title: Pool175_Plate12-4-E22-J7


title: Pool175_Plate12-4-E22-I7

status: Public on May 06 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

molecule: genomic DNA

organism: Mus musculus

source_name: brain

growth_protocol: All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee. The knock-in mouse line, R26R-CAG-loxp-stop-loxp-Sun1-sfGFP-Myc (INTACT) was used for most experiments4 and they were maintained on a C57BL/6J background. 42-49 day old adult male and female INTACT mice were used for the retrograde labeling experiment.

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x1012 to 1x1013 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: tissue

value: brain

tag: source

value: RSP

tag: target

value: AI

tag: Sex

value: female


title: Pool175_Plate12-4-E22-J19

value: VIS

value: male


title: Pool175_Plate12-4-E22-O8


title: Pool175_Plate12-4-E22-I19


title: Pool175_Plate12-4-E22-H7


title: Pool175_Plate12-4-E22-H19


title: Pool175_Plate12-4-E22-G20


title: Pool175_Plate12-4-E22-G7


title: Pool175_Plate12-4-E22-G19


title: Pool175_Plate12-4-E22-D19


title: Pool175_Plate12-4-E22-D7


title: Pool175_Plate12-4-E22-B7


title: Pool175_Plate12-4-E22-B20


title: Pool175_Plate12-4-E22-C19


title: Pool175_Plate12-4-E22-E7


title: Pool175_Plate12-4-E22-A19


title: Pool175_Plate12-4-E22-J20


title: Pool175_Plate12-4-E22-F7


title: Pool175_Plate12-4-E22-B19


title: Pool175_Plate12-4-E22-E19


title: Pool175_Plate12-3-E22-N18


title: Pool175_Plate12-3-E22-N17


title: Pool175_Plate12-3-E22-P18


title: Pool175_Plate12-3-E22-O18


title: Pool175_Plate12-3-E22-N5


title: Pool175_Plate12-3-E22-O5


title: Pool175_Plate12-3-E22-P17


title: Pool175_Plate12-3-E22-N6


title: Pool175_Plate12-3-E22-M5


title: Pool175_Plate12-3-E22-M18


title: Pool175_Plate12-4-E22-C7


title: Pool175_Plate12-3-E22-L6


title: Pool175_Plate12-3-E22-M17


title: Pool175_Plate12-3-E22-P5


title: Pool175_Plate12-3-E22-L5


title: Pool175_Plate12-3-E22-L18


title: Pool175_Plate12-3-E22-L17


title: xenograft_Y537S_clone1_rep2

city: Salt Lake City

first: Jason

last: Gertz

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

description: Homo sapiens xenografted into mouse

library_source: transcriptomic

data_processing:
The raw FASTQ files were filtered for reads specific to human (as compared to mouse) using Xengsort software
FASTQ files containing unambiguous human reads were aligned to hg19 build of the human genome using HISAT2
SAMtools was used to convert SAM files to BAM files
Read counts were normalized and analyzed for differential expression via the DESeq2 package in R
Genes were defined by the University of California Santa Cruz (UCSC) Known Genes and reads that mapped to known genes were assigned with featureCounts
Assembly: hg19
Supplementary files format and content: Gene counts (raw) from unambiguous human reads in a tab-delimited text file

molecule: total RNA

organism: Homo sapiens

source_name: xenografted tumor

growth_protocol: 1.0x10^6 Ishikawa ER wildtype or ER mutant (D538G or Y537S) cells were implanted subcutaneously into six- to nine-week-old female ovariectomized, immunodeficient NRG mice without estrogen supplementation. Thirty-four days post-implantation mice were scrificed and tumors were excised and flash frozen.

extract_protocol:
Approximately 30 mg of flash-frozen xenograft tissue was used for RNA extraction by mechanical homogenization using M tubes (Miltenyi Biotec) using a gentleMACS Octo Dissociator (Miltenyi Biotec) in RLT plus (Qiagen) lysis buffer supplemented with 1% beta-mercaptoethanol (Sigma-Aldrich). RNA was purified using a Quick-RNA Miniprep kit (Zymo Research).
Libraries were generated using Ribo-Zero Gold (Illumina) with the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) using 500 ng of total RNA.

value: xenografted tumor

tag: cell line

value: Ishikawa ER-Y537S Clone 1

tag: cell type

value: endometrioid adenocarcinoma

tag: genotype

value: ESR1 Y537S


title: xenograft_Y537S_clone1_rep1

description: Homo sapiens xenografted into mouse


title: xenograft_Y537S_clone1_rep3

description: Homo sapiens xenografted into mouse


title: xenograft_D538G_clone1_rep3

description: Homo sapiens xenografted into mouse

value: Ishikawa ER-D538G Clone 1

value: ESR1 D538G


title: xenograft_D538G_clone1_rep2

description: Homo sapiens xenografted into mouse


title: Pool175_Plate12-3-E22-M6


title: Pool175_Plate12-3-E22-K5


title: Pool175_Plate12-3-E22-J6


title: Pool175_Plate12-3-E22-K6


title: Pool175_Plate12-3-E22-K17


title: xenograft_WT_clone1_rep2

description: Homo sapiens xenografted into mouse

value: Ishikawa Wildtype Clone 1

value: ESR1 wildtype


title: xenograft_D538G_clone1_rep1

description: Homo sapiens xenografted into mouse


title: xenograft_WT_clone1_rep1

description: Homo sapiens xenografted into mouse


title: xenograft_WT_clone1_rep3

description: Homo sapiens xenografted into mouse


title: Ishikawa_doublefixation_pooled_input

data_processing:
Reads were aligned to hg19 using Bowtie with the following parameters: -m 1 -t --best -q -S -I 32 -e 80 -n 2
SAMtools was used to sort and convert SAM files to BAM files
Peaks with a P-value cutoff of 1 x 10-10 and an mfold parameter between 15 and 100 were called by Model Based Analysis of ChIP-seq-2 (MACS2)
DESeq was used to normalize read counts and perform differential analysis at individual ER or CDK9 bound sites
Assembly: hg19
Supplementary files format and content: Bedgraph files
Supplementary files format and content: narrowPeak files from MACS2

source_name: pooled input of Ishikawa lines

growth_protocol: Ishikawa cells were cultured in full serum media: RPMI-1640 with 10% fetal bovine serum and 1% penicillin-streptomycin. Cells were incubated at 37°C with 5% CO2 for the duration of all experiments. At least 5 days prior to inductions, cells were placed in hormone deprived media: phenol-red free RPMI-1640 media (Thermo Fisher Scientific), since phenol-red is estrogenic, with 10% charcoal-dextran stripped fetal bovine serum (Thermo Fisher Scientific) and 1% penicillin-streptomycin.

extract_protocol:
For FLAG ChIPs (flag tagged ESR1), fixation was performed by treating cells with 1% formaldehyde for 10 minutes at room temperature. For CDK9 ChIPs, a double fixation was performed by treating cells with 2 mM disuccinimidyl glutarate (Thermo Scientific) for 20 minutes at room temperature followed by fixation with 1% formaldehyde for 10 minutes at room temperature. For both fixation methods, the cross-linking reaction was stopped with the addition of glycine to a final concentration of 125 mM. Cells were then washed with cold PBS and harvested via cell scraping in Farnham lysis buffer supplemented with protease inhibitors.
Chromatin immunoprecipitation was performed as previously described (Reddy et al. Genome Research 2009) with an Anti-FLAG (Sigma-Aldrich M2) antibody that recognizes a FLAG tag on ESR1 or an Anti-CDK9 (Abcam ab239364) that recognizes CDK9.

treatment_protocol: Media was changed 1 day prior to estradiol (E2) inductions and cells were treated with either DMSO (vehicle) or 10 nM E2 for 1 hour.

value: pooled input of Ishikawa lines

value: pooled input

tag: chip antibody

tag: treatment


title: Pool175_Plate12-3-E22-J5


title: CDK9_ER_Y537S_Clone1_DMSO_rep2

source_name: Ishikawa ER-Y537S Clone 1

value: ESR1 mutant

value: CDK9 (Abcam ab239364)

value: 1 hr 0.1% DMSO


title: Pool175_Plate12-3-E22-J17

value: brain

value: AI


title: CDK9_ER_Y537S_Clone1_DMSO_rep1


title: Pool175_Plate12-3-E22-I5

value: RSP


title: Pool175_Plate12-3-E22-I6

value: female


title: Pool175_Plate12-3-E22-H6


title: Pool175_Plate12-3-E22-H5

value: male


title: Pool175_Plate12-3-E22-I18

value: VIS


title: CDK9_ER_WT_Clone2_E2_rep2

source_name: Ishikawa ER wildtype Clone 2

value: Ishikawa ER wildtype Clone 2

value: endometrioid adenocarcinoma

value: 1 hr 10 nM E2


title: CDK9_ER_WT_Clone2_E2_rep1


title: Pool175_Plate12-3-E22-H18


title: CDK9_ER_WT_Clone2_DMSO_rep2


title: Pool175_Plate12-3-E22-J18


title: Pool175_Plate12-3-E22-G6


title: CDK9_ER_D538G_Clone1_DMSO_rep2

source_name: Ishikawa ER-D538G Clone 1

value: Ishikawa ER-D538G Clone 1


title: CDK9_ER_WT_Clone2_DMSO_rep1


title: Pool175_Plate12-3-E22-G5


title: CDK9_ER_D538G_Clone1_DMSO_rep1


title: Pool175_Plate12-3-E22-G17


title: Pool175_Plate12-3-E22-F5


title: CUTRUN_HUDEP_D0_KOWT_GATA1_Rep2

city: Beijing

first: Dong

last: Li

state: Beijing

address: No.5 Yiheyuan Road, Haidian District,

department: College of Life Science

country: China

institute: Peking University

data_processing:
Raw sequence data of CUT&RUN were trimmed to barcode using trim_galore (version 0.4.4_dev) and reads were aligned to hg19 version of human genome with bowtie2 (version 2.3.4.1).
Duplicated reads were removed through Picard tool (http://broadinstitute.github.io/picard/) and the low quality of reads (MAPQ < 30) were removed. Reads with the cutoff of inset size < 120bp were selected for transcription factors occupancy and 150-500bp for H3K27ac histone modification as previous studies.
Peaks were calling by SEACR with default parameter with IgG control
The differentiated binding sites of H3K27ac and GATA1 were calculated through diffbind R package with the following parameter (FDR < 0.05) (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind). Co-binding of transcription factors was performed by bedtools and R with 1 bp overlap. The bigwig/ bedgraph files were generated through bamCoverage (https://deeptools.readthedocs.io/en/develop/)
Co-binding of transcription factors was performed by bedtools and R with 1 bp overlap. The bigwig/ bedgraph files were generated through bamCoverage (https://deeptools.readthedocs.io/en/develop/) to visualize peaks in IGV (https://software.broadinstitute.org/software/igv/), and pyGenomeTrack (https://github.com/deeptools/pyGenomeTracks).
Assembly: hg19
Supplementary files format and content: bigWig

source_name: Cord Blood

extract_protocol:
CUT&RUN experiments were carried out as described with modifications. Briefly, 10,000 cells were captured with BioMagPlus Concanavalin A (Bang Cat. # BP531) for 10 min at room temperature. Permeabilization of cells and binding of primary antibodies were performed oner-night at 4℃. After washing away unbound antibody with wash buffer, protein A-MNase was added at a 1:100 ratio and incubated for 2 hours. Cells were washed again and placed in a 0℃-metal block. Then CaCl2 was added to a final concentration of 2 mM to activate protein A-MNase. The reaction was carried out for 30 min and stopped by addition of equal volume of 2XSTOP buffer. The protein-DNA complex was released by centrifugation. DNA was extracted by NEB PCR Cleanup Kit (NEB Cat. # T1030), followed by Qubit fluorometer and bioanalyzer quality control. Protein A-MNase was expressed and purified from BL21(DE) carrying pET-pA-MN. pET-pA-MN was obtained from addgene (Cat#:86973).
The CUT&RUN library preparation was performed with DNA library preparation kit (Vazyme, Cat. # ND607) following with the manufacture’s protocol with minor modifications. Briefly, the temperature dA-tailing was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour. After adaptor ligation, 2X volume of DNA Clean beads (Vazyme, Cat. # N411) was added to the reaction to ensure high recovery efficiency of short fragments. After 15 cycles of PCR amplification, the reaction was cleaned up with 1.2X volume of DNA Clean beads. The final libraries were quantified using a VAHTS Library Quantification Kit (Vazyme, Cat. # NQ101) and a D1000 High Sensitivity DNA chip run on a Bioanalyzer 4250 system (Agilent). Two biological replicates per condition were sequenced in a Novaseq 6000 (S4, PE150, Illumina) by Novogene (Beijing).

