title: ATAC-seq K562, HDAC6 KO, replicate 2

first: Julian

address: Moorenstr. 5

institute: Uniklinik Düsseldorf

description: Library name: ATACseq_HDAC6knock_out_2

data_processing:
Mapping was done via Bowtie2
Reads were filtered for mapping quality >=30, proper pairing and chromosomal origin
PCR duplicates were flagged via MarkDuplicates
After BAM to BED conversion MACS2 was used to call peaks
Differential Accessability was determined through DiffBind
Assembly: hg38
Supplementary files format and content: a tabular differentially accessible gene region matrix

source_name: blood

growth_protocol: K562 were lentivirally transduced to express CAS9 and a guide RNA, sorted via a fluorescence marker & monoclonally selected, 100,000 cells were frozen in cryo media (50% RPMI Glutamax, 40 FCS, 10% DMSO) and send in duplicates to active motif

extract_protocol:
Extraction followed the standard Active Motif protocol for ATAC-seq of cryopreserved samples; Supplier: Active motif, Catalogue number: 53150; Cell sample Preparation 1. Count cells and aliquot 50,000 to 100,000 cells into a fresh 1.5 mL centrifuge tube for each sample. 2. Centrifuge the cells at 500 x g for 5 minute at 4°C. Orient the tubes such that the pellet will be where you expect it to be. If there is no visible pellet, spin an additional 5 minutes at 1,000 x g at 4°C. 3. Gently remove supernatant by pipetting and add 100 μL of ice-cold PBS. Do not resuspend or disturb pellet. Spin once more at 500 x g for 5 minutes at 4°C. 4. Remove supernatant very carefully, ensuring to not disturb the cell pellet. By pipetting, thoroughly resuspend the cell pellet in 100 μL ice-cold ATAC Lysis Buffer. 5. Transfer the resuspended cell pellet to a PCR tube on ice. Immediately spin down at 500 x g for 10 minutes at 4°C. During this time, prepare the Tagmentation Master Mix. 6. After the spin, remove the supernatant very carefully, ensuring the cell pellet is not disturbed (this is a critical step; take extra care to remove the ATAC Lysis Buffer but not lose nuclei). Immediately continue to the Tagmentation Reaction and Purification steps. Tagmentation Reaction and Purification 1. Add 50 μL of Tagmentation Master Mix to each sample (does not have to be on ice). Gently pipette to resuspend nuclei in the Tagmentation Master Mix with a multi-channel pipettor. 2. Incubate the tagmentation reaction at 37°C for 30 minutes in a thermomixer (or similar device) set at 800 rpm. 3. Immediately following the tagmentation reaction, transfer each sample to a clean 1.5 mL microcentrifuge tube. 4. Add 250 μL DNA Purification Binding Buffer and 5 μL 3 M sodium acetate to each sample. 5. If the color of the sample is anything other than bright yellow, add additional 3 M sodium acetate in 5 μL increments until the proper color is achieved. 6. Mix each sample by pipetting. 7. For each sample, place a labeled DNA purification column into a collection tube. 8. Transfer each sample to its corresponding column, close the cap, and centrifuge at 17,000 x g (14,000 rpm) for 1 minute. 9. Discard the flow-through and return the collection tube to the column. 10. Add 750 μL of Wash Buffer (see note above in step 9 the Wash Buffer should have a final concentration of 80% ethanol) to the column and cap the column. 11. Centrifuge at 17,000 x g for 1 minute. 12. Discard the flow-through and return the column to the collection tube. 13. With the column cap open, centrifuge at 17,000 x g for 2 minutes to remove residual Wash Buffer from the column. 14. Transfer each column to a new microcentrifuge tube. 15. Add 35 μL of DNA Purification Elution Buffer to the center of the column matrix, cap the column, and incubate for 1 minute at room temperature. 16. Centrifuge at 17,000 x g for 1 minute. 17. Discard column. DNA purification is complete. 18. Purified DNA can be stored at -20°C, or you may proceed directly with the PCR Amplification of Tagmented DNA steps that follow.
Library preparation followed the standard Active Motif protocol for ATAC-seq; Supplier: Active motif, Catalogue number: 53150 PCR Amplification of Tagmented DNA  1. Set up the PCR reactions by adding the components in the order shown below. If libraries are to be multiplexed for sequencing on the same flow cell, ensure that a unique i5 and/or i7 index combination is used for each. Each sample will require a combination of one i7 Indexed Primer and one i5 Indexed Primer in the PCR amplification reaction. There are 4 x 4 = 16 unique combinations of i7/i5 primers for a total of 16 samples that can be multiplexed. These Indexed Primers are based on Illumina’s Nextera adapters. 2. Perform PCR using the following program on a thermal cycler (with a heated lid): 72°C 5 minutes 98°C for 30 seconds 10 cycles of: 98°C for 10 seconds, 63°C for 30 seconds, 72°C for 1 minute Hold at 10°C. 3. Perform SPRI clean-up with 60 μL SPRI bead solution (1.2X the sample volume), eluting in 20 μL DNA Purification Elution Buffer. Have 400 μL of freshly-prepared 80% ethanol ready per sample: A. Add 60 μL well-mixed, room temperature SPRI Beads to each sample. B. Vortex briefly to mix and incubate for 5 minutes at room temperature to allow beads to bind. C. Apply magnet to collect beads. D. Once the solution is clear, aspirate the supernatant. E. With the magnet still applied to the sample, add 180 μL 80% ethanol to each sample without mixing. F. Incubate for 30 seconds at room temperature. G. Aspirate the supernatant. H. Repeat steps E through G for a second ethanol wash. I. Allow tubes to sit at room temperature so that residual ethanol can evaporate. Once the beads transition from shiny to matte (2-5 minutes), proceed to the next step. J. With the tubes separated from the magnet, add 20 μL DNA Purification Elution Buffer. K. Cap tubes and vortex to mix. L. Incubate samples for 5 minutes at room temperature. M. Apply magnet to collect beads. N. Once the solution is clear, transfer each supernatant containing the eluted DNA to a fresh tube. 4. At this stage, libraries are ready for quantification and sequencing. Use a library quantification kit for next-generation sequencing to quantify the library (e.g. Kapa Biosystems, Catalog No. KR0405). PCR amplified libraries can also be analyzed to assess size distribution with a Bioanalyzer, TapeStation, or similar instrument to assess size distribution.

value: blood

value: chronic myeloid leukemia

value: HDAC6 KO


title: FLC33_H3K27Ac

status: Public on May 23 2025

type: SRA

city: Houston

first: Haopeng

last: Yang

state: TX

address: 7455 Fannin ST

department: Lymphoma and Myeloma

country: USA

institute: The University of Texas MD Anderson Cancer Center

library_source: genomic

data_processing:
CUT&RUN: Sequencing quality control was evaluated by FastQC. Paired-end CUT&RUN raw reads were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using Bowtie2 with options: --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Aligned reads were sorted by coordinates and tested for mapped fragment size distribution by Samtools. The final aligned and sorted Bam files were used for further processing. Visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools with option: --normalizeUsing RPKM -e -bs 50 and evaluated in IGV browser. CUT&RUN peaks were called by MACS2 callpeak with option: -g hs -B -f BAM -q 0.01. IgG controls were used for comparison. Each technical repeat and biological repeat were separately processed.
ATAC-seq: Technical duplicates of each ATAC-seq samples were combined and sequencing quality control was evaluated by FastQC. Fastq files of paired-end ATAC-seq data were trimmed to remove adapter sequences using Trimmomatic and then aligned to version 19 of the human reference genome (hg19) using BWA (Burrows-Wheeler Aligner). Aligned reads were sorted by coordinates and filtered out mitochondrial DNA and black-listed regions by Samtools. Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The final aligned, sorted and filtered Bam files were used for further analysis. ATAC-seq visualization was assessed by converting the final Bam files to Bigwig files using the ‘bamCoverage’ command in deepTools and corrected for Tn5 insertion. ATAC-seq peaks were called from Tn-5 corrected insertions using MACS2 callpeak with option ‘-g hs -q 0.05 -f BAMPE and -B’.
ChIP-seq:The sequencing files were first demultiplexed and trimmed based on the eight-nucleotide barcode using previously described pipeline, allowing one mismatch on the first eight-nucleotide from read 121. The demultiplexed reads were then evaluated by FastQC then aligned to the hg19 genome using BWA (Burrows-Wheeler Aligner). Duplicate read pairs were marked and removed using the ‘MarkDuplicates’ command in picard tools. The H3K27ac peaks were called using MACS2 callpeak with option ‘-g hs -B -f BAM -q 0.01’. Input controls were used for comparison during peak calling.
RNA-seq: Data was trimmed with Trimmomatic, and both pre- and post-trimming quality controls were evaluated by FastQC. The trimmed data were aligned to version 19 of the human reference genome (hg19) using STAR (2-pass). Samples with at least 20 million uniquely mapping reads were retained for further analysis. Reads count was performed with the ‘Htseq-count’ command in HTSeq with option: -m union -f bam -i gene_id -s reverse -t exon --additional-attr=gene_name. Reads count filtering was applied to the DESeqDataSet matrix to keep only rows that have at least 10 reads total.
Assembly: hg19
Supplementary files format and content: bigwig, bed (for CUT&RUN ATAC-seq and ChIP-seq)
Supplementary files format and content: csv files with normalized counts (For RNA-seq)

