title: Atac HD-MSNs_GM02173_#3

tag: cell line


title: mRNA 1_Hypoxia 2h

status: Public on Sep 15 2022

type: SRA

city: GDANSK

first: Rafal

middle: A

last: Bartoszewski

address: Hallera 107

country: Poland

institute: Medical University of Gdansk

library_source: transcriptomic

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
Raw sequence FASTQ files were uploaded to Qiagen's GeneGlobe Data Analysis Center and followed their analysis pipeline.
Differential expression was also analyzed with GeneGlobe using the DESeq2 option for normalization
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited Excel file containing each sample (columns) with UMI values for each microRNA

molecule: total RNA

organism: Homo sapiens

source_name: HUVEC

growth_protocol: Primary human umbilical vein endothelial cells (HUVEC) that were pooled from ten individual donors were purchased from Cellworks (Caltag Medsystems Ltd, UK) and cultured in EGM-2 Bulletkit Medium (Lonza). All experiments were conducted between passage 2 and 6 at a confluence of 70-80%.

extract_protocol: Total RNA (containing both mRNA and miRNA) was isolated using miRNeasy kit (Qiagen). RNA concentrations were calculated based on the absorbance at 260 nm. RNA samples were stored at -70°C until use.

treatment_protocol: Hypoxia was induced in a CO2/O2 incubator/chamber specific for hypoxia research (Invivo2 Baker Ruskin). Briefly, cells were cultured in 35 mm or 60 mm dishes (for RNA isolation and protein isolation, respectively) at 0.9% O2 for the time periods specified (PO2 was 10-12 mm Hg). Control cells were maintained in normoxia in a CO2/O2 incubator (Binder). The hypoxia mimetics – Dimethyloxalylglycine; N-(Methoxyoxoacetyl)-glycine (DMOG, Sigma, D3695) and CoCl2 (Sigma, 60818) were used at final concentrations of 200 µM and 1 mM for 16 h. siRNA transfections. siRNA for HIF1A (Ambion assay id s6539) and EPAS1 (Ambion assay id s4698) were purchased from Ambion. HUVECs were transfected using the Lipofectamine RNAiMax (Invitrogen, 13778030) according to manufacturer's protocol. The siRNAs were used at a final concentrations of 40 nM. The transfected cells were cultured for 2 days prior to further analysis. Ambion siRNA Negative Control 1 (Ambion assay id MC22484) was used as a control. After 24 h, the transfected cells were put into a hypoxia chamber or treated with CoCl2 or DMOG, whereas the control cells remained in an incubator in normoxic conditions.The RIP assay kit for miRNA (#RN1005, MBL) was used following the manufacturer’s protocol. HUVECs (80% confluence) from four 100 mm culture dishes were collected for each condition 17, 18. Cell lysis was conducted in hypoxia or normoxia using a cell scraper and ice-cold PBS and mi-Lysis Buffer(+) was added to the cell pellet. Lysates were snap-frozen and stored at -70°C until use. For immunoprecipitation, 15 µg of anti-EIF2C2/AGO2 (#RN003M, MBL) or mouse IgG2a (isotype control; # M076-3, MBL) and agarose beads (Pierce Protein A/G Agarose, #20421, Thermo Scientific) were used. RNA was isolated using a miRNeasy Mini Kit (Qiagen, Hilden, Germany). 700 µl of QIAzol Lysis Reagent was added to the washed beads and the obtained RNA was eluted in 30 µl of nuclease-free water and used in the next generation RNA sequencing experiments

tag: sample type

value: 10 donors derived endothelial cells

tag: treatment

value: Exposed to hypoxia (1 % Oxygen) for 2 hours


title: Atac HD-MSNs_GM04198_124

city: Saint Louis

first: Youngmi

last: Oh

state: MO

address: 660 S. Euclid Avenue

department: Development department

country: USA

institute: Washington University in St. Louis

library_source: genomic

data_processing:
At least 45 million omni-ATAC reads per sample were processed by Atac-seq Integrative Analysis Pipeline (AIAP, https://github.com/Zhang-lab/ATAC-seq_QC_analysis).
AIAP trims adapters using Cutadapt
AIAP aligns fragments using BWA-MEM to the hg38 human reference genome
AIAP removes low quality reads using methylQA
AIAP normalizes count signal by 10 million input single end reads
AIAP call peaks by macs2 with q-value less than 0.01
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files of biological replicates for ATAC-seq experiments

molecule: genomic DNA

source_name: Dermal fibroblasts

growth_protocol: Direct neuronal reprogramming of human fibroblasts to neurons was performed as previously described (Abernathy et al., 2017; Richner et al., 2015).

extract_protocol:
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)
Omni-ATAC-seq preparation was performed as outlined in Corces et al. (Corces et al., 2017)

value: Coriell GM04198

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: RNA 20_hifa si DMOG

data_processing:
Illumina bcl2fastq version 2.18.0.12 was used for basecalling
STAR version 2.7.3a was used to align the raw sequences to the human genome using parameters: --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Cufflinks version 2.2.1 was used to estimate transcript abundances using parameters: --library-type fr-firststrand -G -L
Cuffmerge merged the samples together and Cuffdiff (using default parameters) was used for differential expression
Genome_build: Gencode GRCh38 p13 Release 32
Supplementary_files_format_and_content: tab-delimited Excel files with sample (columns) and their respective FPKM values for each gene (rows)

value: Treated for 16h with 1mM DMOG

tag: genotype/variation

value: with HIF1A knockdown


title: Plate11-274-Liver

city: Durham

first: Scott

last: Auerbach

state: North Carolina

address: 111 TW Alexander Drive

institute: Division of the National Toxicology Program at NIEHS

description: Plate 11_LIVER_C03

data_processing: Data were processed using the Tempo-SeqR software package

organism: Rattus norvegicus

source_name: Liver

growth_protocol: Male and female SD rats were placed on NTP-2000 diet and housed up to 5 animals per cage. After a 10-14 day quarantine, 8-10 week old animals were randomly assigned to treatment and control groups.

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

treatment_protocol: Each of six chemicals was given at nine doses (5 mL/kg dosing volume) to the treatment groups. A vehicle control group was also included for each treatment group. Rats received the test formulations via gavage for five consecutive days.

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Male

tag: tissue

value: Liver

tag: chemical

value: 10:2 FTOH

tag: concentration

tag: unit

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: mRNA 1_Normoxia (Control group)

value: Normoxia exposed


title: Atac HD-MSNs_ND33947_129

value: NHCDR ND33947


title: MA_H3K27ac_rep2

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

description: MA_27_R2_CHIP_CGTTAGAA-TTCAGGTC_S31_ME_peaks.narrowPeak

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
MACS2 were used for peak calling with following parameter -extsize 200 --nolambda -g mm -p 1e-5
Genome_build: mm10 reference
Supplementary_files_format_and_content: 20 txt files containg  Ascl1, Mef2c, and H3K27ac Peaks of A, M, and AM  infected fibroblast in replicates

organism: Mus musculus

source_name: Mouse Embryonic Fibroblast

growth_protocol: Mice were raised and maintained under standard laboratory conditions.

extract_protocol:
Chromatin were harvested using truChIP® Chromatin Shearing Kit (Covaris, PN 520154) following the manufacturer’s protocol. Briefly, five million cells were cross-linked with Fixing Buffer A at room temperature for 10 minutes. Quenching Buffer E was added to the fixed cells and the cells were incubated at room temperature for an additional 5 minutes. The cells were washed twice with ice-cold PBS. To extract the nuclei, Lysis Buffer B containing 1x protease inhibitors were added to the cells. Incubate the cell on ice for 10 minutes on a rocker at 4 degree. Intact nuclei were collected by centrifugation at 1,700 x g for 5 minutes at 4 degree. The nuclei were washed once with Wash Buffer C and then Shearing Buffer D3.   The pelleted nuclei were resuspended in 1ml Shearing Buffer D3 and transfer to  milliTUBE (Covaris, PN 520135). The chromatin shearing were performed with E220 Focused-ultrasonicator (Covaris) with 60sec on and 30sec off, 14 cycles. The chromatin solution was clarified by centrifugation at 20,000 g at 4C for 45 minutes and then pre-cleared with Dynabeads protein A (Life Technologies) for 2 hours at 4C. The pre-cleared chromatin sample was incubated with 50 mL of Dynabeads protein A loaded with 5 mg antibody (anti-H3K27ac, ab4729; anti-Mef2c, ab211493; anti-Ascl1, ab74065) overnight at 4C. The beads were washed three times with 0.1% SDS lysis buffer, once with 0.1% SDS lysis buffer/0.35 M NaCl, once with 10 mM Tris-Cl (pH 8)/1 mM EDTA/0.5% NP40/ 0.25% LiCl/0.5% NaDOC, and once with TE buffer (pH8.0). The immunoprecipitated material was eluted from the beads by heating for 45 minutes at 68C in 50 mM Tris-Cl (pH 7.5), 10 mM EDTA, 1% SDS. To reverse the crosslinks, samples were incubated with 1.5 mg/ml Pronase at 42C for 2 hr followed by 67C for 6 hr. The samples were then extracted with MinElute PCR purification Kit (QIAGEN) and eluted in TE buffer.
ChIP DNA were then sent to UNC Chapel Hill’s High-Throughput Sequencing Facility libraries for ChIP-seq library preparation with Thruplex DNA Seq Library Prep kit (Takara).

treatment_protocol: MEF were infected with viruses encoding the  reprogramming factors with polybrene(4ug/ml)

tag: cell type

value: Mouse Embryonic Fibroblast

tag: antibody

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)

value: Infected with Ascl1, Mef2c  virus


title: MA_H3K27ac_rep1

description: MA_27_R1_CHIP_TACCGAGG-CCTGAACT_S29_ME_peaks.narrowPeak


title: Plate11-268-Liver

description: Plate 11_LIVER_E02

value: Female


title: mRNA 3_Normoxia (Control group)

value: 10 donors derived endothelial cells


title: RNA 20_DMOG ctrl si

value: Treated for 16h with 1mM DMOG

value: control sample


title: mRNA 1_Hypoxia 8h

value: Exposed to hypoxia (1 % Oxygen) for 8 hours


title: Plate11-261-Liver

description: Plate 11_LIVER_D03

value: Sprague Dawley (SD)

value: Male


title: Atac HD-MSNs_ND33947_128

tag: cell line

value: CTIP2, DLX1, DLX2, MYT1L


title: Mef2c_H3K27ac_rep1_input

description: M_27_R1_CHIP_AGCCTCAT-AGTAGAGA_S21_ME_peaks.narrowPeak

value: No antibody

value: Infected with Mef2c virus


title: Mef2c_H3K27ac_rep2_input

description: M_27_R2_CHIP_GATTCTGC-GACGAGAG_S23_ME_peaks.narrowPeak


title: RNA 20_hif2 si CoCl2

tag: sample type

value: Treated for 16h with 200 µM CoCl2

value: with EPAS1 knockdown


title: Plate11-253-Liver

description: Plate 11_LIVER_A04

value: Liver

value: 10:2 FTOH

value: mg/kg

value: water/tween

value: day

value: TempO-Seq


title: Atac HD-MSNs_ND33947_127

value: NHCDR ND33947


title: RNA 20_hif1a Si CoCl2

value: 10 donors derived endothelial cells

tag: treatment

value: with HIF1A knockdown


title: Atac HD-MSNs_GM02147_123

value: Coriell GM02147

tag: overexpression 1


title: Mef2c_H3K27ac_rep2

value: Mouse Embryonic Fibroblast

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: RNA 20_CoCL2 ctrl si)

value: control sample


title: Plate11-238-Liver

description: Plate 11_LIVER_B02

value: Sprague Dawley (SD)

value: Female


title: Atac HD-MSNs_GM02147_122

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate11-217-Liver

description: Plate 11_LIVER_B04

value: Male


title: Plate11-214-Liver

description: Plate 11_LIVER_A02

value: Liver


title: RNA 20_hif1a si hypoxia 8h

value: Exposed to hypoxia (1 % Oxygen) for 8 hours

tag: genotype/variation


title: Plate11-235-Liver

description: Plate 11_LIVER_A03

tag: strain

value: 10:2 FTOH

value: mg/kg


title: Ascl1_H3K27ac_rep1_input

description: A_27_R1_CHIP_TCGTAGTG-AGACTTGG_S1_ME_peaks.narrowPeak

value: No antibody

value: Infected with Ascl1 virus


title: Ascl1_H3K27ac_rep2_input

description: A_27_R2_CHIP_GGTACCTT-AAGACGTC_S3_ME_peaks.narrowPeak


title: Mef2c_H3K27ac_rep1

value: Infected with Mef2c virus


title: RNA 20_hif si hypoxia 8h

value: 10 donors derived endothelial cells

value: with EPAS1 knockdown


title: RNA 20_hypoxi 8h control


title: Atac HD-MSNs_GM04230_119

value: Coriell GM04230


title: Plate11-212-Liver

description: Plate 11_LIVER_B03

tag: Sex

value: water/tween

value: day

value: TempO-Seq


title: RNA R_8h hypoxia

value: RISC complexes


title: RNA R_normoxia control

value: Normoxia exposed


title: Plate11-211-Liver

description: Plate 11_LIVER_H03

value: Sprague Dawley (SD)

tag: tissue


title: Atac HD-MSNs_ND30013_117

value: NHCDR ND30013

value: CTIP2, DLX1, DLX2, MYT1L


title: MGT_scRNA

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ARC pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R using seurat.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: Two csv files containing RNA count for cells in the two samples, respectively

source_name: cardiac

extract_protocol:
Cells were harvested by trypsin and nuclei were harvested using 10x provided protocol.
Illumina libraries were prepared usingSingle Cell Multiome ATAC  + Gene Expression kit.