value: Cord Blood

value: WT


title: CUTRUN_HUDEP_D0_KOBS12_GATA1_Rep2

value: GATA1 binding site1&2 KO


title: CUTRUN_HUDEP_D0_KOBS1_GATA1_Rep2

value: GATA1 binding site1 KO


title: CUTRUN_HUDEP_D0_KOBS12_GATA1_Rep1


title: Pool175_Plate12-3-E22-E6


title: Pool175_Plate12-3-E22-E17


title: CUTRUN_HUDEP_D0_KOBS1_GATA1_Rep1


title: Pool175_Plate12-3-E22-D6


title: Pool175_Plate12-3-E22-E5


title: Pool175_Plate12-3-E22-D5


title: CUTRUN_HUDEP_D0_KOWT_GATA1_Rep1


title: scRNA_EryPro_KDGATA1

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads of scRNA-seq for each sample were processed by the Cell Ranger (ver. 6.1.1) Pipeline with human reference version GRCh38, then the filtered gene expression matrices were analyzed by the Seurat package (https://github.com/satijalab/seurat)
Cells were further filter by the following criteria: (1) >1000 unique molecular identifiers (UMIs); (2) <25,000 UMIs; (3) <20% UMIs derived from the mitochondrial genome; and (4) >500 genes. The gene expression matrices were normalized and 2000 features with high cell-to-cell variation were calculated via the FindVariableFeatures function.
Normalized data underwent a linear transformation and principal component analysis (PCA) based on variable features using the RunPCA function. Graph-based clustering was performed as per gene expression profiles using the FindNeighbors and FindClusters functions with default parameters, and results were visualized using a nonlinear dimensional reduction UMAP technique running RunUMAP and DimPlot functions.
We identified shared sources of variation across Ery-Pro, knocking-down 48h of siGATA1 Ery-Pro scRNA dataset with FindIntegrationAnchors function and integrated them via anchors from the IntegrateData function with correlation dimensions of 20. Integrated data then were normalized and underwent reducing dimension as performed in individual datasets.
Assembly: hg19
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

extract_protocol:
Single cell RNA (scRNA) sequencing was performed with Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, Cat. # 1000269) targeting 10,000 cells according to the manufacturer’s guidance.
The final libraries were quantified via D1000 High Sensitivity DNA chip running on a Bioanalyzer 4250 system (Agilent). libraries were sequenced in a Novaseq 6000 (S4, PE150, Illumina) by Novogene (Beijing).

value: Erythroid progenitor

value: pooled

value: siGATA1, 48h


title: scRNA_EryPro

description: 10x Genomics


title: RNAseq_EryPro_KDGATA1_72_Rep2

data_processing:
The bulk RNA-seq data were checked the quality by FastQC (version 0.11.7, https://www.bioinformatics.babraham.ac.uk /projects/fastqc/).
Data were aligned to the hg19 reference genome using RNA STAR.
The expression level of each gene was calculated by FeatureCounts then reads counts were normalized to TPM (transcription per million)
Genes with TPM > 0 are considered as expressed genes. DESeq2 was used to calculate the differential expression genes, and fold change > 2 & FDR < 0.05 will be consider significantly different. Gene set enrichment analysis for gene ontology biological processes were performed by using clusterProfiler R package.
Assembly: hg19
Supplementary files format and content: RAW reads counts, export by FeatureCount: RNA_All_Sample_Counts.FC.txt

extract_protocol:
RNA-seq was performed with Single Cell Full Length mRNA-Amplification Kit (Vazyme, Cat. # N712) which is based on SMART-seq2 method.
In brief, two hundred cells were lysed, and reverse transcription was conducted, then 11 cycles of PCR were used to amplify transcriptome library. Quality of whole transcriptome libraries was validated using a D5000 DNA Chip run on a Bioanalyzer 4150 system (Agilent), followed by library preparation using the TruePrep DNA Library Prep Kit (Vazyme, Cat. # TD503) and custom index primers according to the manufacturer’s instructions. The final libraries were quantified using a VAHTS Library Quantification Kit (Vazyme, Cat. # NQ101) and a D1000 High Sensitivity DNA chip run on a Bioanalyzer 4250 system (Agilent). Two biological replicates per condition were sequenced in a Novaseq 6000 (S4, PE150, Illumina) by Novogene (Beijing).

value: siGATA1, 72h


title: Pool175_Plate12-3-E22-D18

value: brain

value: AI


title: RNAseq_EryPro_KDGATA1_72_Rep1


title: Pool175_Plate12-3-E22-B6

value: RSP

value: female


title: Pool175_Plate12-3-E22-C6


title: Pool175_Plate12-3-E22-C17

value: VIS

value: male


title: Pool175_Plate12-3-E22-C18


title: Pool175_Plate12-3-E22-B5


title: Pool175_Plate12-3-E22-B17


title: RNAseq_EryPro_KDCon_72_Rep2

value: siCon, 72h


title: RNAseq_EryPro_KDGATA1_48_Rep1


title: RNAseq_EryPro_KDCon_72_Rep1


title: Pool175_Plate12-3-E22-A5


title: RNAseq_EryPro_KDCon_48_Rep1

value: siCon, 48h


title: RNAseq_EryPro_KDCon_48_Rep2


title: Pool175_Plate12-2-E22-P3


title: scRNA_EryPro_KDCon

description: 10x Genomics


title: Pool175_Plate12-3-E22-A17


title: RNAseq_EryPro_KDGATA1_24_Rep1

value: siGATA1, 24h


title: RNAseq_EryPro_KDCon_24_Rep2

value: Cord Blood

value: siCon, 24h


title: RNAseq_EryPro_KDCon_24_Rep1


title: RNAseq_EryPro_KDGATA1_24_Rep2


title: Pool175_Plate12-2-E22-O4


title: Pool175_Plate12-2-E22-O16


title: RNAseq_EryPre_Rep2

value: Erythroid precursor


title: RNAseq_EryPre_Rep1


title: RNAseq_EryPro_Rep3


title: Pool175_Plate12-2-E22-N15

value: PTLp


title: Pool175_Plate12-2-E22-N16


title: Pool175_Plate12-2-E22-N3


title: RNAseq_EryPro_KDGATA1_48_Rep2

value: Erythroid progenitor


title: Pool175_Plate12-2-E22-O15


title: RNAseq_EryPro_Rep2

value: pooled


title: RNAseq_EryPro_Rep1


title: Pool175_Plate12-2-E22-M3


title: Pool175_Plate12-2-E22-P16


title: Pool175_Plate12-2-E22-M16


title: RNAseq_HSPC_Rep3


title: Pool175_Plate12-2-E22-P15


title: RNAseq_HSPC_Rep2


title: Pool175_Plate12-3-E22-A6


title: Pool175_Plate12-2-E22-L4


title: RNAseq_EryPre_Rep3


title: RNAseq_HSPC_Rep1


title: Pool175_Plate12-2-E22-L3


title: Pool175_Plate12-2-E22-L16


title: Pool175_Plate12-2-E22-N4


title: Pool175_Plate12-2-E22-K3


title: Pool175_Plate12-2-E22-K4


title: Pool175_Plate12-2-E22-K16


title: MC_EryPro_Rep2

data_processing:
The raw reads of Micro-C library were mapped with hg19 and further filtered with HiC-Pro (version 3.10.0, https://github.com/nservant/HiC-Pro). Pairs with multiple hits, MAPQ <10, singleton, dangling end, self-circle, and PCR duplicates were removed. Paired reads with distances shorter than 100 bp were also disregarded.
Correlation of replicates was calculated by Stratum-adjusted Correlation Coefficient (SCC) method with HiCRep (http://github.com/qunhualilab/hicrep) at 10 kb, 20 kb, 50 kb and 100 kb. All biological replicates were processed individually to assess quality and then combined for further analyses and visualization. The valid Micro-C contacts matrices were then normalized by using K-R method and corresponding .cool files were generated at 200 bp, 400 bp, 600 bp, 800 bp, 1 kb, 2 kb, 4 kb, 10 kb, 20 kb, 100 kb, 200 kb bin size. Visualization of .cool files were conducted on Higlass 3D genome server (http://higlass.io).
We utilize Mustache (https://github.com/ay-lab/mustache to call loops with balanced contact matrices at resolutions of 400 bp, 600 bp, 800, 1 kb, 2 kb, 4 kb, 10 kb, and 20 kb using the calling options --pThreshold 0.1 --sparsityThreshold 0.88 -–octaves 2. We then combined all loops at different resolutions. If a loop was detected at different resolutions, we retained the precise coordinates in finer resolutions. Coolpup (https://github.com/open2c/coolpuppy) has implemented the APA function for the .cool file. To further filter and classify loops, we first defined +-2.5 kb of gene TSS as promoter (P) and Non-TSS H3K27ac peaks in each stage (HSPC, Ery-Pro and Ery-Pre) as enhancers (E). GenomicInteractions (https://github.com/ComputationalRegulatoryGenomicsICL /GenomicInteractions)  was used to designated P-P, E-P and E-E loops in respective stages.
Assembly: hg19
Supplementary files format and content: mcool
Supplementary files format and content: bedpe: loop files
Library strategy: Micro-C

extract_protocol:
About 100,000 FACS-purified cells were used for each reaction. In brief, after fixation with 3mM DSG for 30 min followed by 1% formaldehyde for another 10 min, crosslinked cells were permeabilized in ice-cold Micro-C Buffer #1 (50mM NaCl, 10mM Tris-HCl pH = 7.5, 5mM MgCl2, 1mM CaCl2, 0.2% NP-40, 1x Protease Inhibitor Cocktail) for 20 minutes. Chromatin from permeabilized cells was digested by 50U micrococcal nuclease at 37°C for 10 minutes. After digestion, chromatin fragments were then subjected to dephosphorylation, phosphorylation, end-chewing process by T4 PNK and Klenow Fragment in end-repair buffers (50mM NaCl, 10mM Tris-HCl pH = 7.5, 10mM MgCl2, 100ug/mL BSA, 2mM ATP, 5mM DTT, no dNTPs) at 37°C for 30 minutes. Blunt-end and biotin incorporation was achieved by adding biotin-dATP, biotin-dCTP, dGTP, and dTTP and incubated at 25°C for 45 minutes. Chromatin was ligated by T4 DNA ligase at room temperature for 2.5 hours. Unligated ends containing biotin-dNTPs were then removed by exonuclease III in 37°C for 15 minutes.
After reverse-crosslinking, DNA was purified and gel size-selected for dinucleosomal DNA at 200 to 400 bp. DNA fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (ThermoFisher Cat. #: 65602), and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturer’s protocol. Two biological replicates per condition were sequenced in a NovaSeq 6000 (S4, PE150, Illumina) by Novogene (Beijing).


