title: HDAC7-KO_rep2_input

city: Barcelona

first: Maria

last: Vila-Casadesús

state: Barcelona

address: Carrer del Dr. Aiguader, 88

institute: CRG

data_processing:
Library strategy: hydroxyMeDIP-seq
Fastq data were processed with Trim Galore-0.4.2 and Cutadapt-1.6
hMeDIP-seq reads were aligned to the mm10 genome assembly using bowtie2 program
Bigwig were computed using deeptools and RPKM normalization.
Peaks were called with macs2 bdgpeakcall option (-c 250 -l 10 -g 10). Peaks that intersect with peaks in the corresponding input samples were removed.
Genome_build: mm10
Supplementary_files_format_and_content: bw and bed

source_name: Progenitor B cells

extract_protocol:
Bone marrow was extracted from mice legs, B220+CD43+IgM- pro-B cells were isolated on a FACS Aria sorter (BD Biosciences) and genomic DNA was exctracted by using Quick-DNA Miniprep Plus Kit from ZYMO (Cat#D4068). 1ug of genomic DNA/sample was sonicated to 350bp fragments.
Antibody immunoprecipitation: Resulting DNA was incubated and isolated with anti- 5hmC antibody and magnetic beads
Libraries were constructed according to Illumina standard protocols and were preceded by end repair reaction and adaptor ligation.
Amplification of the purified DNA with specific primers

value: Bone marrow

value: 4-6 weeks

value: Hdac7 fl/-


title: WT_rep2_input

status: Public on Jun 28 2022

type: SRA

country: Spain

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

tag: tissue

tag: age

tag: genotype

value: wild-type


title: HDAC7-KO_rep1_input


title: WT_rep1_input


title: B cells isolated from donor 1 at visit D (HIV-) [ETH006586]

city: Silver Spring

first: Rasmi

last: Thomas

state: MD

address: 503 Robert Grant Avenue

department: MHRP

country: USA

institute: Walter Reed Army Institute of Research

library_source: transcriptomic

data_processing:
FASTQ files were generated from BCL files using bcl2fastq
Trimmomatic v0.36 was used to trim low-quality bases from both ends of each read
Trimmed reads were aligned to the human genome using HISAT2 v2.1.0
Read counts per protein-coding gene were determined using subread featureCounts v1.6.4
The trimmed mean of M-values normalization method (TMM), as implemented in the R package edgeR v3.34.0, was used for normalization
Genome_build: GRCh38 build 97
Supplementary_files_format_and_content: matrix file with read counts for each gene and sample
Supplementary_files_format_and_content: matrix file with TMM normalized expression for each gene and sample

molecule: total RNA

organism: Homo sapiens

source_name: B cells

extract_protocol:
Total RNA from sorted peripheral blood cells was extracted using the Single Cell RNA Purification kit from Norgen Biotek Corp
RNA libraries were prepared for sequencing using the Illumina Nextera XT kit

tag: timepoint

value: HIV-

value: B cells

tag: pid


title: PCreMRpos_H2

city: Cambridge

first: Wenjun

last: Yan

state: MA

address: 52 Oxford Street

department: Department of Molecular  and Cellular Biology

institute: Harvard University

description: retrogradely labeled regenerating RGCs in PtenCKO 21pdc

data_processing:
Sequencing reads were first trimmed using Trimmomatic-0.39. Reads were then aligned to mouse genome GRCm38.81 using hisat2, reads per gene per cell were counted using featureCounts.
Assembly: GRCm38
Supplementary files format and content: Gene count matrix in .csv format

source_name: Mouse retina, 6-8 wk old

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90,  (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP and mCherry (for MR+) or without mCherry (MR-)co-expression. Cells were collected directly into 96well plates, 1 cell/well and frozen at -80C.
Cells were processed following published SS2 protocols, using pre-beads clean up and purification and Nextera XT kit from Illumina. Libraries were sequenced on NovaSeq-SP

treatment_protocol: YFP17het-Ptenfl/fl, YFP17het-PtenSocs3fl/fl mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

value: Retina

value: Pten fl/fl - YFP17 het

tag: aav infection

value: AAV2 - Cre

tag: intervention

value: PCreMRpos

value: 6-8 wk old


title: HDAC7-KO_rep2


title: CD4 T cells isolated from donor 7 at visit 14 (setpoint) [ATH006578]

source_name: CD4 T cells

value: setpoint

value: CD4 T cells


title: PCreMRpos_H12


title: CD4 T cells isolated from donor 7 at visit 5 (peak) [ATH006577]

value: peak


title: HDAC7-KO_rep1


title: Group 3 innate lymphoid cell, WT rep1, scRNAseq

city: hangzhou

first: lie

last: wang

state: zhejiang

address: Zijingang Campus, Zhejiang University，Yuhangtang Road 866

department: immunology

country: China

institute: zhejiang universiry

description:
BD Rhapsody
sample tag 1

library_source: transcriptomic single cell

data_processing:
Illumina Casava2.19 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 hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. 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.
The FASTQ files were processed using the BD Rhapsody Targeted analysis pipeline v1.9.1 on the Seven Bridges platform (https://www.sevenbridges.com).
First of all, read pairs with low mean base quality scores (less than 20) were removed. The filtered R1 reads were analyzed to identify the cell label sequences and unique molecular identifiers(UMIs). R2 reads were aligned to the mice reference genome(GRCm38) using Bowtie2. Valid reads with the same cell label, the same UMI sequence, and the same gene were collapsed into a single raw molecule. Recursive substation error correction (RSEC) and distribution-based error correction (DBEC) algorithms were applied to correct sequencing and PCR errors of raw UMI counts. The final single-cell expression matrices containing DBEC-adjusted molecules were used for downstream analysis.
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Csv files include readcount values for each Sample with different sample tag

source_name: small intestine

extract_protocol:
Intestinal ILC3s were sorted from siLP of wild-type and ThPOK-deficient mice. All samples were uniformly resuscitated and washed twice by PBS (with 0.1% BSA), then the cells were 1 ml stain buffer (with 0.1% BSA) and counted. The viability of cells in all samples was assessed >80%.
Cells for all samples were labeled with sample tags (BD Mouse Single-Cell Multiplexing Kit, USA), counted, and multiplexed, ready for single-cell capture. Single-cell capture and cDNA synthesis were performed by the BD Rhapsody Single-Cell Analysis System (BD, USA), according to the manufacturer's instructions.

tag: cell type

value: Group 3 innate lymphoid cell

value: small intestine

value: 6-8 weeks old


title: PCreMRpos_H11


title: CD4 T cells isolated from donor 7 at visit 1 (prepeak) [ATH006576]

value: prepeak


title: CD4 T cells isolated from donor 7 at visit B (HIV-) [ETH006575]


title: PCreMRpos_H10


title: WT_rep2

value: Bone marrow

value: 4-6 weeks


title: CHLA10_shHOXD13_2

city: Boston

first: April

last: Apfelbaum

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

description: molecule: Bru-labeled RNA

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
A coverage determination was then made for every base in the genome using Bedtools v.2.28.0 such that a base covered by one read was recorded as having a coverage of 1/(read length).
Base coverages were used to obtain pseudo-read counts in regions of interest (genes) using bedtools 2 v2.28.0 (bedtools intersect with strand-specific option -s).
Genes were defined for coverage using a method described in Chepelev et al., Nucleic Acids Research, 2009. In short, the exons from all isoforms of a gene were merged to create one meta-transcript with inter-exonic regions defined as intronic. Pseudo-counts covering these meta-transcripts were normalized by reads per kilobase per million (RPKM) using the effective length (sum of lengths of exonic and intronic regions) and by the size of the library (uniquely mapped read count).
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression files for individual samples are tab-delimited text files where the first 6 columns conform to standard BED6 format. Coordinates are for the hg38 reference genome. Column definitions: (1) "chr" - chromosome; (2) "start"; (3) "end"; (4) "name" - gene symbol; (5) "score" (set to 0 as a placeholder); (6) "strand"; (7) "ensembl" - Ensembl gene ID; (8) "effective_length" - sum of feature lengths in meta-transcript, i.e. exons and introns; (10) "counts" - pseudo read count; (11) "rpkm" - RPKM = counts/(effective_length/1x10^3)/(mapped read count/1x10^6). Gene counts and RPKM matrices for combined samples are available as tab-delimited text files (genes.counts.txt and genes.rpkm.txt), where column 1 is Ensembl gene ID and column 2 is gene name.

growth_protocol: A673 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies). CHLA10 was maintained in IMDM media (Fisher scientific) supplemented with 20% FBS, 2mmol/L-glutamine, and 1X Insulin-Transferrin-Selenium (Gibco). Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.

extract_protocol:
Bromouridine (2mM; Sigma #850187) was added to media and cells incubated for 30 min. After labeling, cells were immediately collected by centrifugation and lysed in 1 mL TRIzol (Invitrogen). RNA was extracted according to the TRIzol protocol. Goat anti-mouse IgG magnetic Dynabeads (110.33; Invitrogen) were prepared by washing 50 µL of beads with 200 μl 0.1% BSA in DEPC-PBS three times. Beads were resuspended in 200 μl 0.1% BSA in DEPC-PBS, followed by incubation with 2 μg anti-BrdU mouse monoclonal antibody (555627; BD Biosciences) and 20 U RNaseOUT (10777-019; Invitrogen) for 1 hour at room temperature. Beads were washed three times and resuspended in 200 μl 0.1% BSA in DEPC-PBS containing 20 U RNaseOUT. To isolate BrU labeled RNA, samples were heated at 80°C for 10 min, placed on ice, and 90% of the sample was added to prepared beads and incubated with rotation for 1 hour at room temperature. Nascent RNA bound beads were washed three times with 0.1% BSA in DEPC-PBS. For elution, beads were resuspended in 40 μl DEPC-water and incubated at 95 °C for 10 min, followed by magnetic capture. Supernatant containing purified nascent BrU-containing RNA was removed and quantified (Nanodrop; Thermo Scientific).
cDNA libraries were prepared using reagents in the Illumina TruSeq RNA Prep Kit. Bru-labeled RNA was mixed with first strand buffer and random primers and fragmented by heating at 85 ̊C for 10 minutes. The first strand cDNA was then synthesized, in the presence of Actinomycin D, to result in strand specific reads. After purifying the first strand cDNA using AMPure RNAclean beads (Beckman Coulter), the second strand cDNA was synthesized. The resulting cDNA was purified with AMPure XP beads, followed by cDNA end repair, adenylation, and adapter ligation (TruSeq RNA Prep Kit). The samples were then run on a 3% agarose gel and size-selected by excising gel slices in the 300bp region. These gel slices were purified using the QIAEX II Gel Extraction Kit (Qiagen) and then DNA fragments were enriched using the PCR reagents from the TruSeq RNA Prep Kit. After a final purification using AMPure XP beads, the quality and concentration of the DNA libraries were determined using an Agilent Bioanalyzer.Libraries were sequenced by the University of Michigan Sequencing Core on an Illumina HiSeq 2500 to obtain 50 nucleotide single-end reads.

