of transcripts (count of sequencing) that mapped to genome or exon. Read counts is proportional to gene expression level, gene length and sequencing depth. FPKM (short for the expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) is the most common method of estimating gene expression levels, which takes the effects into consideration of both sequencing depth and gene length on counting of fragments (Mortazavi et al., 2008).
Assembly: hg38
Supplementary files format and content: FPKM

growth_protocol: CORL47 cells were maintained in RPMI 1640 supplemented with 2mM Glutamine, 10% FBS, and 1% antibiotics (P/S) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen #74106) per the manufacturer's instructions including a DNase digestion step.
The libraries for RNA-seq are prepared using NEBNext Ultra II non-stranded kit.  Paired end 150bp sequencing was performed on Novaseq6000 sequencer using S4 flow cell. Sequencing reads were mapped to the hg38 genome by STAR. Statistics for differentially expressed genes were calculated by DESeq2.

treatment_protocol:
CORL47 cells were first infected with lenti-dCas9-VP64_Blast (Addgene #61425) and selected with Blasticidin and then superinfected with pXPR_502-Puro (Addgene #96923) lentivirus  and an sgRNA targeting the promoter of ZFP36L1 (sgZFP36L1-1 and sgZFP36L1-2) or a non-targeting sgRNA (sgControl) and selected with puromycin to make stable cell lines.
Stable cell lines with endogenous CRISPR activation of ZFP36L1 confirmed by RT-qPCR were plated at 200,000 cells/mL in complete media (above) and harvested for RNA after 3 days. Performed in two biological replicates.

value: Small cell lung cancer cell line

value: ZFP36L1 CRISPR activation (sg2)

value: untreated

value: steady state


title: BMSCs, shControl3, Day 3

value: Primary isolated cells

value: mesenchymal stem cells

value: WT

value: miRNA mimic transfection

value: Day 3


title: RNA-seq_TNBC_Tissue1

source_name: Triple negative breast cancer tissue, patient1

value: Triple negative breast cancer IDC


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-ALi2]

value: ALi


title: p38_wt_irradiated_rep1

city: New York

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

tag: Sex

value: male

value: irradiated


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-ALi3]


title: BMSCs, shControl1, Day 3


title: BMSCs, shControl2, Day 3


title: p38_wt_irradiated_rep4


title: p38_wt_unirradiated_rep5

value: unirradiated


title: RNA-seq_TNBC_Tissue9

source_name: Triple negative breast cancer tissue, patient9


title: rna-no-crush-rep3

description: rawEx.tsv.gz


title: p38_wt_irradiated_rep5


title: p38_wt_irradiated_rep3


title: CORL47dCas9VP64_sgZFP36L1#1_biolrep1

value: ZFP36L1 CRISPR activation (sg1)


title: p38_wt_unirradiated_rep4


title: Transcriptome profile from intestinal porcine enterocytes [IPEC1-ALi1]


title: RNA-seq_TNBC_Tissue8

source_name: Triple negative breast cancer tissue, patient8


title: rna-4dpc-rep2

description: rawEx.tsv.gz


title: p38_wt_unirradiated_rep2


title: rna-4dpc-rep1

description: rawEx.tsv.gz


title: CORL47dCas9VP64_sgZFP36L1#1_biolrep2


title: RNA-seq_TNBC_Tissue5

source_name: Triple negative breast cancer tissue, patient5


title: p38_wt_irradiated_rep2


title: p38_wt_unirradiated_rep3


title: rna-3dpc-rep3

description: rawEx.tsv.gz

value: Crush (Day 3)


title: H1876Cas9_sgZFP36L1#1_1nMORY1001_biolrep2

growth_protocol: NCI-H1876 cells were maintained in DMEM/F12 supplemented 5% FBS, antibiotics (P/S), and HITES [10 nM hydrocortisone, Insulin-Transferrin-Selenium (Gemini), and 10 nM beta-estradiol] in humidified atmosphere with 5% CO2 at 37C

treatment_protocol:
NCI-H1876 cells were first transduced with Cas9-Blast lentivirus, selected with blasticidin, and then superinfected with lentiGuide puro ZFP36L1 sgRNAs or non-targeting sgRNAs lentiviruses and selected with puromycin to make stable cell lines.
The cells above were then plated at 250,000 cells/mL in complete media above in the presence of ORY-1001 (1 nM) or DMSO. 7 days later cells were harvested for RNA. Peformed in two biological replicates.

value: ZFP36L1 CRISPR knockdown (sg1)

value: ORY-1001 1 nM (LSD1 inhibitor)

value: Day 7


title: CORL47dCas9VP64_sgControl_biolrep2

value: Small cell lung cancer cell line

value: WT (Non-targeting sgRNA Control)

value: untreated


title: rna-3dpc-rep2

description: rawEx.tsv.gz


title: rna-2dpc-rep2

description: rawEx.tsv.gz

value: Crush (Day 2)


title: rna-no-crush-rep2

description: rawEx.tsv.gz

value: No Crush (Day0)


title: rna-3dpc-rep1

description: rawEx.tsv.gz


title: CORL47dCas9VP64_sgZFP36L1#2_biolrep1

value: ZFP36L1 CRISPR activation (sg2)