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary FL sample 33

growth_protocol: Cell were cultured in RPMI medium with 10% FBS and 1X penicillin/streptomycin.

extract_protocol:
Cells were collected and washed by PBS. After final wash, nuclei were isolated using nuclei extraction buffer and then washed twice with wash buffer. Five-hundred thousand nuclei were counted and incubated with activated Concanavalin A coated beads and subsequently mixed with antibody in antibody buffer for overnight incubation on nutator in a cold room. IgG controls were set in parrel for antibody enrichment and specificity validation. Nuclei were then washed three times with digitonin buffer and incubated with PAG-MNase for 10 minutes at room temperature. After 10 minutes of incubation, nuclei were washed three times again with digitonin buffer and resuspended with prechilled low salt high Ca2+ buffer  to initiate 1-hour digestion at 0 °C. The reaction was terminated by switching into stop buffer and incubating at 37 °C for 10 minutes to release digested DNA from the nuclei. DNA was then purified with Ampure beads size selection (0.5X to remove large fragment and 2X to recover desired nucleosomal DNA fragments).
NGS libraries were generated with KAPA Hyper Prep Kits (Roche KK8502) using 14 cycles of PCR amplification. Libraires were validated on a Tapestation 4200 (Agilent G2991BA), quantified by Qubit High Sensitivity dsDNA Kit (Life Technologies Q32854), multiplexed and sequenced on a NovaSeq6000 using 100-10-10-100bp reads format.

treatment_protocol: For CD40 stimulation, stimulation medium were prepared by incubation of 40 uL of CD40 ligand and 40 uL of cross-linking antibody mixture at room temperature for 30 minutes and subsequently adding into 10 mL of RPMI+10%FBS and 2 uL of IL4. Cells were seeded at 0.5 million per mL of CD40 stimulation medium at 37 °C. Negative control group was set in the absence of CD40 ligand multimer and IL4. For bi-specific antibody experiment, B tumor cell lines were stained with CellTrace™ Far Red and CD4+ T cells were stained with CellTrace™ Violet. After mixing as desired ratio (1:1), cells were cultured in RPMI supplemented with 10% FBS in the presence of 100 ng/mL mosunetuzumab for 12-hour and 24-hour respectively, prior to sorting. Co-culture right after mixing without mosunetuzumab treatment was set as 0-hour treatment group.

tag: tissue

value: Primary FL sample 33

tag: genotype

value: CREBBP WT

tag: treatment

value: sort B cells

tag: time

tag: antibody

value: Mouse recombinant anti-H3K27Ac Active Motif Cat#91193


title: Huh7-KD1

city: Jinan

first: Yu-Chuan

last: Yan

state: Shandong

address: 107 West Wen Hua Road

country: China

institute: Qilu Hospital of Shandong University

description:
Library name: Sample4
HUH7_KD1_tpm

library_source: transcriptomic

data_processing:
To identify DEGs ( differential expression genes) between two different samples, the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances. Essentially, differential expression analysis was performed using the DESeq2 or DEGseq. DEGs with |log2FC| ≧ 1 and FDR≤ 0.05(DESeq2 ) or FDR ≤0.001(DEGseq) were considered to be significantly different expressed genes. In addition, functional- enrichment analysis including GO and KEGG were performed to identify which DEGs were significantly enriched in GO terms and metabolic pathways at Bonferronicorrected P-value ≤0.05 compared with the whole-transcriptome background. GO functional enrichment and KEGG pathway analysis were carried out by Goatools and KOBAS, respectively.
Assembly: hg38
Supplementary files format and content: HUH7_NC_vs_HUH7_KD.deseq2.annot.txt
Supplementary files format and content: HEP3B_NC_vs_HEP3B_KD.deseq2.annot.xls

molecule: total RNA

growth_protocol: Huh7 cells were maintained in high-glucose DMEM supplemented with 10% foetal bovine serum, penicillin (100 IU/ml) and streptomycin (100 μg/ml). Hep3B cells were maintained in MEM-alpha supplemented with 10% foetal bovine serum, penicillin (100 IU/ml) and streptomycin (100 μg/ml).  All the cells were cultured in 25 cm2 polystyrene culture flasks in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted  using an RNA Rapid Extraction Kit (RNAfast200, Fastagen, China) according to the manufacturer’s instructions.
RNA purification, reverse transcription, library construction and sequencing were performed at Shanghai Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) according to the manufacturer’s instructions (Illumina, San Diego, CA). The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina). Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

tag: cell line

tag: cell type

value: Hepatocellular carcinoma

value: FAM111B knockdown


title: ATAC-seq K562, HDAC6 KO, replicate 1

city: Düsseldorf

last: Schliehe-Diecks

country: Germany

description: Library name: ATACseq_HDAC6knock_out_1


title: FLC25_H3K27Ac

source_name: Primary FL sample 25

value: Primary FL sample 25


title: Muscle total RNA, dimt-1 RNAi, biological replicate 4

city: Boston

first: Wayne

last: Mitchell

state: MA

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

description:
Library name: dmt_Input_S4_muscle
genecounts_raw.csv

data_processing:
Fastq files were mapped to the WBCel235 genome using STAR v.2.7.2b
Assembly: WBCel235
Supplementary files format and content: csv file containing raw counts for each sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole-worm lysates

growth_protocol: WBM1339 worms were grown on OP50 until the gravid stage, and eggs were collected by bleaching. Synchronized L1 worms were then poured to control or dimt-1 RNAi plates.

extract_protocol:
RNA was purified using the Rneasy Plus Mini Kit (QIAGEN)
Libraries were prepared with TruSeq Stranded mRNA LT Sample Prep Kit according to TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: At young adult (YA) stage worms were collected for immunoprecipitation (IP). Ribosome IP was performed using anti-FLAG antibody (Sigma F1804) to pull down the FLAG-tagged ribosomal subunits.

value: whole-worm lysates

value: dimt-1 RNAi


title: ATAC-seq K562, empty vector control, replicate 2

description: Library name: ATACseq_ Empty_vector_control_2

value: WT


title: Huh7-NC3

description:
Library name: Sample3
HUH7_NC3_tpm

value: Control group


title: Muscle total RNA, dimt-1 RNAi, biological replicate 3

description:
Library name: dmt_Input_S3_muscle
genecounts_raw.csv


title: tga7_control_root3

type: RNA

city: Bunkyo-ku

first: Yasuhito

last: Sakuraba

state: Tokyo

address: Yayoi 1-1-1

department: Agro-Biotechnology Research Center

country: Japan

institute: The University of Tokyo

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 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 Human Genome Oligo Microarrays (G4112A) 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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k 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 (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: WT and tga7 seedlings were grown on 1/2 MS plates for 5 days and then on nitrogen-sufficient and nitrogen-defficient agar plates for 5 days.

extract_protocol: RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.

treatment_protocol: shoot part and root part from 10 day-old wild-type and tga7 seedlings grown under nitrogen-sufficient and nitrogen-defficient conditions

value: sufficient nitrogen

value: root


title: WT_LN_root1

value: deficient nitrogen


title: ATAC-seq K562, empty vector control, replicate 1

description: Library name: ATACseq_ Empty_vector_control_1

value: blood


title: Huh7-NC1

description:
Library name: Sample1
HUH7_NC1_tpm


title: Huh7-NC2

description:
Library name: Sample2
HUH7_NC2_tpm


title: Muscle total RNA, dimt-1 RNAi, biological replicate 1

description:
Library name: dmt_Input_S1_muscle
genecounts_raw.csv


title: Muscle total RNA, dimt-1 RNAi, biological replicate 2

description:
Library name: dmt_Input_S2_muscle
genecounts_raw.csv


title: Muscle total RNA, control RNAi, biological replicate 4

description:
Library name: Ct_Input_S4_muscle
genecounts_raw.csv

value: control RNAi


title: U2OS AsiSI (4h 4-OHT) - siMePCE #2

city: Austin

first: Blerta

last: Xhemalçe

state: Texas

address: 2500 Speedway

department: Molecular Biosciences

institute: University of Texas at Austin

description: Library name: ngsBX319

data_processing:
The adapter sequences in each raw fastq file (fastq) were trimmed using Trim Galore. The quality of each processed fastq file was then assessed with FastQC. Subsequently, the reads were aligned to the reference human genome hg19 using the STAR method. SAMtools was employed to remove low-quality mapped reads by filtering out reads with a mapping quality score of less than 10. Each gene in each sample was counted using featureCounts.
Assembly: hg19
Supplementary files format and content: CSV file

source_name: U2OS- AiD-DiVA AsiSI -ER

growth_protocol:
U2OS-Flp-In-TREx cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ) and supplemented with 100µg/mL Zeocin and 15 µg/mL Blasticidin.
U2OS- AiD-DiVA AsiSI -ER cells were grown in DMEM containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 μg/mL streptomycin and 2 mM L-glutamine (PSQ) and supplemented with 400µg/mL G418.