treatment_protocol: Cells were treated with 0.5 ug/uL for 72 hours to induce shRNA expression

tag: cell line

value: Ewing sarcoma

tag: labeling agent

value: Bromouridine (Bru)

tag: bru labeling time

tag: time between bru labeling period and rna extraction

value: 0 h


title: PCreMRpos_G9

value: Retina


title: CHLA10_shHOXD13_1

description: molecule: Bru-labeled RNA


title: CHLA10_shNS_3

description: molecule: Bru-labeled RNA


title: CHLA10_shNS_2

description: molecule: Bru-labeled RNA


title: CD4 T cells isolated from donor 6 at visit 5 (peak) [ATH006573]


title: CD4 T cells isolated from donor 6 at visit 14 (setpoint) [ATH006574]


title: CHLA10_shNS_1

description: molecule: Bru-labeled RNA


title: PCreMRpos_G7

value: Pten fl/fl - YFP17 het


title: PCreMRpos_G6

value: AAV2 - Cre


title: CD4 T cells isolated from donor 6 at visit 2 (prepeak) [ATH006572]


title: Forskolin-treated, 18h, biol rep5

city: Calgary

first: Omar

last: Hamed

state: AB

address: 2500 University DR NW

department: Physiology and Pharmacology

country: Canada

institute: University of Calgary

data_processing:
Basecalls were performed using RTA v2
demultiplexing FASTQ conversion was performed using bcl2fastq v2.18.0.12
Sequenced reads were mapped to the reference human transcriptome (GRCh37/hg19) and quantified using Kallisto with 100 bootstraps per sample
Differential expression analysis was performed using the R package Sleuth and transcripts per million (TPM) values were calculated
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes transcripts per million (TPM) values for each sample for each gene described by its HGNC symbol

source_name: Left Lung

growth_protocol: Human primary bronchial epithelial cells grown as monolayers in submersion culture were seeded in 12-well plates (Costar Inc, Corning, NY, USA) containing bronchial epithelial cell growth medium (PromoCell, Heidelberg, Germany) supplemented with penicillin (50 μg ml-1) and streptomycin (10 μg ml-1) and maintained for ∼14 days under a 5% CO2/air atmosphere at 37°C until ∼80% confluent. Cells were cultured for a further 24 h in supplement-free, basal medium (PromoCell) prior to experimentation.

extract_protocol:
Total RNA was extracted using NucleoSpin® RNA kit (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany) and quantified using NanoDrop 2000 (Thermo Fisher Scientific, Wilmington, DE) according to manufacturer's instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra II Directional kit (New England Biolabs Inc., Ipswich, MA) with the poly(A) mRNA magnetic isolation module according to the manufacturer’s instructions. The prepared libraries were validated using the D1000 Screen Tape assay on an Agilent 2200 TapeStation system (Agilent Technologies, Santa Clara, CA) and quantified by Kapa qPCR Library Quantification kit for Illumina (Kapa Biosystems, Boston, MA).

treatment_protocol: Confluent human primary bronchial epithelial cells were cultured for 1, 2, 6 and 18 h with vehicle, TNFα (10 ng ml-1), formoterol (1 nM), TNFα and formoterol in combination or forskolin (10 µM).

tag: Sex

value: Female

tag: ethnicity

value: Caucasian

tag: cause of_death

value: Intracerebral Haemorrhage

value: Left Lung

tag: treatment

value: Forskolin

tag: time


title: CHLA10_shHOXD13_3

description: molecule: Bru-labeled RNA


title: A673_shHOXD13_3

description: molecule: Bru-labeled RNA


title: CD4 T cells isolated from donor 6 at visit B (HIV-) [ETH006571]

value: HIV-

tag: tissue

value: CD4 T cells


title: PCreMRpos_G5

tag: strain

value: PCreMRpos

tag: age

value: 6-8 wk old


title: Forskolin-treated, 18h, biol rep3

value: Hispanic/Latino

value: CNS Tumor

value: Human primary bronchial epithelial cells


title: A673_shHOXD13_2

description: molecule: Bru-labeled RNA

value: Ewing sarcoma

value: Bromouridine (Bru)


title: WT_rep1

value: Bone marrow

value: 4-6 weeks

tag: genotype

value: wild-type


title: A673_shHOXD13_1

description: molecule: Bru-labeled RNA

value: 0 h


title: Forskolin-treated, 18h, biol rep2

value: Female

value: Caucasian


title: PCreMRpos_G4

value: Retina

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre


title: CD4 T cells isolated from donor 5 at Visit 2 (prepeak) [ATH006568]

tag: timepoint

value: prepeak

value: CD4 T cells

tag: pid


title: A673_shNS_3

description: molecule: Bru-labeled RNA


title: Forskolin-treated, 18h, biol rep1

source_name: Right Lung

value: Intracerebral Haemorrhage

value: Right Lung

value: Forskolin


title: CD4 T cells isolated from donor 5 at Visit A (HIV-) [ETH006567]

value: HIV-


title: Forskolin-treated, 18h, biol rep4

value: Male

value: Human primary bronchial epithelial cells


title: A673_shNS_1

description: molecule: Bru-labeled RNA

value: Ewing sarcoma

value: Bromouridine (Bru)


title: PCreMRpos_G12

tag: aav infection

tag: intervention

value: PCreMRpos

value: 6-8 wk old


title: A673_shNS_2

description: molecule: Bru-labeled RNA

tag: cell line

tag: cell type

value: 0 h


title: TNFα + Formoterol - treated, 18h, biol rep5

value: Female

value: Caucasian

value: Left Lung

value: TNFα + Formoterol


title: PCreMRpos_G2

value: Retina

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre


title: PCreMRpos_G11


title: TNFα + Formoterol - treated, 18h, biol rep4

value: Intracerebral Haemorrhage

value: Right Lung


title: CD4 T cells isolated from donor 4 at visit 14 (setpoint) [ATH006566]

value: setpoint

value: CD4 T cells


title: NRVMs, Igfbp3 siRNA, Dox3

city: Los Angeles

first: Junjie

last: Chen

state: California

address: 650 Charles E Young Dr

department: medicine

institute: UCLA

data_processing:
Salmon 1.8 for alignment
Supplementary files format and content: tab-delimited text files include raw counts

organism: Rattus norvegicus

source_name: heart

extract_protocol:
RNeasy Mini Kits (Qiagen)
RNAseq with Ribo-Zero Plus rRNA Depletion Kit

value: heart

value: cardiomyocyte

value: Doxorubicin


title: TNFα + Formoterol - treated, 18h, biol rep3

value: Hispanic/Latino

value: CNS Tumor

value: Human primary bronchial epithelial cells


title: CD4 T cells isolated from donor 5 at Visit 14 (setpoint) [ATH006570]


title: PCreMRpos_G10

value: PCreMRpos

value: 6-8 wk old


title: CD4 T cells isolated from donor 4 at visit 4 (peak) [ATH006565]

value: peak


title: NRVMs, Igfbp3 siRNA, Dox2


title: TNFα + Formoterol - treated, 18h, biol rep2

value: Female

value: Caucasian

value: Left Lung

value: TNFα + Formoterol


title: CD4 T cells isolated from donor 5 at Visit 6 (peak) [ATH006569]


title: PCreMRpos_G8

value: Retina

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre


title: NRVMs, Igfbp3 siRNA, Dox1


title: TNFα + Formoterol - treated, 18h, biol rep1

value: Intracerebral Haemorrhage

value: Right Lung


title: PCreMRpos_G3


title: CD4 T cells isolated from donor 4 at visit 2 (prepeak) [ATH006564]

value: prepeak

value: CD4 T cells


title: NRVMs, siRNA scramble, Dox3

value: heart

value: cardiomyocyte

value: Doxorubicin


title: Formoterol-treated, 18h, biol rep5

value: Human primary bronchial epithelial cells

value: Formoterol


title: CD4 T cells isolated from donor 4 at visit B (HIV-) [ETH006563]

value: HIV-


title: PCreMRpos_F9

value: PCreMRpos

value: 6-8 wk old


title: CD4 T cells isolated from donor 3 at visit 14 (setpoint) [ATH006562]

value: setpoint


title: NRVMs, siRNA scramble, Dox1


title: NRVMs, adenovirus empty, Dox3


title: PCreMRpos_F7


title: CD4 T cells isolated from donor 3 at visit 6 (peak) [ATH006561]

value: peak


title: PCreMRpos_F6

value: Retina


title: CD4 T cells isolated from donor 3 at visit 2 (prepeak) [ATH006560]


title: Formoterol-treated, 18h, biol rep2

value: Female

value: Caucasian

value: Left Lung


title: Formoterol-treated, 18h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: CD4 T cells isolated from donor 3 at visit B (HIV-) [ETH006559]

value: CD4 T cells


title: Formoterol-treated, 18h, biol rep4

value: Male

value: Intracerebral Haemorrhage

value: Right Lung


title: CD4 T cells isolated from donor 2 at visit 14 (setpoint) [ATH006558]


title: PCreMRpos_F4

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre


title: PCreMRpos_F8


title: CD4 T cells isolated from donor 2 at visit 5 (peak) [ATH006557]


title: TNFα-treated, 18h, biol rep5

value: Human primary bronchial epithelial cells

value: TNFα


title: PCreMRpos_F3

value: PCreMRpos

value: 6-8 wk old


title: NRVMs, adenovirus empty, Dox1

value: heart

value: cardiomyocyte

value: Doxorubicin


title: NRVMs, adenovirus empty, Dox2


title: PCreMRpos_F5

value: Retina


title: Formoterol-treated, 18h, biol rep1

value: Female

value: Caucasian

value: Formoterol


title: PCreMRpos_F2


title: CD4 T cells isolated from donor 2 at visit 2 (prepeak) [ATH006556]

value: prepeak

value: CD4 T cells


title: NRVMs, Igfbp3 adenoviral overexpression, Dox2


title: NRVMs, siRNA scramble, Dox2


title: PCreMRpos_F12


title: TNFα-treated, 18h, biol rep4

value: Male

value: Intracerebral Haemorrhage


title: NRVMs, Igfbp3 adenoviral overexpression, Dox1


title: PCreMRpos_F11

value: Pten fl/fl - YFP17 het


title: TNFα-treated, 18h, biol rep3

value: Hispanic/Latino

value: CNS Tumor

value: Left Lung


title: NRVM, 1uM Dox 24, sample 3


title: NRVM, 1uM Dox 24, sample 1


title: TNFα-treated, 18h, biol rep2

value: Human primary bronchial epithelial cells

value: TNFα


title: PCreMRpos_F10

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: NRVM, 1uM Dox 24, sample 2

value: heart

value: cardiomyocyte

value: Doxorubicin


title: Vehicle-treated, 18h, biol rep5

value: Female

value: Caucasian

value: Vehicle


title: CD4 T cells isolated from donor 1 at visit 5 (peak) [ATH006554]