treatment_protocol: For direct cardiac reprogramming, pMXs retrovirus encoding Mef2c, Gata4, Tbx5, and Ascl1 were packaged by transfecting platE cells with Trans-IT as the manufacturer suggested. Viruses were collected from one 10-cm dish were resuspended in 100μl iCM medium(400ml DMEM, 100ml M199, and 50ml FBS). All virus transductions were performed in the iCM medium containing 4 μg/ml of polybrene. For single-cell multiomics, cardiac fibroblasts were transduced with M, G, and T viruses  for MGT induced reprogramming sample or equal amounts of M and A for AM induced reprogramming sample.

value: heart

tag: age

value: 1-3 days

tag: genotype

value: wild type


title: Plate11-242-Liver

description: Plate 11_LIVER_G03

value: Male

value: Liver

tag: chemical

value: 10:2 FTOH

tag: concentration

tag: unit

value: mg/kg


title: AM_scRNA


title: Plate10-320-Kidney

description: Plate 10_KIDNEY_A07

source_name: Kidney

value: Female

value: Kidney

tag: vehicle

tag: duration

tag: platfrom


title: RNA R_negative Igg

value: 10 donors derived endothelial cells

value: Nonspecific antibody used for immunoprecypitation of RISC


title: Atac HD-MSNs_ND30013_116

tag: cell line


title: Atac HD-MSNs_GM02147_121

value: Coriell GM02147


title: Atac HD-MSNs_GM04230_120

value: Coriell GM04230


title: MGT_scATAC

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Raw sequencing data was demultiplexed, debarcoded, mapped to Cell Ranger pre-built mm10 genome, and counted following the Cell Ranger ARC pipeline. The Cell Ranger output of collapsed UMI counts were then processed and analyzed in R using seurat.
Genome_build: Cell Ranger pre-built mm10 reference
Supplementary_files_format_and_content: Two csv files containing peak count for cells in the two samples, respectively


title: Plate10-319-Kidney

description: Plate 10_KIDNEY_G03

value: water/tween

value: day

value: TempO-Seq


title: Ascl1_H3K27ac_rep2

tag: cell type

value: Mouse Embryonic Fibroblast

tag: antibody

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)

value: Infected with Ascl1 virus


title: RNA R_2h hypoxia

tag: sample type

tag: treatment

value: Exposed to hypoxia (1 % Oxygen) for 2 hours

value: RISC complexes


title: Atac HD-MSNs_ND30013_115

value: NHCDR ND30013

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: AM_scATAC

tag: strain

value: heart

value: 1-3 days

value: wild type


title: Plate10-318-Kidney

description: Plate 10_KIDNEY_F07

value: Sprague Dawley (SD)

tag: Sex

value: Female

tag: tissue

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: Plate10-316-Kidney

description: Plate 10_KIDNEY_D06

value: water/tween

value: day


title: LACZ RNA rep2

data_processing:
Data quality was checked with FastQC and MultiQC.
Reads matching adapter sequences or with a mean quality score less than 20 were trimmed with Bbduk. Pseudoalignment was performed with Salmon using the mm10 cDNA transcriptome as reference.
Differential gene expression analysis was performed with DESeq2. Genes with an adjusted p value less than 0.1 and an absolute fold change greater than 1.5 compared to the relevant control.
Genome_build: mm10 reference
Supplementary_files_format_and_content: 1 csv files containg tpm of reprogramming and control group for three reprogramming systems in replicates

extract_protocol:
RNA was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s protocol.
Library preparation was performed with the Roche KAPA Stranded mRNA-Seq kit. Paired-end sequencing was performed on the NovaSeq SP platform to a depth of 4 X 107 reads per sample.

value: Mouse Embryonic Fibroblast

value: Infected with LACZ virus


title: Atac HD-MSNs_GM04230_118

value: Coriell GM04230


title: Ascl1_H3K27ac_rep1

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)

value: Infected with Ascl1 virus


title: LACZ RNA rep1


title: Plate10-313-Kidney

description: Plate 10_KIDNEY_B11

value: Male

value: TempO-Seq


title: A382_P53_1

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were mapped into reference human genome hg19 using TopHat2
Differentially expressed genes were analyzed using a Cufflinks tool, Cuffdiff, by masking structural RNAs
normalized to total mapped reads
RNA-seq files of two sgRNAs for each target gene were treated as replicates
Genome_build: hg19
Supplementary_files_format_and_content: txt, normalized FPKM

molecule: polyA RNA

source_name: glioblastoma

growth_protocol: A382 cells were cultured in DMEM with 10% FBS and penicillin/streptomycin

extract_protocol:
Total RNA was extracted using TRIzol following the manufacture's protocol
RNA-seq libraries were prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. Briefly, polyA RNA was selected by RNA Purification Beads and fragmented enzymatically. The first strands of cDNAs were synthesized using Super Script II reverse transcriptase, and the second strands were synthesized using Master Mix. Double-stranded cDNA was then 3’-adenylated, ligated with index adaptors, and PCR-amplified. The final RNA-seq library was quantified using Bioanalyzer Agilent DNA 1000 Chips

treatment_protocol: Cells were lentivirally infected with sgRNA for knockout or doxycycline for p53 induction

value: A382 expressing doxy-inducible p53

value: day2 after doxycycline induction


title: Atac pre-HD-MSNs_GM04717_106

value: Coriell GM04717

value: CTIP2, DLX1, DLX2, MYT1L


title: A382_PCW_2

value: A382 expressing control vector


title: MGT RNA rep2

value: Infected with MGT virus


title: Atac pre-HD-MSNs_GM04857_114

value: Coriell GM04857


title: A382_PCW_1


title: Plate10-310-Kidney

description: Plate 10_KIDNEY_D07

value: Sprague Dawley (SD)

value: Female

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: sgH2AZ_2_R2

value: day9 after sgH2AZ#2_2 guide RNA infection


title: Atac pre-HD-MSNs_GM04857_113


title: RNA R_16h hypoxia

value: 10 donors derived endothelial cells

value: Exposed to hypoxia (1 % Oxygen) for 16 hours

tag: genotype/variation

value: RISC complexes


title: Plate10-309-Kidney

description: Plate 10_KIDNEY_F04

tag: chemical

value: water/tween

value: day

value: TempO-Seq


title: Atac pre-HD-MSNs_GM04717_108

value: Coriell GM04717


title: IRESG_RNA_rep2

value: Mouse Embryonic Fibroblast

value: Infected with IRESG virus


title: sgH2AZ_2_R1

value: day9 after sgH2AZ#2_1 guide RNA infection


title: IRESG_RNA_rep1


title: A382_P53_2

value: A382 expressing doxy-inducible p53

value: day2 after doxycycline induction


title: Atac pre-HD-MSNs_GM04717_107

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate10-308-Kidney

description: Plate 10_KIDNEY_C09

value: Sprague Dawley (SD)

value: Female

value: Kidney

tag: concentration


title: HF_RNA_rep2

value: Infected with Hnf4a, Foxa3 virus


title: Atac pre-HD-MSNs_GM04829_110

value: Coriell GM04829


title: Atac pre-HD-MSNs_GM04829_111


title: sgH2AZ_1_R2

value: day9 after sgH2AZ#1_2 guide RNA infection


title: Plate10-304-Kidney

description: Plate 10_KIDNEY_C05

value: Male

value: 10:2 FTOH

tag: unit

value: mg/kg


title: sgH2AZ_1_R1

value: day9 after sgH2AZ#1_1 guide RNA infection


title: Plate10-303-Kidney

description: Plate 10_KIDNEY_B06

tag: vehicle

value: water/tween

value: day

value: TempO-Seq


title: Plate10-311-Kidney

description: Plate 10_KIDNEY_H01

tag: duration


title: sgNeg4_2

value: day9 after sgNeg4_2 guide RNA infection


title: HF_RNA_rep1

value: Mouse Embryonic Fibroblast


title: Atac pre-HD-MSNs_GM04829_109


title: Plate10-302-Kidney

description: Plate 10_KIDNEY_D08

tag: platfrom


title: Atac pre-HD-MSNs_GM04831_99

tag: cell line

value: Coriell GM04831


title: TETG_RNA_rep2

tag: cell type

value: Infected with TETG virus


title: TETG_RNA_rep1


title: Plate10-301-Kidney

description: Plate 10_KIDNEY_F11

value: Sprague Dawley (SD)


title: Atac pre-HD-MSNs_GM04857_112

value: Coriell GM04857

value: CTIP2, DLX1, DLX2, MYT1L


title: Atac pre-HD-MSNs_GM04831_98


title: sgRUVBL2_2

value: day9 after sgRUVBL2#2 guide RNA infection


title: BAM_RNA_rep2

value: Infected with Brn2, Ascl1, Myt1l  virus


title: Atac pre-HD-MSNs_GM04861_102

value: Coriell GM04861


title: Plate10-300-Kidney

description: Plate 10_KIDNEY_E03

value: Female

value: Kidney


title: sgRUVBL2_1

value: day9 after sgRUVBL2#1 guide RNA infection


title: BAM_RNA_rep1


title: Atac pre-HD-MSNs_GM04861_100


title: Plate10-299-Kidney

description: Plate 10_KIDNEY_D04

value: 10:2 FTOH

value: mg/kg


title: MGT RNA rep1

value: Infected with MGT virus


title: sgRUVBL1_2

value: day9 after sgRUVBL1#2 guide RNA infection


title: Plate10-298-Kidney

description: Plate 10_KIDNEY_E02

value: water/tween

value: day

value: TempO-Seq


title: sgRUVBL1_1

value: day9 after sgRUVBL1#1 guide RNA infection


title: MGT_RNA_rep1

data_processing:
Data quality was checked with FastQC and MultiQC.
Reads matching adapter sequences or with a mean quality score less than 20 were trimmed with Bbduk. Pseudoalignment was performed with Salmon using the mm10 cDNA transcriptome as reference.
Differential gene expression analysis was performed with DESeq2. Genes with an adjusted p value less than 0.1 and an absolute fold change greater than 1.5 compared to the relevant control.
Genome_build: mm10 reference
Supplementary_files_format_and_content: 1 csv files containg tpm of  Ascl1, Mef2c, and H3K27ac Peaks of A, M, and AM  infected fibroblast in replicates

value: Mouse Embryonic Fibroblast


title: Atac pre-HD-MSNs_GM04855_104

value: Coriell GM04855


title: Atac pre-HD-MSNs_GM04855_105

value: CTIP2, DLX1, DLX2, MYT1L


title: sgMORF4L2_2

value: day9 after sgMORF4L2#2 guide RNA infection


title: MA_RNA_rep1

value: Infected with Mef2c  and Ascl1 virus


title: MA_RNA_rep2


title: Plate10-296-Kidney

description: Plate 10_KIDNEY_C12

value: Sprague Dawley (SD)


title: sgNeg4_1

value: day9 after sgNeg4_1 guide RNA infection


title: Old-MSNs_AG11798_#3

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the Ensembl release 76 primary assemblies with STAR version 2.5.1a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:feature Count version 1.4.6-p52.
Isoform expression of known Ensembl transcripts was estimated with Salmon version 0.8.23.
Sequencing performance was assessed for the total number of aligned reads, the total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.24.
Genome_build: hg38
Supplementary_files_format_and_content: Excel, Differentially expressed genes (DEGs) and adj p-value

extract_protocol:
At day 21, total RNA from reprogramming cells was extracted using the RNeasy Micro Kit (Qiagen)  (Figure 2).
Samples were prepared according to the library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina HiSeq.