title: Pool175_Plate12-2-E22-L15


title: MC_EryPro_Rep1


title: MC_HSPC_Rep2


title: MC_EryPre_Rep1


title: MC_EryPre_Rep2


title: HiChIP_GATA1_Day12_Rep2

data_processing:
In brief, the raw reads of HiChIP library were mapped with hg19 and further filtered with HiC-Pro (version 3.10.0, https://github.com/nservant/HiC-Pro) to remove pairs with multiple hits, MAPQ <10, singleton, dangling end, self-circle, and PCR duplicates.
All biological replicates (HiChIP GATA1, generated in this paper) were processed individually to assess quality and then combined for downstream analyses and visualization (HiChIP of H3K27ac are obtained from public dataset without replicates). Correlation of replicates was calculated by Stratum-adjusted Correlation Coefficient (SCC) method with HiCRep (http://github.com/qunhualilab/hicrep) at 10 kb, 20 kb and 50 kb.
HiChIP datasets then were processed by FitHiChIP (https://github.com/ay-lab/FitHiChIP) after subset to the same valid interaction numbers. The following parameters were used to call HiChIP loops: 5,000 bp resolution, 10000-2000000 distance threshold, FDR 0.05, coverage specific bias correction, merged nearby peak to all interactions, L model for both H3K27ac and GATA1 HiChIP. To simplify the analysis, we designate H3K27ac/ GATA1 peaks in Ery-Pro/ Ery-Pre stage to represent Day5/12 H3K27ac/ GATA1 peaks respectively. GenomicInteractions (https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions) was used to designated P-P, E-P and E-E loops in respective stage.
Differential GATA1 HiChIP loops were identified via “DiffAnalysisHiChIP.r” script of FitHiChIP with parameters as follow: FDR < 0.01, FoldChangeThr > 2
Virtual 4C was performed as described before with minor modifications. In brief, the mates of reads that mapped at the viewpoints region at one side were extract, and visualization was done using average CPM signals per condition at 200 bp bin size and 2 kb window.
Assembly: hg19
Supplementary files format and content: mcool
Supplementary files format and content: loopfiles.tar.gz; compressed package containing WashU.bed.gz and .tbi
Library strategy: HiChIP

extract_protocol:
For GATA1 HiChIP, ten million Day-5 erythroid progenitors / Day-12 erythroblasts generated from ex vivo CD34+ erythroid differentiation culture were used. In brief, after fixation with 1% formaldehyde, cells were digested for 2 hours at 37°C using 375U of MboI (NEB, Cat. #R0147). After biotin filling, proximity ligation was carried out with 4000U T4 DNA Ligase (NEB, Cat. # M0202M) for 2 hours at 25°C. Sonication of re-suspended nuclei was performed by Covaris M220 sonicator. Following an overnight incubation with anti-GATA1 antibody (abcam, Cat.# ab11852), 100 µL Protein A Magnetic Beads were added at 4°C and incubated for 2 hours. Bound DNA–protein complexes were eluted and reverse-crosslinked after a series of washes.
After reverse-crosslinking, ligation fragments containing biotin were immobilized on MyOne Streptavidin C1 beads (ThermoFisher Cat.#: 65602), and the library was prepared using the Tn5 transposome DNA library preparation kit (Vazyme, Cat.# TD502) as per the manufacturer’s protocol. DNA was then subjected to double-size selection using DNA Clean Beads (Vazyme, Cat. # N411) in order to isolate fragments between 300 and 600bp. Two biological replicates per condition were sequenced in a NovaSeq 6000 (S4, PE150, Illumina) by Novogene (Beijing).

value: Erythroid precursor (Day12)


title: Pool175_Plate12-2-E22-J3


title: Pool175_Plate12-2-E22-J16


title: Pool175_Plate12-2-E22-J4


title: MC_HSPC_Rep1


title: HiChIP_GATA1_Day12_Rep1


title: Pool175_Plate12-2-E22-I3


title: HiChIP_GATA1_Day5_Rep2

value: Erythroid progenitor (Day5)


title: Pool175_Plate12-2-E22-J15

value: brain


title: HiChIP_GATA1_Day5_Rep1


title: Pool175_Plate12-2-E22-I16

value: AI


title: Pool175_Plate12-2-E22-H3

value: RSP


title: Pool175_Plate12-2-E22-I15

value: female


title: Pool175_Plate12-2-E22-H16

value: VIS


title: CapC_HUDEP_KDGATA1_Rep1

data_processing:
Capture-C analysis was performed as described before with capC-MAP (https://github.com/cbrackley/capC-MAP) software. In brief, the raw reads were trimmed with cutadapt, and mapped with hg19 reduced genome that consists of reference genome sequences adjacent to DpnII cut sites by bowtie, The read counts per bin were normalized to the sequencing depth per replicate in CPM. Visualization was performed using average CPM signals per condition at bin size 200 bp with 2 kb/ 4 kb window.
Assembly: hg19
Supplementary files format and content: bedGraph: for GATA-KD sample, viewpoints: SLC4A1, TLCD4, and METTL7A respectively
Supplementary files format and content: bedGraph: for GATABS-KO sample, viewpoin :SLC4A1, only
Library strategy: Capture-C

extract_protocol:
One million cells were used for each reaction. In brief, after fixation with 1% formaldehyde, cells were digested overnight at 37 °C using MboI (NEB, Cat. #R0147). Proximity ligation was carried out overnight at 25 °C with T4 DNA Ligase (NEB, Cat. # M0202M).
After reverse-crosslinking, DNA was purified and sheared to 300-500bp fragments using Covaris M220 sonicator, and then library preparation was performed using the DNA library preparation kit (Vazyme, Cat.# ND607) as per the manufacturer’s protocol. Two micrograms indexed and mixed library was use as input for the two rounds downstream hybridization and biotin capture with biotin labeled oligo (Supplementary Table) following with manufacture’s recommendation (Genscript, NGS09612).Two biological replicates per condition were sequenced in a NovaSeq 6000 (S4, PE150, Illumina) by Novogene (Beijing).

value: Erythroblasts

value: differentiation


title: CapC_HUDEP_KDCon_Rep1

value: siCon


title: CapC_HUDEP_KDGATA1_Rep2


title: CapC_HUDEP_KOBS12_Rep2

value: GATA1 binding site1&2 KO


title: Pool175_Plate12-2-E22-G3


title: Pool175_Plate12-2-E22-G4


title: CapC_HUDEP_KOBS1_Rep2

value: Cord Blood

value: GATA1 binding site1 KO


title: CapC_HUDEP_KOBS12_Rep1


title: Pool175_Plate12-2-E22-F4


title: CapC_HUDEP_KDCon_Rep2


title: CapC_HUDEP_KOBS1_Rep1


title: CapC_HUDEP_WT_Rep2

value: WT


title: CeA, Fasted, replicate 1

city: Munich

first: Songwei

last: He

address: Am Klopferspitz 18

country: Germany

institute: Max Planck Institute of Neurobiology

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: C57BL6 mouse brain

extract_protocol:
The mice were deeply anesthetized and then perfused with 10 mL of ice-cold "Cutting Buffer" consisting of Sucrose-HEPES containing (in mM) 110 NaCl, 2.5 KCl, 10 HEPES, 7.5 MgCl2, 25 glucose, 75 sucrose (approximately 350 mOsm/kg), and pH 7.4. All solutions and reagents were kept on ice, unless specified otherwise. The brain was removed and sliced into 300 μm sections using a vibratome in the cutting buffer. The slices were transferred into a "Dissociation Buffer" containing (in mM) 82 Na2SO4, 30 K2SO4, 10 HEPES, 10 glucose, and 5 MgCl2, with a pH of 7.4. The CeA was microdissected under a microscope. Collected tissue was transferred into 600 uL homogenization buffer containing 320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 0.1% NP-40 (70% in H2O, Sigma NP40S), 1 mM β-mercaptoethanol, and 0.4 U/µL SUPERase RNase inhibitor (Invitrogen AM2694). The tissue was homogenized in a 1 mL Wheaton Dounce, filtered through a 20-μm cell strainer (Miltenyi Biotec), and mixed with an equal volume of working solution (50% OptiPrep density gradient medium (Sigma-Aldrich), 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, and 1 mM β-mercaptoethanol). The resulting solution was transferred into a 2 mL centrifuge tube containing a 29% OptiPrep density gradient solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL SUPERase inhibitor). A 35% density solution (96 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl pH 7.8, 0.1 mM EDTA pH 8.0, 1 mM β-mercaptoethanol, 0.03% NP-40, and 0.12 U/µL SUPERase inhibitor) was slowly added below the 29% density and the nuclei were separated by ultracentrifugation using a SH 3000 rotor (20 min, 3000xg, 4 °C). 300 µL of nuclei were collected from the 29%/35% interphase and washed once with 2 mL resuspension solution (0.3% BSA, 0.2 U/µL SUPERase in PBS). The nuclei were centrifuged (300g) for 5 min and resuspended in ~30 µL resuspension solution.
Chromium Single cell 3’ v3.1 protocol, 10x Genomics
Single nuclei RNA-seq

value: C57BL6 mouse brain

tag: age

value: 8 weeks

value: fasted for 20 hours


title: Pool175_Plate12-2-E22-F3


title: CeA, Fed, replicate 3, Htr2a-Cre

value: 12 weeks

value: normal


title: CapC_HUDEP_WT_Rep1


title: CeA, Fed, replicate 1


title: TM4-4

type: RNA

city: nantong

first: Yonghui

last: Zhang

address: 19 Qixiu Road

institute: nantong university

description:
Gene expression after 24hr 10μM nPNP treatment.
Replicate 1

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized in an Agilent Hybridization Oven overnight at a rotation speed of 20 rpm at 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Scanned on an Agilent G2565CA scanner.

data_processing: Feature Extraction v10.7 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and GeneSpring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: cell line, 10μM

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described, and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: TM4 cells were exposed to 10 μM PNP for 24 h.

value: Testicular somatic cell line

value: male

value: 10uM 4-nitrophenol


title: Pool175_Plate12-2-E22-H15

value: brain

value: PTLp

value: AI

value: female


title: TM3-6

description:
Gene expression after 24hr 10μM nPNP treatment.
Replicate 3

treatment_protocol: TM3 cells were exposed to 10 μM PNP for 24 h.


