title: Leaf, b-ionone+botrytis, 24 hours, rep 1 [BIBc24h1]

city: Thuwal

first: Juan Camilo

last: Moreno Beltran

address: King Abdullah University of Science and Technology

country: Saudi Arabia

institute: KAUST

data_processing:
Fastp was used to process Raw data of FASTQ format at first (Cock et al., 2010). This step removes adapter reads, poly-N sequences, and reads with low quality from the raw data.
In Parallel, Q20, Q30, and GC content of cleaned data were calculated. Final cleaned reads were used in all downstream analysis.
All cleaned Paired-end reads were mapped against reference genomes obtained from NCBI, UCSC, and Ensembl genomes and gene model annotations, using HISAT2 software.
HISAT2 enables fast and very accurate alignment of sequencing reads by using a large set of small GFM indexes that collectively cover the whole genome in combination with multiple alignment strategies.
The assembly was done using Stringtie to assemble transcript isoforms for each bam file generated from the mapping step. Gffcompare is able to compare Stringtie assemblies to the reference annotation files and assists in identifying new genes from declared ones.
Assembly: NCBI, UCSC, and Ensembl
Supplementary files format and content: Excel 97-2003 workbook (.xls) including gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for preBI_AvspreM_A
Supplementary files format and content: Excel 97-2003 workbook (.xls) including gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for BI_0hvspreM_B
Supplementary files format and content: Excel 97-2003 workbook (.xls) including gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for Bc_24hvsM_0h
Supplementary files format and content: Excel 97-2003 workbook (.xls) including gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for BIBc24hvsM_0h
Supplementary files format and content: Excel 97-2003 workbook (.xls) including gene id, Tair ATG identifier, normalized data, Log2Fold change, p-value, p-adjust, gene description, read counts and FPKM values for BIBc48hvsM_0h

organism: Arabidopsis thaliana

source_name: Leaf

growth_protocol: Arabidopsis thaliana col-0 seeds were grown on Jiffy soil (Jiffy Product International AS, Norway). They were placed at 4C degrees for three days before being transferred to a growth chamber with 16 h light/8 h dark and 180 µmol m-1 s-1 illumination at 21C day/18C night for four weeks.

extract_protocol:
Total RNA was extracted using the Direct-zol RNA Miniprep Plus Kit (Zymo Research according to the manufacturer’s instructions).  A total of 2ug were used for libraries preparation.
RNA sequencing was performed by Novogene (Novogene Co., Ltd., Beijing, China). A total of 2000 ng total RNA was used to extract messenger RNA, using poly-T oligo-attached magnetic beads. Random hexamer primers were used to synthesize the first strand of cDNA from the fragmented RNA. The second strand was synthesized using either dUTP or dTTP, depending on whether the library was directional or non-directional. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was quantified using Qubit and real-time PCR and detected size distribution using a bioanalyzer device. Libraries were pooled and sequenced using Illumina sequencing and paired-end reads were generated.

treatment_protocol: Arabidopsis plants were sprayed twice with β-ionone (50 μM; dissolved in 1% acetone and 0.05% tween 20) within 24 hours and plants sprayed with mock solution were used as the control. For fungal infection, plants were spray-inoculated with B. cinerea (2.5x105 spores ml-1). For combined treatments b-ionone was applied twice during 24 hours and then plants were infeted with Botrytis cinerea. Samples were harvested after 24 and 48 post infection.

value: Leaf

tag: cell line

value: 24 hours

tag: cell type

value: 4 weeks old

value: wild type

value: b-ionone+botrytis


title: Leaf, Botrytis, 24 hours, rep 1 [Bc_24h_1]

status: Public on Sep 30 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment

value: Botrytis


title: Leaf, b-ionone+botrytis, 24 hours, rep 2 [BIBc24h2]


title: Leaf, b-ionone+botrytis, 48 hours, rep 2 [BIBc48h2]

value: 48 hours


title: Leaf, Mock, 24 hours, rep 3 [M_0h_3]

value: Mock


title: Leaf, b-ionone+botrytis, 48 hours, rep 3 [BIBc48h3]


title: Leaf, Botrytis, 24 hours, rep 3 [Bc_24h_3]


title: Leaf, Mock, 24 hours, rep 3 [preM_B3]

value: Mock (acetone)


title: Leaf, b-ionone+botrytis, 48 hours, rep 1 [BIBc48h1]


title: Leaf, Mock, 24 hours, rep 2 [preM_B2]


title: Leaf, Mock, 24 hours, rep 1 [preM_B1]


title: Leaf, b-ionone, 24 hours, rep 2 [BI_0h_2]

value: b-ionone


title: Leaf, b-ionone, 24 hours, rep 3 [BI_0h_3]


title: Leaf, Mock, 3 hours, rep 3 [preM_A3]

value: 3 hours


title: Leaf, b-ionone, 24 hours, rep 1 [BI_0h_1]


title: Leaf, Mock, 3 hours, rep 1 [preM_A1]


title: Leaf, Mock, 3 hours, rep 2 [preM_A2]


title: Leaf, b-ionone, 3hours, rep 1 [preBI_A1]


title: Leaf, b-ionone, 3hours, rep 2 [preBI_A2]


title: Leaf, Mock, 24 hours, rep 2 [M_0h_2]


title: Leaf, b-ionone+botrytis, 24 hours, rep 3 [BIBc24h3]


title: Leaf, b-ionone, 3hours, rep 3 [preBI_A3]


title: Leaf, Botrytis, 24 hours, rep 2 [Bc_24h_2]


title: Heat-triggered ddm1 seedling D7, rep4

city: Vienna

first: Ruben

last: Gutzat

state: Vienna

address: Dr. Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute GmbH

data_processing:
the raw BAM files were converted to fastq by bedtools (v2.27)
The fastq files were processed by nextflow RNAseq pipeline (v21.02.0) by the following command: "nextflow run nf-core/rnaseq --input /directory --fasta genome.fasta --gtf file.gtf --clip_r1 19 --clip_r2 5 -profile cbe"
The salmon count output file was used for gene expression analysis by DESeq2
Normalized reads were obtained by the DESeq2 analysis
Assembly: TAIR10
Supplementary files format and content: The processed file was the normalized counts from DESeq2 analysis. The table contains the first column is the gene_id, the following columns are replicate of each genotype and treatment, then the mean, and then the standard deviation

source_name: seedlings

growth_protocol: Plants were grown in vitro until D7 and transferred to soil under LED illumination and 8h light/16h darkness cycles, watering twice a week.