value: Coriell AG11798


title: Plate10-295-Kidney

description: Plate 10_KIDNEY_C10

value: Male

value: Kidney


title: sgMORF4L1_2

value: day9 after sgMORF4L1#2 guide RNA infection


title: Plate10-294-Kidney

description: Plate 10_KIDNEY_G01

value: 10:2 FTOH

value: mg/kg


title: MGT_RNA_rep2

value: Infected with MGT virus


title: Atac pre-HD-MSNs_GM04855_103


title: sgMORF4L1_1

value: day9 after sgMORF4L1#1 guide RNA infection


title: M_RNA_rep2

value: Infected with Mef2c virus


title: Plate10-290-Kidney

description: Plate 10_KIDNEY_F05

value: Female

value: water/tween

value: day

value: TempO-Seq


title: Plate10-288-Kidney

description: Plate 10_KIDNEY_D12


title: M_RNA_rep1

value: Mouse Embryonic Fibroblast


title: Old-MSNs_AG11798_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: sgNeg3_R2

value: day9 after sgNeg3_2 guide RNA infection


title: Old-MSNs_AG11798_#2


title: LACZ_RNA_rep2

value: Infected with LacZ virus


title: LACZ_RNA_rep1


title: sgNeg3_R1

value: day9 after sgNeg3_1 guide RNA infection


title: Old-MSNs_AG08379_#3

value: Coriell AG08379


title: Plate10-297-Kidney

description: Plate 10_KIDNEY_H03

value: Sprague Dawley (SD)

value: Kidney


title: Plate10-286-Kidney

description: Plate 10_KIDNEY_F03

value: 10:2 FTOH


title: sgVPS72_2

value: day9 after sgVPS72#2 guide RNA infection


title: Old-MSNs_AG08379_#1


title: A_RNA_rep2

value: Infected with Ascl1 virus


title: sgMORF4L2_1

value: day9 after sgMORF4L2#1 guide RNA infection


title: sgVPS72_1

value: day9 after sgVPS72#1 guide RNA infection


title: A_RNA_rep1


title: Plate10-285-Kidney

description: Plate 10_KIDNEY_F12

value: Male

value: mg/kg


title: Old-MSNs_GM02187_#3

value: Coriell GM02187


title: sgMEAF6_2

value: day9 after sgMEAF6#2 guide RNA infection


title: LACZ_H3K27ac_rep2_input

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the mm10 reference genome using Bowtie2.
MACS2 were used for peak calling with following parameter -extsize 200 --nolambda -g mm -p 1e-5
Genome_build: mm10 reference
Supplementary_files_format_and_content: 12 txt files containg H3K27ac Peaks of reprogramming and control group for three reprogramming systems in replicates

value: Mouse Embryonic Fibroblast

tag: antibody

value: No antibody

value: Infected with LACZ virus


title: Old-MSNs_GM02187_#2

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate10-284-Kidney

description: Plate 10_KIDNEY_F10

value: water/tween

value: day

value: TempO-Seq


title: sgMEAF6_1

value: day9 after sgMEAF6#1 guide RNA infection


title: LACZ_H3K27ac_rep1_input


title: Old-MSNs_GM02187_#1


title: sgGAS41_2

value: day9 after sgGAS41#2 guide RNA infection


title: Plate10-280-Kidney

description: Plate 10_KIDNEY_A02

value: Sprague Dawley (SD)

value: Female

value: Kidney

value: 10:2 FTOH


title: Old-MSNs_AG12956_#3

value: Coriell AG12956


title: Old-MSNs_AG08379_#2

value: Coriell AG08379


title: LACZ_H3K27ac_rep2

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: LACZ_H3K27ac_rep1


title: sgGAS41_1

value: day9 after sgGAS41#1 guide RNA infection


title: Plate10-279-Kidney

description: Plate 10_KIDNEY_H11

value: mg/kg


title: MGT_H3K27ac_rep2_input

value: Mouse Embryonic Fibroblast

value: No antibody

value: Infected with MGT virus


title: Plate10-278-Kidney

description: Plate 10_KIDNEY_H09

value: water/tween


title: sgDMAP1_1

value: day9 after sgDMAP1#1 guide RNA infection


title: Old-MSNs_AG12956_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: sgDMAP1_2

value: day9 after sgDMAP1#2 guide RNA infection


title: Old-MSNs_AG12956_#2


title: Plate10-277-Kidney

description: Plate 10_KIDNEY_E12

value: day

value: TempO-Seq


title: MGT_H3K27ac_rep1_input


title: Old-MSNs_AG10047_#3

value: Coriell AG10047


title: sgTRRAP_2

value: day9 after sgTRRAP#2 guide RNA infection


title: Plate10-276-Kidney

description: Plate 10_KIDNEY_G02

value: Sprague Dawley (SD)

value: Female

value: Kidney

value: 10:2 FTOH


title: MGT_H3K27ac_rep2

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: Plate10-282-Kidney

description: Plate 10_KIDNEY_B02

value: Male

value: mg/kg


title: MGT_H3K27ac_rep1

value: Mouse Embryonic Fibroblast


title: Old-MSNs_AG10047_#2


title: sgTRRAP_1

value: day9 after sgTRRAP#1 guide RNA infection


title: Plate10-275-Kidney

description: Plate 10_KIDNEY_H06

value: water/tween


title: Old-MSNs_AG10047_#1


title: sgING3_2

value: day9 after sgING3#2 guide RNA infection


title: IRESG_H3K27ac_rep2_input

value: No antibody

value: Infected with IRESG virus


title: Old-MSNs_AG04453_#3

value: Coriell AG04453

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate10-274-Kidney

description: Plate 10_KIDNEY_B07

value: day

value: TempO-Seq


title: Plate10-272-Kidney

description: Plate 10_KIDNEY_B05

value: Sprague Dawley (SD)


title: sgMRGBP_2

value: day9 after sgMRGBP#2 guide RNA infection


title: Old-MSNs_AG04453_#2


title: IRESG_H3K27ac_rep2


title: IRESG_H3K27ac_rep1_input


title: sgING3_1

value: day9 after sgING3#1 guide RNA infection


title: Plate10-271-Kidney

description: Plate 10_KIDNEY_E05

value: Kidney

value: 10:2 FTOH


title: Old-MSNs_AG04453_#1


title: Plate10-287-Kidney

description: Plate 10_KIDNEY_A11

value: Female


title: sgMRGBP_1

value: day9 after sgMRGBP#1 guide RNA infection


title: sgACTL6A_2

value: day9 after sgACTL6A#2 guide RNA infection


title: Plate10-270-Kidney

description: Plate 10_KIDNEY_E04

value: mg/kg


title: IRESG_H3K27ac_rep1

value: Mouse Embryonic Fibroblast

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: Young-MSNs_AG11732_#3

value: Coriell AG11732


title: Plate10-269-Kidney

description: Plate 10_KIDNEY_G05

value: water/tween


title: Young-MSNs_AG11732_#2


title: HF_H3K27ac_rep2_input

value: No antibody

value: Infected with Hnf4a, Foxa3 virus


title: HF_H3K27ac_rep1_input


title: Plate10-268-Kidney

description: Plate 10_KIDNEY_H10

value: day


title: Young-MSNs_AG11732_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: HF_H3K27ac_rep2


title: Plate10-267-Kidney

description: Plate 10_KIDNEY_A09

value: Sprague Dawley (SD)

value: TempO-Seq


title: sgTIP60_2

value: day9 after sgTIP60#2 guide RNA infection


title: HF_H3K27ac_rep1


title: sgTIP60_1

value: day9 after sgTIP60#1 guide RNA infection


title: Young-MSNs_GM02171_#3

value: Coriell GM02171


title: Plate10-266-Kidney

description: Plate 10_KIDNEY_C07

value: Female

value: Kidney

value: 10:2 FTOH


title: Young-MSNs_GM02171_#2


title: sgEP400_1

value: day9 after sgEP400#1 guide RNA infection


title: Young-MSNs_GM02171_#1


title: Plate10-263-Kidney

description: Plate 10_KIDNEY_G04

value: Male

value: mg/kg


title: TETG_H3K27ac_rep2_input

value: Mouse Embryonic Fibroblast

value: Infected with TETG virus


title: TETG_H3K27ac_rep1_input

value: No antibody


title: sgNeg2_R2

value: day9 after sgNeg2 _2guide RNA infection


title: TETG_H3K27ac_rep2

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: Plate10-261-Kidney

description: Plate 10_KIDNEY_D10

value: water/tween

value: day


title: Plate10-262-Kidney

description: Plate 10_KIDNEY_F06

value: Sprague Dawley (SD)

value: TempO-Seq


title: Young-MSNs_GM08399_#2

value: Coriell GM08399

value: CTIP2, DLX1, DLX2, MYT1L


title: Young-MSNs_GM08399_#3


title: sgNeg2_R1

value: day9 after sgNeg2_1 guide RNA infection


title: TETG_H3K27ac_rep1


title: sgACTL6A_1

value: day9 after sgACTL6A#1 guide RNA infection


title: BAM_H3K27ac_rep2_input

value: Infected with Brn2, Ascl1, Myt1l  virus


title: sgBRD8_2_R2

value: day9 after sgBRD8#2_2 guide RNA infection


title: Young-MSNs_GM07492_#3

value: Coriell GM07492


title: sgBRD8_2_R1

value: day9 after sgBRD8#2_1 guide RNA infection


title: Young-MSNs_GM08399_#1


title: BAM_H3K27ac_rep1_input

value: Mouse Embryonic Fibroblast


title: Plate10-260-Kidney

description: Plate 10_KIDNEY_A03

value: Female

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: sgBRD8_1_R2

value: day9 after sgBRD8#1_2 guide RNA infection


title: BAM_H3K27ac_rep2

value: Anti-Histone H3K27 antibody - ChIP Grade (ab4729)


title: Plate10-259-Kidney

description: Plate 10_KIDNEY_G10

value: Sprague Dawley (SD)

value: water/tween

value: day


title: Plate10-265-Kidney

description: Plate 10_KIDNEY_C06

value: Male

value: TempO-Seq


title: Plate10-258-Kidney

description: Plate 10_KIDNEY_D05


title: sgEP400_2

value: day9 after sgEP400#2 guide RNA infection


title: sgBRD8_1_R1

value: day9 after sgBRD8#1_1 guide RNA infection


title: Young-MSNs_GM07492_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: sgNeg1_R2

value: day9 after sgNeg1_2 guide RNA infection


title: Young-MSNs_GM00495_#3

value: Coriell GM00495


title: Plate10-256-Kidney

description: Plate 10_KIDNEY_C03


title: BAM_H3K27ac_rep1

value: Mouse Embryonic Fibroblast

value: Infected with Brn2, Ascl1, Myt1l  virus


title: Plate10-254-Kidney

description: Plate 10_KIDNEY_D09

value: Kidney


title: T27, TP2, RF5, 5

city: Bern

first: Ivana

last: Jaric

address: Länggassstrasse 120

department: Animal Welfare Division

country: Switzerland

institute: Vetsuisse Faculty, University of Bern

data_processing:
Library strategy: ATAC-seq
The obtained sequences were adapter trimmed and aligned to the mouse reference genome (ensembl build 102) with Bowtie2 in paired end mode (version 2.3.5.1) keeping only concordant and unique alignments.
We selected and used only uniquely aligned reads for the analysis. Reads aligned to mitochondrial DNA and PCR duplicate reads were eliminated from further analysis. Duplicate read pairs were marked using the MarkDuplicates command from the Picard software suite (version 1.140; broadinstitute.github.io/picard/).
Peaks were then called in each sample separately with MACS2 (version 2.1.4, with the parameters -f BAMPE -g mm --nomodel -q 0.05 --broad --broad-cutoff 0.1 --keep-dup all) as previously reported (Zhang et al. 2017: PMID: 18798982)
For each time point (TP) and rearing facility (RF), peaks were intersected with multovl (version 1.3;  and only peaks found in at least three samples per group (i.e. rearing laboratory; RF) were kept. peaks from all groups were merged with multovl (union of all peaks within groups)
Genome_build: ensembl102
Supplementary_files_format_and_content: Individual peaks in BED format
Supplementary_files_format_and_content: Merged peaks in BED format
Supplementary_files_format_and_content: Raw counts in merged peaks, CSV format
Supplementary_files_format_and_content: Normalized and log2(x+1)-transformed counts (DESeq2) in merged peaks, CSV format

source_name: FACS-sorted neuronal (NeuN+) nuclei

extract_protocol:
with slight modifications. In brief, the ventral hippocampus was dissected from one side of the brain at -20C°, cut into small pieces and stored in Eppendorf DNA LoBind 2mL tubes at -80°C until nuclei preparation. Nuclei preparation and sorting was performed in 5 batches per each time point, with each batch having exactly one samples from each facility in random order. Total nuclei were then extracted using sucrose gradient centrifugation. Neuronal (NeuN+) nuclei were isolated from non-neuronal nuclei (NeuN-) with fluorescence-activated nuclei sorting  using an anti-NeuN antibody conjugated to AlexaFluor-488 on a FACSAria instrument. For a detailed protocol for nuclei isolation and purification of neuronal nuclei, see the methods section.
ATAC-seq libraries were prepared according to Buenrostro et al. 2013 (PMID:24097267) with some modifications. Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (2003419) and IDT for Illumina Nextera DNA UD Indexes (20026930) were used to prepare the libraries.