value: peak

value: CD4 T cells


title: TNFα-treated, 18h, biol rep1

value: Intracerebral Haemorrhage

value: Right Lung


title: CD4 T cells isolated from donor 1 at visit 14 (setpoint) [ATH006552]

value: setpoint


title: PCreMRpos_E9

value: Retina

value: Pten fl/fl - YFP17 het


title: CD4 T cells isolated from donor 1 at visit 1 (prepeak) [ATH006551]

value: prepeak


title: Vehicle-treated, 18h, biol rep4

value: Male

value: Human primary bronchial epithelial cells


title: NRVMs, Igfbp3 siRNA, control3

value: control


title: CD4 T cells isolated from donor 1 at visit D (HIV-) [ETH006553]

value: HIV-


title: NRVMs, Igfbp3 siRNA, control2

value: heart

value: cardiomyocyte


title: PCreMRpos_E8

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: PCreMRpos_E6


title: Vehicle-treated, 18h, biol rep3

value: Female

value: Hispanic/Latino

value: CNS Tumor

value: Left Lung

value: Vehicle


title: CD8 T cells isolated from donor 7 at visit 14 (setpoint) [ATH006620]

source_name: CD8 T cells

value: setpoint

value: CD8 T cells


title: PCreMRpos_E7

value: Retina

value: Pten fl/fl - YFP17 het


title: NRVMs, siRNA scramble, control3


title: Vehicle-treated, 18h, biol rep1

value: Caucasian

value: Intracerebral Haemorrhage

value: Right Lung

value: Human primary bronchial epithelial cells


title: NRVMs, Igfbp3 siRNA, control1

value: heart

value: cardiomyocyte

value: control


title: CD4 T cells isolated from donor 2 at visit B (HIV-) [ETH006555]

value: HIV-

value: CD4 T cells


title: Vehicle-treated, 18h, biol rep2

value: Female


title: PCreMRpos_E5

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: CD8 T cells isolated from donor 7 at visit 5 (peak) [ATH006619]

value: peak


title: CD8 T cells isolated from donor 7 at visit 1 (prepeak) [ATH006618]

value: prepeak

value: CD8 T cells


title: NRVMs, siRNA scramble, control2


title: PCreMRpos_E3

value: Retina

value: Pten fl/fl - YFP17 het


title: Forskolin-treated, 6h, biol rep5

value: Caucasian

value: Intracerebral Haemorrhage

value: Left Lung

value: Forskolin


title: NRVMs, siRNA scramble, control1

value: heart

value: cardiomyocyte


title: CD8 T cells isolated from donor 6 at visit 14 (setpoint) [ATH006617]

value: setpoint


title: NRVMs, adenovirus empty, control2

value: control


title: Forskolin-treated, 6h, biol rep4

value: Male

value: Right Lung

value: Human primary bronchial epithelial cells


title: PCreMRpos_E12

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: NRVMs, adenovirus empty, control1


title: Forskolin-treated, 6h, biol rep2

value: Female


title: PCreMRpos_E11

value: Retina


title: Forskolin-treated, 6h, biol rep1


title: CD8 T cells isolated from donor 6 at visit 2 (prepeak) [ATH006615]

value: prepeak

value: CD8 T cells


title: NRVMs, control2


title: NRVMs, control3


title: PCreMRpos_E10

value: Pten fl/fl - YFP17 het


title: CD8 T cells isolated from donor 6 at visit B (HIV-) [ETH006584]

value: HIV-


title: TNFα + Formoterol - treated, 6h, biol rep5

value: Caucasian

value: Intracerebral Haemorrhage

value: Left Lung

value: TNFα + Formoterol


title: PCreMRpos_D9


title: PCreMRpos_D8


title: CD8 T cells isolated from donor 5 at Visit 14 (setpoint) [ATH006614]

value: setpoint


title: NRVMs, Igfbp3 adenoviral overexpression, control3

value: heart

value: cardiomyocyte

value: control


title: CD8 T cells isolated from donor 5 at Visit 6 (peak) [ATH006613]

value: peak


title: TNFα + Formoterol - treated, 6h, biol rep4

value: Male

value: Right Lung

value: Human primary bronchial epithelial cells


title: PCreMRpos_D7

value: Retina

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: CD8 T cells isolated from donor 7 at visit B (HIV-) [ETH006585]

value: HIV-

value: CD8 T cells


title: TNFα + Formoterol - treated, 6h, biol rep3

value: Female

value: Hispanic/Latino

value: CNS Tumor


title: PCreMRpos_E2

value: Pten fl/fl - YFP17 het


title: Forskolin-treated, 6h, biol rep3

value: Left Lung

value: Forskolin


title: NRVMs, Igfbp3 adenoviral overexpression, control2

value: heart

value: cardiomyocyte

value: control


title: CD8 T cells isolated from donor 6 at visit 5 (peak) [ATH006616]

value: peak


title: TNFα + Formoterol - treated, 6h, biol rep2

value: Caucasian

value: Intracerebral Haemorrhage

value: Human primary bronchial epithelial cells

value: TNFα + Formoterol


title: NRVMs, Igfbp3 adenoviral overexpression, control1


title: CD8 T cells isolated from donor 5 at Visit A (HIV-) [ETH006583]


title: PCreMRpos_D6

value: Retina

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: PCreMRpos_D5


title: PCreMRpos_D4


title: CD8 T cells isolated from donor 4 at visit 14 (setpoint) [ATH006611]

value: setpoint

value: CD8 T cells


title: TNFα + Formoterol - treated, 6h, biol rep1

value: Female

value: Right Lung


title: Formoterol-treated, 6h, biol rep5

value: Left Lung

value: Formoterol


title: NRVMs, control1

value: heart

value: cardiomyocyte


title: CD8 T cells isolated from donor 4 at visit 4 (peak) [ATH006610]

value: peak


title: CD8 T cells isolated from donor 4 at visit B (HIV-) [ETH006582]

value: HIV-


title: Formoterol-treated, 6h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: Formoterol-treated, 6h, biol rep4

value: Male

value: Caucasian

value: Intracerebral Haemorrhage

value: Human primary bronchial epithelial cells


title: CD8 T cells isolated from donor 4 at visit 2 (prepeak) [ATH006609]

value: prepeak


title: CD8 T cells isolated from donor 5 at Visit 2 (prepeak) [ATH006612]


title: PCreMRpos_D12

value: Retina

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: CD8 T cells isolated from donor 3 at visit 14 (setpoint) [ATH006608]

value: setpoint

value: CD8 T cells


title: Formoterol-treated, 6h, biol rep1

value: Female

value: Right Lung

value: Formoterol


title: PCreMRpos_D11


title: CD8 T cells isolated from donor 3 at visit 6 (peak) [ATH006607]

value: peak


title: TNFα-treated, 6h, biol rep5

value: Left Lung

value: TNFα


title: Formoterol-treated, 6h, biol rep2

value: Caucasian


title: CD8 T cells isolated from donor 3 at visit 2 (prepeak) [ATH006606]


title: PCreMRpos_D10


title: CD8 T cells isolated from donor 3 at visit B (HIV-) [ETH006581]

value: HIV-


title: PCreMRpos_D1


title: PCreMRpos_C_H4_S39


title: TNFα-treated, 6h, biol rep4

value: Male

value: Intracerebral Haemorrhage

value: Human primary bronchial epithelial cells


title: TNFα-treated, 6h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: CD8 T cells isolated from donor 2 at visit 14 (setpoint) [ATH006605]


title: TNFα-treated, 6h, biol rep2


title: CD8 T cells isolated from donor 2 at visit 5 (peak) [ATH006604]


title: PCreMRpos_C_H5_S40

value: Retina

value: Pten fl/fl - YFP17 het

value: AAV2 - Cre

value: PCreMRpos


title: PCreMRpos_C_G5_S35

value: 6-8 wk old


title: TNFα-treated, 6h, biol rep1

value: Female

value: Right Lung


title: PCreMRpos_C_G2_S32


title: CD8 T cells isolated from donor 2 at visit 2 (prepeak) [ATH006603]

value: prepeak

value: CD8 T cells


title: PCreMRpos_D3


title: CD8 T cells isolated from donor 2 at visit B (HIV-) [ETH006580]


title: Vehicle-treated, 6h, biol rep4

value: Vehicle


title: PCreMRpos_C_F5_S30


title: PCreMRpos_C_G1_S31


title: Vehicle-treated, 6h, biol rep5

value: Caucasian

value: Left Lung


title: PCreMRpos_C_F4_S29


title: CD8 T cells isolated from donor 1 at visit D (HIV-) [ETH006579]

value: HIV-


title: CD8 T cells isolated from donor 1 at visit 14 (setpoint) [ATH006601]

value: setpoint


title: Vehicle-treated, 6h, biol rep1

value: Intracerebral Haemorrhage

value: Human primary bronchial epithelial cells


title: CD8 T cells isolated from donor 1 at visit 5 (peak) [ATH006602]

value: peak


title: CD8 T cells isolated from donor 1 at visit 1 (prepeak) [ATH006600]


title: PCreMRpos_C_F3_S28

value: Retina


title: Vehicle-treated, 6h, biol rep2


title: PCreMRpos_C_F1_S26

value: Pten fl/fl - YFP17 het


title: NK cells isolated from donor 7 at visit 14 (setpoint) [ATH006662]

source_name: NK cells

value: NK cells


title: PCreMRpos_C_F2_S27

value: AAV2 - Cre

value: PCreMRpos


title: Forskolin-treated, 2h, biol rep4

value: Male

value: Forskolin


title: NK cells isolated from donor 7 at visit 5 (peak) [ATH006661]


title: Forskolin-treated, 2h, biol rep5

value: Female


title: PCreMRpos_C_H1_S36

value: 6-8 wk old


title: PCreMRpos_C_E5_S25


title: Forskolin-treated, 2h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: NK cells isolated from donor 7 at visit 1 (prepeak) [ATH006660]

value: prepeak


title: NK cells isolated from donor 7 at visit B (HIV-) [ETH006599]

value: HIV-


title: PCreMRpos_C_E3_S23


title: Forskolin-treated, 2h, biol rep2

value: Caucasian

value: Left Lung


title: Forskolin-treated, 2h, biol rep1

value: Intracerebral Haemorrhage

value: Right Lung

value: Human primary bronchial epithelial cells


title: Vehicle-treated, 6h, biol rep3

value: Vehicle


title: PCreMRpos_C_E2_S22

value: Retina

value: Pten fl/fl - YFP17 het


title: NK cells isolated from donor 6 at visit 14 (setpoint) [ATH006659]

value: setpoint

value: NK cells


title: NK cells isolated from donor 6 at visit 5 (peak) [ATH006658]

value: peak


title: PCreMRpos_C_D5_S20

value: AAV2 - Cre

value: PCreMRpos


title: TNFα + Formoterol - treated, 2h, biol rep4

value: Male

value: TNFα + Formoterol


title: PCreMRpos_C_D4_S19

value: 6-8 wk old


title: NK cells isolated from donor 6 at visit 2 (prepeak) [ATH006657]