extract_protocol:
The RNA/Protein Plus purification kit from Norgen # 48000 was used for extracting RNA.
Libraries were constructed using the NEBNext Ultra II kit (RNA directional WITH ribosomal removal) following manufacturer’s instructions.

treatment_protocol: Cells were reverse-transfected with siNC (Control) and siMePCE in two rounds at 0h and 48h, and cells were lysed in the SKP buffer supplemented with 10 µL/mL of b-Mercaptoethanol at 96h. U2OS-AsiSI cells were treated with 300 nM of 4-hydroxytamoxifen (4-OHT) starting at 92h and for 4 hrs total to induce sequence-specific double strand breaks at AsiSI sites in actively transcribed regions.

value: U2OS- AiD-DiVA AsiSI -ER

value: siMePCE


title: BxPC3s, 28clones, scRNA

city: Tokyo

first: Kenichi

last: Miyata

institute: JFCR

description: Library name: BxPC3s_28clones_scRNA

library_source: transcriptomic single cell

data_processing:
For scRNA-seq data, raw sequencing reads were processed using Cell Ranger (v6.1.2, 10x Genomics) with default settings and aligned to the GRCh38 human reference genome to generate gene-by-cell expression matrices. Demultiplexing of individual clones was performed using the PseuMO-Tag Decoder pipeline developed in-house. Downstream analyses were carried out using the Seurat R package (v4.0.1). Low-quality cells were removed based on standard quality control criteria.
Assembly: GRCh38
Supplementary files format and content: matrix of gene counts
Supplementary files format and content: matrix of gene names
Supplementary files format and content: matrix of 10x cell barcodes

growth_protocol: The cells were cultured in RPMI medium supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin (Sigma-Aldrich) under physiological oxygen conditions (92% N2, 5% CO2, and 3% O2) at 37°C.

extract_protocol:
Cultured cells were detached using trypsin and passed through a cell strainer to obtain a single-cell suspension. The resulting suspension was cryopreserved in Bambanker (Nippon Genetics) for later use in downstream experiments.
Cryopreserved cell stocks were rapidly thawed at 37 °C, and cell viability was confirmed to exceed 90% before further processing. Equal numbers of viable cells were pooled and loaded onto a 10x Genomics Chromium Controller for single-cell partitioning and barcoding. cDNA synthesis and library preparation were performed using the Chromium Single Cell 3′ v3 protocol (10x Genomics) according to the manufacturer's instructions.

treatment_protocol: shPseuMO-Tag constructs targeting ARID1A (two independent shRNAs: ARI3# and ARI4#) or a nontargeting control (SCR#) were introduced into BxPC3 cells. Following single-cell cloning and approximately 20 cell divisions, 28 clonal subpopulations were established (eight controls and 20 ARID1A knockdowns). Subsequently, all 28 clones were pooled into a single cellular mixture, and scRNA-seq and scATAC-seq were performed to minimize the batch effect while evaluating transcriptional variations within and across clones.

value: controls and ARID1A knockdowns


title: TREx.BCBL1.Rta Dox Repeat2

city: Columbus

first: Zhenyu

last: wu

state: Ohio

address: 281 W Lane Ave

department: Pathology

institute: The ohio state university

data_processing:
Briefly, clean reads were mapped to the hg38 genome using meRanGh from meRanTK.
Conversion rate was calculated based on the mouse Dhfr mRNA spike-in, which revealed the C to T conversion rate >98%. The m5C sites were called using meRanCall from meRanTK (false discovery rate < 0.01). Only sites with a coverage depth ≥ 20, methylation level ≥ 0.2, and methylated cytosine depth ≥ 5 were considered credible.
The m5C annotation was performed using meRanAnnotate command with the customized genomic sequences consist of both human and KSHV genomes.
For pathway analysis, differentially methylated mRNAs were subjected to the pathway enrichment analysis using the R package clusterProfiler  to calculate the significant canonical pathways (P ≤ 0.01).
Assembly: hg38
Supplementary files format and content: tab-delimited files include identified m5c sites for each sample
Library strategy: RNA-BS-seq

growth_protocol: RPMI+10% FBS

extract_protocol:
Total RNA was first extracted from samples using Trizol, and mRNA was then purified from total RNA using mRNA Dynabeads purification kit (Invitrogen). RNA concentration was measured by NanoDrop. DNA-free DNA Removal Kit (Invitrogen, Cat#AM1906) was utilized to avoid DNA contamination.
(Bisuflite treated mRNA)  500 ng of cellular mRNAs and 1 ng in vitro transcribed mouse Dhfr mRNA were mixed as input for RNA bisulfite conversion using EZ RNA Methylation Kit (Zymo R5001). Then BS-treated mRNA were submitted to GENEWIZ (South Plainfield, NJ 07080) for quality control, followed by the library preparation. Sequencing was carried out on an Illumina HiSeq platform with the configuration of 2 × 150 bp (paired end), and > 20 million reads per sample were achieved
RNA Bisfulfite-seq

treatment_protocol: Doxcycline 2ug/ml

value: B cell lymphoma

value: Doxcycline 2ug/ml


title: TREx.BCBL1.Rta Dox Repeat1


title: Muscle total RNA, control RNAi, biological replicate 3

description:
Library name: Ct_Input_S3_muscle
genecounts_raw.csv


title: WT_control_root3


title: U2OS AsiSI (4h 4-OHT) - siNC #2

description: Library name: ngsBX318

value: siNC


title: TREx.BCBL1.Rta Mock Repeat2

value: Mock


title: U2OS-Flp-In-TREx - siMePCE #2

description: Library name: ngsBX317


title: Muscle total RNA, control RNAi, biological replicate 2

description:
Library name: Ct_Input_S2_muscle
genecounts_raw.csv


title: TREx.BCBL1.Rta Mock Repeat1


title: Muscle total RNA, control RNAi, biological replicate 1

description:
Library name: Ct_Input_S1_muscle
genecounts_raw.csv


title: tga7_control_root1


title: U2OS-Flp-In-TREx - siNC #2

description: Library name: ngsBX316


title: Muscle ribosome-bound mRNA, dimt-1 RNAi, biological replicate 4

description:
Library name: dmt_IP_S4_muscle
genecounts_raw.csv

source_name: Muscle

value: Muscle


title: U2OS AsiSI (4h 4-OHT) - siMePCE #1

description: Library name: ngsBX315


title: tga7_LN_shoot2

value: shoot


title: Blood cells, biological replicate 2

first: Tal

middle: Deborah

last: Scully

address: 200 Longwood Ave

department: Systems Biology

institute: Harvard Medical School

description:
Library name: Cr_blood_230518_2
10x Genomics, Chromium Next GEM Single Cell 3′ v3.1

data_processing:
Single cell analysis (alignment, cell identification, gene counts) done by 10X Genomics Cell Ranger 6.1.2. No additional cell filtering or preprocessing was done on processed data files Cr_blood_230518_1_raw_unfiltered_matrix.h5 and Cr_blood_230518_2_raw_unfiltered_matrix.h5.
Assembly: Ciona robusta genome HT 2019 assembly with KY21 gene models (Ghost Database http://ghost.zool.kyoto-u.ac.jp/download_ht.html ), plus mitochondrial genes from Ensembl KH (GCA_000224145.1) Ciona intestinalis genome. Fasta and gtf files for the combined genome are available on https://github.com/AllonKleinLab/paper-data/tree/master/Scully_mannitol_2025/C_robusta_genome_HT2019_KY21_with_Ensembl_mito
Supplementary files format and content: H5 Hierarchical Data Format