value: C57BL/6JRj (Janvier Labs)

value: ventral hippocampus

tag: age

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)

tag: group


title: Plate10-253-Kidney

description: Plate 10_KIDNEY_A05

value: Sprague Dawley (SD)

value: 10:2 FTOH

value: mg/kg

value: water/tween


title: sgNeg1_R1

tag: treatment

value: day9 after sgNeg1_1 guide RNA infection


title: Young-MSNs_GM00495_#1

tag: overexpression 1

tag: overexpression 2


title: T24, TP2, RF4, 5

tag: strain

tag: Sex


title: ChIP_sgBRD8_H3K4me3

data_processing:
Sequence reads were mapped into reference human genome hg19 by using Bowtie2.
Peakcaling was done by using MACS2 FDR cutt off 5% with narrow peak and broad peak option for BRD8, p53, and histones seperately.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Cell lysates were clarified from sonicated nulcei; BRD8, p53, and histone-DNA complexes were isolated with Flag or histone antibody.
Libraries were constructed using Illumina TruSeq ChIP Sample Prep kit following manufacture's protocol. Briefly, 50 µl of ChIP DNA was end-repaired, 3’-adenyl tailed, and then ligated with different index adaptors. The adaptor-ligated DNA was size selected (250-300 bp) using agarose gel electrophoresis, followed by PCR amplification. The amplified DNA was purified with AMPure XP beads (Beckman Coulter).

treatment_protocol: For BRD8 ChIP-seq, A382 cells were infected with BRD8 cDNA with fusion to triple FLAG

value: A382 expressing cas9 and sgBRD8

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgBRD8 lentivirus

tag: chip antibody

value: H3K4me3 (EMD Millipore, 07-473)


title: Plate10-252-Kidney

description: Plate 10_KIDNEY_A04

value: Male

tag: tissue

tag: chemical

value: day

value: TempO-Seq


title: T4, TP2, RF2, 5


title: Young-MSNs_GM03440_#3

value: Coriell GM03440

value: CTIP2, DLX1, DLX2, MYT1L


title: Young-MSNs_GM07492_#2

value: Coriell GM07492


title: Young-MSNs_GM03440_#2


title: ChIP_sgNeg_H3K4me3

value: A382 expressing cas9 and sgNeg

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgNeg lentivirus


title: ChIP_sgBRD8_H3K27ac

value: H3K27ac (Abcam, Ab4729)


title: T25, TP2, RF1, 5

value: C57BL/6JRj (Janvier Labs)

value: ventral hippocampus

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: Plate10-251-Kidney

description: Plate 10_KIDNEY_H12

value: Sprague Dawley (SD)

value: Kidney

value: 10:2 FTOH

tag: concentration

tag: unit

value: mg/kg

value: water/tween


title: Plate10-249-Kidney

description: Plate 10_KIDNEY_F09

value: Female

tag: vehicle

tag: duration

value: day

value: TempO-Seq


title: Young-MSNs_GM03440_#1

tag: cell line

value: Coriell GM03440

value: CTIP2, DLX1, DLX2, MYT1L


title: ChIP_sgNeg_H3K27ac

value: A382 expressing cas9 and sgNeg

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgNeg lentivirus


title: T19, TP2, RF2, 4

value: C57BL/6JRj (Janvier Labs)


title: Input_sgBRD82

value: A382 expressing cas9 and sgBRD8

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgBRD8 lentivirus


title: HD-MSNs_GM02173_#3

value: Coriell GM02173


title: T20, TP2, RF4, 4

value: ventral hippocampus

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: Plate10-248-Kidney

description: Plate 10_KIDNEY_B03

value: Sprague Dawley (SD)

value: Kidney

value: 10:2 FTOH

value: mg/kg

tag: platfrom


title: Input_sgNeg2


title: HD-MSNs_GM02173_#2


title: Young-MSNs_GM00495_#2

value: Coriell GM00495


title: T18, TP2, RF1, 4


title: Plate10-247-Kidney

description: Plate 10_KIDNEY_B10

value: Female

value: water/tween

value: day

value: TempO-Seq


title: ChIP_sgBRD8_H2AZ

value: H2AZ (Abcam, Ab4174)


title: T17, TP2, RF3, 4

value: C57BL/6JRj (Janvier Labs)


title: HD-MSNs_GM04198_#3

value: Coriell GM04198

value: CTIP2, DLX1, DLX2, MYT1L


title: HD-MSNs_GM02173_#1

value: Coriell GM02173


title: ChIP_sgNeg_H2AZ

value: A382 expressing cas9 and sgNeg

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgNeg lentivirus


title: T21, TP2, RF3, 5

value: ventral hippocampus

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: Input_sgBRD81

value: A382 expressing cas9 and sgBRD8

value: Stable cell line was generated by infecting A382 with FLAG-cas9 and sgBRD8 lentivirus


title: Plate10-250-Kidney

description: Plate 10_KIDNEY_C11

value: Sprague Dawley (SD)

value: Female

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: HD-MSNs_GM04198_#2


title: Input_sgNeg1


title: T14, TP2, RF1, 3

value: C57BL/6JRj (Janvier Labs)


title: T16, TP2, RF5, 4


title: HD-MSNs_GM04198_#1

value: Coriell GM04198


title: Plate10-244-Kidney

description: Plate 10_KIDNEY_E10

value: Male

value: water/tween

value: day

value: TempO-Seq


title: HD-MSNs_ND33947_#3

value: NHCDR ND33947

value: CTIP2, DLX1, DLX2, MYT1L


title: ChIP_H3K4me3

value: H3K4me3 (EMD Millipore, 07-473)


title: T13, TP2, RF3, 3

value: ventral hippocampus

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: Plate10-243-Kidney

description: Plate 10_KIDNEY_G08

value: Sprague Dawley (SD)


title: Plate10-242-Kidney

description: Plate 10_KIDNEY_B08

value: Kidney


title: HD-MSNs_ND33947_#2


title: ChIP_H3K27ac

value: H3K27ac (Abcam, Ab4729)


title: T12, TP2, RF5, 3


title: ChIP_H2AZ

value: H2AZ (Abcam, Ab4174)


title: Plate10-241-Kidney

description: Plate 10_KIDNEY_E06

value: 10:2 FTOH

value: mg/kg


title: HD-MSNs_ND33947_#1


title: Plate10-240-Kidney

description: Plate 10_KIDNEY_G11

value: Female


title: T11, TP2, RF4, 3

value: C57BL/6JRj (Janvier Labs)


title: Plate10-246-Kidney

description: Plate 10_KIDNEY_H02

value: water/tween

value: day


title: HD-MSNs_GM02147_#3

value: Coriell GM02147


title: Input_HistoneMark


title: Plate10-239-Kidney

description: Plate 10_KIDNEY_D11

value: TempO-Seq


title: T10, TP2, RF1, 2


title: Plate10-245-Kidney

description: Plate 10_KIDNEY_A08

value: Male


title: T15, TP2, RF2, 3

value: ventral hippocampus


title: ChIP_p53

value: A382 expressing inducible FLAG_p53

value: Stable cell line was generated by infecting A382 with inducible FLAG-TP53 lentivirus

value: FLAG(Sigma-Aldrich, F1804)


title: Plate10-236-Kidney

description: Plate 10_KIDNEY_C08

value: Sprague Dawley (SD)


title: T9, TP2, RF3, 2

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: HD-MSNs_GM02147_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: T8, TP2, RF5, 2


title: Input_p53


title: Plate10-235-Kidney

description: Plate 10_KIDNEY_A10

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: ChIP_BRD8

value: A382 expressing FLAG_BRD8

value: Stable cell line was generated by infecting A382 with FLAG-BRD8 lentivirus


title: HD-MSNs_GM04230_#3

value: Coriell GM04230


title: HD-MSNs_GM04230_#2


title: T7, TP2, RF4, 2

value: C57BL/6JRj (Janvier Labs)


title: Plate10-233-Kidney

description: Plate 10_KIDNEY_H07

value: Male

value: water/tween

value: day

value: TempO-Seq


title: T6, TP2, RF2, 2

value: ventral hippocampus


title: HD-MSNs_GM04230_#1


title: T5, TP2, RF3, 1


title: Nucleolin binding targets_3, LPS stimulation

city: Seoul

first: Taeyun

middle: Andrew

last: Lee

address: 262 Seongsan-no, Seodaemun-gu

department: Systems Biology

country: South Korea

institute: Yonsei University

data_processing:
Processed reads were aligned to the reference genome (mm10) by the Bowtie algorithm, allowing for two alignment errors (mutation, insertion, or deletion).
For each read, only the best mapping was reported out of a maximum of 10 genomic matches.
After the conversion subtraction, reads that mapped to only one genomic location were retained for further analysis.
The PAR-CLIP data were analyzed by using the PARpipe analysis, which is a pipeline wrapper for PARalyzer (v.1.5) (https://ohlerlab.mdc-berlin.de/software/PARpipe_119/).
Raw sequencing reads were aligned to the mouse genome (mm10) and overlapped, and uniquely aligned reads were assembled into groups.
Those groups with greater read kernel density estimates than the background, a read depth of at least three, and at least two independent diagnostic T-to-C mutations indicating crosslinking were considered high-confidence binding sites or clusters and annotated using the following database (gencode.v24.chr_patch_hapl_scaff_fixed.annotation.gtf).
Assembly: UCSC mm10 Mus musculus genome
Supplementary files format and content: Excel files include the information about NCL-binding targets and sequences analyzed by PARpipe

growth_protocol: RAW 264. 7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37 °C

extract_protocol:
The cells were washed with PBS, and irradiated with 0.15 mJ cm-2 and 365 nm ultraviolet (UV) light in a UV crosslinker to crosslink the labeled RNA to RNA-binding proteins. After isolation of nucleoli from cell lysates, nucleolar extracts were treated with 1 U ml-1 RNase T1 and NCL proteins were immunoprecipitated with anti-NCL antibodies and Protein A/G sepharose beads. The immunoprecipitates were further digested with 100 U ml-1 RNase T1 and the beads were washed in lysis buffer and suspended in one bead volume of dephosphorylation buffer. RNAs were dephosphorylated and radioactively labeled with [γ -32P]-ATP. The protein-RNA complexes were separated by SDS-PAGE and visualized by autoradiography. The radioactive bands migrated as a 110 kDa were eluted from the gel and all proteins in eluted bands were removed by digestion with 0.2 mg ml-1 proteinase K. The RNAs were isolated by acidic phenol/chloroform extraction and ethanol precipitation.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW 264. 7 cells were incubated in medium supplemented with 100 μM 4-thiouridine (4SU) for 16 h, in the absence or presence of LPS for 12 h.

tag: cell type

value: Macrophage

value: LPS 12 h


title: Plate10-232-Kidney

description: Plate 10_KIDNEY_E08

value: Sprague Dawley (SD)


title: Input_BRD8


title: HD-MSNs_ND30013_#3

value: NHCDR ND30013


title: Nucleolin binding targets_2, LPS stimulation


title: T26, TP2, RF5, 1

tag: age

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: Plate10-231-Kidney

description: Plate 10_KIDNEY_F02

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: T3, TP2, RF4, 1

tag: group


title: HD-MSNs_ND30013_#2

value: CTIP2, DLX1, DLX2, MYT1L


title: HD-MSNs_GM02147_#2

value: Coriell GM02147


title: Nucleolin binding targets_1, LPS stimulation

tag: treatment


title: Plate10-230-Kidney

description: Plate 10_KIDNEY_G06

value: Female


title: HD-MSNs_ND30013_#1

tag: overexpression 1


title: Nucleolin binding targets_3, normal conditions

value: Normal conditions


title: Plate10-229-Kidney

description: Plate 10_KIDNEY_H04

value: water/tween

value: day


title: T2, TP2, RF2, 1

value: C57BL/6JRj (Janvier Labs)

value: ventral hippocampus


title: pre-HD-MSNs_GM04717_#3

value: Coriell GM04717

tag: overexpression 2


title: Nucleolin binding targets_2, normal conditions

value: Macrophage


title: Plate10-228-Kidney

description: Plate 10_KIDNEY_H08

tag: strain

value: Sprague Dawley (SD)

value: TempO-Seq


title: Plate10-234-Kidney

description: Plate 10_KIDNEY_G09

tag: Sex

value: Male


title: T1, TP2, RF1, 1

value: 14 weeks (TP2)

value: male

value: hexane (freezing condition)


title: pre-HD-MSNs_GM04717_#2


title: S25, TP1, RF5, 5

value: 8 weeks (TP1)


title: Plate10-226-Kidney

description: Plate 10_KIDNEY_E11

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: MYC deficient cells stimulated with RANKL rep2

city: NEW YORK CITY

first: Kyung-Hyun

last: Park-min

state: NY

address: 535 E 70th st

institute: Hospital for Special Surgery

data_processing:
Basecalling was performed using bcl2fastq (version bcl2fastq-1.8.4)
Sequenced reads were preprocessed with fastp (with parameters fastp -q 15 -n 10 -l 20)
After preprocessing, sequenced reads were mapped to mm10 whole genome using STAR v2.7.3a (with parameters --outFilterMultimapNmax 1  --outSAMstrandField intronMotif --quantMode GeneCounts), using gencode mm10 annotation
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts, filtered gene counts (min expression cutoff of 5 CPM) and log CPMs from edgeR for every gene and every sample

source_name: Bone marrow-derived macrophages

growth_protocol: Mouse bone marrow-derived macrophages (BMDMs) were prepared from bone marrow cells from 8-week-old wild type and myeloid specific MYC deficient mice as described previously (Bae et al., 2017). Non-adherent mouse bone marrow cells were cultured with α-MEM w/o nucleosides (Invitrogen) supplemented with 10% premium FBS (R&D systems), 1% L-glutamine (Invitrogen), and 1% penicillin/streptomycin (Invitrogen). Mouse BMDM were cultured with RANKL for one day and mRNAs were prepared.