extract_protocol:
Stem cell nuclei were directly collected for mRNA-seq protocol. Total RNA from seedlings and inflorescence meristems were collected by TRI agent and chloroform. The aquaous phased was collected and then adding 1 volume of isopropanol for RNA precipitation overnight. The pellets were washed  twice with 75% ethanol, then dried and resuspended with RNA-free water.
SMART-Seq V2
Illumina NovaSeq SP SR100

treatment_protocol: After heat-heat triggered (D7), shoot apical meristem were collected for isolating stem cell nuclei and somatic nuclei. The remaining plants were transferred to soil and grew until D28 for the next time point of nuclei isolation.

tag: ecotype

value: seedlings

value: Inflorescence meristems

value: heat-triggered

tag: time


title: Heat-triggered ddm1 seedling D7, rep1


title: Leaf, Mock, 24 hours, rep 1 [M_0h_1]


title: Heat-triggered poliv seedling D7, rep3

value: poliv


title: Heat-triggered poliv seedling D7, rep4


title: Heat-triggered ddm1 seedling D7, rep2


title: Heat-triggered ddm1 seedling D7, rep3


title: Heat-triggered poliv seedling D7, rep1


title: Heat-triggered poliv seedling D7, rep2


title: Control ddm1 seedling D7, rep3

value: control


title: Control poliv seedling D7, rep4


title: Heat-triggered wt seedling D7, rep2

value: wt


title: Heat-triggered wt seedling D7, rep1


title: Heat-triggered wt seedling D7, rep3


title: Control ddm1 seedling D7, rep4


title: Control ddm1 seedling D7, rep1


title: Control poliv seedling D7, rep3


title: Control wt seedling D7, rep4


title: Control poliv seedling D7, rep1


title: Control wt seedling D7, rep1


title: Control wt seedling D7, rep3


title: Control wt seedling D7, rep2


title: Control ddm1 seedling D7, rep2


title: Heat-triggered wt seedling D7, rep4


title: Heat-triggered ddm1 inflorescence meristem D28, rep1

source_name: Inflorescence apices

value: Inflorescence apices


title: Heat-triggered ddm1 inflorescence meristem D28, rep3


title: Heat-triggered poliv inflorescence meristem D28, rep4


title: Heat-triggered ddm1 inflorescence meristem D28, rep2


title: Heat-triggered poliv inflorescence meristem D28, rep3


title: Control ddm1 inflorescence meristem D28, rep4


title: Control ddm1 inflorescence meristem D28, rep3


title: Heat-triggered wt inflorescence meristem D28, rep4


title: Heat-triggered poliv inflorescence meristem D28, rep2


title: Heat-triggered wt inflorescence meristem D28, rep1


title: Heat-triggered wt inflorescence meristem D28, rep3


title: Heat-triggered wt inflorescence meristem D28, rep2


title: Heat-triggered poliv inflorescence meristem D28, rep1


title: Control ddm1 inflorescence meristem D28, rep1


title: Control ddm1 inflorescence meristem D28, rep2


title: Control poliv inflorescence meristem D28, rep2


title: Control poliv inflorescence meristem D28, rep3


title: Control wt inflorescence meristem D28, rep4


title: Control wt inflorescence meristem D28, rep1


title: Control poliv inflorescence meristem D28, rep1


title: Control ddm1 stem cell nuclei D28, rep3

source_name: Inflorescence meristems

value: stem cell nuclei


title: Control wt inflorescence meristem D28, rep2


title: Heat-triggered wt stem cell nuclei D28, rep3


title: Heat-triggered poliv stem cell nuclei D28, rep3


title: Heat-triggered wt stem cell nuclei D28, rep1


title: Heat-triggered wt stem cell nuclei D28, rep4


title: Heat-triggered poliv stem cell nuclei D28, rep1


title: Heat-triggered ddm1 stem cell nuclei D28, rep3


title: Heat-triggered poliv stem cell nuclei D28, rep4


title: Heat-triggered poliv stem cell nuclei D28, rep2


title: Heat-triggered wt stem cell nuclei D28, rep2


title: Control ddm1 stem cell nuclei D28, rep4


title: Heat-triggered ddm1 stem cell nuclei D28, rep1


title: Control ddm1 stem cell nuclei D28, rep1


title: Control poliv stem cell nuclei D28, rep3


title: Control wt stem cell nuclei D28, rep3


title: Control poliv stem cell nuclei D28, rep1


title: Control poliv stem cell nuclei D28, rep2


title: Control wt stem cell nuclei D28, rep4


title: Control ddm1 stem cell nuclei D28, rep2


title: Heat-triggered ddm1 stem cell nuclei D28, rep2


title: Control wt stem cell nuclei D28, rep2


title: Control poliv inflorescence meristem D28, rep4


title: Control poliv stem cell nuclei D28, rep4


title: Control wt somatic nuclei D7, rep6

source_name: Shoot apical meristems

value: Shoot apical meristems

value: somatic nuclei


title: Control wt somatic nuclei D7, rep5


title: Control wt somatic nuclei D7, rep3


title: Control ddm1 stem cell nuclei D7, rep6


title: Control ddm1 stem cell nuclei D7, rep4


title: Control ddm1 stem cell nuclei D7, rep5


title: Control wt somatic nuclei D7, rep4


title: Control poliv stem cell nuclei D7, rep8


title: Control ddm1 stem cell nuclei D7, rep8


title: Control wt somatic nuclei D7, rep2


title: Control wt somatic nuclei D7, rep1


title: Control wt stem cell nuclei D28, rep1


title: Control poliv stem cell nuclei D7, rep5


title: Control ddm1 stem cell nuclei D7, rep2


title: Control ddm1 stem cell nuclei D7, rep1


title: Control poliv stem cell nuclei D7, rep7


title: Control wt stem cell nuclei D7, rep7


title: Control ddm1 stem cell nuclei D7, rep3


title: Control ddm1 stem cell nuclei D7, rep7