title: TM4-2

description:
Gene expression after 24hr 0μM nPNP treatment.
Replicate 2

source_name: cell line, 0μM


title: TM3-4


title: TM4-6


title: TM3-3

description:
Gene expression after 24hr 0μM nPNP treatment.
Replicate 3


title: TM3-2


title: TM4-1

description:
Gene expression after 24hr 0μM nPNP treatment.
Replicate 1


title: TM4-3


title: Pool175_Plate12-2-E22-F16

value: VIS


title: TM3-5

description:
Gene expression after 24hr 10μM nPNP treatment.
Replicate 2


title: CUTRUN_EryPre_IgG

data_processing:
Raw sequence data of CUT&RUN were trimmed to barcode using trim_galore (version 0.4.4_dev) and reads were aligned to hg19 version of human genome with bowtie2 (version 2.3.4.1).
Duplicated reads were removed through Picard tool (http://broadinstitute.github.io/picard/) and the low quality of reads (MAPQ < 30) were removed. Reads with the cutoff of inset size < 120bp were selected for transcription factors occupancy and 150-500bp for H3K27ac histone modification as previous studies.
Peaks were calling by SEACR with default parameter with IgG control
The differentiated binding sites of H3K27ac and GATA1 were calculated through diffbind R package with the following parameter (FDR < 0.05) (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind). Co-binding of transcription factors was performed by bedtools and R with 1 bp overlap. The bigwig/ bedgraph files were generated through bamCoverage (https://deeptools.readthedocs.io/en/develop/)
Co-binding of transcription factors was performed by bedtools and R with 1 bp overlap. The bigwig/ bedgraph files were generated through bamCoverage (https://deeptools.readthedocs.io/en/develop/) to visualize peaks in IGV (https://software.broadinstitute.org/software/igv/), and pyGenomeTrack (https://github.com/deeptools/pyGenomeTracks).
Assembly: hg19
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

value: Erythroid precursor

value: pooled

tag: antibody

value: IgG


title: Scml2-KO_ICSI-F2_sperm_rep1

city: Shinjuku-ku

first: Akihiko

last: Sakashita

state: Tokyo

address: 35 Shinanomachi

department: Department of Molecular Biology,

country: Japan

institute: Keio University School of Medicine

description: run0133_lane9_read1_indexN701=Scml2-KO-F2-spz-rep1

data_processing:
Basecalls performed using bcl2fastq version 2.20.0.
RNA-seq  reads were aligned to the mm10 genome using Hisat2 version 2.1.0. and bowtie2 version 2.3.3.1.
Alignment output file (.bam) was input to the featureCounts function, a part of the Subread package, to quantify uniquely aligned reads on respective annotated transcript loci (NCBI RefSeq transcripts).
Read count output file (.txt) was input to the DESeq2 package version 1.16.1, to detect differentially expressed genes between two biological samples.
Genome_build: mm10
Supplementary_files_format_and_content: Read count data (.txt) from quantification step

source_name: Scml2-KO-F2 spermatozoa

growth_protocol: Mice were maintained and fed ad libitum with standard diet and water in a temperature- and light-controlled room (23℃±3℃, 12 light/12 dark cycle), according to the guidelines of the Institutional Animal Care and Use Committee at Cincinnati Children’s Hospital Medical Center and Yamanashi University, and fed ad libitum with standard diet and water

extract_protocol:
For RNA-seq analysis, total RNA from liver tissue was extracted with TRIzol reagent (Thermo Fisher Scientific) and purified it using a RNeasy Plus Mini Kit (QIAGEN) with genomic DNA elimination according to the manufacturer's instructions. For the preparation of sperm RNA-seq library, we extracted total RNA from the swim-up separated motile sperm using a RNeasy Plus Mini Kit (QIAGEN) with genomic DNA elimination according to the manufacturer's instructions.
Preparation of RNA-seq libraries were carried out using TruSeq Stranded mRNA Library Prep kit (Illumina, for liver) and SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, for spermatozoa) following manufacturer’s instructions.

treatment_protocol: Through mating between wild-type males and Scml2+/- female, Scml2-KO(-/y) male mice were born at expected ratios according to Mendel’s Law. Since Scml2-KO male mice showed infertility with abnormal sperm morphology, F1 generations from littermate wild-type and Scml2-KO males were generated using assisted reproductive technologies (ICSI and ROSI, see below). To generate F2 mice, single F1 male progenies were continuously housed with 1-to-3 C57BL/6 females, and litters were weaned at 3 weeks of age.

tag: tissue/cell type

value: spermatozoa

value: 8-12 weeks

tag: genotype/generation

tag: background strain


title: Pool175_Plate12-2-E22-G16


title: Scml2-KO_ICSI-F2_sperm_rep2

description: run0133_lane9_read1_indexN702=Scml2-KO-F2-spz-rep2


title: CUTRUN_EryPro_IgG

value: Cord Blood

value: Erythroid progenitor


title: Pool175_Plate12-2-E22-E4

value: RSP


title: Scml2-KO_ICSI-F1_liver_rep1

description: run0224_lane99_read1_indexUDI0029-UDI0029=Scml2KO-ICSI-F1-liver-rep1

source_name: Scml2-KO-F1 male liver tissue

value: liver


title: Scml2-KO_ICSI-F1_liver_rep2

description: run0224_lane99_read1_indexUDI0030-UDI0030=Scml2KO-ICSI-F1-liver-rep2


title: Ctrl_ICSI-F1_liver_rep2

description: run0224_lane99_read1_indexUDI0028-UDI0028=Ctrl-ICSI-F1-liver-rep2

source_name: Ctrl-F1 male liver tissue


title: Liver, KO6ZT22

city: College Station

first: Jerome

last: Menet

state: Texas

address: Texas A&M University Biology Department 3258 TAMU College Station, TX 77843

department: Biology

institute: Texas A&M University

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT22; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed

data_processing:
Libraries were sequenced on an Illumina NextSeq. Base calling and demultiplexing were performed with the accompanying software
Sequenced reads were trimmed to remove the first 12nt, trailing and embedded polyA sequences, poor quality bases at the 3' end, and removed if under 36nt
Trimmed reads were aligned to mm10 transcriptome using STAR v2.4.2a with options "--outSAMstrandField intronMotif --quantMode GeneCounts --outFilterIntronMotifs RemoveNoncanonical"
Read counts were quantified to raw values with the R package GenomicRanges
Genes over 10 reads total for 70% of the samples were kept and TMM-normalized with the R package edgeR
Generation of BED files: All 36 WT (total RNA) samples were trimmed to their 3’-most mapped nucleotide and formed into peaks using two commands from HOMER “makeTagDirectory -precision 3 -totalReads all -fragLength 1 -keepAll” and  “findPeaks -strand separate -tbp 0 -fragLength 1 -size 10 -minDist 25 -ntagThreshold 2 –region”
All reads were then further filtered to those with only 6 or more adenine residues in a row and where the 20 genomic bases downstream were not adenine rich, resulting in reads that sequenced part of the poly(A) tail
This second set of reads then took the 3’ most read that was not part of the poly(A) tail and used to form peaks using HOMER with “makeTagDirectory -precision 3 -totalReads all -fragLength 1 -keepAll” and “findPeaks -strand separate -tbp 0 -fragLength 1 -size 10 -minDist 25 -ntagThreshold 5 –region”
The two resulting peak files were concatenated resulting in 86780 prospective PAS, and PAS were then assigned to genes with summarizeOverlaps from the R package GenomicRanges
For all 144 samples, read counts per PAS were quantified to raw values with the R package GenomicRanges, and any PAS with over 10 reads total for 70% of the samples were kept and TMM-normalized with the R package edgeR
Finally, PAS were filtered by both their total expression and relative expression to their parent gene based on gene expression in the 36 WT samples; any PAS under 0.5 TMM or under 0.5% of the total expression for its gene was discarded. PAS under 5 TMM or less than 10% of the transcript total was kept if it was within 75nt of a PAS from PolyA_DB. This resulted in a total of 29199 high-confidence PAS
Genome_build: mm10, GRCm38.p5
Supplementary_files_format_and_content: Tab-delimited text files with RAW (non-normalized and unfiltered) or TMM values for each gene and sample

source_name: Liver

growth_protocol: Male C57BL/6J WT and Bma1-/- mice were housed in a 12 hour light:12 hour dark facility with ad libitum access to water and food

extract_protocol:
RNA WAS extracted using TRIzol reagent, treated with DNaseI, and purified with an acid phenol-chloroform extraction
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used for all samples
3' RNA-Seq

tag: strain

value: Liver

tag: time

tag: fraction

value: total RNA


title: CUTRUN_HSPC_IgG

tag: tissue


title: Pool175_Plate12-2-E22-E3

tag: source


title: Liver, KO6ZT18

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT18; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Pool175_Plate12-2-E22-E16

tag: target

value: male


title: Liver, KO6ZT14

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT14; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, KO6ZT10

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT10; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: CUTRUN_HUDEP_KOBS12_GATA1_Rep1

value: GATA1 binding site1&2 KO


title: Pool175_Plate12-2-E22-D4

value: brain

tag: Sex


title: CUTRUN_HUDEP_KOBS1_GATA1_Rep2

tag: cell line

value: GATA1 binding site1 KO


title: Liver, KO6ZT06

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT06; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, KO6ZT02

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT02; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Ctrl_ICSI-F1_liver_rep1