extract_protocol:
Total RNAs were harvested
mRNA-seq

treatment_protocol: Cells were stimulated with or without RANKL (50 ng/ml) for one day

value: MYC f/fLysM cre

value: Bone marrow-derived early osteoclasts

tag: genotype

value: MYC cKO

value: RANKL


title: S24, TP1, RF4, 5

value: C57BL/6JRj (Janvier Labs)

tag: tissue

value: ventral hippocampus


title: Plate10-227-Kidney

description: Plate 10_KIDNEY_G07

value: Female

tag: chemical

value: water/tween

value: day


title: MYC deficient cells stimulated with RANKL rep1


title: Plate10-225-Kidney

description: Plate 10_KIDNEY_D02

value: Sprague Dawley (SD)

tag: concentration

value: TempO-Seq


title: S23, TP1, RF2, 5

value: male


title: pre-HD-MSNs_GM04857_#2

value: Coriell GM04857

value: CTIP2, DLX1, DLX2, MYT1L


title: pre-HD-MSNs_GM04857_#3


title: Plate10-224-Kidney

description: Plate 10_KIDNEY_C04

value: Kidney

tag: unit


title: Control cells stimulated with RANKL rep1

value: LysM cre

value: WT


title: pre-HD-MSNs_GM04829_#3

value: Coriell GM04829


title: Plate10-223-Kidney

description: Plate 10_KIDNEY_G12

value: 10:2 FTOH

value: mg/kg

tag: vehicle


title: S21, TP1, RF3, 5

value: 8 weeks (TP1)

value: hexane (freezing condition)


title: CH12_PROCap_WT

city: Vienna

first: Tobias

last: Neumann

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
True-seq barcoded primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-cap

data_processing:
Library strategy: PRO-cap
The Illumina reads were adapter trimmed on their 3′ ends using cutadapt v1.15; --match-read-wildcards -f fastq -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
Afterwards, four nucleotides from their 5′ end were removed with fastx_trimmer (http://hannonlab.cshl.edu/fastx_toolkit; version 0.0.13; -Q33 -t 5).
The trimmed reads >18 nucleotides were aligned with bowtie v1.0.0 (-S -p 10 --trim5 0 --trim3 0 -v 2 --best --strata --tryhard -m 1 --phred33-quals --chunkmbs 256) to the mouse mm9 genome.
The aligned reads were sorted by position with samtools v1.9.
Strand-specific and undirected occupancy profiles were generated with deepTools bamCoverage v2.2.2.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of rpm-normalized read densities

growth_protocol: CH12 cells cultured in complete RPMI medium

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of all 4 biotynilated NTPs.After trizol extraction of total RNA
total extraction with trizol, labeled RNA enrichement .3' and 5' linker attachment. cDNA preparation and PCR
Single molecule indexing with random 10-mers via adapter ligation.TrusSeq indexed primers for multiplexing were used in the PCR step to generate barcoded libraries

treatment_protocol: no treatment

tag: agent

value: unstimulated


title: Plate10-222-Kidney

description: Plate 10_KIDNEY_C02

value: Female

tag: duration


title: pre-HD-MSNs_GM04829_#2

tag: cell line


title: S20, TP1, RF4-4

value: C57BL/6JRj (Janvier Labs)

value: ventral hippocampus


title: CH12_SNSSeq_shMcm_exp2_rep2

description: SNS-seq

data_processing:
Library strategy: SNS-seq
SNS-seq
The 3' adaptors were removed using cutadapt (v1.4.2, Read1: cutadapt --match-read-wildcards -O 4 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were aligned to the mouse genome (mouse genome build NCBI m37, GCA_000001635.18) using bowtie (v 1.0.0, -v 2 --best --strata --tryhard -m 1 --chunkmbs 256)
replicates were pooled by condition and experiment with samtools merge 1.9 and peaks were called using MACS2 2.1.2.1 with --nomodel --extsize 275 -q 0.05 -g mm using sheared genomic DNA as control
Peak sets for each condition were overlapped between experiments with BEDTools intersect 2.27.1 using default parameters retaining only those peaks per condition that were found in both experiment
retained peaks were then clustered by genome-wide median interpeak distance with ClusterScan 0.2.1 using -n 2 and -d to 17,625 bp and 13,544 kb for WT and KD and peaks that are part of a cluster were retained
filtered peak sets were then merged merged with BEDTools merge 2.27.1
Genome_build: NCBI m37, GCA_000001635.18
Supplementary_files_format_and_content: CH12_unstimulated_IS.bed is a BED file containing the genomic positions of the merged initiation sites for WT and KD with the columns chrom, start, end, name, score, strand
Supplementary_files_format_and_content: CH12_unstimulated_IZ.bed is a BED file containing the genomic position of the clusters inferred by ClusterScan

growth_protocol: CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.

extract_protocol:
Genomic DNA was extracted and short nascent DNA was enriched via size selection and lamda exonuclease digestion
Libraries were prepared following standard Illumina protocols

tag: knockdown

value: shMcm


title: Nucleolin binding targets_1, normal conditions

tag: cell type

value: Macrophage

value: Normal conditions


title: Plate10-221-Kidney

description: Plate 10_KIDNEY_D03

value: Sprague Dawley (SD)

value: water/tween

value: day

tag: platfrom

value: TempO-Seq


title: pre-HD-MSNs_GM04717_#1

value: Coriell GM04717

value: CTIP2, DLX1, DLX2, MYT1L


title: pre-HD-MSNs_GM04829_#1

value: Coriell GM04829


title: CH12_SNSSeq_shMcm_exp2_rep1

description: SNS-seq


title: S18, TP1, RF1, 4

tag: age

value: male

tag: treatment

tag: group


title: Plate10-220-Kidney

description: Plate 10_KIDNEY_E07

tag: strain

value: Male

value: Kidney

value: 10:2 FTOH

value: mg/kg


title: pre-HD-MSNs_GM04831_#3

value: Coriell GM04831

tag: overexpression 1

tag: overexpression 2


title: Control cells stimulated with RANKL rep2

value: LysM cre

value: Bone marrow-derived early osteoclasts

tag: genotype

value: WT

value: RANKL


title: CH12_SNSSeq_shLacZ_exp2_rep2

description: SNS-seq

value: shLacZ


title: pre-HD-MSNs_GM04831_#2


title: CH12_SNSSeq_shLacZ_exp2_rep1

description: SNS-seq


title: pre-HD-MSNs_GM04857_#1

value: Coriell GM04857


title: S22, TP1, RF1, 5

value: C57BL/6JRj (Janvier Labs)

tag: tissue

value: ventral hippocampus

value: 8 weeks (TP1)

tag: Sex

value: hexane (freezing condition)


title: pre-HD-MSNs_GM04831_#1

value: CTIP2, DLX1, DLX2, MYT1L


title: CH12_SNSSeq_shMcm_exp1_rep2

description: SNS-seq

value: shMcm


title: Plate10-217-Kidney

description: Plate 10_KIDNEY_A06

value: Sprague Dawley (SD)

value: Male

tag: chemical

tag: concentration

tag: unit

value: water/tween

value: day

value: TempO-Seq


title: CH12_SNSSeq_shMcm_exp1_rep1

description: SNS-seq


title: pre-HD-MSNs_GM04861_#3

value: Coriell GM04861


title: S19, TP1, RF2, 4

value: male


title: Plate10-216-Kidney

description: Plate 10_KIDNEY_F08

value: Kidney

value: 10:2 FTOH

value: mg/kg

tag: vehicle

tag: duration


title: CH12_SNSSeq_shLacZ_exp1_rep2

description: SNS-seq

tag: cell line

tag: knockdown

value: shLacZ


title: pre-HD-MSNs_GM04861_#2


title: S14, TP1, RF1, 3

value: C57BL/6JRj (Janvier Labs)


title: Plate10-215-Kidney

description: Plate 10_KIDNEY_B04

tag: platfrom


title: CH12_SNSSeq_shLacZ_exp1_rep1

description: SNS-seq


title: S13, TP1, RF3, 3

value: ventral hippocampus

tag: age


title: S12, TP1, RF5, 3

value: 8 weeks (TP1)

tag: treatment


title: Plate10-213-Kidney

description: Plate 10_KIDNEY_H05


title: pre-HD-MSNs_GM04855_#3

value: Coriell GM04855


title: S17, TP1, RF3, 4

value: hexane (freezing condition)

tag: group


title: Plate10-219-Kidney

description: Plate 10_KIDNEY_B09

tag: strain


title: CH12_RNASeq_C23_rep3

description: ribozomal RNA depleted RNA

data_processing:
RNA-seq
Read alignment: 3' adaptors or reads were removed using cutadapt  (v1.4.2, Read1: cutadapt --match-read-wildcards -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) and trimmed reads with a length of less than 18bp were discarded.
The trimmed reads were filtered with a contaminants database consisting of rDNA sequences (gi|374088139, gi|38176281) with bowtie2(v2.1.0 --very-sensitive-local).
The recovered non matching reads were aligned to the genome/transcriptome using STAR-align (v2.4.2a, STAR  --outSAMstrandField None --outFilterIntronMotifs RemoveNoncanonical --outFilterMismatchNoverLmax 0.1 --outFilterMismatchNmax 10 --outFilterScoreMinOverLread 0.30 --outFilterMatchNminOverLread 0.30 --outFilterMatchNmin 30 --chimSegmentMin 15 --quantMode TranscriptomeSAM --chimJunctionOverhangMin 15 --twopassMode Basic --outSAMtype SAM --outSAMattributes All --outReadsUnmapped Fastx intronMotif --alignIntronMax 200000  --outSJfilterIntronMaxVsReadN 10000 20000 30000 50000 --outSJfilterOverhangMin 20 12 12 12 --outFilterType BySJout --alignMatesGapMax 0  --outFilterMultimapNmax 20).
The STAR-index used for alignment was generated from the combination of the mouse genome build NCBI m37 (GCA_000001635.18) and a transcriptome GTF file created from all refGenes and ensGenes gtfs downloaded from the UCSC Table Browser on the 1. March 2014.
Unique mappers from the resulting BAM file were used to create unstranded, stranded and reverse stranded coverage tracks for visualisation using bedtools (v2.27, bedtools genomecov -split -bg, bedtools genomecov  -split -bg -strand '+' ,bedtools genomecov -split -bg -strand '-') and bedGraphToBigWig from the kent-tools (bedGraphToBigWig v4, bedGraphToBigWig -blockSize=256 -itemsPerSlot=1024).
Normalised coverage tracks were created by dividing the coverage at each position with the total number of aligned reads per million.
Differential gene expression analysis: Read counts for genes were quantified using featureCounts v2.0.0.
As a reference, we downloaded all mm9 refSeq genes from the UCSC table browser (https://hgdownload.soe.ucsc.edu/goldenPath/mm9/bigZips/genes/) on February 28, 2020.
In addition, we downloaded the Igh, Igk and Igl gene Ensembl Gene IDs from IMGT (http://www.imgt.org, August 11, 2020) and extracted the corresponding genes from Gencode M25 (www.gencodegenes.org) and lifted them over to mm9 coordinates and added them in addition to the Elambda 3_1 enhancer.
Differential gene expression analysis was performed with DESeq2 v1.22.2 and shrinking log2-foldchanges with ashr v2.2-47.
To test for unchanged genes, we applied a threshold-based Wald test testing for absolute log-foldChanges < 1.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: Tab-delimited table with TPMs and DESeq2 log2-foldchanges, adjusted p-values and control TPMs

extract_protocol:
Cells were harvested and total RNA was extracted with Trizol reagent.
Library preparation for total RNA-Seq was performed using the Corall Total RNA-seq kit from Lexogen following their instructions.