value: prepeak


title: TNFα + Formoterol - treated, 2h, biol rep3

value: Female

value: Hispanic/Latino

value: CNS Tumor


title: NK cells isolated from donor 5 at Visit 14 (setpoint) [ATH006656]


title: TNFα + Formoterol - treated, 2h, biol rep2

value: Caucasian

value: Intracerebral Haemorrhage

value: Left Lung


title: NK cells isolated from donor 6 at visit B (HIV-) [ETH006598]

value: HIV-


title: PCreMRpos_C_D1_S16

value: Retina

value: Pten fl/fl - YFP17 het


title: PCreMRpos_C_D2_S17


title: PCreMRpos_C_D3_S18


title: NK cells isolated from donor 5 at Visit 6 (peak) [ATH006655]

value: NK cells


title: TNFα + Formoterol - treated, 2h, biol rep1

value: Right Lung

value: Human primary bronchial epithelial cells


title: NK cells isolated from donor 5 at Visit 2 (prepeak) [ATH006654]


title: Formoterol-treated, 2h, biol rep4

value: Formoterol


title: PCreMRpos_C_C4_S14

value: AAV2 - Cre

value: PCreMRpos


title: PCreMRpos_C_C3_S13

value: 6-8 wk old


title: NK cells isolated from donor 5 at Visit A (HIV-) [ETH006597]


title: Formoterol-treated, 2h, biol rep3


title: TNFα + Formoterol - treated, 2h, biol rep5

value: TNFα + Formoterol


title: Formoterol-treated, 2h, biol rep2

value: Female


title: PCreMRpos_C_C1_S11


title: NK cells isolated from donor 4 at visit 2 (prepeak) [ATH006651]

value: prepeak


title: NK cells isolated from donor 4 at visit 4 (peak) [ATH006652]

value: peak


title: PCreMRpos_C_B4_S9


title: TNFα-treated, 2h, biol rep5

value: Caucasian

value: TNFα


title: PCreMRpos_C_C2_S12


title: NK cells isolated from donor 4 at visit B (HIV-) [ETH006596]


title: Formoterol-treated, 2h, biol rep1

value: Intracerebral Haemorrhage


title: NK cells isolated from donor 3 at visit 14 (setpoint) [ATH006650]

value: setpoint


title: PCreMRpos_C_C5_S15

value: Retina


title: NK cells isolated from donor 3 at visit 6 (peak) [ATH006649]


title: PCreMRpos_C_B1_S6

value: Pten fl/fl - YFP17 het


title: PCreMRpos_C_A5_S5


title: NK cells isolated from donor 3 at visit 2 (prepeak) [ATH006648]

value: NK cells


title: Vehicle-treated, 2h, biol rep5

value: Left Lung

value: Vehicle


title: PCreMRpos_C_B2_S7


title: NK cells isolated from donor 4 at visit 14 (setpoint) [ATH006653]


title: NK cells isolated from donor 2 at visit 5 (peak) [ATH006646]


title: PCreMRpos_C_B3_S8


title: PCreMRpos_C_A4_S4


title: Formoterol-treated, 2h, biol rep5

value: Human primary bronchial epithelial cells

value: Formoterol


title: PCreMRpos_C_A3_S3

value: AAV2 - Cre

value: PCreMRpos


title: Vehicle-treated, 2h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: Vehicle-treated, 2h, biol rep4

value: Male

value: Right Lung


title: TNFα-treated, 2h, biol rep3

value: Female


title: PCreMRpos_C9

value: 6-8 wk old


title: TNFα-treated, 2h, biol rep1

value: Caucasian

value: Intracerebral Haemorrhage

value: TNFα


title: PCreMRpos_C_A2_S2

value: Retina

value: Pten fl/fl - YFP17 het


title: NK cells isolated from donor 2 at visit 2 (prepeak) [ATH006645]

value: prepeak

value: NK cells


title: TNFα-treated, 2h, biol rep2

value: Left Lung

value: Human primary bronchial epithelial cells


title: NK cells isolated from donor 1 at visit 14 (setpoint) [ATH006643]

value: setpoint


title: NK cells isolated from donor 1 at visit 5 (peak) [ATH006644]

value: peak


title: Vehicle-treated, 2h, biol rep2

value: Vehicle


title: PCreMRpos_C7

value: AAV2 - Cre

value: PCreMRpos


title: NK cells isolated from donor 3 at visit B (HIV-) [ETH006595]

value: HIV-


title: TNFα-treated, 2h, biol rep4

value: Male

value: Right Lung


title: Forskolin-treated, 1h, biol rep4

value: Caucasian

value: Forskolin


title: PCreMRpos_C_A1_S1

value: 6-8 wk old


title: PCreMRpos_C6

value: Retina


title: PCreMRpos_C5

value: Pten fl/fl - YFP17 het


title: PCreMRpos_C4


title: PCreMRpos_C8


title: Vehicle-treated, 2h, biol rep1

value: Female

value: Intracerebral Haemorrhage


title: RNA KIKI 2

city: Montreal

first: Michael

last: Witcher

state: Quebec

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

department: Experimental Medicine

institute: McGill University

data_processing:
Reads were trimmed with Trimmomatics (Bolger et al. 2014) using the following condition: ILLUMINACLIP:$Adapters:2:30:10:8:true, HEADCROP:4, SLIDINGWINDOW:4:30, LEADING:3, TRAILING:3, MINLEN:30.
Alignment on hg19 human genome was performed with STAR 2.5.4b (Dobin et al. 2013) default parameters, and converted into bam format using Samtools 1.9 (Li et al. 2009).
Differential expression analysis was generated using FeatureCounts count matrix (Liao et al. 2014)
Genome_build: hg19
Supplementary_files_format_and_content: Count Matrix from featureCount

source_name: CTCF ZF1M/ZF1M MCF10A

growth_protocol: MCF10A cell line and mutants were maintained in DMEM/F12 50/50 (Wisent, #319-085-CL) supplemented with EGF (100μg/ml, Wisent, #511-110-UM), Insulin (10mg/ml, Wisent, #H511-016-U6), Hydrocortisone (1mg/ml, Sigma, #H0888-1G), Horse Serum (2%, Wisent, #065150) and Choleratoxin (1mg/ml, Sigma, #C8052-2MG) in an incubator at 37C and 5% CO2.

extract_protocol:
Total RNA was extracted according to Sigma RNA Extraction Kit (Sigma, #RTN350-1KT) protocol. RNA quantity and quality was measured using Nanodrop.
RNA was sent to Genome Quebec for polyA RNA library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

value: Breast

value: CTCF ZF1M/ZF1M


title: RNA KIKI 3


title: NK cells isolated from donor 2 at visit B (HIV-) [ETH006594]

value: NK cells


title: PCreMRpos_C3


title: Forskolin-treated, 1h, biol rep5

value: Left Lung

value: Human primary bronchial epithelial cells


title: Forskolin-treated, 1h, biol rep2


title: TNFα + Formoterol - treated, 1h, biol rep4

value: TNFα + Formoterol


title: TNFα + Formoterol - treated, 1h, biol rep5


title: PCreMRpos_C12

value: AAV2 - Cre

value: PCreMRpos


title: NK cells isolated from donor 1 at visit 1 (prepeak) [ATH006642]

value: prepeak


title: TNFα + Formoterol - treated, 1h, biol rep2


title: TNFα + Formoterol - treated, 1h, biol rep1

value: Right Lung


title: Forskolin-treated, 1h, biol rep1

value: Caucasian


title: NK cells isolated from donor 2 at visit 14 (setpoint) [ATH006647]

value: setpoint


title: PCreMRpos_C10

value: 6-8 wk old


title: PCreMRpos_C2

value: Retina


title: RNA KIKI 1


title: NK cells isolated from donor 1 at visit D (HIV-) [ETH006593]

value: HIV-


title: PCreMRpos_C1

value: Pten fl/fl - YFP17 het


title: RNA KI 3

source_name: CTCF ZF1M/- MCF10A

value: CTCF ZF1M/-


title: PCreMRpos_C11


title: TNFα + Formoterol - treated, 1h, biol rep3

value: Female

value: Hispanic/Latino

value: CNS Tumor


title: Formoterol-treated, 1h, biol rep4

value: Male

value: Intracerebral Haemorrhage

value: Formoterol


title: Formoterol-treated, 1h, biol rep3

value: Left Lung

value: Human primary bronchial epithelial cells


title: RNA KI 2

value: Breast


title: RNA KI 1


title: CTCF_KIKI input

data_processing:
Reads were trimmed with Trimmomatics (Bolger et al. 2014) using the following parameters: ILLUMINACLIP:$Adapters:2:30:10, LEADING:30, TRAILING:30, SLIDINGWINDOW:4:30, MINLEN:30.
Alignment on hg19 human genome was performed using BWA (Li et al. 2009) default conditions.
Sam files generated by BWA were converted to bam format using Samtools (Li et al. 2009).
Peak calling was performed with MACS2 (Zhang et al. 2008) default condition and normalization on the respective Input dataset of each cell lines.
Bigwig files used for visualization were generated from the fragment pileup bedGraph using the BedGraphToBigwig function.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files

extract_protocol:
70-80% confluent cells were fixed 10 minutes in 4% formaldehyde and stored at -80C. The pellets were subsequently resuspended in 1ml of ChIP-buffer [0.25% NP-40, 0.25% Triton X-100, 0.25% Sodium Deoxycholate, 0.005% SDS, 50nM Tris (pH8), 100mM NaCl, 5mM EDTA, 1X PMSF, 2mM NaF, 1X P8340 Cocktail Inhibitor (Roche)] and sonicated with a probe sonicator (Fisher Scientific Sonic Dismembrator Model 500) using the following cycles: 5 cycles at 20% power, 5 cycles at 25% power, and 5 cycles at 30% power. Each cycle lasts 10 seconds, and the samples are kept on ice between each cycle to avoid overheating. Next, the samples are spun at high speed in a microcentrifuge for 30 minutes. Then, lysates are collected and protein concentration measured using the Bradford assay, as described above. Based on protein concentrations, samples are diluted to 2mg/ml proteins in ChIP-buffer and 50ul/ml of Protein G Plus-Agarose Suspension Beads (Calbiochem, IP04-1.5ML) are added for 3h to preclear. 2% of the sample is collected as input and kept at -20 °C until DNA purification. Immunoprecipitation is carried out at 4°C overnight with 1ml of sample, 60ul of beads and primary antibody. The beads are then washed once with Wash1, Wash2, Wash3 [0.10% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris (pH 8), 150/200/500mM NaCl for Wash 1,2,3 respectively], Wash LiCl [0.25M LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1mM EDTA, 10mM Tris (pH8)] and twice with TE buffer [10mM Tris (pH8), 1mM EDTA]. Then, beads are resuspended in elution buffer [1% SDS, 0.1M NaHCO3]. The samples are decrosslinked overnight at 65 °C. 20µg of Proteinase K (Sigma, # 39450-01-6) is added for 1h at 42 °C. Then, DNA is purified using BioBasic DNA collection column (BioBasic, #SD5005). DNA concentration was assessed via Picogreen assay (Invitrogen, #P7589).
Library were preapred at Genome Quebec using  NEB Ultra II DNA kit (no shearing).