description: run0224_lane99_read1_indexUDI0027-UDI0027=Ctrl-ICSI-F1-liver-rep1


title: Liver, KO5ZT22


title: Pool175_Plate12-2-E22-D3

value: AI

value: female


title: CUTRUN_HUDEP_KOBS1_GATA1_Rep1

tag: cell type


title: Liver, KO5ZT18

tag: genotype


title: TM4-5

value: Testicular somatic cell line

value: 10uM 4-nitrophenol


title: Pool175_Plate12-2-E22-C4


title: CUTRUN_HUDEP_KOWT_GATA1_Rep2

value: WT


title: Liver, KO5ZT14


title: Liver, KO5ZT06


title: CUTRUN_HUDEP_KOBS12_GATA1_Rep2


title: Pool175_Plate12-2-E22-B4


title: CUTRUN_HUDEP_KOWT_GATA1_Rep1


title: Liver, KO4ZT22


title: Liver, KO5ZT02


title: Liver, KO4ZT18


title: Pool175_Plate12-2-E22-B3


title: CUTRUN_HUDEP_KDGATA1_GATA1_Rep2

value: pooled


title: Liver, KO4ZT14


title: TM3-1


title: Liver, KO4ZT06


title: Liver, KO4ZT10


title: Liver, KO4ZT02


title: Pool175_Plate12-2-E22-A4


title: CUTRUN_HUDEP_KDGATA1_GATA1_Rep1


title: CUTRUN_HUDEP_KDCon_GATA1_Rep2


title: Pool175_Plate12-2-E22-C3


title: Liver, KO5ZT10


title: Liver, KO3ZT22


title: CUTRUN_HUDEP_KDCon_GATA1_Rep1


title: Liver, KO3ZT18


title: Pool175_Plate12-1-E22-P2


title: Pool175_Plate12-1-E22-P14

value: PTLp


title: Liver, KO3ZT02


title: Liver, KO2ZT22


title: Liver, KO3ZT06


title: CUTRUN_EryPre_RUNX1_Rep1

value: Cord Blood

value: Erythroid precursor


title: CUTRUN_EryPro_RUNX1_Rep2

value: Erythroid progenitor


title: Pool175_Plate12-1-E22-P1

value: RSP


title: Liver, KO2ZT14

value: Liver


title: CUTRUN_EryPro_RUNX1_Rep1


title: Liver, KO3ZT10

value: total RNA


title: Liver, KO2ZT10


title: Pool175_Plate12-1-E22-P13


title: Pool175_Plate12-1-E22-O2


title: Pool175_Plate12-2-E22-A16

value: VIS

value: male


title: CUTRUN_HSPC_RUNX1_Rep2


title: Liver, KO2ZT02


title: Liver, KO3ZT14


title: CUTRUN_EryPre_RUNX1_Rep2


title: Liver, KO1ZT18


title: Liver, KO1ZT22


title: Pool175_Plate12-1-E22-O1

value: brain


title: CUTRUN_HSPC_RUNX1_Rep1


title: CUTRUN_EryPre_ETV6_Rep2


title: Liver, KO1ZT14


title: Liver, KO1ZT10


title: Liver, KO2ZT18


title: CUTRUN_EryPre_ETV6_Rep1


title: Liver, KO1ZT06


title: Pool175_Plate12-1-E22-N14


title: Liver, KO1ZT02


title: Pool175_Plate12-2-E22-B16


title: Pool175_Plate12-1-E22-N1


title: CUTRUN_EryPro_ETV6_Rep2


title: Pool175_Plate12-1-E22-M2


title: Liver, PO6ZT18

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT18; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed

extract_protocol:
Polysomal RNA was extracted from frozen tissue by crushing under LN2 in a polysome buffer containing 100ug/mL cycloheximide, ultracentrifuged at 41000rpm in a sucrose gradient, and fractionated. Fractions contains polysomal RNA then underwent the RNA extraction procedure detailed below
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used for all samples
3' RNA-Seq

value: Wild-type

value: polysomal RNA


title: Liver, PO6ZT14

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT14; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, PO6ZT10

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT10; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, PO6ZT06

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT06; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, PO6ZT02

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT02; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: CUTRUN_HSPC_ETV6_Rep2


title: Pool175_Plate12-1-E22-M13

value: AI

value: female


title: Pool175_Plate12-1-E22-O14


title: CUTRUN_HSPC_ETV6_Rep1


title: Liver, KO2ZT06


title: Pool175_Plate12-1-E22-M1


title: Pool175_Plate12-1-E22-L14


title: CUTRUN_EryPre_CEBPA_Rep2

value: CEBPA


title: Pool175_Plate12-1-E22-L13


title: Liver, PO5ZT22

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT22; polysomal RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, PO5ZT14


title: Liver, PO5ZT02


title: Liver, PO6ZT22


title: Liver, PO4ZT22


title: CUTRUN_EryPro_ETV6_Rep1


title: Liver, PO4ZT18


title: Liver, PO5ZT18


title: Liver, PO4ZT14


title: CUTRUN_EryPro_CEBPA_Rep2


title: Liver, PO4ZT10


title: CUTRUN_EryPre_CEBPA_Rep1


title: Liver, PO5ZT06


title: Liver, PO4ZT06


title: CUTRUN_HSPC_CEBPA_Rep2


title: Pool175_Plate12-1-E22-L1


title: Liver, PO4ZT02


title: Pool175_Plate12-1-E22-K2


title: CUTRUN_HSPC_CEBPA_Rep1


title: Pool175_Plate12-1-E22-K13


title: Liver, PO5ZT10


title: Liver, PO3ZT14


title: Liver, PO3ZT22


title: Liver, PO3ZT18


title: CUTRUN_EryPre_GATA2_Rep2


title: Liver, PO3ZT10


title: Liver, PO3ZT06


title: CUTRUN_EryPro_CEBPA_Rep1


title: Liver, PO3ZT02


title: Pool175_Plate12-1-E22-J1


title: CUTRUN_EryPro_GATA2_Rep2


title: Pool175_Plate12-1-E22-J13


title: Liver, PO2ZT18


title: CUTRUN_EryPre_GATA2_Rep1


title: Liver, PO2ZT22


title: Liver, PO2ZT14


title: Pool175_Plate12-1-E22-I2


title: Liver, PO2ZT10


title: CUTRUN_EryPro_GATA2_Rep1


title: Pool175_Plate12-1-E22-I14


title: Liver, PO2ZT06


title: CUTRUN_HSPC_GATA2_Rep2


title: Liver, PO2ZT02


title: Pool175_Plate12-1-E22-K1


title: CUTRUN_HSPC_GATA2_Rep1


title: Pool175_Plate12-1-E22-I13


title: Liver, PO1ZT14


title: Pool175_Plate12-1-E22-I1


title: Liver, PO1ZT18


title: CUTRUN_EryPre_GATA1_Rep2


title: Pool175_Plate12-1-E22-H2


title: Liver, PO1ZT06


title: Liver, NU6ZT14

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT14; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed

extract_protocol:
Nuclear RNA was extracted from frozen tissue by homogenization followed by washing twice with hypotonic buffer and then centrifuged on a sucrose cushion at 20000g. Nuclei were isolated and then underwent the RNA extraction procedure detailed below
3' mRNA libraries were prepared following manufacturer instructions for Lexogen's QuantSeq 3' mRNA-Seq Kit. 2μg input total RNA was used for all samples
3' RNA-Seq

value: nuclear RNA


title: Liver, NU6ZT18

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT18; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Pool175_Plate12-1-E22-H13


title: CUTRUN_EryPro_GATA1_Rep2

value: pooled


title: Liver, NU6ZT10

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT10; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Pool175_Plate12-1-E22-G2


title: Liver, PO1ZT22


title: Pool175_Plate12-1-E22-H14

value: PTLp


title: Liver, NU6ZT22

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT22; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, PO1ZT02


title: Liver, NU5ZT22


title: Pool175_Plate12-1-E22-G14


title: Liver, NU6ZT06

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT06; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: CUTRUN_HSPC_GATA1_Rep2

value: Cord Blood


title: CUTRUN_EryPro_GATA1_Rep1


title: Liver, PO1ZT10


title: Liver, NU5ZT18


title: Pool175_Plate12-1-E22-G13


title: Liver, NU5ZT14


title: CUTRUN_HSPC_GATA1_Rep1


title: Liver, NU5ZT06


title: Liver, NU5ZT02

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT02; nuclear RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, NU5ZT10


title: CUTRUN_EryPre_H3K27ac_Rep1

value: Erythroid precursor


title: CUTRUN_EryPre_GATA1_Rep1


title: Pool175_Plate12-1-E22-F2


title: Pool175_Plate12-1-E22-G1


title: Liver, NU6ZT02


title: Liver, NU4ZT22


title: CUTRUN_EryPro_H3K27ac_Rep2

value: Erythroid progenitor


title: Liver, NU4ZT18


title: Pool175_Plate12-1-E22-F14


title: Liver, NU4ZT14


title: CUTRUN_EryPro_H3K27ac_Rep1


title: Liver, NU4ZT10


title: Pool175_Plate12-1-E22-F13


title: CUTRUN_HSPC_H3K27ac_Rep2


title: CUTRUN_EryPre_H3K27ac_Rep2


title: Liver, NU4ZT06


title: Liver, NU4ZT02


title: Pool175_Plate12-1-E22-F1

value: RSP


title: CUTRUN_HSPC_H3K27ac_Rep1


title: Liver, NU3ZT22

value: Liver


title: Liver, NU3ZT18


title: Liver, NU3ZT14


title: iPSC Cell Line B, Methadone Treatment, Biological Replicate 4 [BTREAT4]

first: Gabriel

last: Haddad

state: California

department: Pediatrics

institute: University of California, San Diego

data_processing:
Read alignment to the hg19 genome was performed through the RNA-Seq Alignment (STAR, Version 2.0.2) application in the Illumina BaseSpace Sequence Hub.
Mapped reads were assigned to genomic meta-features (genes) using the Rsubread (Version 2.6.4) package featureCounts in R.
Expression level filtering was performed using the edgeR (Version 3.34.1) function filterbyExpr, using default parameters.
Assembly: hg19
Supplementary files format and content: A comma separated values (CSV) file including CPM values per gene for each sequenced sample.

source_name: Cortical organoids

growth_protocol: Human cortical organoids were generated and maintained using a protocol previously described by Muotri and colleagues (Trujillo et al., 2018; Trujillo and Muotri, 2018). iPSCs used to form organoids were derived from two healthy individuals, and were passaged an equal number of times before beginning 3D cultures.

extract_protocol:
RNA was harvested using the Direct-Zol Miniprep Plus Kit (Zymo) according to the manufacturer’s instructions.
PolyA+ selected libraries were prepared with the TruSeq mRNA Stranded Library Prep Kit with TruSeq UDI96 indexed adaptors (Illumina).

treatment_protocol: Human cortical organoids were treated with 1μM methadone (Sigma) or a vehicle of nuclease-free water (Invitrogen) for 50 days, beginning at Day 9 of differentiation and ending at Day 60. Methadone or vehicle were added to the media each day of media change according to the normal differentiation protocol.

value: Cortical organoids

value: B

value: Methadone Treatment


title: Pool175_Plate12-1-E22-E2

value: brain


title: Liver, NU3ZT02

value: Wild-type


title: Liver, NU3ZT06


title: Pool175_Plate12-1-E22-L2


title: iPSC Cell Line B, Methadone Treatment, Biological Replicate 2 [BTREAT2]


title: Liver, NU2ZT22


title: Liver, NU2ZT18


title: Liver, NU3ZT10


title: Pool175_Plate12-1-E22-E1


title: Pool175_Plate12-1-E22-E14


title: iPSC Cell Line B, Methadone Treatment, Biological Replicate 3 [BTREAT3]


title: Liver, NU2ZT10


title: Pool175_Plate12-1-E22-D14


title: Pool175_Plate12-1-E22-D13


title: Liver, NU2ZT14


title: iPSC Cell Line B, Methadone Treatment, Biological Replicate 1 [BTREAT1]


title: Liver, NU2ZT02


title: Liver, NU1ZT22


title: iPSC Cell Line B, Control (Vehicle), Biological Replicate 3 [BCTRL3]

value: Control (Vehicle)


title: Pool175_Plate12-1-E22-D1

value: AI


title: Pool175_Plate12-1-E22-C2

value: female


title: Liver, NU1ZT18


title: iPSC Cell Line B, Control (Vehicle), Biological Replicate 2 [BCTRL2]


title: Pool175_Plate12-1-E22-C14


title: Liver, NU1ZT06


title: Liver, NU1ZT02


title: iPSC Cell Line B, Control (Vehicle), Biological Replicate 1 [BCTRL1]


title: Liver, WT6ZT18

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT18; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed

value: total RNA


title: Pool175_Plate12-1-E22-C1


title: Liver, WT6ZT22

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT22; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: iPSC Cell Line A, Methadone Treatment, Biological Replicate 3 [ATREAT3]

value: A


title: Liver, NU1ZT10

value: nuclear RNA


title: Pool175_Plate12-1-E22-C13

value: PTLp


title: Liver, WT6ZT06

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT06; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, WT6ZT14