tag: clone


title: S16, TP1, RF5, 4


title: pre-HD-MSNs_GM04855_#2

tag: overexpression 1

tag: overexpression 2

value: CTIP2, DLX1, DLX2, MYT1L


title: Plate10-218-Kidney

description: Plate 10_KIDNEY_A12

value: Sprague Dawley (SD)

tag: tissue


title: Plate10-211-Kidney

description: Plate 10_KIDNEY_B12

tag: Sex

value: Male


title: CH12_RNASeq_C23_rep2

description: ribozomal RNA depleted RNA


title: Plate10-212-Kidney

description: Plate 10_KIDNEY_E09

tag: chemical

value: water/tween


title: S15, TP1, RF2, 3


title: S11, TP1, RF4, 3


title: S9, TP1, RF3, 2


title: pre-HD-MSNs_GM04855_#1


title: CH12_RNASeq_C23_rep1

description: ribozomal RNA depleted RNA


title: Plate1-190-Liver

description: Plate 1_LIVER_B08

value: Female

value: Liver

value: PFHxSAm

tag: concentration

value: day


title: SETD5-3

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

institute: Korea Research Institute of Bioscience and Biotechnology

data_processing:
Illumina Casava1.7 software used for basecalling.
The reads were mapped to mm10 using STAR v2.5.1.
Read counts were calculated using a STAR standard protocol.
Heat map was constructed using Mev (v. 4.9.0). Statistical analyses were performed using R (v. 3.3.0) and PYTHON (v. 2.7.6).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2CPM (count per million) values for each sample

source_name: SETD5-deficient Huh7

growth_protocol: Huh7 cells were cultured in DMEM. The DMEM media was supplemented with 10% (v/v) heat-inactivated fetal bovine serum and 1% (v/v) antibiotic-antimycotic.

extract_protocol:
Total RNA was isolated from cells using the RNeasy RNA extraction Mini-Kit (Qiagen) and the quality of the RNA was confirmed by agarose gel electrophoresis.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. The sequencing library was prepared using the IlluminaTruSeq Stranded mRNA LT Sample Prep Kit (Illumina).
The mRNA derived from total RNA using poly-T oligo-attached magnetic beads was fragmented and converted into cDNA. Adapters were ligated to the cDNA and the fragments were amplified by PCR.

treatment_protocol: siRNA transfection employed RNAiMAX (invitrogen) reagents for gene silencing.

tag: cell type

value: human hepatocellular carcinoma cells

tag: genotype/variation


title: pre-HD-MSNs_GM04861_#1

value: Coriell GM04861


title: CH12_RNASeq_C13_rep2

description: ribozomal RNA depleted RNA


title: Plate1-189-Liver

description: Plate 1_LIVER_G01

data_processing: Data were processed using the Tempo-SeqR software package

tag: unit

value: mg/kg

tag: vehicle

tag: duration

value: TempO-Seq


title: CTL-3

source_name: control Huh7

tag: cell line

value: control


title: S8, TP1, RF5, 2

value: C57BL/6JRj (Janvier Labs)

value: ventral hippocampus

tag: age

value: male


title: Plate1-188-Liver

description: Plate 1_LIVER_C12

tag: platfrom


title: S7, TP1, RF4, 2

value: 8 weeks (TP1)

tag: treatment

value: hexane (freezing condition)

tag: group


title: CH12_RNASeq_C13_rep1

description: ribozomal RNA depleted RNA

tag: clone


title: SETD5-2


title: CH12_RNASeq_WT_rep3

description: ribozomal RNA depleted RNA

value: WT


title: Plate1-187-Liver

description: Plate 1_LIVER_G02

tag: strain

value: Sprague Dawley (SD)


title: S5, TP1, RF3, 1


title: S6, TP1, RF2, 2


title: CTL-2


title: S10, TP1, RF1, 2


title: SETD5-1


title: CH12_RNASeq_WT_rep2

description: ribozomal RNA depleted RNA


title: CTL-1


title: S4, TP1, RF5, 1


title: Plate1-185-Liver

description: Plate 1_LIVER_D03

value: Male

value: water/tween


title: S3, TP1, RF4, 1


title: CH12_RNASeq_WT_rep1

description: ribozomal RNA depleted RNA


title: CH12_RNASeq_C13_rep3

description: ribozomal RNA depleted RNA


title: Plate1-184-Liver

description: Plate 1_LIVER_C02

value: Liver


title: CH12_RNASeq_shMcm_d3_rep3

description: ribozomal RNA depleted RNA

tag: knockdown

value: shMcm


title: S2, TP1, RF2, 1

tag: tissue


title: Unblocked_control

city: Xiamen

first: Huifen

last: Cao

email: hfcao_bnu@163.com, hfcao@hqu.edu.cn

state: Fujian

address: 668 Jimei Road

department: School of Biomedical Sciences

country: China

institute: Huaqiao University

description: bacterial spike-in controls in background of human genome DNA

data_processing:
The genomic and mitochondrial AP site mapping was performed the same way as in the SSiNGLe-ILM protocol (https://protocolexchange.researchsquare.com/article/pex-920/v2) with the two additional filtering steps. One, PCR duplicates were removed. Two, a read-pair was used only if the first base of the read 2 aligned to the reference sequence. The coordinate of one base upstream of the first aligning base of the read 2 was assigned as the position of the AP site. In the samples used for the chrM analysis, reads were aligned separately to the chrM genome sequences and processed in the same way. Then, the coordinates of AP sites mapping to chrM were added to the BED files containing AP sites mapping to the nuclear genome.
Genome_build: HG19(GRCh37) for human reads, mm10 (GRCm38) for the mouse reads and sequences corresponding to the bacterial spike-ins listed in the file spike-ins.fa for the reads from the spike-in control experiments.
Supplementary_files_format_and_content: The *spike-ins.bed files contain coordinates of AP sites in the sequences of spike-ins. All other BED files contain coordinates of AP sites mapped to either mouse or human genomes. The 4th columns show the number of reads representing the AP site.

growth_protocol: Human CML leukemia cell line K562 was obtained from Cell Bank of Chinese Academy of Sciences, and human cervical carcinoma HeLa cell line was obtained from National Infrastructure of Cell Line Resource. Cells were cultured in RPMI 1640 (Thermo Fisher Scientific) supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS, ExCell Bio) and 1% (v/v) pen-strep (HyClone) at 37 °C and 5% CO2.

extract_protocol:
12 male mice of C57BL/6J strain from 4 age groups (3-, 12-, 19- and 22-month-old) were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80C prior to DNA isolation. Genomic DNA from human cell lines and the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer's protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer?s instructions. All DNA samples were eluted in UltraPure? DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20C.
Library construction method: SSiNGLe-AP method

treatment_protocol: Two million K562 or HeLa cells were seeded at 1 million cells per ml of culture medium without penicillin-streptomycin solution in 6-well plates. After 16 hr, cells were treated with 1.5 mM MMS (Sigma) for 1 hr or grown without MMS as control. One microgram of the K562 or HeLa genomic DNA was used directly as input into the SSiNGLe-AP protocol. For the MX treatment, after DNase fragmentation, the purified genomic DNA was incubated at 37C for 30 min in 20 µl of 50 mM K3PO4 (pH 7.0) buffer with or without 33 mM MX (Abmole). The DNA was recovered by ethanol precipitation, dissolved in 15 µl water and subjected to SSiNGLe-AP procedure starting from the blocking step preceded by denaturation. All samples were processed with SSiNGLe-AP protocol based on APE1, with exception of some samples where Endo IV was used instead as indicated.

tag: spike-in

value: Leptotrichia wadei


title: P-A-3


title: CH12_RNASeq_shMcm_d3_rep2

description: ribozomal RNA depleted RNA


title: S1, TP1, RF1, 1

tag: Sex


title: Plate1-182-Liver

description: Plate 1_LIVER_B11

tag: chemical

value: PFHxSAm

tag: concentration

value: day


title: P-A-2


title: CH12_RNASeq_shMcm_d3_rep1

description: ribozomal RNA depleted RNA


title: CH12_RNASeq_shLacZ_d3_rep3

description: ribozomal RNA depleted RNA

value: shLacZ


title: Plate1-181-Liver

description: Plate 1_LIVER_B10

value: mg/kg

value: TempO-Seq


title: Plate1-186-Liver

description: Plate 1_LIVER_D08

value: Female


title: P-A-1


title: 22-S-3

source_name: Sperm

value: Sperm

value: 22 months


title: N-A-3


title: CH12_RNASeq_shLacZ_d3_rep2

description: ribozomal RNA depleted RNA


title: 22-S-2


title: Plate1-180-Liver

description: Plate 1_LIVER_B05


title: Plate1-179-Liver

description: Plate 1_LIVER_A07


title: N-A-2


title: 22-S-1


title: N-A-1


title: CH12_RNASeq_shLacZ_d3_rep1

description: ribozomal RNA depleted RNA


title: Plate1-178-Liver

description: Plate 1_LIVER_E11


title: Plate1-183-Liver

description: Plate 1_LIVER_H01


title: CH12_C13KI_lateS_rep2

description:
Repli-Seq
CH12_RT_C13KI_loess.bw

data_processing:
Library strategy: Repli-seq
Repli-seq
All RepliSeq analysis was wrapped into the reproducible Nextflow workflow repliseq-nf available at https://github.com/t-neumann/repliseq-nf loosely following the steps previously described in Marchal et al., 2018:
Raw reads from  replicates of early (E) and late (L) fractions were trimmed with trim_galore v0.6.5 and aligned to the mouse mm9 reference sequence using bwa mem v0.7.17  and unmapped reads, secondary alignments and multimapping reads were filtered with samtools v1.9.
Replicates were merged using samtools and read duplicates were filtered using picardTools MarkDuplicates.
E/L log2 ratios were calculated in 5kb windows using deeptools bamCompare v3.4.1.
Loess smoothing was performed with bedtools v2.29.2 and a custom R script using the preprocessCore package v1.46.0 with a span size of 300 kb and bigwig tracks were produced using kent_tools v377.
The correlation between replicates was assessed with deepTools multiBamSummary.
Genome_build: NCBI mm9
Supplementary_files_format_and_content: bigWig of loess smoothed E/L log2 ratios.

growth_protocol: CH12 cells cultured in complete RPMI medium with IL4/CD40/TGF beta stimulation.

extract_protocol:
BrdU labled DNA was extracted via phenol, phenol-chlorophorm extraction and subjected to immunoprecipitation
Repli-seq was performed as previously described (Marchal C, 2018). In brief,  Cells were fixed and incubated with a mix of RNase A  and propidium iodide  . For each sample, three fractions were sorted: G1 phase, early S phase and late S phase cells, 50 000 cells per fraction Sorted cells were lysed . Extracted DNA was sonicated for 9 min in a Diagenode Bioruptor resulting in 100-500 bp DNA fragments . Sonicated DNA was subjected to end-repair and adapter ligation using the NEBNext® Ultra™ II DNA Library Prep Kit (NEB) following the NEB protocol. Adapter-ligated DNA was incubated with 25 mg/ml of anti-BrdU antibody (BD Pharmingen) for 4h with rotation followed by incubation with 40 μg of anti-mouse IgG antibody (Sigma) for 1h with rotation (light protected) which was followed by DNA purification

treatment_protocol: Two million asynchronously dividing cells were seeded and incubated with 100mM BrdU for 2h in a light protected environment to maintain BrdU stability.

tag: cell cycle phase

value: lateS


title: CH12_C13KI_lateS_rep1

description:
Repli-Seq
CH12_RT_C13KI_loess.bw


title: 19-S-2

value: 19 months


title: PMN-Mito-JLRNASEQ-2

city: Moncton

first: Eric

middle: P

last: Allain

state: New Brunswick

address: 330 University ave

department: Medical Genetics

country: Canada

institute: Vitalité Health Network

data_processing:
FASTQ reads from PMNLs were assessed using fastqc version 0.11.9 and quality trimmed using Trimmomatic version 0.39 prior to alignment to the hg38 genome using STAR version 2.7.
Feature quantification was performed using featureCounts version 2.0.1 with the gencode human annotation version 37
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated count table with gene counts for all 12 samples.

source_name: Polymorphonuclear Neutrophils

growth_protocol: Blood collected from healthy donors in tubes containing the anticoagulant acid citrate dextrose (ACD) and then centrifuged at 275g for 15 min at room temperature (RT). The hematocrits were processed to remove erythrocytes by dextran sedimentation. After a centrifugation step at 800g for 10 min at RT on a lymphocyte separation medium cushion (density of 1.077 g/ml, Corning), PMNL were obtained (>95%), verified by flow cytometry. Remaining erythrocytes were lysed by hypotonic lysis and PMNL were counted and resuspended at 107 cells/ml in HBSS supplemented with 1.6 mM CaCl2 and 0.3 U/ml adenosine deaminase (Sigma-Aldrich).