title: Control poliv stem cell nuclei D7, rep1


title: Control wt stem cell nuclei D7, rep8


title: Control wt stem cell nuclei D7, rep6


title: Control wt stem cell nuclei D7, rep5


title: Control poliv stem cell nuclei D7, rep2


title: Control wt stem cell nuclei D7, rep4


title: Control poliv stem cell nuclei D7, rep3


title: Control poliv stem cell nuclei D7, rep4


title: Control wt stem cell nuclei D7, rep3


title: Control wt stem cell nuclei D7, rep2


title: Control poliv stem cell nuclei D7, rep6


title: Control wt stem cell nuclei D7, rep1


title: Heat-triggered wt somatic nuclei D7, rep6


title: Heat-triggered wt somatic nuclei D7, rep5


title: Heat-triggered wt somatic nuclei D7, rep4


title: Heat-triggered wt somatic nuclei D7, rep3


title: Heat-triggered wt somatic nuclei D7, rep2


title: Heat-triggered wt somatic nuclei D7, rep1


title: Heat-triggered poliv  stem cell nuclei D7, rep8


title: Heat-triggered ddm1  stem cell nuclei D7, rep3


title: Heat-triggered ddm1  stem cell nuclei D7, rep7


title: Heat-triggered ddm1  stem cell nuclei D7, rep4


title: Heat-triggered ddm1  stem cell nuclei D7, rep5


title: Heat-triggered poliv  stem cell nuclei D7, rep5


title: Heat-triggered ddm1  stem cell nuclei D7, rep6


title: Heat-triggered poliv  stem cell nuclei D7, rep7


title: Heat-triggered poliv  stem cell nuclei D7, rep2


title: Heat-triggered ddm1  stem cell nuclei D7, rep1


title: Heat-triggered poliv  stem cell nuclei D7, rep3


title: Heat-triggered poliv  stem cell nuclei D7, rep6


title: Heat-triggered wt stem cell nuclei D7, rep6


title: Heat-triggered wt stem cell nuclei D7, rep7


title: Heat-triggered wt stem cell nuclei D7, rep8


title: Heat-triggered poliv  stem cell nuclei D7, rep4


title: Heat-triggered ddm1  stem cell nuclei D7, rep8


title: Heat-triggered ddm1  stem cell nuclei D7, rep2


title: Heat-triggered wt stem cell nuclei D7, rep4


title: Heat-triggered wt stem cell nuclei D7, rep3


title: Heat-triggered wt stem cell nuclei D7, rep5


title: Heat-triggered wt stem cell nuclei D7, rep2


title: Heat-triggered poliv  stem cell nuclei D7, rep1


title: Heat-triggered wt stem cell nuclei D7, rep1


title: Control ddm1 stem cell nuclei D28 rep2

library_source: genomic

data_processing:
the raw BAM files were converted to fastq by bedtools (v2.27)
Read adapters were removed by trim_galore (v0.6.2) with additional parameter "--clip_r1 13 --three_prime_clip_r1 12"
Reads were mapped to TAIR10 genome by bismark (v0.22.2), and deduplicated by deduplicated_bismark
Methylpy (v1.2.9) was used to call methylation of the deduplicated files.
Assembly: TAIR10
Supplementary files format and content: The processed file is methylation levels of genomic features. The table contains the first column is the gene_id, the following columns are the methylation, coverage, and methylation level.

molecule: genomic DNA

extract_protocol:
Stem cell nuclei were collected in lysis buffer and DNA was isolated by the Quick-gDNA MicroPrep kit (#3020 Zymo Research)
Pico Methyl-Seq prep kit (Zymo Research #D5456)
Illumina NovaSeq SP SR100

treatment_protocol: After heat-heat triggered (D7), the plants were transferred to soil and grew until D28. Infloresence meristems were collected for preparing isolation stem cell nuclei for bisulfite-seq.

value: Control


title: Control ddm1 stem cell nuclei D28 rep1


title: Control poliv stem cell nuclei D28 rep2


title: Control poliv stem cell nuclei D28 rep1


title: Control wt stem cell nuclei D28 rep2


title: Heat-triggered ddm1 stem cell nuclei D28 rep2


title: Heat-triggered poliv stem cell nuclei D28 rep1


title: Control wt stem cell nuclei D28 rep1


title: Heat-triggered ddm1 stem cell nuclei D28 rep1


title: Heat-triggered wt stem cell nuclei D28 rep1


title: Heat-triggered wt stem cell nuclei D28 rep2


title: Thalami of saline injected Maged1 cKO mice-TIC

city: Lyon

first: Leonardo

last: Beccari

address: 8 Avenue Rockefeller

country: France

institute: Institute NeuroMyoGene (PGNM)

description: ChIPmentation

data_processing:
ChIPmentation sequencing data were analyzed using the public Galaxy server (Afgan E et al 2018) (doi:10.1093/nar/gky379) and personalized R scripts. First, adapter sequences were trimmed from both R1 and R2 adapters using Cutadpat v3 (Martin M et al 2011; CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -q 30 -m 15), and mapped against the mouse mm10 genome assembly using Bowtie2 (v 2.3.4.1) (Langmead B et al 2012). Only alignments with a mapping quality above 30 were kept (samtools v1..2 Danecek et al. 2021).
Significantly enriched regions were called using MACS2 (v 2.1.1.20160309.3) with broadpeak calling parameters (Zhang Y et al 2008). The bam files from TIC samples were used as a control for MACS peak calling. Coverage files were normalized by the number of millions of valid paired reads of each sample.

organism: Mus

source_name: Thalamus

growth_protocol: Conditional knockout mice were generated by crossing heterozygous Maged1 loxp/WT or homozygous Maged1 loxp/loxp females with different population selective Cre male mice. The Cre-mediated deletion of Maged1 was obtained using mice expressing Cre-recombinase under the control of the vGluT2 promoter. Maged1 WT or Maged1 cKO adult animals (2-4 months ) were used for ChIPmentation/RNAseq experiments.