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT14; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: Liver, WT6ZT10

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT10; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: iPSC Cell Line A, Methadone Treatment, Biological Replicate 1 [ATREAT1]


title: Liver, NU2ZT06


title: iPSC Cell Line A, Control (Vehicle), Biological Replicate 3 [ACTRL3]


title: Liver, WT5ZT22


title: Pool175_Plate12-1-E22-B13


title: Liver, WT6ZT02

description:
Fed under ad-libitum feeding paradigm; sacrificed at ZT02; total RNA
Gene_RAW_Table.txt
Gene_TMM_Table.txt
PAS_RAW_Table.txt
PAS_TMM_Table.txt
PAS_unfiltered.bed
PAS_filtered.bed


title: iPSC Cell Line B, Control (Vehicle), Biological Replicate 4 [BCTRL4]


title: Liver, WT5ZT18


title: iPSC Cell Line A, Control (Vehicle), Biological Replicate 2 [ACTRL2]


title: Liver, WT5ZT14


title: Pool175_Plate12-1-E22-A2


title: Pool175_Plate12-1-E22-B1


title: Liver, WT5ZT06


title: iPSC Cell Line A, Methadone Treatment, Biological Replicate 2 [ATREAT2]


title: iPSC Cell Line A, Control (Vehicle), Biological Replicate 1 [ACTRL1]


title: Pool175_Plate12-1-E22-B14


title: Liver, WT5ZT02


title: Liver, WT4ZT22


title: Pool175_Plate12-1-E22-A14


title: Liver, WT4ZT18


title: Scml2-KO_ICSI-F1_sperm_rep2

source_name: Scml2-KO-F1 spermatozoa

value: spermatozoa

value: 8-12 weeks


title: Pool175_Plate12-1-E22-A1


title: Pool175_Plate12-1-E22-A13


title: Liver, WT4ZT14


title: Scml2-KO_ICSI-F1_sperm_rep1


title: Ctrl_ICSI-F1_sperm_rep1

source_name: Ctrl-F1 spermatozoa


title: Liver, WT4ZT06


title: Liver, WT4ZT10


title: Pool175_Plate11-6-K20-P11

source_name: brain

value: AUD


title: Ctrl_ICSI-F1_sperm_rep2


title: Pool175_Plate11-6-K20-P12


title: Liver, WT5ZT10


title: RRBS: t081o

city: Moscow

first: Alexey

middle: Igorevich

last: Kalinkin

state: Russia

address: Moskvorechie st., 1

department: Epigenetics

country: Russia

institute: RCMG

data_processing:
Basecalls performed using Ion Torrent Suite 4.0
XmaI-RRBS reads were aligned to the hg19 genome assembly using Bismark v0.12.2 with bowtie2 v2.2.3 with settings --non_directional -L 24 --rdg 0,3 --rfg 0,3. Cutadapt 3.4 was used to clean sequencing adapters.
Data were filtered to remove artificial methylation using custom script
Methylation state called using bismark_methylation_extractor
Assembly: hg19
Supplementary files format and content: .cov files were generated using bismark_methylation_extractor

source_name: Breast

extract_protocol:
Phenol:chloroform protocol after proteinase K treatment
XmaI-RRBS protocol as in: Tanas AS, Borisova ME, Kuznetsova EB et al. Rapid and affordable genome-wide bisulfite DNA sequencing by XmaI-reduced representation bisulfite sequencing. Epigenomics. 9 (6), 833-847 (2017).

value: Tissue

value: Breast Cancer

tag: patient

tag: chemotherapy status

value: post-chemo

tag: surgery status

value: Post-surgery

tag: t (tumor)

tag: n (node)

tag: m (metastasis)


title: RRBS: t083o


title: RRBS: tko096o


title: RRBS: t072o


title: RRBS: tsh054o


title: Liver, WT4ZT02

value: Liver


title: Pool175_Plate11-6-K20-O24

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.) or snmC-seq3 protocol described in (Liu, H. et al., Biorxiv. 2023:2023-04.). The libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: brain


title: Liver, WT3ZT22

value: Wild-type


title: RRBS: t071o


title: RRBS: tch056o


title: Liver, WT3ZT18


title: Liver, WT3ZT14


title: RRBS: t070o


title: RRBS: t069o


title: Pool175_Plate11-6-K20-O12


title: Pool175_Plate11-6-K20-O11


title: Liver, WT3ZT10


title: RRBS: t068o


title: Liver, WT3ZT06


title: Pool175_Plate11-6-K20-N24


title: RRBS: t066o


title: Liver, WT3ZT02


title: RRBS: t065o


title: pfc, RES, scRNAseq

city: Chongqing

first: Peng

last: Xie

address: 1st, Youyi Street

institute: The first affiliated hospital of Chongqing medical university

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Read alignment and count summarization were performed using CellRanger
Nucleus expressing fewer than 200 genes and cells with a mitochondrial UMI rate higher than 20% were excluded. Mitochondrial genes were removed from the expression matrix but used for cell expression regression to avoid cell status effect in clustering analysis and marker analysis of each cluster.
Assembly: Mfa5.0
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

organism: Macaca fascicularis

source_name: prefrontal cortex

extract_protocol:
single nucleus were collected using   the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: prefrontal cortex

value: prefrontal cortex cells


title: pfc, DL, scRNAseq

description: 10x Genomics

value: female


title: Pool175_Plate11-6-K20-N12

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2 & 3

value: AI


title: Pool175_Plate11-6-K20-N11


title: Liver, WT2ZT22

value: total RNA


title: Pool175_Plate11-6-K20-O23


title: RRBS: t064o


title: pfc, HC, scRNAseq

description: 10x Genomics


title: Pool175_Plate11-6-K20-M24


title: Liver, WT2ZT18


title: H7

description: ST transcriptomes

source_name: Dorsolateral prefrontal cortex

growth_protocol: The M. fascicularis facilities, housing and primate laboratories used in this study are accredited by the Association for Assessment and Accreditation of Laboratory Animal Care.Animals were housed in an environmentally controlled facility (22 ± 1 °C temperature, 50 ± 5% relative humidity, and 12 h light/12 h dark cycle with lights on at 7:00). Behaviors were videotaped with webcams around the enclosures at daytime without human interference.

extract_protocol:
single nucleus were collected using   the 10X Genomics Chromium Controller Instrument and Chromium Single Cell 3’ V3.1 Reagent Kits (10X Genomics, Pleasanton, USA) .ST transcriptomes were collected using 10X Chromium Spatial Gene Expression Slide & Reagent Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Dorsolateral prefrontal cortex

value: Dorsolateral prefrontal cortex cells

tag: group

value: healthy control


title: RRBS: t062o


title: Pool175_Plate11-6-K20-N23


title: Liver, WT2ZT14

tag: strain


title: RRBS: t061o


title: Pool175_Plate11-6-K20-L24


title: Liver, WT2ZT10

tag: time


title: S2_6_NS

city: jinan

first: hai

middle: yan

last: liu

address: huaxianchanglu

institute: bohao

description: Competing endogenous RNA expression in decidua derived from cesarean sections

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8 x 60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Decidua derived from mice of LPS treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

extract_protocol: The total RNA of decidua was extracted using Trizol.

treatment_protocol: LPS (100 μg/kg body weight) was intraperitoneally injected into the mice at 14 days of pregnancy. PTB has been found after approximately 48 h of treatment. When bleeding found in vagina, the decidua  were selected in asepsis condition. The decidua were analyzed for expression of specific genes compared with cesarean sections.

tag: developmental stage

value: 17 days of pregnancy

value: Decidua


title: S2_5_NS

tag: tissue


title: H3

description: ST transcriptomes


title: H6

description: ST transcriptomes


title: Liver, WT2ZT06

tag: fraction


title: Pool175_Plate11-6-K20-L12

tag: source

value: AUD

tag: target


title: Pool175_Plate11-6-K20-L23

tag: Sex


title: RRBS: t060o

tag: cell type

value: Tissue

value: Breast Cancer


title: Pool175_Plate11-6-K20-L11


title: RRBS: t059o

value: post-chemo

value: Post-surgery


title: D6

description: ST transcriptomes

value: depressive-like


title: S1_2_1_NS

source_name: Decidua derived from mice of cesarean sections


title: S1_2_2_NS


title: S1_1_NS


title: Pool175_Plate11-6-K20-K24

value: brain


title: Liver, WT2ZT02

tag: genotype

value: Wild-type

value: Liver


title: Liver, WT1ZT22


title: RRBS: t055o

tag: patient


title: D7

description: ST transcriptomes


title: S2_4_NS


title: R5

description: ST transcriptomes

value: resilient in low social rank


title: RRBS: t054o

tag: chemotherapy status


title: Pool175_Plate11-6-K20-K23

value: AI

value: female


title: Liver, WT1ZT14

value: total RNA


title: Liver, WT1ZT18


title: R4

description: ST transcriptomes

value: Dorsolateral prefrontal cortex

value: Dorsolateral prefrontal cortex cells


title: Pool175_Plate11-6-K20-K12


title: R3

description: ST transcriptomes


title: RRBS: tsh042

value: pre-chemo

tag: surgery status

value: Pre-surgery


title: Pool175_Plate11-6-K20-K11

value: AUD


title: RRBS: tk069

value: Tissue

tag: t (tumor)


title: Liver, WT1ZT06


title: Pool175_Plate11-6-K20-J23


title: Liver, WT1ZT10


title: D6-dpfc

description: single nucleus RNA-Seq


title: RRBS: t042

value: Breast Cancer

tag: n (node)


title: D5-dpfc

description: single nucleus RNA-Seq


title: D7-dpfc

description: single nucleus RNA-Seq


title: Pool175_Plate11-6-K20-J12


title: Liver, WT1ZT02


title: RRBS: tch040

tag: m (metastasis)


title: RRBS: t046


title: Pool175_Plate11-6-K20-J24


title: D4-dpfc

description: single nucleus RNA-Seq

tag: group


title: RRBS: t031


title: mHLC3

city: Phiadelphia

first: Corbett

middle: T

last: Berry

address: 3800 Spruce St

institute: University of Pennsylvania

description: Passage 3

data_processing:
Transcript counting with salmon (v0.14.1)
Sumarize to genes with Tximport (v1.16.0)
normalization/differential testing with DESeq2 (v1.28.1)
Genome_build: EnsDb.Hsapiens.v86

source_name: DKC1 A353V iPSCs

growth_protocol: Every iPSC lines were maintained on vitronectin (Stem cell Tech.) coated plate using StemMACS™ iPS-Brew XF medium (Miltenyi Biotec). The medium was changed every day.

extract_protocol:
Total RNAs were isolated from HBs (Day 10) and HEPs (Day 17) using TRIzol™ Reagent (Thermo Fisher Scientific) and cleaned up with RNA Clean & Concentrator-5 kit (Zymo Research).
Isolated RNAs were submitted to Genewiz sequencing facility for RNA-sequencing. All submitted samples had at least 9.5 of RNA integrity number (RIN). Libraries were prepared by Poly A selection from total RNA and sequenced using HiSeq 2 x 150 bp sequencing (Illumina).