value: CTCF ZF1M/ZF1M


title: Formoterol-treated, 1h, biol rep5

value: Caucasian


title: CTCF_KI input


title: Formoterol-treated, 1h, biol rep2


title: RNA WT 2

source_name: WT MCF10A

value: WT


title: CTCF_KIKI_2


title: RNA WT 3


title: PCreMRpos_B7

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: RNA WT 1


title: Forskolin-treated, 1h, biol rep3

value: Forskolin


title: PCreMRpos_B8

value: Retina

value: Pten fl/fl - YFP17 het


title: TNFα-treated, 1h, biol rep5

value: Female

value: TNFα


title: PCreMRpos_B9


title: PCreMRpos_B2


title: CTCF_KI_1

value: CTCF ZF1M/-


title: PCreMRpos_B4


title: CTCF_KIKI_1


title: Formoterol-treated, 1h, biol rep1

value: Intracerebral Haemorrhage

value: Right Lung


title: TNFα-treated, 1h, biol rep2

value: Left Lung


title: CTCF_KI_2


title: PCreMRpos_B5


title: TNFα-treated, 1h, biol rep4

value: Male

value: Human primary bronchial epithelial cells


title: PCreMRpos_B12


title: PCreMRpos_B3


title: PCreMRpos_B6


title: PCreMRpos_B11


title: ALKBH1 with 5EC treatment rep2

city: princeton

first: Ang

last: Li

state: NJ

address: Washington Road

department: chemistry

institute: princeton university

data_processing:
NovaSeq Control Software (NVCS) v1.7 was used for the sequencing run and base calling
alignment(STAR), filtering and peak-calling(Paraclu) were performed by using ICOUNT version2.0.0
Genome_build: GRCh38
Supplementary_files_format_and_content: bed peaks file

growth_protocol: 30 x 10 cm dish Flp-In T-Rex 293 cells expressing 3xFlag-ALKBH1 were treated with 1 mg/mL tetracycline once the cells reached 60% confluency.

extract_protocol:
Cells were washed twice with cold PBS and then 500 µl lysis buffer (50 mM Tris–HCL pH 7.4, 100 mM NaCl, 1% NP-40, 0.1% SDS and 0.5% sodium deoxycholate) was added to each dish. Lysates were treated with Turbo DNase (AM2239) and a low (1:200) or high (1:50) concentration of RNaseI (AM2295) at 37 °C for 3 mins with rotation after which they were centrifuged at 13000  rpm for 15 min at 4°C. The supernatant was incubated with anti-FLAG beads (200 μl Protein G beads and 15 µg anti-Flag M2 antibody) at 4 °C overnight with rotation, and the immunoprecipitated material was then washed 3 times with high-salt buffer and then once with CutSmart buffer (NEB) washing. The beads were treated with Quick-CIP (NEB) at 37 °C for 30 mins with rotation, washed twice with high-salt buffer, and then incubated with preadenylated and biotin labeled L3 linker by using T4 RNA ligase I (NEB) at 16 °C overnight. After washing 3 times with high-salt buffer, the beads were boiled with 60 μl sample buffer and 3 μl was analyzed by Western blot for biotinylation with the chemiluminescent nucleic acid detection module (Thermo). The rest of the sample was gel purified based on the position of the biotin signal. Immunoprecipitated RNA was recovered using D-tube dialyzer midi (Merck-Millipore) and digested with proteinase K (NEB).
Reverse transcription was performed using oligonucleotides containing randomized barcodes (UMIs) and two inversely oriented adaptor regions separated by a BamHI restriction site. cDNAs were size-purified (70-80nt, 80-100nt and 100-150nt) on TBE-Urea gels and then circularized by CircLigase II (Epicentre). Circularized cDNAs were digested with BamHI and linearized cDNAs were amplified using Solexa primers and submitted for Illumina sequencing.
Iclip-seq

treatment_protocol: After 12 hr,the medium was changed to fresh medium containing 1 mg/mL tetracycline (Control) or 1 mg/mL tetracycline and 100 mM 5-EC (5-EC-iCLIP) and cultured for another 12 hr.

value: Hek


title: TNFα-treated, 1h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: ALKBH1 with 5EC treatment rep1

source_name: Flp-In T-Rex 293 cells expressing 3xFlag-ALKBH1


title: TC32_shHOXD13_3

data_processing:
Adapter trimming of paired-end fastq files was performed using Trim Galore (Babraham Institute).
Trimmed reads were then aligned to GRCh38 using STAR aligner (Dobin, et al 2013) with `--quantMode GeneCounts` to count the number of reads per gene while mapping.
Differential expression analysis was performed using the default parameters from the DESeq2 package (Love et al, 2014).
Genome_build: Hg38
Supplementary_files_format_and_content: .txt files with count data

molecule: polyA RNA

growth_protocol: TC32 was maintained in RPMI 1640 media (Gibco) supplemented with 10% FBS (Atlas Biologicals) and 2mmol/L-glutamine (Life Technologies).  Cells were cultured at 37°C with 5% CO2 and were split according to ATCC and COG recommendations.

extract_protocol:
RNA was extracted using the Quiagen Rneasy Kit
polyA-capture mRNA
Libraries were prepared with NEBNext Ultra II RNA Library Prep kit and Paired end 150 bp sequencing was performed on a Novaseq600

value: Ewing sarcoma

value: HOXD13 knockdown


title: Vehicle-treated, 1h, biol rep4

value: Caucasian

value: Vehicle


title: PCreMRpos_B1

value: Retina

value: AAV2 - Cre

value: PCreMRpos

value: 6-8 wk old


title: TC32_shHOXD13_2


title: TC32_shHOXD13_1


title: PCreMRpos_A9

value: Pten fl/fl - YFP17 het


title: Vehicle-treated, 1h, biol rep2

value: Female

value: Intracerebral Haemorrhage


title: TC32_shNS_3

value: shNS

value: control


title: Vehicle-treated, 1h, biol rep1

value: Right Lung

value: Human primary bronchial epithelial cells


title: PCreMRpos_A8


title: TNFα-treated, 1h, biol rep1

value: TNFα


title: TC32_shNS_2


title: PCreMRpos_A7


title: Vehicle-treated, 1h, biol rep5

value: Left Lung


title: TC32_shNS_1

value: Ewing sarcoma


title: PCreMRpos_A6


title: PCreMRpos_A5


title: PCreMRpos_B10


title: PCreMRpos_A3


title: HEK293-cfCas13d-PPARG-g1-rep1

city: Shanghai

first: Hui

last: Yang

state: Shanghai

address: 320 Yueyang Road

institute: CAS Center for Excellence in Brain Science and Intelligence Technology

description:
NM10-1
35μg plasmids containing cfCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

data_processing:
RNA quality was evaluated and sequenced using Illumina NovaSeq 6000, raw data from the sequencer were first underwent quality control using FastQC.
Reads are treated using trim_galore, where illumina adapter sequence and low quality (phred score <20) at the 3’ end were trimmed, and the paired reads were removed if any of the two reads doesn’t meet the minimum length (20bp)
Clean reads were then aligned to human genome (grch38) using hisat2.
For each sample, we count the reads hit on each transcript using htseq-count.
Genome_build: grch38
Supplementary_files_format_and_content: Matrix table with FPKM values for every gene and every sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human embryonic kidneys

growth_protocol: KEK293 Cells were cultured in the DMEM medium supplemented with 10% FBS, penicillin (100 units/ml)/streptomycin (100 µg/ml ) and 0.1 mM non-essential amino acids in the incubator at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted with TRIZOL-based method, fragmented and reverse transcribed to cDNAs with HiScript Q RT SuperMix for qPCR (Vazyme, Biotech) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For transcriptome sequencing, 35μg all-in-one plasmids containing Cas13 (dCas13d, Cas13d or cfCas13d), EGFP, mCherry, targeting gRNA for each endogenous gene were transfected into HEK293 cells cultured in 10-cm dishes. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: cfCas13d + PPARG-g1


title: Vehicle-treated, 1h, biol rep3

value: Hispanic/Latino

value: CNS Tumor


title: ATRA treated BKO-98 SH SY5Y 12-BKO-98-RA-3

city: Newcastle

first: John

last: Casement

address: Framlington Place

department: Bioinformatics Support Unit

country: United Kingdom

institute: Newcastle University

data_processing:
Reads were quantified against transcripts using Salmon (version 0.9.1)
Gene level counts were obtained from transcript level counts using the R package tximport (version 1.4.0)
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data file count_table.txt is a tab-delimited text file containing a matrix of gene level counts. Rows are features (ensembl gene Ids) and columns are  samples

source_name: Human neuroblastoma cell line

growth_protocol: 50:50 mixture of Minimum Essential Medium (MEM) and F12 (hams) medium containing 10% FBS and 1% pen/strep

extract_protocol:
RNA prepared using Qiagen Rneasy kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four biological replicates of both wild type and BKO-98 clone were treated with either (10 μM) ATRA or ethanol (0.01 % V/V) for 24 hours.

value: Derived from SK-N-SH line from the bone marrow of a 4 year old female


title: ATRA treated BKO-98 SH SY5Y 16-BKO-98-RA-4


title: untreated BKO-98 SH SY5Y 15-BKO-98-Con-4


title: untreated WT SH SY5Y 13-WT-Con-4

description:
untreated WT SH SY5Y
13-WT-Con-4


title: ATRA treated WT SH SY5Y 14-WT-RA-4

description:
ATRA treated WT SH SY5Y
14-WT-RA-4


title: PCreMRpos_A2

value: Retina

value: AAV2 - Cre


title: PCreMRpos_A12

value: PCreMRpos

value: 6-8 wk old


title: untreated BKO-98 SH SY5Y 11-BKO-98-Con-3


title: ATRA treated WT SH SY5Y 10-WT-RA-3

description:
ATRA treated WT SH SY5Y
10-WT-RA-3


title: untreated WT SH SY5Y 9-WT-Con-3

description:
untreated WT SH SY5Y
9-WT-Con-3


title: HEK293-Cas13d-PPARG-g1-rep2

description:
NW10-2
35μg plasmids containing Cas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: Cas13d + PPARG-g1


title: HEK293-Cas13d-PPARG-g1-rep1

description:
NW10-1
35μg plasmids containing Cas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-cfCas13d-PPARG-g1-rep3

description:
NM10-3
35μg plasmids containing cfCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-PPARG-g1-rep3

description:
ND10-3
35μg plasmids containing dCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: dCas13d + PPARG-g1-Control