organism: Ciona robusta

extract_protocol:
Ciona robusta adults were collected from the wild in Carlsbad, California, USA by M-REP. They arrived in the lab <24 hours after collection, where they were kept at 17–18ºC in 35–40 ppt artificial seawater (Instant Ocean SS15-10) and fed 6–7 days a week with 15 mL of Phyto-Feast (Reef Nutrition). Blood was collected 7 days after arrival in the lab, during which time animals remained healthy by visual inspection. To reduce movement during dissection, animals were relaxed by incubating 3–5 adults for 3–4 hours at 4 °C in 400 mL artificial seawater from the aquarium system with 5 g of 99% L-menthol crystals (Thermo Scientific A10474). Volume and weight measurements were approximate. To collect blood, animals were dissected to expose a large blood vessel adjacent to the heart and running along the endostyle (“ventral vessel” in Millar 1953). Blood was drawn from the vessel with a zero dead space tuberculin syringe with a 25G needle (Exelint 26046), then transferred to a microcentrifuge tube on ice. This tube had first been coated with bovine serum albumin (BSA) by washing with 0.5 mL of 10% (v./v.) BSA (Sigma 9048-46-8) in Dulbecco’s phosphate-buffered saline (DPBS, Gibco 14200075). Blood was harvested from 7. Equal blood volumes were then pooled for animals A, B, C, D, and then again for animals A, E, F, G, such animal A contributed blood to both pools. Blood was then filtered through a 40 µm strainer (pluriSelect 43-10040-60) and transferred to a microcentrifuge tube, which had been coated with bovine serum albumin (BSA) by washing with 0.5 mL of 10% (v./v.) BSA (Sigma 9048-46-8) in Dulbecco’s phosphate-buffered saline (DPBS, Gibco 14200075). Blood cells were pelleted by spinning at 800 g for 10 minutes at 4 °C in a swinging bucket centrifuge (Eppendorf Centrifuge 5810R). The supernatant was removed, and cells were resuspended in 0.7 M D-mannitol (Sigma Aldrich M4125) in 1X PBS (gibco 70011-044) (PBS-M). This PBS-M buffer was optimized for scRNA-seq of cells adapted to high salinity environments. Cells were then filtered through a 40 µm strainer once more to remove large clumps.
Library preparation was done with Chromium Next GEM Single Cell 3′ v3.1 Kits (10X Genomics 1000123, 1000127, and 1000190). We followed the manufacturer’s guidelines except for the preparation of the RT mix prior to cell encapsulation. The manufacturer’s protocol directs users to add nuclease-free water, followed by cell suspension; instead of adding nuclease-free water, we added an equivalent volume of PBS-M.

value: wild-caught animals from Carlsbad, CA, USA


title: U2OS AsiSI (4h 4-OHT) - siNC #1

description: Library name: ngsBX314


title: Blood cells, biological replicate 1

description:
Library name: Cr_blood_230518_1
10x Genomics, Chromium Next GEM Single Cell 3′ v3.1


title: tga7_control_root2


title: Muscle ribosome-bound mRNA, dimt-1 RNAi, biological replicate 2

description:
Library name: dmt_IP_S2_muscle
genecounts_raw.csv

value: dimt-1 RNAi


title: SHIP1 cKO 3

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

data_processing:
RNA-Seq reads were mapped to the mouse genome (GRCm38, version M12 (Ensembl 87)) with STAR (Dobin et al., 2013, version-2.7.3a) using the following parameters –outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000. Reads were assigned to genes using FeatureCounts (Liao et al., 2014, version-v2.0.0) with the following parameters: -T 2 -t exon -g gene_id -s 2. For the differential expression analyses we used DESeq2 (Love et al., 2014, version-1.32.0) with default parameters. We filtered genes that had less 5 counts in at least 3 samples.
Assembly: GRCm38, version M12 (Ensembl 87)
Supplementary files format and content: Gene counts as calculated by featureCounts in tab separated format

organism: Mus musculus

source_name: Hippocampi

growth_protocol: Mice were bred in the animal facility, with food and water ad libitum, at 20-22°C. Control and SHIP1 cKO male littermates were used.

extract_protocol:
Microglial cells were fluorescently sorted by means of FACS, gating for YFP+/DAPI-/ RedDotTM1 Far-Red Nuclear Stain+ (Anawa, #40060), directly in IB lysis buffer from SPLIT RNA Extraction Kit (Lexogen, #K00848). RNA extraction was performed following the manufacturer’s instructions.
RNA DNBSEQ Eukaryotic Transcriptome was sequenced by BGI genomics

treatment_protocol: In order to obtain experimental animals, Inpp5dfl/+ mice were crossed with Cx3cr1CreErt2-ires-YFP;CreErt2-ires-YFP;Inpp5dfl/+. The litters were injected with 40μL of tamoxifen (dissolved in 10% EtOH and 90% Corn Oil, at 2 mg/mL. Sigma-Aldrich, #T5648) at P3 and P4. Toe clipping of pups was performed between P6 and P12, followed by DNA extraction (KAPAMouse Genotyping Kit, Sigma-Aldrich, #KK7302) and genotyping (Inpp5d Forward: 5'-ACT GAT TTC CCA AGT GCT TCT-3'. Inpp5d Reverse: 5'-CCT TGA ACA CCT CTG CCA AC-3') .

value: Hippocampi

value: Microglia

tag: time of_tamoxifen_injection

value: Postanatal day 3 and 4

value: CX3CR1-creert2-YFP/+ ; Inpp5d fl/fl

tag: time of_collection

value: Postnatal day 15


title: SHIP1 cKO 2


title: Muscle ribosome-bound mRNA, dimt-1 RNAi, biological replicate 1

description:
Library name: dmt_IP_S1_muscle
genecounts_raw.csv


title: WT_LN_shoot3

value: deficient nitrogen


title: U2OS-Flp-In-TREx - siNC #1

description: Library name: ngsBX312


title: tga7_LN_shoot1


title: SHIP1 cKO 1


title: tga7_LN_shoot3


title: Muscle ribosome-bound mRNA, control RNAi, biological replicate 4

description:
Library name: Ct_IP_S4_muscle
genecounts_raw.csv

value: control RNAi


title: WT_control_root1

value: sufficient nitrogen

value: root


title: RS4-11 cells, Treatment rep2

city: Mainz

first: Giuseppe

last: Petrosino

state: --- Select a state ---

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Reads were aligned on the Homo sapiens genome assembly hg38 (ENSEMBL release 98) using STAR (version 2.7.10a, parameters: --outMultimapperOrder Random --outSAMattributes NH HI AS nM MD –outSJfilterReads Unique --outSAMunmapped Within --outFilterMismatchNoverReadLmax 0.04 –outFilterMismatchNmax 999 –sjdbOverhang 79).
The featureCounts program (version 2.0.0, parameter: -s2) was used to count the number of reads overlapping genes.
Differentially expressed genes (DEGs) were determined using DESeq2 (release: 1.34.0) with corrected pvalue (Benjamini and Hochberg, FDR) < 0.05.
Assembly: hg38
Supplementary files format and content: Tab-separated values (TSV) files include raw counts for each Sample.
Supplementary files format and content: XLSX file includes TPM values for each Sample.

source_name: Blood

growth_protocol: RS4-11 cells were maintained in RPMI-1640 medium supplemented with 10% FCS and 1% Penicillin/Streptomycin in humidified atmosphere at 37°C with 5% CO2

extract_protocol:
Cells were harvested and total RNA was isolated using the NucleoSpin RNA kit (Machery-Nagel).
NGS library prep was performed with Illumina's Stranded mRNA Prep Ligation Kit following Stranded mRNA Prep Ligation ReferenceGuide (June 2020) (Document # 1000000124518 v00). Libraries were prepared with a starting amount of 1000 ng and amplified in 9 PCR cycles. After PCR purification, an additional round of purification was performed using 1x of AMPure XP beads. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life technologies). All 9 samples (three replicates of untreated HEL cells and three replicates of MERCK60 treated and SIAH2 KO cells) were pooled in equimolar ratio and sequenced on 1 NextSeq500 high output FC, SR for 1x79 cycles plus 10 cycles for the index read and 2 dark cycle upfront R1.

treatment_protocol: Controls were incubated for 8 hours without treatment. Treated cells were incubated for 8 hours with 15µM of the HDAC10 inhibitor PZ48.

value: Blood

value: Adult B acute lymphoblastic leukemia

value: HDAC10 inhibition


title: WT_LN_shoot1


title: U2OS-Flp-In-TREx - siMePCE #1

description: Library name: ngsBX313

value: siMePCE


title: WT_LN_shoot2


title: Muscle ribosome-bound mRNA, dimt-1 RNAi, biological replicate 3

description:
Library name: dmt_IP_S3_muscle
genecounts_raw.csv

value: Muscle


title: Muscle ribosome-bound mRNA, control RNAi, biological replicate 3

description:
Library name: Ct_IP_S3_muscle
genecounts_raw.csv


title: Control 3

value: CX3CR1-creert2-YFP/+ ; Inpp5d +/+


title: RS4-11 cells, Control rep2

value: Control


title: WT_control_root2


title: Muscle ribosome-bound mRNA, control RNAi, biological replicate 1

description:
Library name: Ct_IP_S1_muscle
genecounts_raw.csv


title: RS4-11 cells, Treatment rep1


title: tga7_control_shoot3

value: shoot


title: Control 2

value: Hippocampi


title: RS4-11 cells, Control rep1


title: WT_control_shoot3


title: Control 1

value: Microglia


title: D_RT_2

status: Public on May 22 2025

city: San Francisco

first: Alan

last: Ashworth

state: CA

address: 1450 3rd Street, HD-271

department: Helen Diller Family Comprehensive Cancer Center

institute: University of California, San Francisco

description: biological replicate 2

data_processing:
Reads were aligned to the reference genome using Bowtie2 (PMID: 22388286).
Gene expression level is calculated with RSEM (PMID: 21816040).
Assembly: Homo_sapiens_9606.UCSC.hg38.v2201
Supplementary files format and content: Processed files are provided for each sample containing TPM, FPKM, and read counts.