treatment_protocol: iPSCs were differentiatied into HLCs by previous protocol with some modification as followed. iPSCs were replated onto matrigel coated plate at 0.8x105 cells/cm2 in StemMACS™ iPS-Brew XF medium (Miltenyi Biotec) with 10μM Y-27632 (Selleck Chemicals). After 1day, medium was changed to RPMI-1640 (Lonza) containing 50 ng/ml Activin A (PeproTech), 0.5 mg/ml bovine serum albumin (Sigma-Aldrich), 1x B27 supplement (Gibco), and 0.5 mM sodium butylate (SB, Sigma). Then concentration of SB in this medium was changed to 0.1 mM for 4 days culture, in order to induce definitive endoderm differentiation. For the HB induction, definitive endoderm cells were cultured in RPMI-1640 (Lonza) supplemented with 10 ng/mL HGF (Peprotech), and 10 ng/mL FGF4 (Peprotech), 0.5 mg/ml bovine serum albumin (Sigma-Aldrich), and 1x B27 supplement (Gibco) for 5 days. Then, HB stage cells were treated Hepatocyte Culture Medium (without EGF supplement, Lonza) with 10 ng/mL HGF, 10 ng/mL OSM (PeproTech), and 0.1 mM Dexamethasone (Dex). For the inhibition of signaling pathways in differentiating DKC1 mutant HEPs, inhibitors were added to HB induction medium (Day 5 – Day 10). Cell cultures were maintained in a 37 °C, 4% CO2, and 5% O2 environment, and medium was changed every day.

tag: amino acid 353

value: Val

tag: differentiation

value: HEP

tag: replicate


title: D3-dpfc

description: single nucleus RNA-Seq

tag: tissue

value: depressive-like


title: mHLC2

description: Passage 2


title: Liver, NU1ZT14

tag: strain

tag: time

tag: fraction

value: nuclear RNA


title: D2-dpfc

description: single nucleus RNA-Seq


title: Pool175_Plate11-6-K20-J11

value: brain

tag: source

tag: target

tag: Sex


title: Pool175_Plate11-6-K20-I12


title: Pool175_Plate11-6-K20-I23


title: RRBS: t057o

tag: cell type

tag: patient

value: post-chemo

value: Post-surgery


title: RRBS: t029

tag: chemotherapy status

tag: surgery status


title: mHLC4

description: Passage 4


title: D1-dpfc

description: single nucleus RNA-Seq


title: Pool175_Plate11-6-K20-H23

value: AI


title: RRBS: t018

tag: t (tumor)

tag: n (node)


title: cHLC4

description: Passage 4

value: Ala


title: R5-dpfc

description: single nucleus RNA-Seq

tag: group

value: resilient in low social rank


title: Pool175_Plate11-6-K20-H12

value: female


title: RRBS: t080

tag: m (metastasis)


title: R4-dpfc

description: single nucleus RNA-Seq

value: Dorsolateral prefrontal cortex

value: Dorsolateral prefrontal cortex cells


title: RRBS: t025

value: pre-chemo

value: Pre-surgery


title: RRBS: t030

value: Tissue


title: RRBS: t023

value: Breast Cancer


title: Pool175_Plate11-6-K20-G24

value: AUD


title: mHLC1

description: Passage 1

tag: amino acid 353

value: Val

tag: differentiation

value: HEP


title: R3-dpfc

description: single nucleus RNA-Seq

tag: tissue


title: Pool175_Plate11-6-K20-G23


title: H7-dpfc

description: single nucleus RNA-Seq

value: healthy control


title: RRBS: t045


title: R1-dpfc

description: single nucleus RNA-Seq


title: mHB3

description: Passage 3

value: HB

tag: replicate


title: mHB4

description: Passage 4


title: mHB2

description: Passage 2


title: Pool175_Plate11-6-K20-F24

value: brain


title: cHLC3

description: Passage 3


title: H6-dpfc

description: single nucleus RNA-Seq


title: RRBS: t032


title: Pool175_Plate11-6-K20-H11


title: Pool175_Plate11-6-K20-F23


title: RRBS: t017


title: H5-dpfc

description: single nucleus RNA-Seq


title: RRBS: t090


title: cHLC1

description: Passage 1


title: cHB4

description: Passage 4


title: R2-dpfc

description: single nucleus RNA-Seq


title: cHB3

description: Passage 3


title: RRBS: t022


title: cHLC2

description: Passage 2


title: RRBS: t089


title: Pool175_Plate11-6-K20-G12


title: H4-dpfc

description: single nucleus RNA-Seq


title: H3-dpfc

description: single nucleus RNA-Seq


title: CD11b+F4/80+ cells, Vegfr-3ΔLBD/ΔLBD, JEV-infected,rep2

city: Shanghai

first: Linlin

last: Qi

state: Shanghai

address: 333 Nanchen Road, Baoshan District

institute: Shanghai University

data_processing:
Trinity (https://github.com/trinityrnaseq/trinityrnaseq/wiki)
The raw paired end reads were trimmed and quality controlled by fastp with default parameters. Then clean data from the samples were used to do de novo assembly with Trinity
To increase the assembly quality, all the assembled sequencs were filtered by CD-Hit and transrate.
The raw reads were deposited into the NCBI database (Mus_musculus. GRCm38.89). Use Cufflinks or StringTie software to splice each sample.
BUSCO ( Benchmarking Universal Single-Copy Orthologs， http://busco.ezlab.org )
Assembly: GRCm38.89
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: CD11b+F4/80+ cells

growth_protocol: CD11b+F4/80+ cells were isolated from the brain of the PBS- or JEV- injected mice 5 days post infection by FACS

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
The sequencing libraries were constructed according to the manufacturer’s protocols.Purified amplicons were pooled in equimolar and sequenced on an Illumina MiSeq platform (Illumina, San Diego, USA) according to the standard protocols by Majorbio Bio-Pharm Technology Co. Ltd. (Shanghai, China).

treatment_protocol: Vegfr-3ΔLBD/ΔLBD mice (KO) and littermate WT mice were intravenously injected with JEV (7×106 TCID50)

value: CD11b+F4/80+ cells

value: macrophages

tag: genotype

tag: treatment

value: JEV-infected

tag: time point

value: Day 5


title: CD11b+F4/80+ cells, Vegfr-3ΔLBD/ΔLBD, JEV-infected,rep1


title: cHB2

description: Passage 2

value: Ala


title: RRBS: t014


title: cHB1

description: Passage 1


title: H2-dpfc

description: single nucleus RNA-Seq

value: Dorsolateral prefrontal cortex


title: CD11b+F4/80+ cells,WT, JEV-infected,rep1

value: WT


title: RRBS: t021

value: pre-chemo


title: H1-dpfc

description: single nucleus RNA-Seq

value: Dorsolateral prefrontal cortex cells


title: mHB1

description: Passage 1


title: B5_CT16_130517liver_12am_AR4_1 (CT16_rep2)

status: Public on May 05 2023

city: Suita

first: Arthur

last: Millius

state: Osaka

address: iFReC 6F

department: iFReC

institute: Osaka University

description:
AR4
processed data for this replicate is in file B5_readsByFragment.txt on GSM6070364.

data_processing:
After quality control using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reads were clipped using fastx_clipper (with parameters -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n) and processed with fastx_trimmer (with parameters -Q33 -f 2), both from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
We then used Bowtie 2.1.0.0 (Langmead and Salzberg, 2012) to map the resulting reads to rRNA sequences. Reads that were successfully aligned to these sequences are discarded, and only unaligned reads were used for downstream analysis.
These reads that did not align to rRNA were mapped to the mouse mm10 reference genome. Using samtools 0.1.19.0 and egrep, we extracted reads for which an exact match between the sequence and the reference could be found.
Using reads aligned to a unique location, we then calculated transcript density profiles. This relies on assignment each footprint alignment (i.e., each read) to a specific A site nucleotide based on the length of the fragment. The initial assumption is that this site will be close to the center of the read. To calculate the best offset, we considered a metagene that captured all reads and their position relative to the start site and calculated the offset that optimized phasing. The best results were obtained when the offset from the 5' end of the alignment was: 26 nt long, +13; 27-28 nt long, +15; 29-30 nt long, +16; 31-32 nt long, +17. Reads shorter than 26 or longer than 32 nucleotides were discarded. Using this offset, we assigned each read to a unique nucleotide, and constructed transcript density profiles by counting the number of reads whose A site was assigned to each nucleotide position.
For each transcript, non-overlapping five-codon windows were then tiled across the coding region and the transcript was considered well-translated if it had a median value of at least 2 reads per window (excluding the excluding the first fifteen and the last five codons).Using all well-translated transcripts, we created file where each transcript is represented across all samples by its RPKM value. We used this file in JTK_CYCLE (Hughes et al., 2010) to identify all rhythmic transcripts with a circadian period (i.e., period between 20 and 28 h). We used a threshold of 0.05 on the adjusted p-value to assess significance.
Assembly: mm10
Supplementary files format and content: Columns in XX_readsbyFragment.txt are RefSeqID, length of 5'UTR, numbers of reads in 5'UTR, length of CDS, numbers of reads in CDS, length of 3'UTR, and numbers of reads in 3'UTR.
Library strategy: Ribosome profiling

source_name: whole liver tissue

growth_protocol: Eight-to-ten week-old wild-type male mice (C57BL/6N, Japan SLC) were entrained under 12-h light (400 lx) 12-h dark (LD) for two weeks.