extract_protocol:
Cells were lysed in RiboZol (Amresco) and kept at -80℃ until use. Total RNA was extracted and purified using the RNeasy Mini Kit (Qiagen), following the procedures described by the manufacturer
Library was prepared using 25 ng RNA input and the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB). First, ribosomal RNA was removed using the NEBNext rRNA Depletion Kit v2 (Human/Mouse/Rat)(NEB) as indicated by the manufacturer’s instructions. Briefly, samples with a RIN between 2 and 6 were fragmented for 8 min at 94°C whereas samples with a RIN ≥7 were fragmented for 15 min at 94°C for a target insert size of 200 bp. Next, the first and the second cDNA strand were synthesized, followed by an Ampure XP bead (Beckman Coulter) clean up. Then the samples were end-prepped, and the adaptor was ligated. Adaptor was diluted following the manufacturer’s instructions. The adaptor-ligated samples were purified with Ampure XP beads before being amplified. For the PCR enrichment, a different Unique Dual Index Primer Pair (NEB) was added to each sample and 14 cycles were used. A last purification using Ampure XP beads was done to obtain the final library. If needed, libraries were pooled at the same concentration and the last bead purification was done a second time to remove adapter-dimer. The quality of the library was assessed as follows; size distribution was determined with the D1000 assay on the Tapestation (Agilent). The dsDNA HS assay from Qubit (ThermoFisher Scientific was used to evaluate the concentration.

treatment_protocol: PMNL were either left unstimulated (native) or primed for 30 min at 37℃ with 100 U/ml tumor necrosis factor-alpha (TNF-α), (Cederlane) and 10 ng/ml granulocyte-macrophage colony-stimulating factor (GM-CSF), (Cederlane) to simulate PMNL in tissue inflammatory tissues16. Cells were then washed and subsequently activated for 2 hrs in presence of either functional platelet-derived mitochondria, 25 µg/ml MTD5 or 1 µM N-formyl-methionyl-leucyl-phenylalanine (fMLP) (Sigma-Aldrich)17 at indicated concentrations in HBSS supplemented with 1.6 mM CaCl2.

tag: cell type

value: Polymorphonuclear Neutrophils

tag: condition

value: Mito-Stimulated

tag: replicate


title: Plate1-177-Liver

description: Plate 1_LIVER_A12

extract_protocol: All animals were euthanized the day after the last dose of chemical was administered and the liver and kidney were removed during necropsy. Two samples from each the left liver lobe and right kidney were collected within five minutes of termination for toxicogenomic evaluation. Tissue samples were cut into approximately 5 cubic mm pieces, aliquoted into screw-cap tubes, flash frozen in liquid nitrogen, and stored at -80 degreees C. RNA was extracted from one of the two collected samples and the extraction batch information recorded in the metadata along with the quantity and quality of each RNA sample. The RNA samples and metadata file were sent to BioSpyder for evaluation using the whole transcriptome TempOSeq platform with a minimum of 10 million reads/sample.

value: Sprague Dawley (SD)

tag: unit

tag: vehicle

tag: duration


title: 19-S-1

tag: age


title: PMN-Mito-JLRNASEQ-27


title: Plate1-176-Liver

description: Plate 1_LIVER_B03

value: water/tween

tag: platfrom


title: CH12_C13KI_earlyS_rep2

description:
Repli-Seq
CH12_RT_C13KI_loess.bw

tag: cell line

tag: clone

value: earlyS


title: Plate1-175-Liver

description: Plate 1_LIVER_G06

tag: strain

value: Male

value: Liver


title: CH12_C13KI_earlyS_rep1

description:
Repli-Seq
CH12_RT_C13KI_loess.bw


title: PMN-Mito-JLRNASEQ-24


title: 12-S-3

tag: tissue

value: 12 months


title: Plate1-174-Liver

description: Plate 1_LIVER_H05

value: PFHxSAm

value: day


title: CH12_C2KI_lateS_rep2

description:
Repli-Seq
CH12_RT_C2KI_loess.bw


title: PMN-Mito-JLRNASEQ-21


title: 12-S-2


title: Plate1-173-Liver

description: Plate 1_LIVER_F04

value: mg/kg


title: PMN-DAMPs-JLRNASEQ-3

value: DAMP-Stimulated


title: CH12_C2KI_lateS_rep1

description:
Repli-Seq
CH12_RT_C2KI_loess.bw


title: 12-S-1


title: PMN-DAMPs-JLRNASEQ-28


title: 19-S-3


title: Plate1-172-Liver

description: Plate 1_LIVER_A09

value: TempO-Seq


title: Plate1-171-Liver

description: Plate 1_LIVER_C10


title: CH12_C2KI_earlyS_rep2

description:
Repli-Seq
CH12_RT_C2KI_loess.bw


title: 3-S-2

value: Sperm

value: 3 months


title: PMN-DAMPs-JLRNASEQ-25


title: CH12_C2KI_earlyS_rep1

description:
Repli-Seq
CH12_RT_C2KI_loess.bw


title: Plate1-170-Liver

description: Plate 1_LIVER_C07

value: Female


title: PMN-DAMPs-JLRNASEQ-22


title: CH12_WTKI_lateS_rep2

description:
Repli-Seq
CH12_RT_WTKI_loess.bw

value: WTKI

value: lateS


title: Plate1-169-Liver

description: Plate 1_LIVER_G12


title: 3-S-1


title: 22-P-3

source_name: PBMC

value: PBMC

value: 22 months


title: CH12_WTKI_lateS_rep1

description:
Repli-Seq
CH12_RT_WTKI_loess.bw


title: 22-P-2


title: PMN-JLRNASEQ-26

value: Polymorphonuclear Neutrophils

value: Control


title: CH12_WTKI_earlyS_rep2

description:
Repli-Seq
CH12_RT_WTKI_loess.bw

value: earlyS


title: PMN-JLRNASEQ-23


title: Plate1-168-Liver

description: Plate 1_LIVER_H09

value: Sprague Dawley (SD)

value: Liver

value: water/tween


title: 19-P-3

value: 19 months


title: Plate1-167-Liver

description: Plate 1_LIVER_F09

value: PFHxSAm

value: mg/kg

value: day


title: 22-P-1


title: 3-S-3

value: Sperm


title: PMN-JLRNASEQ-20


title: CH12_WTKI_earlyS_rep1

description:
Repli-Seq
CH12_RT_WTKI_loess.bw


title: Plate1-166-Liver

description: Plate 1_LIVER_H04

value: TempO-Seq


title: PMN-JLRNASEQ-1


title: CH12_C13_lateS_rep2

description:
Repli-Seq
CH12_RT_C13_loess.bw


title: CH12_C13_lateS_rep1

description:
Repli-Seq
CH12_RT_C13_loess.bw


title: 19-P-2


title: WT_Treated_rep2

city: Singapore

first: Rui

last: Yokomori

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute of Singapore, National University of Singapore

description: Replicate 2

data_processing:
RNA-seq reads were mapped to transcript sequences of curated RefSeq (NM and NR transcripts) using salmon (version 1.4.0) with the options “--gcBias --seqBias –posBias”.
The index file for the transcript sequences was created with default settings.
Transcript-level read counts were converted to gene-level read counts using tximport (version 1.18.0).
Differentially expressed genes were estimated using DESeq2 (version 1.30.0).
Supplementary_files_format_and_content: txt file for differentially expressed genes

source_name: CAL-1 cells

growth_protocol: CAL-1 cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was harvested using the miRNeasy Mini Kit (Qiagen).
Strand-specific library construction and 150-bp paired-end sequencing with a sequencing depth of 130M reads on the NovaSeq6000 platform were performed at Macrogen.

treatment_protocol: METTL3 KO was induced with Tetracycline and cells were then treated with DMSO or GSK595 for 72 hours, after which total RNA were harvested.

value: BPDCN-patient derived cell line

tag: genotype

value: WT

tag: treatment

value: GSK595 Treated


title: Plate1-165-Liver

description: Plate 1_LIVER_C08

tag: Sex

value: Male

tag: chemical


title: WT_Treated_rep1

description: Replicate 1


title: 19-P-1

value: PBMC


title: Plate1-164-Liver

description: Plate 1_LIVER_F11

tag: concentration


title: Plate1-163-Liver

description: Plate 1_LIVER_E10


title: CH12_C13_earlyS_rep1

description:
Repli-Seq
CH12_RT_C13_loess.bw

tag: cell cycle phase


title: CH12_C13_earlyS_rep2

description:
Repli-Seq
CH12_RT_C13_loess.bw


title: WT_DMSO_rep2

description: Replicate 2

tag: cell type

value: DMSO


title: Plate1-162-Liver

description: Plate 1_LIVER_A03


title: 12-P-3

value: 12 months


title: CH12_WT_lateS_rep2

description:
Repli-Seq
CH12_RT_WT_loess.bw

value: lateS


title: WT_DMSO_rep1

description: Replicate 1


title: 12-P-2


title: 12-P-1


title: Plate1-161-Liver

description: Plate 1_LIVER_G08

value: Sprague Dawley (SD)


title: METTL3_KO_Treated_rep2

description: Replicate 2

value: METTL3 KO


title: CH12_WT_lateS_rep1

description:
Repli-Seq
CH12_RT_WT_loess.bw


title: 3-P-3

value: 3 months


title: METTL3_KO_Treated_rep1

description: Replicate 1


title: METTL3_KO_DMSO_rep2

description: Replicate 2


title: CH12_WT_earlyS_rep2

description:
Repli-Seq
CH12_RT_WT_loess.bw

value: earlyS


title: Plate1-159-Liver

description: Plate 1_LIVER_F10

value: Female

value: Liver

value: PFHxSAm

value: water/tween


title: 3-P-2


title: CH12_WT_earlyS_rep1

description:
Repli-Seq
CH12_RT_WT_loess.bw


title: Plate1-160-Liver

description: Plate 1_LIVER_D07

value: mg/kg

value: day

value: TempO-Seq


title: Plate1-158-Liver

description: Plate 1_LIVER_G07


title: 3-P-1


title: CH12_shMcm_d3_G1S_rep2

description:
Repli-Seq
CH12_RT_shMcm_loess.bw

tag: knockdown

value: shMcm


title: METTL3_KO_DMSO_rep1

description: Replicate 1

value: BPDCN-patient derived cell line


title: Plate1-157-Liver

description: Plate 1_LIVER_D09

tag: unit


title: 22-M-3

source_name: Bone marrow

value: Bone marrow

value: 22 months


title: HC60, BCR-Seq

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Library strategy: BCR-seq
Illumina bcl2fastq software used for for basecalling.
Barcoded, full-length TCR V(D)J segments could be enriched from amplified cDNA from 5′ libraries via PCR amplification with primers specific to the TCR prior to library construction using a Chromium Single-Cell V(D)J Enrichment kit according to the manufacturer’s protocol (10X Genomics). If both T cells are expected to be present in the partitioned cell population, TCR transcripts can be enriched in separate reactions from the same amplified cDNA material. Cell Ranger for V(D)J (https://support.10xgenomics.com/single-cell-vdj) is a set of analysis pipelines that process Chromium single cell 5′ RNA-seq output to assemble, quantify, and annotate paired V(D)J transcript sequences. Cell Ranger workflow starts by demultiplexing the Illumina sequencer's base call files (BCLs) for each flowcell directory into FASTQ files. Cell calling is performed independently of V(D)J read filtering and assembly. A clonotype is a set of cells that share the same paired receptor sequences (presumably derived from the same progenitor cell) Cell barcodes are grouped together into clonotypes if they share the same set of productive CDR3 nucleotide sequences by exact match. Repertoire informations of all samples are exhibited using a set of basic features: CDR3 abundance, CDR3 bases length, Variable (V) and Joining (J) segment usage(the frequency of associated reads for each of V/J gene present in samples), the length of V/J gene in CDR3 region, and V-J gene paired frequency in CDR3 junctions. We use hierarchical cluster (https://stat.ethz.ch/R-manual/Rdevel/library/stats/html/hclust.html) and Kruskal’s Non-metric Multidimensional Scaling (isoMDS, https://cran.r-project.org/web/ packages/MASS/MASS.pdf) to estimate Immune Repertoires similarity.
Genome_build: GRCh38_v96
Supplementary_files_format_and_content: filtered_contig_annotations.zip

source_name: Healthy control, Peripheral blood

extract_protocol:
Retrieving the PBMC-containing cryo-tubes from the -196℃ liquid nitrogen storage tank and placing them in a 37℃ water bath for rapid thawing. PBMCs were mixed with 10 mL washing medium (90% DMEM+10% FBS) in a 15-mL polypropylene tube and centrifuged at 500g for 20 min. The supernatant was then aspirated (repeat twice). The cell pellets were resuspended with 500 μl× PBS (0.04% BSA) in the sterile RNase-free vacutainer tubes and added with 5 ml 1× red blood cell lysis buffer (MACS 130-094-183, 10×) and incubated at room temperature for 10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 500g for 20 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in 1× PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C (repeat twice). The cell pellet was resuspended in 50 μl of 1× PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single cell suspensions were counted using a Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
manufacturer's protocols for 5'barcoded GEX and V(D)J BCR