growth_protocol: 22Rv1 cells were cultured in RPMI1640 media supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
total RNA was isolated using Qiagen RNeasy kit and treated with Dnase.
polyA selected, strand specific

treatment_protocol: Cells were hormone-deprived in phenol red-free RPMI media containing charcoal stripped serum  supplemented with 10% FBS and 1% Pen/Strep  for 3 days. Cells were treated with indicated concentrations of  DHT, RBN-2397 or tapnarof for 48 hours before RNA was collected

value: prostate cancer cell lines

value: 5 nM DHT + 100 nM RBN2397 + 100 nM tapinarof


title: D_RT_1

description: biological replicate 1


title: Control 4

value: Postanatal day 3 and 4

value: Postnatal day 15


title: Muscle ribosome-bound mRNA, control RNAi, biological replicate 2

description:
Library name: Ct_IP_S2_muscle
genecounts_raw.csv

value: control RNAi


title: D_T_2

description: biological replicate 2

value: 5 nM DHT + 100 nM tapinarof


title: WT_control_shoot2

value: sufficient nitrogen


title: D_2

description: biological replicate 2

value: 5 nM DHT + DMSO


title: D_R_2

description: biological replicate 2

value: 5 nM DHT + 100 nM RBN2397


title: D_1

description: biological replicate 1


title: V_2

description: biological replicate 2

value: vehicle


title: D_T_1

description: biological replicate 1


title: V_1

description: biological replicate 1


title: D_R_1

description: biological replicate 1


title: tga7_control_shoot1


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

city: Davis

first: Aron Judd

middle: Perez

last: Mendiola

state: CA California

address: 1 Shields Avenue

department: Medical Microbiology and Immunology

institute: University of California - Davis

description:
Library name: CF556
Column name in clamsrw_rawcounts.txt: CF556

data_processing:
Reads were processed using TrimGalore, Samtools, and STAR (https://github.com/benlaufer/RNA-seq).
Raw counts from each experiment were experiment and sex stratified and normalized (logcpm) using Limma-Voom for the final paper. The processed data made available here has not been normalized and only contains raw counts.
Assembly: mm10
Supplementary files format and content: tab-delimited data includes raw counts for wild-type circadian atlas
Supplementary files format and content: tab-delimited data includes raw counts for CLAMS and RW experiment

source_name: left pre-frontal cortex

extract_protocol:
RNA were isolated from 10 - 20 mg prefrontal cortex using All Prep DNA/RNA/Protein kit (Qiagen).
RNA was submitted for library preparation and sequencing to Novogene. Libraries were prepared using NEBNext Ultra II Directional RNA library prep kit for Illumina. Ribosomal RNA was cleaned up using NEBNext rRNA Depletion kit. Libraries were sequenced on the Novaseq S4.

treatment_protocol:
Wild-type mice housed in home cage 12:12 light cycle were sacrificed every three hours at zeitgeiber time 0 – 21 (ZT0, ZT3, ZT6, ZT9, ZT12, ZT15, ZT18, ZT21) to generate a circadian atlas for the prefrontal cortex. Mice were euthanized at ~12 weeks of age for tissue collection.
Male and female offspring (WT/WT, Snord116+/+Ctg-/-; HET/WT, Snord116+/-Ctg-/-; WT/TG, Snord116+/+Ctg+/-; HET/TG, Snord116+/-Ctg+/- were moved at ~8 weeks of age into lightcontrolled incubator housing for a 7-day acclimation to the new housing. All mice were randomly divided into two entrainment groups, 12:12 or 11:11 light/dark (L:D) where they were housed in both entrainment groups at 22°C. After 15 days, one group of entrained mice were transferred to new cages equipped with running wheel actograms, where they remained at the entrained light cycles for an additional 7 days (22 d entrainment total). A different group of entrained mice were moved to indirect calorimetry chambers after 22 days of entrainment. Micce were euthanized at the same timepoint ZT6 the end of each study and RNA was collected from ZT6 prefrontal cortex and submitted to Novogene for library prepration and sequencing.

value: left pre-frontal cortex

tag: Sex

value: female

tag: timepoint collected

value: ZT06 biol rep 4

tag: lighting condition_collected

value: HET/TG, Snord116+/-Ctg+/-

tag: entrainment

tag: experiment

value: Indirect Calorimetry (CLAMS)


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF500
Column name in clamsrw_rawcounts.txt: CF500

value: ZT06 biol rep 3


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF297
Column name in clamsrw_rawcounts.txt: CF297

value: ZT06 biol rep 2


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF511
Column name in clamsrw_rawcounts.txt: CF511


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF77
Column name in clamsrw_rawcounts.txt: CF77


title: WT_control_shoot1

value: shoot


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF278
Column name in clamsrw_rawcounts.txt: CF278

value: ZT06 biol rep 1


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF501
Column name in clamsrw_rawcounts.txt: CF501


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF177
Column name in clamsrw_rawcounts.txt: CF177

value: HET/WT, Snord116+/-Ctg-/-


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF57
Column name in clamsrw_rawcounts.txt: CF57

value: WT/TG, Snord116+/+Ctg+/-


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF321
Column name in clamsrw_rawcounts.txt: CF321


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF505
Column name in clamsrw_rawcounts.txt: CF505


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF369
Column name in clamsrw_rawcounts.txt: CF369


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF377
Column name in clamsrw_rawcounts.txt: CF377


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF410
Column name in clamsrw_rawcounts.txt: CF410


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF495
Column name in clamsrw_rawcounts.txt: CF495


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF55
Column name in clamsrw_rawcounts.txt: CF55


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF417
Column name in clamsrw_rawcounts.txt: CF417


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF58
Column name in clamsrw_rawcounts.txt: CF58

value: WT/WT, Snord116+/+Ctg-/-


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF420
Column name in clamsrw_rawcounts.txt: CF420


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF502
Column name in clamsrw_rawcounts.txt: CF502


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF358
Column name in clamsrw_rawcounts.txt: CF358


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF552
Column name in clamsrw_rawcounts.txt: CF552


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF367
Column name in clamsrw_rawcounts.txt: CF367


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF320
Column name in clamsrw_rawcounts.txt: CF320


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF419
Column name in clamsrw_rawcounts.txt: CF419


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM414
Column name in clamsrw_rawcounts.txt: CM414

value: male


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF356
Column name in clamsrw_rawcounts.txt: CF356


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM116
Column name in clamsrw_rawcounts.txt: CM116


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF418
Column name in clamsrw_rawcounts.txt: CF418


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF366
Column name in clamsrw_rawcounts.txt: CF366


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF276
Column name in clamsrw_rawcounts.txt: CF276


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF75
Column name in clamsrw_rawcounts.txt: CF75


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF540
Column name in clamsrw_rawcounts.txt: CF540


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM176
Column name in clamsrw_rawcounts.txt: CM176


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM151
Column name in clamsrw_rawcounts.txt: CM151


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM95
Column name in clamsrw_rawcounts.txt: CM95


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM135
Column name in clamsrw_rawcounts.txt: CM135


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM326
Column name in clamsrw_rawcounts.txt: CM326


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM299
Column name in clamsrw_rawcounts.txt: CM299


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CF184
Column name in clamsrw_rawcounts.txt: CF184


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM137
Column name in clamsrw_rawcounts.txt: CM137


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM281
Column name in clamsrw_rawcounts.txt: CM281


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM144
Column name in clamsrw_rawcounts.txt: CM144


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM174
Column name in clamsrw_rawcounts.txt: CM174


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM149
Column name in clamsrw_rawcounts.txt: CM149


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM283
Column name in clamsrw_rawcounts.txt: CM283


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM119
Column name in clamsrw_rawcounts.txt: CM119


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM105
Column name in clamsrw_rawcounts.txt: CM105


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM132
Column name in clamsrw_rawcounts.txt: CM132


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM97
Column name in clamsrw_rawcounts.txt: CM97


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM106
Column name in clamsrw_rawcounts.txt: CM106


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM109
Column name in clamsrw_rawcounts.txt: CM109


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM94
Column name in clamsrw_rawcounts.txt: CM94


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM126
Column name in clamsrw_rawcounts.txt: CM126


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM98
Column name in clamsrw_rawcounts.txt: CM98


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM150
Column name in clamsrw_rawcounts.txt: CM150


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM107
Column name in clamsrw_rawcounts.txt: CM107


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM133
Column name in clamsrw_rawcounts.txt: CM133


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM143
Column name in clamsrw_rawcounts.txt: CM143


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM123
Column name in clamsrw_rawcounts.txt: CM123


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA840
Column name in clamsrw_rawcounts.txt: RNA840

value: Running Wheel (RW)


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM327
Column name in clamsrw_rawcounts.txt: CM327


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 12:12 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM117
Column name in clamsrw_rawcounts.txt: CM117