extract_protocol:
Lysates were incubated on ice for 5-10 min, triturated through a 26-G needle 10 times, clarified by centrifugation (20,000 × g for 10 min at 4 °C), and 300 µl of supernatant was transferred to a new tube. Unbound RNA was digested by the addition of 7.5 µl RNAse I (ThermoFisher) for 45 min and then stopped by 10 µl SUPERase In RNAse Inhibitor (ThermoFisher). The digestion was transferred to 13 mm × 51 mm polycarbonate ultracentrifuge tubes, layered on top of 0.9 ml sucrose cushion (150 mM NaCl, 20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 mM DTT, 100 µg/ml cycloheximide, 1 M sucrose, 10 U/ml SUPERase In), centrifuged in a TLA100.3 rotor at 70,000 rpm at 4 °C for 4 h. Ribosome pellets were resuspended in 0.7 ml Qiazol and mRNA was recovered using the miRNeasy RNA extraction kit (Qiagen) according to the manufacturer's instructions.
RNA was precipitated from the elution by the addition of 38.5 µl water, 1.5 µl GlycoBlue (ThermoFisher), and 10 µl 3 M sodium acetate pH 5.5 followed by 150 µl isopropanol, stored overnight at -80 °C, pelleted by centrifugation (20,000 × g for 30 min at 4 °C), and resuspended in 5 µl 10 mM Tris pH 8. Approximately 2–4 µg RNA was separated on a 15% (wt/vol) polyacrylamide TBE-urea gel at 200 V for 65 min in 1× TBE, and fragments between 26 and 34 nt were excised and recovered in 400 µl RNA gel extraction buffer (300 mM sodium acetate pH 5.5, 1 mM EDTA, and 0.25% (wt/vol) SDS) overnight. RNA was precipitated by the addition of 1.5 µl GlycoBlue and 500 µl, stored at -80 °C for >30 min, pelleted by centrifugation (20,000 × g for 30 min at 4 °C), and resuspended in 10 µl 10 mM Tris pH 8. RNA was dephosphorylated by T4 PNK (Takara Bio), precipitated and recovered as previously described, resuspended in 8.5 µl 10 mM Tris, and 1.5 µl of preadenylated and 3' blocked miRNA cloning linker (1/5rApp/CTGTAGGCACCATCAAT/3ddC/, IDT) was added. The linker mixture was denatured for 90 s at 80 °C, cooled to room temperature, ligated by T4 Rnl2 (NEB) for ~5 h at room temperature, precipitated, recovered, and separated by 15% TBE-urea gel electrophoresis. Ligation products were recovered overnight in RNA gel extraction buffer, precipitated, and recovered in 10 µl 10 mM Tris pH 8. Ligated RNA was reverse transcribed at 48 °C for 30 min using SuperScript III (ThermoFisher) with the reverse transcription primer (5′-(Phos)-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC-(SpC18)-CACTCA-(SpC18)- TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3′, where SpC18 indicates a hexa-ethyleneglycol spacer). Reverse transcription products were precipitated, recovered, separated by 15% TBE-urea gel electrophoresis, and recovered overnight in DNA gel extraction buffer (300 mM NaCl, 10 mM Tris pH 8, and 1 mM EDTA). The cDNA was precipitated, recovered, resuspended in 15 µl 10 mM Tris pH 8, and circularized by CircLigase (EpiCentre) for 1 h at 60 °C. rRNA was depleted by combining 5 µl circularization reaction with 1 µl of subtraction oligo pool, 1 µl 20× SSC, and 3 µl water, incubating at 37 °C for 15 min and binding to MyOne Streptavidin C1 DynaBeads (ThermoFisher) at 37 °C for 15 min with mixing at 1000 rpm. Eluate was precipitated, recovered, and resuspended in 5 µl 10 mM Tris pH 8. rRNA-depleted cDNA was PCR amplified by Phusion High-Fidelity DNA Polymerase (NEB) in a 20 µl reaction (denature 94 °C for 15 s, anneal 55 °C for 10 s, extend 72 °C for 10 s) for 12-16 cycles. PCR products were separated on a 8% TBE gel, recovered overnight in DNA gel extraction buffer, precipitated, recovered, and resuspended in 15 µl 10 mM Tris pH 8. Libraries were quantified using the high-sensitivity DNA chip on the Agilent BioAnalyzer according to the manufacturer's protocol, pooled, and amplified on the Illumina HiSeq system according to the manufacturer's protocol.

treatment_protocol: Twenty-four hours after transferring to constant darkness (DD), wild-type mice were sacrificed every 4 h over one day (CT0, CT4, CT8, CT12, CT16, CT20, and CT24) for ribosome profiling analysis.

tag: stain

tag: age

value: 8-10 week-old

value: male

value: whole liver tissue

value: wild-type

tag: time

tag: protocol

value: RiboProf library


title: B7_CT00_130517liver_8am (CT24_rep2)

tag: Sex


title: B5_CT16_130517liver_12am (CT16_rep2)


title: B6_CT20_130517liver_4am (CT20_rep2)


title: B4_CT12_130516liver_8pm (CT12_rep2)


title: B2_CT04_130516liver_12pm (CT04_rep2)


title: B3_CT08_130516liver_4pm (CT08_rep2)


title: B1_CT00_130516liver_8am (CT00_rep2)


title: A7_CT00_130517liver_8am (CT24_rep1)


title: CD11b+F4/80+ cells,WT, JEV-infected,rep2

tag: cell type


title: A5_CT16_130517liver_12am (CT16_rep1)


title: A6_CT20_130517liver_4am (CT20_rep1)


title: A4_CT12_130516liver_8pm (CT12_rep1)


title: A3_CT08_130516liver_4pm (CT08_rep1)


title: A1_CT00_130516liver_8am (CT00_rep1)


title: A2_CT04_130516liver_12pm (CT04_rep1)


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 3)

city: Stanford

first: Sai

last: Gourisankar

address: 240 Pasteur Dr, Rm 4700

department: Chemical Systems Biology

institute: Stanford

data_processing:
kallisto
Sequence reads were trimmed for adaptor sequence and quality using cutadapt with options --nextseq-trim=20 --minimum-length=1
Trimmed sequence reads were pseudoaligned using kallisto quant
Assembly: human gencode v33 for human cell lines, mouse gencode vM24 for mouse tissue
Supplementary files format and content: csv files with TPMs quantified from kallisto

source_name: Mouse liver

growth_protocol: Cell lines maintained in 10 % FBS + RPMI + antibiotics

extract_protocol:
RNA was harvested using Trisure and Zymo Direct-zol RNA purification kit
RNA libraries were made using NEB Ultra II RNA library prep kit using polyA enrichment

treatment_protocol: Drug or DMSO treated with final concentration of DMSO as 0.1% in all cases

value: Mouse liver

tag: strain

value: 10 mg/kg q.d. 5-day IP dosing

value: 5 days


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 2)

source_name: Mouse lung

value: Mouse lung


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 3)


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 1)


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 2)

source_name: Mouse spleen

value: Mouse spleen


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 1)


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 1)


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 1)


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 3)


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 2)


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 2)


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 2)


title: Pool175_Plate11-6-K20-E24

value: brain

tag: source

value: AUD

tag: target

value: AI

value: female


title: Pool175_Plate11-6-K20-F11


title: Pool175_Plate11-6-K20-F12


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 1)

value: WT


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of Vehicle (mouse 3)


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 3)


title: Mouse spleen from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 2)


title: Mouse liver from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 1)


title: Pool175_Plate11-6-K20-E11


title: Mouse lung from 10 mg/kg q.d. 5-day IP dosing of TCIP1 (mouse 3)


title: Pool175_Plate11-6-K20-D23


title: Pool175_Plate11-6-K20-D12


title: Pool175_Plate11-6-K20-E12


title: Pool175_Plate11-6-K20-D11


title: Pool175_Plate11-6-K20-C12


title: Pool175_Plate11-6-K20-C23


title: Pool175_Plate11-6-K20-E23


title: Pool175_Plate11-6-K20-C11


title: Pool175_Plate11-6-K20-B12


title: Pool175_Plate11-6-K20-B24


title: Pool175_Plate11-6-K20-B11


title: Pool175_Plate11-5-K20-O22


title: Pool175_Plate11-5-K20-P21


title: Pool175_Plate11-6-K20-A23


title: Pool175_Plate11-5-K20-P10


title: Pool175_Plate11-6-K20-A12


title: Pool175_Plate11-6-K20-D24


title: Pool175_Plate11-5-K20-O21


title: Pool175_Plate11-5-K20-N9


title: Pool175_Plate11-5-K20-P9


title: Pool175_Plate11-5-K20-O10


title: Pool175_Plate11-5-K20-M9


title: Pool175_Plate11-5-K20-N10


title: Pool175_Plate11-5-K20-N22


title: Pool175_Plate11-5-K20-L22


title: Pool175_Plate11-5-K20-M10


title: Pool175_Plate11-5-K20-L9


title: Pool175_Plate11-5-K20-K22


title: Pool175_Plate11-5-K20-K21


title: Pool175_Plate11-5-K20-L21


title: Pool175_Plate11-5-K20-K9


title: Pool175_Plate11-5-K20-K10


title: Pool175_Plate11-5-K20-L10


title: Pool175_Plate11-6-K20-B23


title: Pool175_Plate11-6-K20-A11


title: Pool175_Plate11-5-K20-J9


title: Pool175_Plate11-5-K20-J22


title: Pool175_Plate11-5-K20-J10


title: Pool175_Plate11-5-K20-I9


title: Pool175_Plate11-5-K20-G22


title: Pool175_Plate11-5-K20-H10


title: Pool175_Plate11-5-K20-I21


title: Pool175_Plate11-5-K20-H22


title: Pool175_Plate11-5-K20-G21


title: Pool175_Plate11-5-K20-H9


title: Pool175_Plate11-5-K20-F22


title: Pool175_Plate11-5-K20-H21


title: Pool175_Plate11-5-K20-F9


title: Pool175_Plate11-5-K20-J21


title: Pool175_Plate11-5-K20-E10


title: Pool175_Plate11-5-K20-E9


title: Pool175_Plate11-5-K20-F10


title: Pool175_Plate11-5-K20-E22


title: Pool175_Plate11-5-K20-D9


title: Pool175_Plate11-5-K20-I10


title: Pool175_Plate11-5-K20-E21


title: Pool175_Plate11-5-K20-C10


title: Pool175_Plate11-5-K20-C21


title: Pool175_Plate11-5-K20-D10


title: Pool175_Plate11-5-K20-C9


title: Pool175_Plate11-5-K20-C22


title: Pool175_Plate11-5-K20-B22


title: Pool175_Plate11-5-K20-F21


title: Pool175_Plate11-5-K20-D21


title: Pool175_Plate11-5-K20-B9


title: Pool175_Plate11-5-K20-B21


title: Pool175_Plate11-5-K20-B10


title: Pool175_Plate11-4-K20-P8


title: Pool175_Plate11-5-K20-A21


title: Pool175_Plate11-5-K20-D22


title: Pool175_Plate11-5-K20-A10


title: Pool175_Plate11-4-K20-P20


title: Pool175_Plate11-4-K20-P19


title: Pool175_Plate11-4-K20-O8


title: Pool175_Plate11-4-K20-O7


title: Pool175_Plate11-4-K20-O20


title: Pool175_Plate11-4-K20-O19


title: Pool175_Plate11-4-K20-K20


title: Pool175_Plate11-4-K20-M8


title: Pool175_Plate11-4-K20-N8


title: Pool175_Plate11-4-K20-N7


title: Pool175_Plate11-5-K20-A9


title: Pool175_Plate11-4-K20-K8


title: Pool175_Plate11-4-K20-L8


title: Pool175_Plate11-4-K20-L20


title: Pool175_Plate11-4-K20-L7


title: Pool175_Plate11-4-K20-N19


title: Pool175_Plate11-4-K20-I8


title: Pool175_Plate11-4-K20-L19


title: Pool175_Plate11-4-K20-J19


title: Pool175_Plate11-4-K20-K7


title: Pool175_Plate11-4-K20-P7


title: Pool175_Plate11-4-K20-I20


title: Pool175_Plate11-4-K20-I19


title: Pool175_Plate11-4-K20-H7


title: Pool175_Plate11-4-K20-M20


title: Pool175_Plate11-4-K20-H8


title: Pool175_Plate11-4-K20-H20


title: Pool175_Plate11-4-K20-H19


title: Pool175_Plate11-4-K20-G8


title: Pool175_Plate11-4-K20-J8


title: Pool175_Plate11-4-K20-K19


title: Pool175_Plate11-4-K20-J20


title: Pool175_Plate11-4-K20-F8


title: Pool175_Plate11-4-K20-G7


title: Pool175_Plate11-4-K20-G20


title: Pool175_Plate11-4-K20-F7


title: Pool175_Plate11-4-K20-E8


title: Pool175_Plate11-4-K20-E7


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