title: PCreMRpos_A11

value: Pten fl/fl - YFP17 het


title: ATRA treated BKO-98 SH SY5Y 8-BKO-98-RA-2


title: PCreMRpos_A10


title: PCCreMRpos_H9

value: AAV2-Cre / AAV-CNTF

value: PCCreMRpos


title: HEK293-cfCas13d-PPARG-g1-rep2

description:
NM10-2
35μg plasmids containing cfCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-PPARG-g1-rep2

description:
ND10-2
35μg plasmids containing dCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-PPARG-g1-rep1

description:
ND10-1
35μg plasmids containing dCas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-Cas13d-PPARG-g1-rep3

description:
NW10-3
35μg plasmids containing Cas13d, EGFP, mCherry, PPARG-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: untreated BKO-98 SH SY5Y 7-BKO-98-Con-2

description:
untreated BKO-98 SH SY5Y
7-BKO-98-Con-2


title: PCCreMRpos_H7


title: ATRA treated WT SH SY5Y 6-WT-RA-2

description:
ATRA treated WT SH SY5Y
6-WT-RA-2


title: PCCreMRpos_H8


title: HEK293-cfCas13d-CA2-g1-rep3

description:
MHg11-3
35μg plasmids containing cfCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: cfCas13d + CA2-g1


title: HEK293-cfCas13d-CA2-g1-rep2

description:
MHg11-2
35μg plasmids containing cfCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-cfCas13d-CA2-g1-rep1

description:
MHg11-1
35μg plasmids containing cfCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: untreated WT SH SY5Y 5-WT-Con-2

description:
untreated WT SH SY5Y
5-WT-Con-2


title: PCCreMRpos_H10


title: untreated BKO-98 SH SY5Y 3-BKO-98-Con-1

description:
untreated BKO-98 SH SY5Y
3-BKO-98-Con-1


title: PCCreMRpos_H6


title: PCCreMRpos_H3


title: ATRA treated BKO-98 SH SY5Y 4-BKO-98-RA-1


title: HEK293-Cas13d-CA2-g1-rep3

description:
Hg11-3
35μg plasmids containing Cas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: Cas13d + CA2-g1


title: PCCreMRpos_G9


title: HEK293-Cas13d-CA2-g1-rep2

description:
Hg11-2
35μg plasmids containing Cas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: untreated WT SH SY5Y 1-WT-Con-1

description:
untreated WT SH SY5Y
1-WT-Con-1


title: HEK293-Cas13d-CA2-g1-rep1

description:
Hg11-1
35μg plasmids containing Cas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_G8


title: PCCreMRpos_G6


title: PCCreMRpos_G5


title: HEK293-dCas13d-CA2-g1-rep3

description:
DHg11-3
35μg plasmids containing dCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: dCas13d + CA2-g1-Control


title: CtPtenCreCD90CD45R1

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-NoCrush.csv

data_processing:
Sample demultiplexing with the mkfastq function from Cell Ranger software(version 2.1.0, 10X Genomics)
Sample alignment with the count function from Cell Ranger software(version 2.1.0, 10X Genomics)
Assembly: GRCm38
Supplementary files format and content: csv files including gene expression matrix from samples at different time points using each intervention

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90,  (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP co-expression. Collected cells were loading into 10X Chromium Single Cell A Chips at ~1,000 cells/ul. For SS2 cells were collected based on high CD90 and GFP w/o and w/ high MicroRuby. Single cells were dropped into 96-well plates, one cell/well, frozen at -80C.
Single cell libraries were made with Chromium 3’ v2 platform (10X Genomics, Pleasanton, CA) following the manufacturer’s protocol. Briefly, single cells were partitioned into Gel bead in EMulsion (GEMs) in the GemCode instrument with cell lysis and barcoded reverse transcription of RNA, followed by amplification, shearing and 5’ adaptor and sample index attachment. On average, approximately 10,000 single cells were loaded on each channel and approximately 6,000 cells were recovered. Libraries were sequenced on at the Broad institute using Illumina HiSeq 2500 or at the Bauer Core Facility at Harvard University using NovaSeq-SP

treatment_protocol: YFP17het-Ptenfl/fl, YFP17het-PtenSocs3fl/fl and C57BL/6J mice were used. Retinas were dissected in Ames solution (Sigma-Aldrich; equilibrated with 95% O2/5% CO2 for all use) immediately following enucleation.

value: retina

tag: 10x kit version

tag: aav injection

tag: days after crush

value: NoCrush


title: PCCreMRpos_G10

description: retrogradely labeled regenerating RGCs in PtenCKO 21pdc


title: CtPtenCreCD90R1


title: PCCreMRpos_G3


title: HEK293-dCas13d-CA2-g1-rep2

description:
DHg11-2
35μg plasmids containing dCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-CA2-g1-rep1

description:
DHg11-1
35μg plasmids containing dCas13d, EGFP, mCherry, CA2-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: CrPtenCre7dCD90R1

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC7d.csv


title: HEK293-cfCas13d-RPL4-g3-rep3

description:
MH53-3
35μg plasmids containing cfCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: cfCas13d + RPL4-g3


title: ATRA treated WT SH SY5Y 2-WT-RA-1

description:
ATRA treated WT SH SY5Y
2-WT-RA-1


title: PCCreMRpos_F6


title: HEK293-cfCas13d-RPL4-g3-rep2

description:
MH53-2
35μg plasmids containing cfCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-cfCas13d-RPL4-g3-rep1

description:
MH53-1
35μg plasmids containing cfCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: CrPtenCre2dCD90R3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC2D.csv


title: PCCreMRpos_F5


title: CtPtenSocs3CreCNTFCD90

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-NoCrush.csv

value: Pten fl/fl - Socs3 fl/fl - YFP17 het


title: CtPtenSocs3NoCreCD90

value: No AAV injected


title: CtPtenNoCreCD90R1


title: PCCreMRpos_F4

value: Retina


title: CtPtenSocs3CNTFCreRGC2


title: PCCreMRpos_E8


title: CtCreRGCS2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Control-NoCrush.csv

value: YFP17 het


title: HEK293-Cas13d-RPL4-g3-rep3

description:
WH53-3
35μg plasmids containing Cas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: Cas13d + RPL4-g3


title: PCCreMRpos_E7

value: 6-8 wk old


title: HEK293-Cas13d-RPL4-g3-rep2

description:
WH53-2
35μg plasmids containing Cas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-RPL4-g3-rep3

description:
DH53-3
35μg plasmids containing dCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: dCas13d + RPL4-g3-Control


title: CrPtenSocs3NoCre2dRGCS1

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-ONC2D.csv


title: CtCreRGCS1


title: HEK293-Cas13d-RPL4-g3-rep1

description:
WH53-1
35μg plasmids containing Cas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_E3


title: CrPtenSocs3Cre7dCNTFCD90S2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-ONC7d.csv


title: HEK293-dCas13d-RPL4-g3-rep2

description:
DH53-2
35μg plasmids containing dCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_E12

description: retrogradely labeled regenerating RGCs in PtenCKO 21pdc


title: HEK293-dCas13d-RPL4-g3-rep1

description:
DH53-1
35μg plasmids containing dCas13d, EGFP, mCherry, RPL4-targeting gRNA g3 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_F8


title: CrPtenSocs3Cre7dCNTFCD90S1


title: PCCreMRpos_D9


title: HEK293-cfCas13d-PPIA-g2-rep3

description:
M52-3
35μg plasmids containing cfCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: cfCas13d + PPIA-g2


title: HEK293-cfCas13d-PPIA-g2-rep2

description:
M52-2
35μg plasmids containing cfCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_D8

value: Pten fl/fl - YFP17 het


title: PCCreMRpos_D7

value: AAV2-Cre / AAV-CNTF


title: HEK293-Cas13d-PPIA-g2-rep3

description:
H52-3
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: Cas13d + PPIA-g2


title: PCCreMRpos_D5

value: PCCreMRpos


title: CrPtenSocs3Cre2dCNTFCD90S2


title: HEK293-Cas13d-PPIA-g2-rep2

description:
H52-2
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: CrPtenSocs321dS2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-ONC21d.csv


title: CrPtenSocs3Cre2dCNTFCD90S1


title: HEK293-Cas13d-PPIA-g2-rep1

description:
H52-1
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_D12


title: PCCreMRpos_D3


title: CrPtenNoCre2dRGCS3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC2D.csv


title: CrPtenNoCre2dRGCS2


title: PCCreMRpos_E1


title: CrPtenSocs321dS1


title: HEK293-dCas13d-PPIA-g2-rep3

description:
D52-3
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: dCas13d + PPIA-g2-Control


title: PCCreMRpos_C7


title: CrPtenCre7dRGCS2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC7d.csv


title: PCCreMRpos_C6


title: CrCre2dRGCS3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Control-ONC2D.csv


title: HEK293-dCas13d-PPIA-g2-rep1

description:
D52-1
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_D1


title: CrCre2dRGCS2


title: CrCre2dRGCS1


title: PCCreMRpos_C5


title: HEK293-cfCas13d-PPIA-g1-rep3

description:
MHe54-3
35μg plasmids containing cfCas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: cfCas13d + PPIA-g1


title: HEK293-cfCas13d-PPIA-g2-rep1

description:
M52-1
35μg plasmids containing cfCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_C4


title: Cr7dYfpCreRGC3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Control-ONC7d.csv

value: retina


title: HEK293-cfCas13d-PPIA-g1-rep1

description:
MHe54-1
35μg plasmids containing cfCas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: Cr7dYfpCreRGC2


title: HEK293-dCas13d-PPIA-g2-rep2

description:
D52-2
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g2 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-Cas13d-PPIA-g1-rep3

description:
He54-3
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: Cas13d + PPIA-g1


title: PCCreMRpos_C1

description: retrogradely labeled regenerating RGCs in PtenCKO 21pdc


title: HEK293-Cas13d-PPIA-g1-rep2

description:
He54-2
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-Cas13d-PPIA-g1-rep1

description:
He54-1
35μg plasmids containing Cas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: HEK293-dCas13d-PPIA-g1-rep3

description:
DHe54-3
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.

value: dCas13d + PPIA-g1-Control


title: Cr7dYfpCreRGC1


title: Cr7dPtenSocs3CNTFCreRGC3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-ONC7d.csv

value: Pten fl/fl - Socs3 fl/fl - YFP17 het


title: HEK293-dCas13d-PPIA-g1-rep2

description:
DHe54-2
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: Cr7dPtenCreS3


title: Cr7dPtenCNTFCreS2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-CNTF-ONC7d.csv


title: PCCreMRpos_B8


title: HEK293-dCas13d-PPIA-g1-rep1

description:
DHe54-1
35μg plasmids containing dCas13d, EGFP, mCherry, PPIA-targeting gRNA g1 was transfected into HEK293 cells and cultured in 10-cm dishes for two days. Then 600,000 dual-positive EGFP+/mCherry+ (top 15%) cells were sorted out to make a pool for sequencing.