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA732
Column name in clamsrw_rawcounts.txt: RNA732


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA779
Column name in clamsrw_rawcounts.txt: RNA779


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA164
Column name in clamsrw_rawcounts.txt: RNA164


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA797
Column name in clamsrw_rawcounts.txt: RNA797


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA114
Column name in clamsrw_rawcounts.txt: RNA114


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA738
Column name in clamsrw_rawcounts.txt: RNA738


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA759
Column name in clamsrw_rawcounts.txt: RNA759


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA120
Column name in clamsrw_rawcounts.txt: RNA120


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA753
Column name in clamsrw_rawcounts.txt: RNA753


title: female, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA173
Column name in clamsrw_rawcounts.txt: RNA173


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA837
Column name in clamsrw_rawcounts.txt: RNA837


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA142
Column name in clamsrw_rawcounts.txt: RNA142


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA811
Column name in clamsrw_rawcounts.txt: RNA811


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA128
Column name in clamsrw_rawcounts.txt: RNA128


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA381
Column name in clamsrw_rawcounts.txt: RNA381


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA141
Column name in clamsrw_rawcounts.txt: RNA141


title: female, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA626
Column name in clamsrw_rawcounts.txt: RNA626


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 11:11 L:D entrainment, Indirect Calorimetry (CLAMS) D:D

description:
Library name: CM110
Column name in clamsrw_rawcounts.txt: CM110


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA279
Column name in clamsrw_rawcounts.txt: RNA279


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA831
Column name in clamsrw_rawcounts.txt: RNA831


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA122
Column name in clamsrw_rawcounts.txt: RNA122


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA514
Column name in clamsrw_rawcounts.txt: RNA514


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA760
Column name in clamsrw_rawcounts.txt: RNA760


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA140
Column name in clamsrw_rawcounts.txt: RNA140


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA798
Column name in clamsrw_rawcounts.txt: RNA798


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA121
Column name in clamsrw_rawcounts.txt: RNA121


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA778
Column name in clamsrw_rawcounts.txt: RNA778


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA172
Column name in clamsrw_rawcounts.txt: RNA172


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA740
Column name in clamsrw_rawcounts.txt: RNA740


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM589
Column name in clamsrw_rawcounts.txt: RM589


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM507
Column name in clamsrw_rawcounts.txt: RM507


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM607
Column name in clamsrw_rawcounts.txt: RM607


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM620
Column name in clamsrw_rawcounts.txt: RM620


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM544
Column name in clamsrw_rawcounts.txt: RM544


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA277
Column name in clamsrw_rawcounts.txt: RNA277


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA308
Column name in clamsrw_rawcounts.txt: RNA308


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM512
Column name in clamsrw_rawcounts.txt: RM512


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM610
Column name in clamsrw_rawcounts.txt: RM610


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM548
Column name in clamsrw_rawcounts.txt: RM548


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM588
Column name in clamsrw_rawcounts.txt: RM588


title: female, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RNA180
Column name in clamsrw_rawcounts.txt: RNA180


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM81
Column name in clamsrw_rawcounts.txt: RM81


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM503
Column name in clamsrw_rawcounts.txt: RM503


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM554
Column name in clamsrw_rawcounts.txt: RM554


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM62
Column name in clamsrw_rawcounts.txt: RM62


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM78
Column name in clamsrw_rawcounts.txt: RM78


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM372
Column name in clamsrw_rawcounts.txt: RM372


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM371
Column name in clamsrw_rawcounts.txt: RM371


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM79
Column name in clamsrw_rawcounts.txt: RM79


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM274
Column name in clamsrw_rawcounts.txt: RM274


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM310
Column name in clamsrw_rawcounts.txt: RM310


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM579
Column name in clamsrw_rawcounts.txt: RM579


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM303
Column name in clamsrw_rawcounts.txt: RM303


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM61
Column name in clamsrw_rawcounts.txt: RM61


title: male, HET/TG, Snord116+/-Ctg+/- , ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM593
Column name in clamsrw_rawcounts.txt: RM593


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM412
Column name in clamsrw_rawcounts.txt: RM412


title: male, HET/WT, Snord116+/-Ctg-/- , ZT06 biol rep 3, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM609
Column name in clamsrw_rawcounts.txt: RM609


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM304
Column name in clamsrw_rawcounts.txt: RM304


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM275
Column name in clamsrw_rawcounts.txt: RM275


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM413
Column name in clamsrw_rawcounts.txt: RM413


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM370
Column name in clamsrw_rawcounts.txt: RM370


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM302
Column name in clamsrw_rawcounts.txt: RM302


title: female, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B46
Column name in circadian_atlas_rawcounts.txt: B46

value: ZT21 biol rep 5

value: wildtype circadian atlas


title: male, WT/TG, Snord116+/+Ctg+/-, ZT06 biol rep 2, 11:11 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM306
Column name in clamsrw_rawcounts.txt: RM306


title: female, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B44
Column name in circadian_atlas_rawcounts.txt: B44

value: ZT18 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B22
Column name in circadian_atlas_rawcounts.txt: B22

value: left pre-frontal cortex

value: ZT21 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B24
Column name in circadian_atlas_rawcounts.txt: B24

value: female

value: ZT21 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B23
Column name in circadian_atlas_rawcounts.txt: B23

value: ZT21 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B21
Column name in circadian_atlas_rawcounts.txt: B21

value: ZT18 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B43
Column name in circadian_atlas_rawcounts.txt: B43

value: ZT18 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B20
Column name in circadian_atlas_rawcounts.txt: B20

value: ZT18 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B42
Column name in circadian_atlas_rawcounts.txt: B42

value: ZT15 biol rep 6


title: female, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B19
Column name in circadian_atlas_rawcounts.txt: B19

value: ZT18 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B18
Column name in circadian_atlas_rawcounts.txt: B18

value: ZT15 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B40
Column name in circadian_atlas_rawcounts.txt: B40

value: ZT15 biol rep 4

value: WT/WT, Snord116+/+Ctg-/-


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B16
Column name in circadian_atlas_rawcounts.txt: B16

value: ZT15 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B39
Column name in circadian_atlas_rawcounts.txt: B39

value: ZT12 biol rep 6


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, Running Wheel (RW) L:D

description:
Library name: RM427
Column name in clamsrw_rawcounts.txt: RM427

value: male

value: ZT06 biol rep 4

value: Running Wheel (RW)


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B37
Column name in circadian_atlas_rawcounts.txt: B37

value: left pre-frontal cortex

value: ZT12 biol rep 4

value: wildtype circadian atlas


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B15
Column name in circadian_atlas_rawcounts.txt: B15

value: female

value: ZT12 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B14
Column name in circadian_atlas_rawcounts.txt: B14

value: ZT12 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B38
Column name in circadian_atlas_rawcounts.txt: B38

value: ZT12 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B13
Column name in circadian_atlas_rawcounts.txt: B13

value: ZT12 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B36
Column name in circadian_atlas_rawcounts.txt: B36

value: ZT09 biol rep 6


title: female, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B45
Column name in circadian_atlas_rawcounts.txt: B45

value: ZT21 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B35
Column name in circadian_atlas_rawcounts.txt: B35

value: ZT09 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B34
Column name in circadian_atlas_rawcounts.txt: B34

value: ZT09 biol rep 4

value: WT/WT, Snord116+/+Ctg-/-


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B12
Column name in circadian_atlas_rawcounts.txt: B12

value: ZT09 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B11
Column name in circadian_atlas_rawcounts.txt: B11

value: ZT09 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B41
Column name in circadian_atlas_rawcounts.txt: B41

value: ZT15 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B7
Column name in circadian_atlas_rawcounts.txt: B7

value: ZT06 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B10
Column name in circadian_atlas_rawcounts.txt: B10

value: left pre-frontal cortex

value: ZT09 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B9
Column name in circadian_atlas_rawcounts.txt: B9

value: ZT06 biol rep 6

value: wildtype circadian atlas


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B8
Column name in circadian_atlas_rawcounts.txt: B8

value: female

value: ZT06 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B33
Column name in circadian_atlas_rawcounts.txt: B33

value: ZT06 biol rep 3


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B31
Column name in circadian_atlas_rawcounts.txt: B31

value: ZT06 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B32
Column name in circadian_atlas_rawcounts.txt: B32

value: ZT06 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B17
Column name in circadian_atlas_rawcounts.txt: B17

value: ZT15 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B6
Column name in circadian_atlas_rawcounts.txt: B6

value: ZT03 biol rep 6


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B4
Column name in circadian_atlas_rawcounts.txt: B4

value: ZT03 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B30
Column name in circadian_atlas_rawcounts.txt: B30

value: ZT03 biol rep 3

value: WT/WT, Snord116+/+Ctg-/-


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B5
Column name in circadian_atlas_rawcounts.txt: B5

value: ZT03 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B29
Column name in circadian_atlas_rawcounts.txt: B29

value: ZT03 biol rep 2


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: B3
Column name in circadian_atlas_rawcounts.txt: B3