extract_protocol:
Microdissected mouse thalami from WT were crosslinked in freshly prepared methanol free 1% formaldehyde solution (Thermofisher #28906) for 10 min at room temperature. The crosslinking reaction was stopped with  0,125M Glycine solution and the samples were washed 3x with PBS and sored at -80C.  Samples were then resuspended in cell lysis buffer (10 mM Tris pH 8.0, 10mM NaCl, 0,2% NP40, 1x EDTA free Proteinase inhibitor cocktail- PIC; Sigma # 11836170001) and nuclei were released by homogenization with a pestle B –douncer, centrifuged 8 min at  600g (4C) and resuspended in 130ul of sonication buffer (50 mM Tris pH 8.0, 10mM EDTA, 0,25% SDS, 1x PIC). After 15 min at 4C the resuspended nuclei were transferred to Covaris sonication microtubes (Covaris # 520045) and sonicated in a Covaris S220 ( to fragment chromatin to an average size of 200-400bp. Sheared chromatin was centrifuged at >13.000g  for 10 min to eliminate cell debris, and transferred to a new 1,5ml tubes and diluted 2,5x with ChIP dilution buffer (20mM HEPES pH 7.3, 1mM EDTA, 0,1% NP40, 150mM NaCl, 1x PIC). Anti-H2AK119ub antibody–Dynabeads protein G complexes were added to the diluted chromatin and incubated overnight at 4C with gentle rotation. For that, for each ChIP sample,  25ul of Dynabeads protein G magnetic beads (Thermofisher #) were transferred to a 1,5 ml tubes and washed twice with 1 ml of blocking buffer (PBS1x, 5mgr/ml BSA, 0,5% Tween 20, 1XPIC), resuspended in 200ul of blocking buffer and conjugated with 4ugr of anti-H2AK119ub antibody (Cell Signaling, 8240S) for 3h at 4C in a rotating platform. Subsequently beads- antibody complexes were washed twice and resuspended in 15ul of blocking buffer and added to the diluted chromatin. For each wash, the beads were incubated 5 min at 4C on a rotating platform, collected for 2 min in a magnetic stand and resuspended in 1 ml of blocking buffer. After overnight incubation chromatin –antibody- Dynabead complexes were washed twice with 1ml of RIPA/low salt buffer (10 mM Tris pH 8.0, 140mM NaCl, 0,1%, 1mM EDTA, Sodium Deoxicholate, 0,1% SDS, 0,1% Triton X100, 1XPIC), twice with 1ml of RIPA/high salt buffer (10 mM Tris pH 8.0, 500mM NaCl, 0,1%, 1mM EDTA, 0,1% Sodium Deoxicholate, 0,1% SDS, 0,1% Triton X100, 1XPIC), twice with 1ml of LiCl buffer (10 mM Tris pH 8.0, 250mM LiCl, 1mM EDTA, 0,5% Sodium Deoxicholate, 0,5% NP40, 0,1%, 1XPIC) and twice with 1ml 10mM Tris pH8.0. Washes were performed as described for the beads- antibody conjugation. After the last wash beads were resuspended in 200ul of 10mM Tris pH8.0 and transferred to a new tube, collected with the magnet and resuspended in 24ul of Tagmentation Mix (1:1 Illumina  2x Tagmentation buffer: 10mM Tris pH8.0). Resuspended chromatin- antibody complexes were incubated for 5 min at 37C and 1ul of  Illumina TDE1 enzyme was added to each sample. After mixing each ChIP sample was tagmented for exactly 7 min at 37C  and the reaction was immediately stopped by the addition of 1 ml of RIPA/low salt buffer. Samples were then washed once more with 1ml of RIPA/low salt buffer and once with 1ml TE buffer (10 mM Tris pH 8.0, 1mM EDTA). Finally, chromatin was eluted by resuspending beads in 100 ul of Elution buffer  (10 mM Tris pH 8.0, 5mM EDTA, 0.1% SDS, 0.3M NaCl) supplemented with 50ugr of proteinase K and incubating at 65C overnight in an agitating thermoblock with heated lid. For Total Imput Chromatin (TIC) samples, 10 ul of sonicated chromatin were diluted 10x in elution buffer with 50ugr of proteinase K and decrosslinked at 65C overnight. In all cases, decrosslinked DNA was treated with 20ugr of RNAseA  for 10 min at 37C, and purified with the Qiagen minielute PCR purification kit (Qiagen # 28004).
H2Aub ChIPmentation samples were quantified using the KAPA Library Quantification Kit (Roche #KK4923). The rest of each sample (20ul) was used for library amplification using Nextera single-index primers as described in Schmidl C et al. Using the KAPA HiFi hotstart ready mix (Roche # KK2601). The number of cycles used to amplify each library was determined as the Ct value of the qPCR reaction +1. For library quantification and amplification the KAPA HiFi polymerase was preactivated by heating at 98C for 30 sec. In all cases, a nick repair step was performed before PCR amplification by incubating the PCR reactions at 72c for 6 min. PCR-amplified libraries were purified and size selected for fragments of 200-250bp using the Pronex paramagnetic beads (Promega # NG2001) according to manufacturer instructions. For Total Imput Chromatin library preparation, approx 10-20ng of TIC samples were diluted in Illumina Tagmentation buffer and tagmented with the TDE1 enzyme as for ChIP samples. Finally, DNA was re-purified with the Qiagen minielute PCR purification kit and size-selected with the Pronex paramagnetic beads.Finally, libraries were quantified using the Qubit High Sensitivity DNA quantification kit (ThermoFisher # Q32851) and analyzed by Fragment analyzer.
ChIPmentation

treatment_protocol: Maged1 WT or Maged1 cKO mice were injected for three days with saline solution, followed by 5 days of cocaine or saline vehicle administration (20 mg/kg, intraperitoneal).

value: Thalamus

value: no antibody (TIC)

value: 2-4 months old mice

value: saline


title: wt col-0 rep7

data_processing:
illumina NovaSeq RTA System software
data were processed with nf-core/rnaseq (https://github.com/nf-core/rnaseq)
deviation from default pipeline options (star_salmon): parameters for trimming: --clip_r1 19 --clip_r2 9 --three_prime_clip_r1 5 --three_prime_clip_r2 5
counts table was analysed with Deseq2 and p-Values calculated with Wald-test
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and transposon for every sample

source_name: shoot apex

growth_protocol: seedlings were grown on soil at standard growth conditions (16h light/8h dark) and shoot apices harvested 7 days after germination

extract_protocol:
total RNA was extracted using Trizol reagent
Smart-seq3 (according to Hagemann-Jensen et. al, https://doi.org/10.1038/s41587-020-0497-0)

tag: developmental age

value: 7 days after germination

value: shoot apex


title: wt col-0 rep4


title: 8WG16_JK06_1hrauxin_L3_rep1 [HW06]

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

country: USA

institute: NYU

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
Supplementary files format and content: ChIP-seq: input normalized bigwigs

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: Mixed developmental stage embryos were obtained by bleaching gravid adults. To isolate synchronized L2/L3 worms, gravid adults were bleached and embryos were hatched overnight in M9 buffer. The resulting starved L1s were grown for 24 hours at 22°C. L3 worms were kept on plates with or without auxin prior to collection.

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.

tag: strain

tag: developmental stage

tag: antibody target

tag: antibody (vendor, cat#, lot#)


title: input_CA1200_1hrauxin_L3_rep2 [JK194]

value: input


title: 8WG16_JK05_1hrauxin_L3_rep3 [JK200]


title: input_JK06_1hrauxin_L3_rep1 [HW09]


title: Thalami of saline injected Maged1 WT mice-TIC

description: ChIPmentation

value: Maged1 Loxp


title: Thalami of cocaine injected Maged1 cKO mice-TIC

description: ChIPmentation

value: cocaine


title: wt col-0 rep3


title: wt col-0 rep8


title: input_JK05_1hrauxin_L3_rep1 [HW08]


title: input_JK06_1hrauxin_L3_rep2 [JK196]


title: 8WG16_JK06_1hrauxin_L3_rep2 [JK199]


title: Thalami of cocaine injected Maged1 WT mice-TIC

description: ChIPmentation


title: Thalami of saline injected Maged1 cKO mice-H2AK119ub_ replicate3

description: ChIPmentation


title: wt col-0 rep5


title: wt col-0 rep6


title: 8WG16_JK05_1hrauxin_L3_rep1 [HW04]


title: 8WG16_JK05_1hrauxin_L3_rep2 [JK198]


title: wt col-0 rep2


title: 8WG16_CA1200_1hrauxin_L3_rep2 [JK197]