title: PCCreMRpos_B11


title: Cr7dPtenCNTFCreS1


title: HS_REC_siLONP1_rep3

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
Raw reads were aligned using STAR version 2.7.3a to build version hg38 of the human genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package and R (version 3.6.3)
Normalization and differential analysis were carried out using edgeR R package.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Colon cancer cells

growth_protocol: SW620 were maintained in Glutamax RPMI 1640 supplemented with gentamycin and 10% foetal bovine serum (FBS) at 37°C, 5%CO2.

extract_protocol:
RNA was extracted by using RNeasy minikit following manufacturer’s instructions.
Libraries were prepared usinn  TruSeq™ Stranded mRNA e Total RNA according to manufacturer’s instructions

treatment_protocol: SW620 cells were grown at 37°C,  then kept at 42°C for 1 hour and left to recover at 37°C for 1 hour.

value: Lonp1 siRNA

tag: condition

value: Kept at 42°C for one hour and left to recover at 37°C for one hour


title: MCF7-TWIST1 RNA-Seq

city: Houston

first: Xiaobin

last: Yu

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

data_processing:
The paired-end reads were mapped to the human genome (UCSC hg38) using STAR with NCBI RefSeq genes as the reference. STAR generated read counts for each RNA was used as the measurement of gene expression.
DESeq2 was used to analyze the gene-based read counts to detect differentially expressed genes between the groups of interest.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include DESeq2 values.

source_name: Human breast cancer cell

growth_protocol: MCF7-TWIST1 and MCF7-Ctrl cell lines were cultured in DMEM medium supplemented with 10% fetal bovine serum (10437028; Thermo Fisher) and 1% penicillin (10000 IU)/streptomycin (10000 µg/ml) solution (30-002-CI; Corning). Cells were maintained at 37°C in a 5% CO2 cell culture incubator.

extract_protocol:
Total RNA samples were extracted from both MCF7-TWIST1 and MCF7-Ctrl using the TRIzol reagent (15596018; Thermo Fisher) followed by purification with the RNeasy Mini Kit (74106; Qiagen) according to manufacturer's instructions. Quality of the samples were checked by using the NanoDrop spectrophotometer and Agilent Bioanalyzer 2100.
250 ng of total RNA samples (measured by picogreen) that had passed the quality check was used for creating a double-stranded DNA library. ERCC RNA Spike-In Controls were added to each sample according to the manufacturer’s protocol. The fragmented and 3’ poly (A)-selected portion of total RNA together with random primers were used to create the cDNA. In the process of second strand synthesis, dTTP was replaced with dUTP to quench the second strand during amplification amd thereby achieve strand specificity. The created cDNA fragments were blunt ended, attached with an adenosine to the 3' end, and finally ligated with unique adapters to the end. The ligated products were amplified with 15 PCR cycles. The resulting libraries were quantitated using the NanoDrop Spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter-ligated fragments, the libraries were further quantitated by qPCR by using the Applied Biosystems ViiA7 Real-Time PCR System and a KAPA Library Quant Kit.

treatment_protocol: TWIST1 was overexpressed in luminal breast cancer cell line MCF7.

value: Breast


title: PCCreMRpos_B2

value: Retina


title: PCCreMRpos_B12

value: 6-8 wk old


title: PCCreMRpos_B1


title: MCF7-Ctrl RNA-Seq


title: Cr2dPtenCreRGC5

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC2D.csv


title: HS_REC_siLONP1_rep2


title: MCF7-TWIST1 ChIP-Seq

data_processing:
ChIP-Seq data was analyzed using the online platform Galaxy (https://usegalaxy.org/). Briefly, the adaptor sequence and low-quality ends were removed using Trim Galore!. Cleaned reads were mapped into the Human Reference Genome hg38 by using Bowtie2. Peak calling was performed with MACS2 with a cutoff q value < 0.05. Visualization of ChIP-Seq track results was achieved by IGV tools.
Genome_build: hg38
Supplementary_files_format_and_content: wig files include Flag-TWIST1 peaks in MCF7-TWIST1 cells and Flag peaks in MCF7-Ctrl cells.

source_name: Breast cancer cells

extract_protocol:
ChIP assays were performed using the SimpleChIP Enzymatic Chromatin IP Kit (Magnetic Beads) (9005S; Cell Signaling Technology) according to the manufacturer’s instructions. Sample quality checks were performed by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 DNA quantitation assay and Agilent Bioanalyzer.
The Rubicon ThruPlex DNA-Seq library preparation system (p/n R400523, protocol QAM-328-001) was used to prepare ChIP-Seq libraries for sequencing on the Illumina NGS sequencing instruments. 1 ng of ChIP’d DNA was used for generating a double-stranded DNA library. The genomic DNA fragments were blunt ended and then the 5' end of the fragments were ligated with stem-loop adapters with blocked 5' end, leaving a nick at the 3' end. Then, the 3' end was extened during library synthesis and Illumina-compatible indexes were incorporated with 11 amplification cycles. The fragments were purified by using the AMPure XP Bead Purification System. Fragments with a size smaller than 200 bp as well as unincorporated PCR reagents and nucleotides were removed. The resulting libraries were quantitated by using the NanoDrop ND-1000 spectrophotometer and the fragment sizes were assessed with the Agilent Bioanalyzer. To determine the concentration of adapter ligated fragments, the libraries were quantitated by qPCR by using the Applied Biosystems ViiA7 TM Real-Time PCR System and a KAPA Library Quant Kit.

treatment_protocol: Flag-TWIST1 was overexpressed in luminal breast cancer cell line MCF7.

tag: chip antibody

value: anti-FLAG (Sigma-Aldrich; Cat# F1804; RRID:AB_262044)

value: Untreated


title: HS_REC_siLONP1_rep1

tag: treatment


title: PCCreMRpos_C3

source_name: Mouse retina, 6-8 wk old

value: Pten fl/fl - YFP17 het


title: PCCreMRpos_B9

value: AAV2-Cre / AAV-CNTF


title: Cr2dPtenCreRGC4


title: PCCreMRpos_A3


title: PCCreMRpos_A8


title: MCF7-Ctrl ChIP-Seq


title: Cr7dPtenCreS4

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-ONC7d.csv


title: CHLA10_shNS_IgG

data_processing:
library strategy: CUT&RUN
Paired-end reads were aligned to hg38 using Bowtie2.3.5 with the following command: bowtie2 --end-to-end --very-sensitive --no-overlap --no-dovetail --no-unal --no-mixed --no-discordant -q -I 10 -X 700 -x path/to/Bowtie2/indices -1 read1.fastq.gz -2 read2.fastq.gz
Peaks were called using MACS2.2.7 with both treatment-only and IgG-controlled modes with the following parameters: --format BAMPE --gsize hs --keep-dup all -q 0.05. For H3K27me3, broad peak calling was turned on using --broad --broad-cutoff 0.1.
IgG-controlled narrow peaks were kept if they overlapped with treatment-only peaks from the same sample, q-value is less than 0.01 and fold enrichment is over 2; treatment-only broad peaks were kept if they overlap with IgG-controlled peaks from the same sample, peak width is at least 2 Kbp, q-value is less than 0.01 and fold enrichment is over 2.
For HOXD13, in addition to MACS2 narrow peak calling and peak filtering described above, SEACR 1.2 was also run with stringent mode and IgG control. Filtered MACS2 peaks that overlap with SEACR peaks were passed on to the downstream analyses.
genome coverage profiles were generated using BEDTools with the following command: bedtools genomecov -scale <scale factor to count per million> -bg -pc -ibam path/to/bam
Genome_build: Hg38
Supplementary_files_format_and_content: peak files in MACS2 narrow/broad peak format
Supplementary_files_format_and_content: genome coverage files (.bw) normalized to count per million

extract_protocol:
Cells were bound to concanavalin A-coated magnetic beads , permeabilized with digitonin, and bound with primary antibodies. Samples are then arrayed in a 96-well plate and processed on a Beckman Biomek FX liquid handling robot equipped with a 96S Super Magnet Plate. The MNase digestion reaction is performed at 0–4 °C after the addition of 2 mM CaCl2.  Chromatin fragments released into the supernatant arae collected for the next steps.
Methods from (Janssens et al. 2018 Methodology: "Chromtin fragments are used as the substrate for end-repair and ligation with barcoded Y-adapters. Prior to ligation, the A-tailing step is performed at 58 °C to preserve sub-nucleosomal fragments in the library. End-repair and adapter ligation reactions were performed on a separate thermocycler. Chromatin proteins are then digested with Proteinase K, and adapter ligated DNA fragments are purified on the Biomek FX using two rounds of pre-PCR Ampure bead cleanups with size selection. PCR enrichment reactions are performed on a thermocycler using the KAPA PCR kit (KAPA Cat#KK2502). Two rounds post-PCR Ampure bead cleanups with size selection are performed on the Biomek FX to remove unwanted proteins and self-ligateed adapters. The size distributions of AutoCUT&RUN libraries were analyzed on an Agilent 4200 TapeStation, and library yield was quantified by Qubit Fluorometer (Thermo Fisher). Up to 24 barcoded AutoCUT&RUN libraries were pooled per lane at equimolar concentration for paired-end 25 × 25 bp sequencing on a 2-lane flow cell on the Illumina HiSeq 2500 platform at the Fred Hutchinson Cancer Research Center Genomics Shared Resource."

value: Ewing sarcoma

tag: antibody


title: Cr21dPtenSocs3CNTFCreRGC3

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_PtenScos3-CNTF-ONC21d.csv

tag: tissue


title: HS_REC_siCtrl_rep3

value: Scrambled siRNA


title: HS_REC_siCtrl_rep2


title: A673_CHLA10_pooled_data

description: RNA data

data_processing:
Bcl2fastq2  Conversion Software (Illumina) was used to generate de-multiplexed Fastq files
CellRanger (3.1) Pipeline (10X Genomics) was used to align reads and generate count  matrices
Supplementary_files_format_and_content: tar.gz containing .mtx.gz, and .tsv.gz files for the mRNA, ADT, and HTO data to be read into R for use in the Seurat/monocle3 pipeline.