value: ZT00 biol rep 6


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: B26
Column name in circadian_atlas_rawcounts.txt: B26

value: left pre-frontal cortex

value: ZT00 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: B27
Column name in circadian_atlas_rawcounts.txt: B27

value: ZT00 biol rep 5


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: B2
Column name in circadian_atlas_rawcounts.txt: B2

value: ZT00 biol rep 2

value: wildtype circadian atlas


title: female, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B28
Column name in circadian_atlas_rawcounts.txt: B28

value: female

value: ZT03 biol rep 1


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: B1
Column name in circadian_atlas_rawcounts.txt: B1

value: ZT00 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A46
Column name in circadian_atlas_rawcounts.txt: A46

value: male

value: ZT21 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A45
Column name in circadian_atlas_rawcounts.txt: A45

value: ZT21 biol rep 4


title: male, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A22
Column name in circadian_atlas_rawcounts.txt: A22

value: ZT21 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A24
Column name in circadian_atlas_rawcounts.txt: A24

value: ZT21 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A44
Column name in circadian_atlas_rawcounts.txt: A44

value: ZT18 biol rep 5

value: WT/WT, Snord116+/+Ctg-/-


title: male, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A21
Column name in circadian_atlas_rawcounts.txt: A21

value: ZT18 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT21 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A23
Column name in circadian_atlas_rawcounts.txt: A23

value: ZT21 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A20
Column name in circadian_atlas_rawcounts.txt: A20

value: left pre-frontal cortex

value: ZT18 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A40
Column name in circadian_atlas_rawcounts.txt: A40

value: ZT15 biol rep 4


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A41
Column name in circadian_atlas_rawcounts.txt: A41

value: ZT15 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A17
Column name in circadian_atlas_rawcounts.txt: A17

value: ZT15 biol rep 2

value: wildtype circadian atlas


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A42
Column name in circadian_atlas_rawcounts.txt: A42

value: ZT15 biol rep 6


title: male, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A43
Column name in circadian_atlas_rawcounts.txt: A43

value: ZT18 biol rep 4


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A39
Column name in circadian_atlas_rawcounts.txt: A39

value: male

value: ZT12 biol rep 6


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A15
Column name in circadian_atlas_rawcounts.txt: A15

value: ZT12 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A13
Column name in circadian_atlas_rawcounts.txt: A13

value: ZT12 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A14
Column name in circadian_atlas_rawcounts.txt: A14

value: ZT12 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A37
Column name in circadian_atlas_rawcounts.txt: A37

value: ZT12 biol rep 4


title: female, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: B25
Column name in circadian_atlas_rawcounts.txt: B25

value: female

value: ZT00 biol rep 3

value: WT/WT, Snord116+/+Ctg-/-


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A36
Column name in circadian_atlas_rawcounts.txt: A36

value: left pre-frontal cortex

value: ZT09 biol rep 6


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A35
Column name in circadian_atlas_rawcounts.txt: A35

value: ZT09 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A12
Column name in circadian_atlas_rawcounts.txt: A12

value: ZT09 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A11
Column name in circadian_atlas_rawcounts.txt: A11

value: ZT09 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A34
Column name in circadian_atlas_rawcounts.txt: A34

value: ZT09 biol rep 4

value: wildtype circadian atlas


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A8
Column name in circadian_atlas_rawcounts.txt: A8

value: ZT06 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT09 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A10
Column name in circadian_atlas_rawcounts.txt: A10

value: male

value: ZT09 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A7
Column name in circadian_atlas_rawcounts.txt: A7

value: ZT06 biol rep 4


title: male, WT/WT, Snord116+/+Ctg-/-, ZT18 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A19
Column name in circadian_atlas_rawcounts.txt: A19

value: ZT18 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A32
Column name in circadian_atlas_rawcounts.txt: A32

value: ZT06 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A31
Column name in circadian_atlas_rawcounts.txt: A31

value: ZT06 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A5
Column name in circadian_atlas_rawcounts.txt: A5

value: ZT03 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A4
Column name in circadian_atlas_rawcounts.txt: A4

value: ZT03 biol rep 4


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A16
Column name in circadian_atlas_rawcounts.txt: A16

value: ZT15 biol rep 1

value: WT/WT, Snord116+/+Ctg-/-


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A30
Column name in circadian_atlas_rawcounts.txt: A30

value: left pre-frontal cortex

value: ZT03 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A6
Column name in circadian_atlas_rawcounts.txt: A6

value: ZT03 biol rep 6


title: male, WT/WT, Snord116+/+Ctg-/-, ZT15 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A18
Column name in circadian_atlas_rawcounts.txt: A18

value: ZT15 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT12 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A38
Column name in circadian_atlas_rawcounts.txt: A38

value: ZT12 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A3
Column name in circadian_atlas_rawcounts.txt: A3

value: ZT00 biol rep 6

value: wildtype circadian atlas


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A29
Column name in circadian_atlas_rawcounts.txt: A29

value: male

value: ZT03 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 5, 12:12 L:D entrainment, circadian atlas

description:
Library name: A27
Column name in circadian_atlas_rawcounts.txt: A27

value: ZT00 biol rep 5


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A25
Column name in circadian_atlas_rawcounts.txt: A25

value: ZT00 biol rep 3


title: male, WT/WT, Snord116+/+Ctg-/-, ZT03 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A28
Column name in circadian_atlas_rawcounts.txt: A28

value: ZT03 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 2, 12:12 L:D entrainment, circadian atlas

description:
Library name: A2
Column name in circadian_atlas_rawcounts.txt: A2

value: ZT00 biol rep 2


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 1, 12:12 L:D entrainment, circadian atlas

description:
Library name: A1
Column name in circadian_atlas_rawcounts.txt: A1

value: ZT00 biol rep 1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 6, 12:12 L:D entrainment, circadian atlas

description:
Library name: A9
Column name in circadian_atlas_rawcounts.txt: A9

value: ZT06 biol rep 6


title: D3 AP+PBS-4

city: SHANGHAI

first: jing

last: jiang

state: China

address: CHINA SHANGHAI

institute: SHANGHAI GENERAL HOSPITAL

description:
Library name: Sample28
D3AP-4

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
Assembly: Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Supplementary files format and content: tab-delimited text file includes fpkm for each Sample

source_name: Pancreas

extract_protocol:
RNA was harvested using RNeasy Micro Kit (Qiagen). 10 ng of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Pancreas

value: macrophage

value: WT

tag: strain


title: D3 AP+PBS-1

description:
Library name: Sample25
D3AP-1


title: D3 AP+PBS-2

description:
Library name: Sample26
D3AP-2


title: D3 AP+PBS-3

description:
Library name: Sample27
D3AP-3


title: D3 AP+Lac-3

description:
Library name: Sample23
D3AL-3


title: D3 AP+Lac-4

description:
Library name: Sample24
D3AL-4


title: D3 AP+Lac-2

description:
Library name: Sample22
D3AL-2


title: D3 AP+Lac-1

description:
Library name: Sample21
D3AL-1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT06 biol rep 3, 12:12 L:D entrainment, circadian atlas

description:
Library name: A33
Column name in circadian_atlas_rawcounts.txt: A33

value: left pre-frontal cortex

value: ZT06 biol rep 3

value: WT/WT, Snord116+/+Ctg-/-


title: D1 AP+PBS-6

description:
Library name: Sample20
D1AP-6


title: D1 AP+PBS-5

description:
Library name: Sample19
D1AP-5


title: D1 AP+PBS-3

description:
Library name: Sample17
D1AP-3


title: D1 AP+PBS-4

description:
Library name: Sample18
D1AP-4


title: D1 AP+PBS-2

description:
Library name: Sample16
D1AP-2


title: D1 AP+Lac-6

description:
Library name: Sample14
D1AL-6


title: D1 AP+Lac-4

description:
Library name: Sample12
D1AL-4


title: D1 AP+PBS-1

description:
Library name: Sample15
D1AP-1


title: D1 AP+Lac-3

description:
Library name: Sample11
D1AL-3


title: D1 AP+Lac-5

description:
Library name: Sample13
D1AL-5


title: D1 AP+Lac-2

description:
Library name: Sample10
D1AL-2


title: D1 AP+Lac-1

description:
Library name: Sample9
D1AL-1


title: male, WT/WT, Snord116+/+Ctg-/-, ZT00 biol rep 4, 12:12 L:D entrainment, circadian atlas

description:
Library name: A26
Column name in circadian_atlas_rawcounts.txt: A26

value: ZT00 biol rep 4


title: D0-5

description:
Library name: Sample8
D0-5


title: D0-2

description:
Library name: Sample5
D0-2


title: D0-4

description:
Library name: Sample7
D0-4


title: D0-1

description:
Library name: Sample4
D0-1


title: NC-3

description:
Library name: Sample3
NC-3


title: NC-2

description:
Library name: Sample2
N-2


title: NC-1

description:
Library name: Sample1
NC-1


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27me3, biol rep3

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgasse 19

country: Austria

institute: Medical University of Vienna

description:
Library name: HDAC1-cKO early-non-TexProg H3K27me3 biol rep3
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.stringent.bed