title: Heat-triggered poliv stem cell nuclei D28 rep2

value: poliv

value: heat-triggered


title: Thalami of saline injected Maged1 cKO mice-H2AK119ub_ replicate 2

description: ChIPmentation


title: wt col-0 rep1


title: 8WG16_CA1200_1hrauxin_L3_rep1 [HW02]


title: input_JK05_1hrauxin_L3_rep2 [JK195]


title: input_CA1200_1hrauxin_L3_rep1 [HW07]


title: Thalami of saline injected Maged1 cKO mice-H2AK119ub_ replicate 1

description: ChIPmentation


title: wt21 rep8


title: PQN85_CA1200_1hrauxin_L3_rep2 [JK191]


title: wt21 rep7


title: PQN85_JK05_1hrauxin_L3_rep2 [JK192]


title: Thalami of cocaine injected Maged1 cKO mice-H2AK119ub_ replicate 2

description: ChIPmentation


title: wt21 rep6


title: wt21 rep5


title: Thalami of saline injected Maged1 WT mice-H2AK119ub_ replicate 3

description: ChIPmentation


title: Thalami of cocaine injected Maged1 cKO mice-H2AK119ub_ replicate 1

description: ChIPmentation


title: Thalami of saline injected Maged1 WT mice-H2AK119ub_ replicate 2

description: ChIPmentation


title: wt21 rep3


title: wt21 rep2


title: input_JK06_1hrauxin_L3_rep1 [JK138]

data_processing:
ChIP-seq: Bowtie2 version 2.4.2 was used to align 75 bp single-end reads to WS220 or its variants based on perturbation with default parameters (Langmead and Salzberg, 2012). Bam sorting and indexing was performed using samtools version 1.11 (Danecek et al., 2021). BamCompare tool in Deeptools version 3.5.0 was used to normalize for the sequencing depth using CPM and create ChIP-Input coverage and ChIP/Input ratios with a bin size of 10 bp and 200 bp read extension (Ramírez et al., 2016). Reads with a minimum mapping quality of 1 were used, and mitochondrial DNA, PCR duplicates, and blacklisted regions were removed (Amemiya et al., 2019). For DPY27 ChIP-seq data, the ratio values are used to rescale the data such that autosomes have mean of 0 and X-chromosome has mean of 1.
Hi-C:  data was mapped to ce10 (WS220) reference genome or its variant that corrosponds to the perturbation using default parameters of the Juicer pipeline version 1.5.7 (Durand et al., 2016).
Assembly: WS220 or its variants based on rex insertion or chromosome fusion
Supplementary files format and content: ChIP-seq: input normalized bigwigs
Supplementary files format and content: Hi-C:  hic matrix files

extract_protocol:
ChIP-seq: L2/L3s and adult worms were dounce-homogenized in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate; 150 mM NaCl) and sonicated in 0.1% sarkosyl to obtain chromatin fragments between 200 and 800 bp. 2 mg of protein extract and 3 to 10 ug of antibody was used per ChIP.
Hi-C: Crosslinked worms were resuspended in 20 ul of PBS per 50ul of worm pellet then dripped into liquid nitrogen containing mortar. The worms were grounded with pestle until fine powder. Grounded worms were crosslinked again in 2% formaldehyde using the TC buffer as described by the Arima High Coverage Hi-C kit, which uses four 4-base cutters. The Arima manufacturer’s protocol was followed.
ChIP-seq: half of the ChIP DNA and 30 ng of input DNA were ligated to Illumina TruSeq adapters and amplified by PCR. Library DNA between 250 and 600 bp was gel purified.
Hi-C: Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.

tag: antibody (vendor, cat#)


title: input_JK06_noauxin_L3_rep2 [JK139]


title: input_JK05_1hrauxin_L3_rep2 [JK128]


title: GFP_JK06_1hrauxin_L3_rep2 [JK150]

value: GFP


title: input_JK05_noauxin_L3_rep2 [JK127]


title: GFP_JK06_1hrauxin_L3_rep1 [JK148]


title: input_JK06_noauxin_L3_rep1 [JK137]


title: GFP_JK06_noauxin_L3_rep2 [JK149]


title: GFP_JK06_noauxin_L3_rep1 [JK147]


title: Thalami of cocaine injected Maged1 WT mice-H2AK119ub_ replicate 2

description: ChIPmentation


title: input_JK05_1hrauxin_L3_rep1 [JK126]


title: wt21 rep1


title: input_JK05_noauxin_L3_rep1 [JK125]


title: Thalami of cocaine injected Maged1 WT mice-H2AK119ub_ replicate 1

description: ChIPmentation


title: GFP_JK05_1hrauxin_L3_rep2 [JK132]


title: ddm1 rep4


title: wt21 rep4


title: GFP_JK05_noauxin_L3_rep2 [JK131]


title: Thalami of saline injected Maged1 WT mice-H2AK119ub_ replicate 1

description: ChIPmentation


title: ddm1 rep3


title: A549_3D_BACH1_KO_H3K27ac_rp1

city: Nanjing

first: Zhiqiang

last: Huang

state: Jiangsu

address: Hankou 22

department: Medical School

country: China

institute: Nanjing University

description:
3D cultured cells
CUT&Tag

data_processing:
Sequencing files (FASTQ) were aligned to the GRCh37/hg19 version of Human reference genome using Bowtie2 (-p 20 --end-to-end –very -sensitive) (Langmead and Salzberg, 2012). Peak calling was computed via MACS2 . The sequencing tags (SAM) and peak file (BED) were then read and imported to the HOMER(Heinz et al., 2010) for statistical analysis. BedGraph files were imported into IGV software for data visualization.
Assembly: hg19
Supplementary files format and content: Bedgraph files contain the genomic coordinates and p value of each peak.
Library strategy: CUT&Tag

organism: Homo sapiens

source_name: A549 cells, 3D cultured lung carcinoma

growth_protocol: CRISPR/Cas9-mediated BACH1 knockout  A549 cells were maintained in advanced 10% FBS DMEM  3D culture medium.  ZFN-mediated HIF1A knock out  were maintained in normal 10% FBS DMEM medium

extract_protocol:
In brief, 105 of the 3D organoid cells were used for the CUT&Tag. The experiments were based on digitonin (Sigma, D5628) mediated cell permeabilization and concanavalin A coated magnetic beads (Bangs Laboratories, BP531) immobilization. Two biological replicates were used for all experiments. H3K27ac (Abcam, ab4729), HIF1a(Novus Biologicals,NB100-134) and BACH1(R&D, AF5776) were used as the primary antibodies. Anti-goat (Sigma, SAB3700280) and anti-rabbit (EpiCypher, 13-0047) secondary antibodies were followed for 1-hour incubation. PA-Tn5 (EpiCypher, 15-1117) was loaded for 1-hour incubation.
The cleaved DNA by Tn5 was extracted using a DNA Clean & Concentrator-5 Kit (Zymo Research, D4013). Library preparation was conducted using IDT primers (Illumina, 20027213) and NEB PCR enzyme mix (NEB, M0541S).