source_name: A673 and CHLA10 cells pooled

extract_protocol: Libraries generated using the 3’ V3 10X Genomics Chromium Controller following the manufacturer’s  protocol (CG000183)

tag: disease

value: HTO labeled by cell type (HTO1- A673, HTO2- CHLA10)


title: PCCreMRpos_A6

data_processing:
Sequencing reads were first trimmed using Trimmomatic-0.39. Reads were then aligned to mouse genome GRCm38.81 using hisat2, reads per gene per cell were counted using featureCounts.
Assembly: GRCm38
Supplementary files format and content: Gene count matrix in .csv format

extract_protocol:
Retinas were dissected in oxygenated AMES, digested in papain, and dissociated to single cell suspensions using manual trituration in ovomucoid solution. Single cell suspensions were incubated with 0.5ul of anti-CD90,  (Thermo Fisher Scientific) for 10 million cells per 100µl. Cells were sorted using a MoFlo Astrios. Cellular debris, doublets, and dead cells were excluded, and RGCs were collected based on high CD90 and GFP and mCherry (for MR+) or without mCherry (MR-)co-expression. Cells were collected directly into 96well plates, 1 cell/well and frozen at -80C.
Cells were processed following published SS2 protocols, using pre-beads clean up and purification and Nextera XT kit from Illumina. Libraries were sequenced on NovaSeq-SP

tag: strain

value: PCCreMRpos

tag: age


title: CHLA10_shNS_H3K27me3_1

value: H3K27me3:cell signaling 9733S (1:100)


title: CHLA10_shNS_H3K27me3_2


title: PCCreMRpos_A2


title: PCCreMRpos_A12


title: CHLA10_shNS_H3K4me3_2


title: HS_siLONP1_rep3

value: Kept at 42°C for one hour


title: Posterior_E10_5

city: Minneapolis

first: Daniel

last: Garry

state: MN

address: 2231 6th Street SE, 4th Floor

department: Lillehei Heart Institute

institute: University of Minnesota

data_processing:
Illumina 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 bowtie2 v2.2.4 with default parameters.
The ATAC-seq peaks were called by MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files; bigwig files

extract_protocol:
Limb bud tissues were digested in 200 ml of TripLE (ThermoFisher 12605010) at 37°C in two cycles of 5 min incubation followed by trituration. Cells were cooled on ice for 5 min between incubations. Digestion was stopped with 1ml of medium with 10% fetal calf serum that was filtered through a 50 mm mesh filter (Partec). Cells were collected by centrifugation and stained with staining medium containing 0.2 mg each of CD31-APC, Tie2-APC, CD45-APC and 0.5 mg anti CD16/CD32, and EYFP positive, APC negative live cells were sorted on FACSAria (BD). Cells from EYFP negative embryos were used as a negative control for FACS sorting.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols

tag: time

tag: genotype/variation


title: HS_REC_siCtrl_rep1


title: Etv2CKO_posteriorHL_rep1


title: Anterior_E10_5


title: HS_siLONP1_rep2


title: CHLA10_shNS_H3K4me3_1


title: CtCrePCS2

description:
Retina ganglion cells collected by CD90+ FACS
count_mat_Pten-CNTF-NoCrush.csv

value: retina

value: NoCrush


title: HL_E9_5


title: CtCrePCS1


title: CHLA10_shNS_H3K4me1_2


title: Etv2_OE_rep6


title: HS_siLONP1_rep1

value: Lonp1 siRNA


title: Etv2CKO_posteriorHL_rep2


title: HS_siCtrl_rep3


title: Cr7dPtenScos3CNTFCreS6

value: Pten fl/fl - Socs3 fl/fl - YFP17 het


title: CHLA10_shNS_H3K27ac_2

value: H3K27ac:Millipore MABE647 (1:50)


title: CHLA10_shNS_H3K27ac_1


title: Etv2_OE_rep5


title: PCCreMRpos_A11

value: Retina

tag: aav infection


title: CHLA10_shNS_H3K4me1_1


title: Cr7dPtenScos3CNTFCreS4


title: Etv2_OE_rep4


title: Etv2_OE_rep3


title: CHLA10_IgG


title: Ctrl_siLONP1_rep3

value: Kept at 37°C


title: HS_siCtrl_rep1


title: Etv2_OE_rep2


title: Cr7dPtenScos3CNTFCreS5


title: Ctrl_siLONP1_rep2


title: Etv2_OE_rep1


title: Ctrl_siLONP1_rep1


title: STZ+SGLT2i [SGL2]

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

data_processing:
Illumina RTA v3.1.5 was used for basecalling and Illumina bcl2fastq2 was used for fastq file generation
PE50 reads were quality checked with package FastQC, then trimmed using Trimgalore (with default settings). Trimmed reads were mapped to murine genome annotation (mm10) using STAR with default settings. .
Mapped reads were then counted using RsubRead.  Normalization and log2 transformation was done with edgeR.
Assembly: mm10
Supplementary files format and content: txt files containing log2 normalized counts per million (log2cpm) per sample

source_name: renal tissue

growth_protocol: Wild-type mice (C57BL/6, age 8-10 weeks) were obtained from Janvier Lab (S.A.S., St. Berthevin Cedex, France). Only male mice were used throughout this study.

extract_protocol:
RNA was extracted from renal tissue using RNeasy Mini Kit (QIAGEN, Germany) and RNA concentration was measured using nanodrop (2000C, Peq lab, Germany). The quality and integrity of RNA were controlled with an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).
The RNA sequencing library was generated from 500ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher) for mRNA purification followed by NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) according to manufacture´s protocols.

treatment_protocol: In wild-type mice (C57BL/6, age 8-10 weeks) mice hyperglycemia was induced using low dose streptozotocin (STZ) injection. A subset of hyperglycemic mice were treated with a sodium-glucose co-transporter 2 inhibitor.  Mice were sacrificed at the end of study period and kidney samples were isolated and RNAseq was performed.

value: Type-1 DM + glycemic control

value: renal tissue


title: CHLA10_HOXD13

value: rabbit anti-HOXD13 (1:20)


title: STZ+SGLT2i [SGL1]


title: HS_siCtrl_rep2


title: STZ [DM2]

value: Type-1 DM


title: Ctrl_siCtrl_rep2


title: A673_shNS_IgG

value: Ewing sarcoma


title: WT_Control_rep7


title: WT_Control_rep8


title: Ctrl_siCtrl_rep3

value: Scrambled siRNA


title: WT_Control_rep6


title: Control [C9]

value: Control


title: A673_shNS_H3K27me3_2


title: A673_shNS_H3K27me3_1


title: Control [C8]


title: Ctrl_siCtrl_rep1


title: STZ [DM1]


title: Control [C2]


title: A673_shNS_H3K4me3_2


title: A673_shNS_H3K4me3_1


title: WT_Control_rep3


title: WT_Control_rep2


title: WT_Control_rep4


title: WT_Control_rep5


title: t-SVZ

city: Chengdu

first: Weibo

last: Liang

address: Renmin South Road

institute: Sichuan University

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 10%  passed the cell quality filtering and mitochondria genes were removed in the expression table.
Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.
PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCm38Ensembl92
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: subventricular zone (SVZ)

growth_protocol: All mice were housed in cages with ad libitum access to food and water and acclimated to standard conditions (12 h light/dark cycle, temperature: 22–25 °C, relative humidity: 40-60%) for at least one week before the experiment.

extract_protocol:
Mice were sacrificed 48 hours post injury, and the SVZ was micro-dissected (n=3 per group) and washed in precooled PBS to remove residual blood. Then, the tissue was flash-frozen in liquid nitrogen and transferred to -80 ℃ until further use.NLB buffer (X-100 (Sigma-Aldrich, St Louis, MO, USA), 0.2 U/μL RNase Inhibitor (Takara, Kyoto, Japan), 250 mM Sucrose, 10 mM Tris-HCl, 3 mM MgAc2, 0.1% Triton 0.1 mM EDTA) was used to homogenize the frozen tissue. Different concentrations of sucrose were applied to purify the nuclei using sucrose density gradient centrifugation. A final concentration of around 1000 nuclei/μL was used for scRNA-Seq.
The scRNA-Seq libraries were built using the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3 Reagent Kits (10X Genomics, Pleasanton, CA, USA). Briefly, the acquired cell nuclei were loaded into several channels to obtain single-cell Gel Bead-In-Emulsions (GEMs). After reverse transcription, barcoded cDNA was released from the GEM and then purified. After amplification, the barcoded cDNA went through fragmentation, ligation with adaptors, and amplified with index PCR. The Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, Waltham, MA, USA) was applied to quantify the final libraries, and the size distribution was determined by the High Sensitivity DNA chip using Bioanalyzer 2200 (Agilent Technologies, Santa Clara, CA, USA). Novaseq6000 (Illumina, San Diego, CA, USA) was used for sequencing on a 150 bp paired-end run.

treatment_protocol: Each mTBI mouse received a single mild controlled cortical impact (CCI).Sham-operated control mice underwent the same procedures except for the impact.

value: subventricular zone (SVZ)

tag: stress

value: mTBI (Mild Traumatic Brain Injury)


title: LimbWT_10_25_rep1


title: c-SVZ

value: Sham (Control)


title: LimbWT_10_25_rep2


title: HL_GFP_pos_rep3


title: WT_Control_rep1


title: A673_IgG

tag: cell line


title: Etv2cKO_E10_25_rep5


title: liver tissue (tumour-free) from Pt#015, liver slice, post-recovery

type: RNA

city: London

first: Elena

last: Palma

state: -- US/Canada Only --

address: 111 Coldharbour Lane

institute: The Roger Williams Institute of Hepatology

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their template for analysis (Instructions for Analyzing RT2 Profiler PCR Array Results with this Template).
For the normalization it uses the average of five housekeeping genes: ACTB, B2M, GAPDH, HPRT1 , RPLP0.

label: SYBR Green

source_name: liver, tumour-free from patient with LM-NEN

label_protocol: cDNA was synthesized with RT2 First Strand Kit (Qiagen).

growth_protocol: After slicing the original tissue, each slice was cultured into a 12-well plate for 2 hours (recovery step) in 1.5 mL supplemented Williams Medium E: William’s E Medium (ThermoFisher Scientific), 5% Human AB serum (Pan-Biotech), Penicillin/Streptomycin (ThermoFisher Scientific), 2 mM Glutamine (ThermoFisher Scientific), ITS (10 mg/L Insulin + 5.5 mg/L Transferrin + 6.7 µg/L Sodium selenite, ThermoFisher Scientific), 1nM epidermal growth factor (ThermoFisher Scientific), 100nM Glucagon (Merck), 1µM Corticosterone (Merck). After the recovery slices were collected, preserved in AllProtect Tissue Reagent (Qiagen) and stored at -80C until RNA extraction.

extract_protocol: Total RNA was isolated with Allprep Mini Kit (Qiagen) according to manifacturer's instructions.

tag: sample type

value: control

tag: primary tumour type

value: LM-NEN

tag: gender

value: M

tag: ethnicity

value: caucasian

tag: primary tumour site

value: lung

tag: tumour grade

tag: fibrosis score

value: UA


title: liver tissue (tumour-free) from Pt#062, liver slice, post-recovery

value: F

value: pancreatic


title: HL_GFP_pos_rep2


title: liver tissue (tumour-free) from Pt#051, liver slice, post-recovery

value: small bowel


title: liver tissue (tumour-free) from Pt#045, liver slice, post-recovery


title: tumour (cholangio carcinoma) from Pt#024, tumour slices, post-recovery

source_name: tumour, primary liver cancer HCC

value: test

value: CCA

value: cholangio carcinoma


title: HL_GFP_pos_rep1


title: liver tissue (tumour-free) from Pt#024, liver slice, post-recovery

source_name: liver, tumour-free from patient with CCA


title: A673_shNS_H3K27ac_1

tag: cell type

value: Ewing sarcoma

tag: antibody

value: H3K27ac:Millipore MABE647 (1:50)


title: Etv2cKO_E10_25_rep4


title: Etv2cKO_E10_25_rep3