data_processing:
Alignment of raw reads to mm10 genome was done with bowtie2 (version 2.5.0).
Blacklisted regions were removed via bedtools intersect (v2.29.1).
Duplicates were marked and for controls removed with Picard tools MarkDuplicates (version: 3.3.0-5-g46d23b4e4-SNAPSHOT).
Reads which mapped to mm10 as proper pairs were merged to one BAM file per sample using samtools merge (version 1.21).
RPKM normalized coverage files in BigWig format were generated with deeptools bamCoverage (version 3.5.6).
Peaks were called with SEACR (version 1.3) for H3K27ac and H3K27me3 samples against IgG background, and with MACS3 (version 3.0.3) for HDAC1 against KO background and RUNX3 against IgG background samples.
Assembly: mm10
Supplementary files format and content: BigWig files for merged replicates
Supplementary files format and content: BED (from SEACR) or narrowPeak (from MACS3) files for merged replicates, except for controls
Library strategy: CUT&Run

source_name: spleen

extract_protocol:
10 spleens per genotype were pooled, single-cell suspensions were prepared, then enriched for CD8+ T cells using the Miltenyi REAlease CD8a Microbead Kit for mouse. Cells were sorted for viability, TCRb, CD8, CD44, PD1 and then either Ly108 (early-TexProg) or PD-1 (early-non-TexProg). Nuclei were isolated, incubated with antibodies (HDAC1, H3K27ac, Runx3, H3K27me3, or IgG) and fragmented with MNase, DNA was isolated with NEB Monarch PCR and DNA clean up.
CUT&RUN Libraries were prepared from 2 ng using NEBNext Ultra II DNA Library Prep Kit, cleaned up using 0.9x volume of SPRI beads and subjected to PE150 sequencing.

value: spleen


title: mouse, WT, early-non-TexProg, IgG, biol rep3

description:
Library name: WT early-non-TexProg IgG biol rep3
CnR-20241114-CD8--Tim3--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, Runx3, biol rep3

description:
Library name: WT early-non-TexProg Runx3 biol rep3
CnR-20241114-CD8--Tim3--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-non-TexProg, IgG, biol rep3

description:
Library name: HDAC1-cKO early-non-TexProg IgG biol rep3
CnR-20241114-CD8--Tim3--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-non-TexProg, HDAC1, biol rep3

description:
Library name: HDAC1-cKO early-non-TexProg HDAC1 biol rep3
CnR-20241114-CD8--Tim3--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27ac, biol rep3

description:
Library name: HDAC1-cKO early-non-TexProg H3K27ac biol rep3
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, HDAC1-cKO, early-non-TexProg, Runx3, biol rep3

description:
Library name: HDAC1-cKO early-non-TexProg Runx3 biol rep3
CnR-20241114-CD8--Tim3--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-non-TexProg, H3K27me3, biol rep3

description:
Library name: WT early-non-TexProg H3K27me3 biol rep3
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, IgG, biol rep3

description:
Library name: HDAC1-cKO early-TexProg IgG biol rep3
CnR-20241114-CD8--Ly108--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, HDAC1, biol rep3

description:
Library name: WT early-non-TexProg HDAC1 biol rep3
CnR-20241114-CD8--Tim3--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Tim3--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, Runx3, biol rep3

description:
Library name: HDAC1-cKO early-TexProg Runx3 biol rep3
CnR-20241114-CD8--Ly108--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, H3K27ac, biol rep3

description:
Library name: HDAC1-cKO early-TexProg H3K27ac biol rep3
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, WT, early-TexProg, H3K27me3, biol rep3

description:
Library name: WT early-TexProg H3K27me3 biol rep3
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.stringent.bed


title: mouse, WT, early-TexProg, Runx3, biol rep3

description:
Library name: WT early-TexProg Runx3 biol rep3
CnR-20241114-CD8--Ly108--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, HDAC1, biol rep3

description:
Library name: HDAC1-cKO early-TexProg HDAC1 biol rep3
CnR-20241114-CD8--Ly108--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, H3K27ac, biol rep3

description:
Library name: WT early-non-TexProg H3K27ac biol rep3
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.stringent.bed


title: D0-3

description:
Library name: Sample6
D0-3


title: mouse, WT, early-TexProg, H3K27ac, biol rep3

description:
Library name: WT early-TexProg H3K27ac biol rep3
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27ac.merged.stringent.bed


title: mouse, WT, early-TexProg, HDAC1, biol rep3

description:
Library name: WT early-TexProg HDAC1 biol rep3
CnR-20241114-CD8--Ly108--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Ly108--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27me3, biol rep2

description:
Library name: HDAC1-cKO early-non-TexProg H3K27me3 biol rep2
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27me3.merged.stringent.bed


title: mouse, HDAC1-cKO, early-non-TexProg, IgG, biol rep2

description:
Library name: HDAC1-cKO early-non-TexProg IgG biol rep2
CnR-20241114-CD8--Tim3--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-TexProg, IgG, biol rep3

description:
Library name: WT early-TexProg IgG biol rep3
CnR-20241114-CD8--Ly108--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-non-TexProg, H3K27ac, biol rep2

description:
Library name: HDAC1-cKO early-non-TexProg H3K27ac biol rep2
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-HDAC1-KO-H3K27ac.merged.stringent.bed


title: mouse, HDAC1-cKO, early-non-TexProg, Runx3, biol rep2

description:
Library name: HDAC1-cKO early-non-TexProg Runx3 biol rep2
CnR-20241114-CD8--Tim3--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-non-TexProg, H3K27me3, biol rep2

description:
Library name: WT early-non-TexProg H3K27me3 biol rep2
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27me3.merged.stringent.bed


title: mouse, WT, early-non-TexProg, IgG, biol rep2

description:
Library name: WT early-non-TexProg IgG biol rep2
CnR-20241114-CD8--Tim3--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-non-TexProg, HDAC1, biol rep2

description:
Library name: HDAC1-cKO early-non-TexProg HDAC1 biol rep2
CnR-20241114-CD8--Tim3--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, HDAC1-cKO, early-TexProg, IgG, biol rep2

description:
Library name: HDAC1-cKO early-TexProg IgG biol rep2
CnR-20241114-CD8--Ly108--T-HDAC1-KO-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, Runx3, biol rep2

description:
Library name: WT early-non-TexProg Runx3 biol rep2
CnR-20241114-CD8--Tim3--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Tim3--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, H3K27me3, biol rep3

description:
Library name: HDAC1-cKO early-TexProg H3K27me3 biol rep3
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, HDAC1, biol rep2

description:
Library name: HDAC1-cKO early-TexProg HDAC1 biol rep2
CnR-20241114-CD8--Ly108--T-HDAC1-KO-HDAC1.merged.sorted.rpkm.BigWig


title: mouse, WT, early-non-TexProg, HDAC1, biol rep2

description:
Library name: WT early-non-TexProg HDAC1 biol rep2
CnR-20241114-CD8--Tim3--T-WT-HDAC1.merged.sorted.rpkm.BigWig
Tim3--T-WT-HDAC1-keepdup-maxgap-minlen-dedupKOctrl_peaks.narrowPeak


title: mouse, HDAC1-cKO, early-TexProg, Runx3, biol rep2

description:
Library name: HDAC1-cKO early-TexProg Runx3 biol rep2
CnR-20241114-CD8--Ly108--T-HDAC1-KO-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-HDAC1-KO-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak


title: mouse, WT, early-non-TexProg, H3K27ac, biol rep2

description:
Library name: WT early-non-TexProg H3K27ac biol rep2
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Tim3--T-WT-H3K27ac.merged.stringent.bed


title: mouse, HDAC1-cKO, early-TexProg, H3K27me3, biol rep2

description:
Library name: HDAC1-cKO early-TexProg H3K27me3 biol rep2
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-HDAC1-KO-H3K27me3.merged.stringent.bed


title: mouse, WT, early-TexProg, IgG, biol rep2

description:
Library name: WT early-TexProg IgG biol rep2
CnR-20241114-CD8--Ly108--T-WT-IgG.merged.sorted.rpkm.BigWig


title: mouse, WT, early-TexProg, H3K27me3, biol rep2

description:
Library name: WT early-TexProg H3K27me3 biol rep2
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.sorted.rpkm.BigWig
CnR-20241114-CD8--Ly108--T-WT-H3K27me3.merged.stringent.bed


title: tga7_control_shoot2

value: sufficient nitrogen

value: shoot


title: mouse, WT, early-TexProg, Runx3, biol rep2

description:
Library name: WT early-TexProg Runx3 biol rep2
CnR-20241114-CD8--Ly108--T-WT-RUNX3.merged.sorted.rpkm.BigWig
Ly108--T-WT-RUNX3-keepdup-maxgap-minlen_peaks.narrowPeak