treatment_protocol: The BACH1 Con/ BACH1 KO and HIF1 Con/ HIF1 KO  A549 cells were harvested by using cell recovery solution.

value: Lung

tag: group

value: BACH1 KO cells

value: Epithelial cells


title: GFP_JK05_1hrauxin_L3_rep1 [JK130]


title: Thalami of cocaine injected Maged1 WT mice-H2AK119ub_ replicate 3

description: ChIPmentation


title: GFP_JK05_noauxin_L3_rep1 [JK129]


title: A549_3D_BACH1_KO_H3K27ac_rp2

description:
3D cultured cells
CUT&Tag


title: input_JK06_1hrauxin_L3_rep2 [JK186]


title: A549_3D_BACH1_Con_H3K27ac_rp2

description:
3D cultured cells
CUT&Tag

value: WT cells


title: ddm1 rep2


title: input_JK06_1hrauxin_L3_rep1 [JK140]


title: input_CA1200_1hrauxin_L3_rep1 [JK171]


title: input_JK05_1hrauxin_L3_rep2 [JK170]


title: ago9 rep3


title: SMC3_JK06_1hrauxin_L3_rep2 [JK185]


title: input_CA1200_1hrauxin_L3_rep2 [JK172]


title: input_JK05_1hrauxin_L3_rep1 [JK169]


title: SMC3_JK06_1hrauxin_L3_rep1 [JK167]


title: SMC3_CA1200_1hrauxin_L3_rep2 [JK166]


title: ago9 rep4


title: ddm1 rep1


title: ago9 rep2


title: A549_3D_BACH1_Con_H3K27ac_rp1

description:
3D cultured cells
CUT&Tag


title: A549_3D_HIF1_KO_BACH1_rp1

description:
3D cultured cells
CUT&Tag

value: HIF1A KO cells


title: ago9 rep1


title: ago5ago9 rep4


title: A549_3D_HIF1_Con_BACH1_rp2

description:
3D cultured cells
CUT&Tag


title: A549_3D_HIF1_Con_BACH1_rp1

description:
3D cultured cells
CUT&Tag


title: SMC1_JK06_1hrauxin_L3_rep2 [JK184b]


title: A549_3D_HIF1_KO_BACH1_rp2

description:
3D cultured cells
CUT&Tag


title: ago5ago9 rep3


title: A549_3D_BACH1_KO_BACH1_rp2

description:
3D cultured cells
CUT&Tag


title: SMC1_CA1200_1hrauxin_L3_rep1 [JK159b]


title: SMC1_JK05_1hrauxin_L3_rep2 [JK158b]


title: A549_3D_BACH1_KO_BACH1_rp1

description:
3D cultured cells
CUT&Tag


title: ago5ago9 rep2


title: A549_3D_BACH1_Con_BACH1_rp2

description:
3D cultured cells
CUT&Tag


title: SMC1_JK05_1hrauxin_L3_rep1 [JK157b]


title: ago5ago9 rep1


title: 2.02yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_55

type: genomic

city: Kolkata

first: Mayur

last: Parihar

state: West Bengal

address: 14 Major Arterial Road (E-W)

department: Pathology

country: India

institute: Tata Medical Center

description: hybridized to Affymetrix CytoScan HD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using ChAS v1.5.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

label: biotin

source_name: WBC from Bone Marrow

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: DNA extracted from mononuclear cell from Bone Marrow in EB at -20C

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, Qubit and agarose gel electrophoresis.

treatment_protocol: treatment is according to IciCLe protocol of InPOG

tag: subject id

tag: disease

value: B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL)

tag: age

tag: gender

value: Female


title: A549_3D_BACH1_Con_BACH1_rp1

description:
3D cultured cells
CUT&Tag

tag: cell type


title: 4.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_53

description: hybridized to Affymetrix CytoScan HD

value: Male


title: Hypoxia_HIF1A_NB100-134_2

description:
3D cultured cells
CUT&Tag
merged_Hypoxia_HIF1A_NB100_134_MACS2.bedgraph

tag: tissue

value: Hypoxia,WT cells


title: SMC3_JK05_1hrauxin_L3_rep2 [JK164]


title: 5.5yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_51

description: hybridized to Affymetrix CytoScan HD


title: ago5 rep3

value: 7 days after germination


title: Hypoxia_HIF1A_NB100-134_1


title: 9.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_50

description: hybridized to Affymetrix CytoScan HD


title: SMC1_CA1200_1hrauxin_L3_rep2 [JK160b]


title: ago5 rep2

value: shoot apex


title: 4.4yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_49

description: hybridized to Affymetrix CytoScan HD


title: 3.9yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_48

description: hybridized to Affymetrix CytoScan HD


title: Normoxia_HIF1A_NB100-134_2

description:
3D cultured cells
CUT&Tag
merged_Normoxia_HIF1A_NB100_134_MACS2.bedgraph

value: Normoxia,WT cells


title: ago5 rep1


title: Normoxia_HIF1A_NB100-134_1


title: 2.19yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_45

description: hybridized to Affymetrix CytoScan HD


title: 5.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_43

description: hybridized to Affymetrix CytoScan HD


title: 3.6yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_46

description: hybridized to Affymetrix CytoScan HD


title: Wang_ChIP_antiParB_BWX5470

city: Bloomington

first: Xindan

last: Wang

state: IN

address: 1001 E 3rd St

institute: Indiana University at Bloomington

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
Assembly: NC_022898.1
Supplementary files format and content: Files ending with .csv: comma-separated values files of ChIP-seq results.
header information: position, value
column information: genome position; number of reads at each genome position

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol:
Bacillus subtilis strains were derived from the prototrophic strain PY79 (Youngman et al 1983, PMID: 6300908). Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus) at specified temperature.
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

extract_protocol:
ChIP-seq experiments were performed using anti-ParB.
Standard library construction protocol was used for Illumina Nextseq550 sequencing platforms. Illumina Truseq indexes were used.