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

value: female

tag: disease symptom

value: Healthy control

tag: disease state

tag: thymalfasin treatment

value: No


title: Plate1-156-Liver

description: Plate 1_LIVER_A05

value: Sprague Dawley (SD)

tag: vehicle

tag: duration

tag: platfrom


title: CH12_shMcm_d3_lateS_rep2

description:
Repli-Seq
CH12_RT_shMcm_loess.bw

tag: cell line

value: lateS


title: CH12_shMcm_d3_lateS_rep1

description:
Repli-Seq
CH12_RT_shMcm_loess.bw


title: Plate1-154-Liver

description: Plate 1_LIVER_F06

tag: strain

value: Male

tag: tissue

value: Liver


title: Plate1-155-Liver

description: Plate 1_LIVER_D12

tag: Sex

value: PFHxSAm

value: water/tween


title: HC39, BCR-Seq

tag: age


title: HC36, BCR-Seq


title: 19-M-3

value: 19 months


title: CH12_shMcm_d3_earlyS_rep2

description:
Repli-Seq
CH12_RT_shMcm_loess.bw

value: earlyS


title: 19-M-2


title: HC31, BCR-Seq

value: male


title: 22-M-1


title: Plate1-153-Liver

description: Plate 1_LIVER_E12

tag: chemical

tag: concentration

value: mg/kg

value: day

value: TempO-Seq


title: CH12_shMcm_d3_earlyS_rep1

description:
Repli-Seq
CH12_RT_shMcm_loess.bw

value: shMcm

tag: cell cycle phase


title: Plate1-152-Liver

description: Plate 1_LIVER_F02


title: 19-M-1

value: Bone marrow


title: CH12_shLacZ_d3_G1S_rep2

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw

tag: knockdown

value: shLacZ


title: Plate1-151-Liver

description: Plate 1_LIVER_E02

tag: unit


title: CH12_shMcm_d3_G1S_rep1

description:
Repli-Seq
CH12_RT_shMcm_loess.bw


title: 12-M-3

value: 12 months


title: 22-M-2

value: 22 months


title: Plate1-150-Liver

description: Plate 1_LIVER_B12

value: Sprague Dawley (SD)

value: Female


title: 12-M-2


title: HC20, BCR-Seq

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

value: Healthy control

value: Yes


title: CH12_shLacZ_d3_lateS_rep2

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw

value: lateS


title: HC21, BCR-Seq

tag: disease symptom

tag: disease state


title: CH12_shLacZ_d3_G1S_rep1

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw


title: HC58, BCR-Seq

tag: thymalfasin treatment

value: No


title: 12-M-1


title: Plate1-149-Liver

description: Plate 1_LIVER_G09

value: Liver

value: PFHxSAm

tag: vehicle

value: water/tween

tag: duration


title: CH12_shLacZ_d3_lateS_rep1

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw

tag: cell line


title: Plate1-147-Liver

description: Plate 1_LIVER_C04

tag: strain

value: mg/kg

value: day

tag: platfrom

value: TempO-Seq


title: HC05, BCR-Seq

tag: tissue

value: female


title: HC07, BCR-Seq

tag: age


title: Plate1-148-Liver

description: Plate 1_LIVER_C03

tag: Sex

tag: chemical


title: HC01, BCR-Seq


title: HC23, BCR-Seq

value: male


title: 3-M-2

value: Bone marrow

value: 3 months


title: 3-M-1


title: Plate1-146-Liver

description: Plate 1_LIVER_B07

value: Sprague Dawley (SD)

value: Female

tag: concentration


title: CH12_shLacZ_d3_earlyS_rep2

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw

tag: knockdown

value: shLacZ

tag: cell cycle phase

value: earlyS


title: Plate1-145-Liver

description: Plate 1_LIVER_D04

value: Male

tag: unit


title: COV164, BCR-Seq

source_name: COVID-19, Peripheral blood

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

value: symptomatic

value: Severe Recovery

tag: disease duration

value: long term

tag: patient comorbidity


title: COV165, BCR-Seq

tag: disease symptom

tag: disease state

tag: thymalfasin treatment

value: No


title: 22-L-2

tag: strain

value: Liver

value: 22 months


title: COV163, BCR-Seq

value: female

value: Yes


title: Plate1-142-Liver

description: Plate 1_LIVER_B06

value: PFHxSAm

value: mg/kg

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: 22-L-3

tag: tissue

tag: age


title: 22-L-1


title: COV166, BCR-Seq


title: 19-L-3

value: 19 months


title: Plate1-144-Liver

description: Plate 1_LIVER_G03

value: Sprague Dawley (SD)

tag: Sex

value: Male

tag: chemical

tag: concentration


title: 3-M-3

value: Bone marrow

value: 3 months


title: Plate1-143-Liver

description: Plate 1_LIVER_F08

tag: unit


title: Liver, CCl4_v-A12, Week 6_1

city: Zurich

first: Jing

last: Chen

state: Other

address: Winterthurerstrasse 190

institute: University of Zurich

description: 250 paired-end reads

data_processing:
iRepertoire pipeline
Raw fastq files were demultiplexed based barcode
The ends of sequence reads were trimmed for quality,
Paired ends were stitched into monolithic sequences,
Sequences were aligned with IMGT references
Identify CDRs based on positional information
Remove erroneous sequences with filters.
Assembly: IMGT references and numbering scheme
Supplementary files format and content: Tab-delimited txt files with sequecing reads foe the features of interest
Library strategy: TCR-seq

source_name: liver

extract_protocol:
Total RNA was extracted using Rneasy midi plus kit (Qiagen). 50ng of total RNA was used for the sequencing
targeted multiplex PCR (arm-PCR)

treatment_protocol:
Mice were immunized with ADAM12 vaccine (v-A12) or control vaccine (v-CTRL)
Mice were treated with carbon tetracholoride (CCl4) or olive oil (sham) 3 times/per week for 6 weeks. Livers were harvested for RNA extraction

value: liver

tag: genotype

value: WT

tag: treatment

value: carbon tetracholoride, ADAM12 vaccine

tag: time

value: Week 6


title: Liver, CCl4_v-A12, Week 6_2

description: 250 paired-end reads


title: Liver, CCl4_v-CTRL, Week 6_2

description: 250 paired-end reads

value: carbon tetracholoride, control vaccine


title: Plate1-141-Liver

description: Plate 1_LIVER_E05

source_name: Liver

value: Liver


title: CH12_shLacZ_d3_earlyS_rep1

description:
Repli-Seq
CH12_RT_shLacZ_loess.bw

tag: cell line

tag: knockdown

value: shLacZ

tag: cell cycle phase

value: earlyS


title: 19-L-2


title: Plate1-140-Liver

description: Plate 1_LIVER_H06

value: Female

value: PFHxSAm

value: mg/kg


title: Liver, CCl4_v-A12, Week 6_3

description: 250 paired-end reads


title: Liver, sham_v-A12, Week 6_2

description: 250 paired-end reads

value: olive oil, ADAM12 vaccine


title: COV159, BCR-Seq

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

tag: gender

value: female

tag: disease symptom

value: symptomatic

tag: disease state

value: Severe Recovery

tag: thymalfasin treatment

value: No

tag: disease duration

value: long term

tag: patient comorbidity

value: Yes


title: Liver, sham_v-A12, Week 6_1

description: 250 paired-end reads

tag: tissue

value: liver

value: WT

value: Week 6


title: COV158, BCR-Seq

tag: age


title: COV161, BCR-Seq

value: male


title: 12-L-3

tag: strain

value: Liver

value: 12 months


title: Plate1-139-Liver

description: Plate 1_LIVER_H12

value: Sprague Dawley (SD)

tag: Sex

value: Female

tag: chemical

value: PFHxSAm

tag: concentration

tag: unit

tag: vehicle

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: COV126, BCR-Seq

value: Peripheral blood

tag: cell type

value: peripheral blood mono-nuclear cells (PBMCs)

value: symptomatic

value: short term


title: Plate1-138-Liver

description: Plate 1_LIVER_C06

value: mg/kg


title: 12-L-2


title: 12-L-1


title: COV119, BCR-Seq

tag: gender

value: Severe Recovery

value: No


title: Liver, sham_v-CTRL, Week 6_2

description: 250 paired-end reads

value: liver

tag: genotype

value: WT

tag: treatment

value: olive oil, control vaccine

tag: time

value: Week 6


title: Plate1-137-Liver

description: Plate 1_LIVER_C05

value: Sprague Dawley (SD)

value: Liver


title: Liver, sham_v-CTRL, Week 6_1

description: 250 paired-end reads


title: 3-L-3

value: 3 months


title: 19-L-1

value: 19 months


title: 3-L-2


title: 30S no treatment

city: El Paso

first: Eda

last: Kocui

state: TX

address: 500 W. University Avenue

department: Chemistry and Biochemistry

institute: University of Texas at El Paso

data_processing:
Library strategy: SHAPE-MaP
Base calls were performed uising Illumina RTA version 1.18. 54
The next generation sequencing reads were aligned to the rrlB and rrsB  genes of Bl21 (DE3)  E Coli and the mutations were counted using Shape-Mapper 1.2

organism: Escherichia coli

source_name: Escherichia Coli cells

growth_protocol: The cells were grown at 37ºC in 200 mL of media containing 10g/L tryptone, 1g/L yeast extract, 100μg/mL carbenicillin, and 34μg/mL chloramphenicol. When the cell reached an optical density at 600 nm of about 0.3, the cell growth was arrested by adding 200 ml of ice.

extract_protocol:
The ribosomal particles were isoalate using a  20-40% gradients were made in a buffer consisting of 20mM HEPES KOH pH 7.5, 150mM NH4Cl, 1mM MgCl2 and 4mM BME.
The NGS sequencing library was performed following the randomer workflow of the Selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) protocol(Smola et al. 2015)

treatment_protocol: the isolated ribosomal particles were treated with CMCT and NaHCO3 , NaHCO3 alone, KMnO4, or no chemical treatment

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing wild-type  DbpA

value: no treatment

tag: molecule

value: 16S ribosomal RNA


title: Plate1-135-Liver

description: Plate 1_LIVER_A11

value: Male

tag: tissue

value: PFHxSAm

value: water/tween

value: day

value: TempO-Seq


title: COV045, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

tag: age

value: female

tag: disease symptom

value: symptomatic

tag: disease state

value: Severe Recovery

tag: thymalfasin treatment

value: Yes

tag: disease duration

value: short term

tag: patient comorbidity

value: No


title: Liver, CCl4_v-CTRL, Week 6_1

description: 250 paired-end reads

value: liver

value: WT

value: carbon tetracholoride, control vaccine

value: Week 6


title: Plate1-136-Liver

description: Plate 1_LIVER_G10

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Female

value: Liver

tag: chemical

tag: concentration

tag: unit

value: mg/kg

tag: vehicle


title: COV037, BCR-Seq

tag: cell type

tag: gender


title: 30S KMnO4 6min treatment

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing R331A DbpA

tag: treatment

value: 16S ribosomal RNA


title: 50S no treatment

value: BLR (DE3) deltaDbpA, expressing wild type  DbpA

value: no treatment

tag: molecule

value: 23S ribosomal RNA


title: Plate1-134-Liver

description: Plate 1_LIVER_F07

value: Male

tag: tissue

value: PFHxSAm

value: water/tween

tag: duration

value: day

tag: platfrom

value: TempO-Seq


title: 30S KMnO4 3min treatment


title: Plate1-133-Liver

description: Plate 1_LIVER_D11


title: 22-H-3

source_name: Heart

value: Heart

tag: age

value: 22 months


title: COV057, BCR-Seq

value: Peripheral blood

value: peripheral blood mono-nuclear cells (PBMCs)

value: male

tag: disease symptom

value: symptomatic

tag: disease state

value: Severe

tag: thymalfasin treatment

value: Yes

tag: disease duration

value: short term


title: COV047, BCR-Seq

value: No

tag: patient comorbidity


title: Plate1-132-Liver

description: Plate 1_LIVER_D05

tag: strain

value: Sprague Dawley (SD)

tag: Sex

value: Liver

tag: chemical

tag: concentration

value: mg/kg


title: 22-H-2


title: COV029, BCR-Seq

tag: cell type

tag: gender


title: 50S KMnO4 6min treatment

tag: genotype/variation

value: BLR (DE3) deltaDbpA, expressing wild-type  DbpA

tag: treatment

value: 23S ribosomal RNA


title: COV055, BCR-Seq

tag: tissue

value: Severe Recovery

value: long term


title: 50S KMnO4 3min treatment

tag: molecule


title: 22-H-1

value: Heart