value: steady state


title: RNA-seq_BT549_rep1

source_name: Triple negative breast cancer B cell

value: Triple negative breast cancer B cell


title: RNA-seq_HCC70_rep1

source_name: Triple negative breast cancer A cell

value: Triple negative breast cancer A cell


title: RNA-seq_HCC70_rep2


title: RNA-seq_TNBC_Tissue6

source_name: Triple negative breast cancer tissue, patient6

value: Triple negative breast cancer IDC


title: p38_dn_irradiated_rep5

value: male

value: irradiated


title: CORL47dCas9VP64_sgControl_biolrep1


title: RNA-seq_TNBC_Tissue4

source_name: Triple negative breast cancer tissue, patient4


title: rna-2dpc-rep1

description: rawEx.tsv.gz


title: H1876Cas9_sgZFP36L1#1_1nMORY1001_biolrep1


title: RNA-seq_BT549_rep2


title: H1876Cas9_nosite1_1nMORY1001_biolrep2

value: WT (Non-targeting sgRNA Control, nosite1)


title: p38_wt_unirradiated_rep1

value: unirradiated


title: H1876Cas9_nosite1_DMSO_biolrep2

value: DMSO


title: p38_dn_irradiated_rep2


title: p38_dn_irradiated_rep4


title: rna-1dpc-rep3

description: rawEx.tsv.gz

value: Crush (Day 1)


title: H1876Cas9_nosite1_1nMORY1001_biolrep1

value: ORY-1001 1 nM (LSD1 inhibitor)

value: Day 7


title: RNA-seq_HCC1954_rep2

source_name: Her2+ cell

value: Her2+ cell


title: p38_dn_irradiated_rep3


title: rna-1dpc-rep2

description: rawEx.tsv.gz


title: H1876Cas9_nosite1_DMSO_biolrep1

value: Small cell lung cancer cell line


title: RNA-seq_ZR7530_rep2

source_name: Luminal B cell

value: Luminal B cell


title: rna-1dpc-rep1

description: rawEx.tsv.gz


title: atac.no.crush.rep6

description: atac.3dpc.rep6.macs2_peaks.narrowPeak_rmBlk

data_processing:
For ATAC-seq, Raw sequencing fastq files were assessed for quality, adapter content and duplication rates with FastQC, trimmed using trim-galore and aligned with bowtie2.The reference genome was mouse GRCm38 vM11. Samtools was used to calculate the read statistics, and Picard Tools was used to remove duplicate.
MACS2 was used to call peaks on each sample. Peaks from each sample were merged to a set of union peaks across all conditions using bedtools merge. The consensus peaks were further annotated to the transcriptional start site of genes in a distance of +-2 kb from the gene start using ChIPseeker. Gencode vM24 was used for annotations.
We obtained the number of reads for consensus peaks (hereafter referred to as peaks) across samples using featureCounts from the Subread package, and the GC content using bedtools nuc.
We then calculated normalization factors for each peak accounting for GC content, peak width, and total number of unique non-mitochondrial fragments sequenced using conditional quantile normalization from cqn package. To obtain differential accessible peak-regions (DAR) comparing injured vs uninjured RGCs, we used a negative binomial regression with normalization based on the size factors from cqn and implemented in DEseq2 with default parameters (fitType=“parametric”,test=“Wald”). Normalized peak-count matrix with batch effects regressed out was used for subsequent analysis.
mm10
peak files in bed format for each sample

extract_protocol:
Samples were dissociated in papain, followed by FACS sorting. For ATAC-seq, 50,000 - 100,000 sorted RGCs were lysed in 100 µL ice-cold Resuspension Buffer (RSB, 10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, pH=7.4) with 0.1% NP40, 0.1% Tween- 20, and 0.01% Digitonin. Cell lysis were washed with 1 ml of cold ATAC-RSB containing 0.1% Tween-20 but NO NP40 or digitonin, and centrifuged at 4 °C for 10 minutes at 500 x g. Pelleted nuclei were resuspended gently in 50 µL transposition mix (25 ul 2x TD buffer, 2.5 ul transposase (100nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, 5 ul H2O) and incubated for 30 minutes at 37 °C. DNA was cleaned using Zymo DNA Clean and Concentrator-5 Kit.
Purified DNA was PCR amplified 5 cycles in a 50 µL reaction with Illumina Nextera adaptors using NEBNext High Fidelity 2x Master Mix. To determine the number of additional cycles to amplify the libraries, a side qPCR reaction was performed using 5 µL (10%) of the pre-amplified PCR. We used the Ct value of the qPCR at ¼ maximum fluorescence as the number of additional cycles. Final PCR products were cleaned using Zymo DNA Clean and Concentrator-5 Kit, and quantified by the KAPA Library Quantification kit prior to pooling and sequencing.

value: No Crush (Day0)


title: RNA-seq_ZR7530_rep1


title: p38_dn_unirradiated_rep5


title: atac.no.crush.rep5

description: atac.3dpc.rep5.macs2_peaks.narrowPeak_rmBlk


title: p38_dn_irradiated_rep1


title: RNA-seq_T47D_rep1

source_name: Luminal A cell

value: Luminal A cell


title: atac.no.crush.rep4

description: atac.3dpc.rep4.macs2_peaks.narrowPeak_rmBlk


title: p38_dn_unirradiated_rep4