tag: growth condition

value: CH, 37C

tag: genotype

value: pelB::Psoj spo0J R80A (delta_parS) KCK cat, delta_spo0J spec

tag: chip target

value: ChIP using anti-ParB antibodies


title: 6.9yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_56

description: hybridized to Affymetrix CytoScan HD


title: 5.19yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_44

description: hybridized to Affymetrix CytoScan HD


title: ago5 rep4

tag: ecotype


title: 6.6yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_54

description: hybridized to Affymetrix CytoScan HD


title: 4.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_52

description: hybridized to Affymetrix CytoScan HD


title: ago4ago9 rep3

tag: developmental age


title: ago4ago9 rep2


title: 10.7yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_40

description: hybridized to Affymetrix CytoScan HD


title: 2.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_39

description: hybridized to Affymetrix CytoScan HD


title: Wang_ChIP_antiParB_BWX5466

value: pelB::Psoj opt KCK-spo0J (delta_parS) tet, delta_spo0J spec


title: Wang_ChIP_antiParB_BWX5444

value: pelB::Psoj spo0J (delta_parS) KCK cat, delta_spo0J spec


title: ago4ago9 rep1


title: 5.4yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_37

description: hybridized to Affymetrix CytoScan HD


title: Wang_ChIP_antiParB_BWX2034

value: pelB::Psoj spo0J delta_parS cat, delta_spo0J spec


title: 3.8yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_47

description: hybridized to Affymetrix CytoScan HD


title: ago4ago5ago9 rep3


title: Wang_ChIP_antiParB_BWX5468

value: pelB::Psoj opt KCK-spo0J R80A (delta_parS) tet, delta_spo0J spec


title: 2.3yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_35

description: hybridized to Affymetrix CytoScan HD


title: ago4ago5ago9 rep2


title: 2.1yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_32

description: hybridized to Affymetrix CytoScan HD


title: 4.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_33

description: hybridized to Affymetrix CytoScan HD


title: Wang_ChIP_antiParB_BWX2032

value: pelB::Psoj spo0J R80A delta_parS cat, delta_spo0J spec


title: ago4ago5ago9 rep1


title: 2.4yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_42

description: hybridized to Affymetrix CytoScan HD


title: 1.8yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_41

description: hybridized to Affymetrix CytoScan HD


title: ago4 rep4


title: 3.4yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_30

description: hybridized to Affymetrix CytoScan HD


title: 2.18yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_38

description: hybridized to Affymetrix CytoScan HD


title: ago4 rep3


title: ago4ago5ago9 rep4


title: 2.9yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_36

description: hybridized to Affymetrix CytoScan HD


title: ago4 rep2


title: 5.4yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_25

description: hybridized to Affymetrix CytoScan HD


title: 4.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_26

description: hybridized to Affymetrix CytoScan HD


title: ago4ago9 rep4


title: ago4 rep1


title: 4.07yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_22

description: hybridized to Affymetrix CytoScan HD


title: 2.9yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_21

description: hybridized to Affymetrix CytoScan HD


title: mouse choroid plexus from SCNx mouse sacrificed at time 36

city: Prague 4

first: Martin

last: Sládek

address: Videnska 1083

country: Czech Republic

institute: Institute of Physiology of the Czech Academy of Sciences

data_processing:
NextSeq 2000 P3 (50 cycles, SE), Nextflow 22.10.6
nf-core/rnaseq 3.10.1
mapped to Mm_39 by STAR_ALIGN 2.7.9a
read counts and transcripts per million (TPM) were calculated by Salmon 1.9.0, Samtools 1.16.1, Cutadapt 3.4 and Stringtie 2.2.1
Genes with average TPM > 1 across the whole group were analyzed for circadian rhythmicity using eJTK, ARSER and BioCycle.
Assembly: Genome Reference Consortium Mouse Build 39 (Mm_39_104_nf310)
Supplementary files format and content: salmon.merged.gene_counts.tsv - gene_id (ENSEMBL gene ID), gene_name, counts in columns named after samples
Supplementary files format and content: salmon_merged_counts_KO.csv -  gene_id (ENSEMBL gene ID), gene_name, counts in columns named after samples

organism: Mus musculus

source_name: choroid plexus

growth_protocol: C57Bl6J mice were housed individually in a temperature-controlled facility at 21-25°C with free access to food and water. The light/dark cycle was maintained with 12 h of light and 12 h of darkness (LD12:12); lights were turned on and off at 06:00. For KO mice tamoxifen was provided ad libitum through the diet (tamoxifen citrate 0.4g/kg; Envigo TD.130860) under 12:12 LD cycle (07:00 light-on and 19:00 light-off). The tamoxifen-induced flox recombination was tested in liver samples through qPCR (data not shown).

extract_protocol:
After exposure to constant darkness to verify absence of locomotor activity rhythms as a marker of SCN lesioning success, the mice of both groups (n = 12 per group) were returned to the original LD12:12 regime for one week to synchronize with the LD cycle. Subsequently, the lights were not switched on in the morning (assigned as circadian time, CT0), and mice remained in constant darkness for the following two days during which they were sacrificed every 4 h (from CT0 to CT44, 12 time points). ChP from the 4th ventricle was removed by pincers and immediately immersed into RNAlater. FoxJ1-ERT2-Cre+/-; Bmal1fl/fl (KO) mice were sacrificed at two time points; 7 h after the lights on for the day time point, i.e., Zeitgeber time (ZT)7 and 6 h after the lights off for the night time point, i.e., ZT18, at Taipei Medical University, Taipei, Taiwan. Whole brains were removed, frozen on dry ice, embedded in OCT compound (Sakura Finetek), and then cold-shipped to Prague. Upon arrival, they were sectioned on cryocut and ChP from the 4th ventricle was sampled by laser-capture microdissection.
rRNA depletion, polyA RNA enrichment, library preparation using KAPA mRNA HyperPrep Kit (Roche, Switzerland; for WT samples) or Smarter Stranded totRNA-seq low input kit (Takara, Japan; for KO samples)

treatment_protocol: The surgical ablation of the SCN and sham surgery were performed as previously described (10.1371/journal.pbio.3001637).

value: choroid plexus

tag: cell line

value: tissue

tag: treatment

value: SCN lesion

tag: time

value: adult

tag: Sex

value: male


title: mouse choroid plexus from SCNx mouse sacrificed at time 32


title: mouse choroid plexus from ChP-specific Bmal1-KO mouse sacrificed at time 7

value: FoxJ1-ERT2-Cre+/-; Bmal1fl/fl

value: tamoxifen


title: mouse choroid plexus from ChP-specific Bmal1-KO mouse sacrificed at time 18


title: mouse choroid plexus from SCNx mouse sacrificed at time 40


title: 3.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_20

description: hybridized to Affymetrix CytoScan HD

value: B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL)

value: Male


title: 2.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_34

description: hybridized to Affymetrix CytoScan HD


title: mouse choroid plexus from SCNx mouse sacrificed at time 28


title: 2.5yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_19

description: hybridized to Affymetrix CytoScan HD

value: Female


title: mouse choroid plexus from SCNx mouse sacrificed at time 44


title: mouse choroid plexus from SCNx mouse sacrificed at time 24


title: Sample 39_wt_dapi_R3

data_processing:
samples 1-40: NextSeq 550 RTA software, samples 41-67: illumina NovaSeq System software
data were processed with nf-core/rnaseq (https://github.com/nf-core/rnaseq)
deviation from default pipeline options (star_salmon): parameters for trimming samples 1-40: --clip_r1 19 --clip_r2 9 --three_prime_clip_r1 5 --three_prime_clip_r2 5
counts table was analysed with Deseq2 and p-Values calculated with Wald-test
Genome_build: Tair10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and transposon for every sample

molecule: nuclear RNA

source_name: seedling

growth_protocol: for samples 1-40: seedlings were grown on soil at standard growth conditions (16h light/8h dark) and shoot apices harvested 7 days after germination. For samples 41-67, pollen was harvested accoding to (DOI: 10.1111/j.1365-313X.2004.02147.x)

extract_protocol:
for samples 1-40: nuclei were extracted according to (DOI: 10.1007/978-1-0716-0179-2_7) and per replicate 100 nuclei sorted into (SmartSeq-) lysis buffer. For samples 41-67: nuclei were extracted according to (DOI: 10.1007/s00497-015-0258-2) into Trizol and total RNA extracted.
for samples 1-40: Smart-seq3 (according to Hagemann-Jensen et. al, https://doi.org/10.1038/s41587-020-0497-0), for samples 41-67: Smart-seq2 (DOI: 10.1038/nmeth.2639) from 2ng of RNA

value: 7 days after germination

value: non stem cells


title: 2.9yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_18

description: hybridized to Affymetrix CytoScan HD


title: 3.7yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_28

description: hybridized to Affymetrix CytoScan HD


title: 1.5yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_31

description: hybridized to Affymetrix CytoScan HD


title: 5.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_27

description: hybridized to Affymetrix CytoScan HD


title: 1.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_17

description: hybridized to Affymetrix CytoScan HD


title: 4.17yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_29

description: hybridized to Affymetrix CytoScan HD


title: 5.4yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_23

description: hybridized to Affymetrix CytoScan HD


title: 10.08yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_16

description: hybridized to Affymetrix CytoScan HD


title: mouse choroid plexus from SCNx mouse sacrificed at time 20


title: Sample 37_wt_cherry_R8

value: stem cells


title: 4.4yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_15

description: hybridized to Affymetrix CytoScan HD


title: 3.5yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_14

description: hybridized to Affymetrix CytoScan HD


title: 2.7yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_24

description: hybridized to Affymetrix CytoScan HD


title: Sample 40_wt_dapi_R4


title: Sample 36_wt_cherry_R7


title: 2.7yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_13

description: hybridized to Affymetrix CytoScan HD


title: 4.03yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_11

description: hybridized to Affymetrix CytoScan HD


title: 1.9yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_9

description: hybridized to Affymetrix CytoScan HD


title: Sample 35_wt_cherry_R5


title: 2.3yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_10

description: hybridized to Affymetrix CytoScan HD


title: 3.3yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_12

description: hybridized to Affymetrix CytoScan HD


title: 9.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_8

description: hybridized to Affymetrix CytoScan HD


title: Sample 34_wt_cherry_R4


title: Sample 33_wt_cherry_R3


title: mouse choroid plexus from SCNx mouse sacrificed at time 8


title: mouse choroid plexus from SCNx mouse sacrificed at time 12


title: mouse choroid plexus from SCNx mouse sacrificed at time 4


title: Sample 38_wt_dapi_R2


title: 3.6yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_6

description: hybridized to Affymetrix CytoScan HD


title: 6.3yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_5

description: hybridized to Affymetrix CytoScan HD


title: 4.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_7

description: hybridized to Affymetrix CytoScan HD


title: Sample 32_ago9_dapi_R4


title: mouse choroid plexus from control mouse sacrificed at time 44

value: sham surgery


title: mouse choroid plexus from SCNx mouse sacrificed at time 0


title: 2.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_4

description: hybridized to Affymetrix CytoScan HD


title: Sample 31_ago9_dapi_R3


title: mouse choroid plexus from control mouse sacrificed at time 40


title: Sample 30_ago9_dapi_R2


title: 2.08yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_2

description: hybridized to Affymetrix CytoScan HD


title: mouse choroid plexus from SCNx mouse sacrificed at time 16


title: 2.8yo Female High hyperdiploid Acute Lymphoblastic Leukemia Patient_3

description: hybridized to Affymetrix CytoScan HD


title: 2.7yo Male High hyperdiploid Acute Lymphoblastic Leukemia Patient_1

description: hybridized to Affymetrix CytoScan HD


title: Metabolic cycle 4, biol rep 3

first: Christine

last: Mayr

address: 417 E 68th Street

department: Cancer Biology and Genetics

institute: MSKCC

description:
ymc4.F.bedgraph
ymc4.R.bedgraph

data_processing:
Low-quality ends were trimmed by trimmomatic (version: 0.39; average quality per base < 15, 4 bp window). 3'-adapters were removed by cutadapt (version: 2.3)
Reads with at least two terminal adenylates were selected. The number of terminal adenylates were recorded and appended to read ID. All terminal adenylates were trimmed off from each read, and remaining sequence was mapped to yeast genome (version: 64.1.1) using hisat2 (version: 2.1.0).
Only reads with high mapping quality (mapq > 30) were kept. Only those reads whose number of terminal adenylates (labels in their IDs) exceeds the number of consecutive adenylates in adjacent genomic regions.
Bedgraph files containing genome coverage for each sample were generated by bedtools (genomecov function; version: v2.26.0)
Assembly: sacCer3
Supplementary files format and content: F.bedgraph (Bedgraph file of genome coverage on plus strand; all three biological replicates combined)
Supplementary files format and content: R.bedgraph (Bedgraph file of genome coverage on minus strand; all three biological replicates combined)
The bedgraph files are the read coverage of 3’-seq data. They represent the location of cleavage and polyadenylation sites.

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Yeast strain BY4741 was grown in YPD medium. An overnight culture was inoculated into 600 ml of YPD with a starting OD600 of 0.2. When the culture was grown to mid-log phase, it was dispensed by 100 ml and each was subjected to either control (30°C for 20 min or 2 h) or one of the three stress conditions (diauxic shift, DNA damage, heat shock). For metabolic cycles, yeast strain CEN.PK was cultivated as described elsewhere (Nocetti and Whitehouse, Genes & Dev., 2016).

extract_protocol:
The total RNA from each sample was extracted by hot phenol method.
An oligo(dT) primer containing a VN-anker, a uridine, the sequence of the sequencing adapter, and biotin (/5BiosG/CAGACGTGTGCTCTTCCGATCTTTTTTTTrUTT TTTTTTVN) was attached to streptavidin-coated magnetic beads (Invitrogen, M280). Total RNA was incubated for 5 min at 65°C, followed by incubation with the coated magnetic beads for 10 min at 45°C. First strand synthesis was carried out using SuperScript III reverse transcriptase (Invitrogen) at 50°C. The enzyme was inactivated by incubation for 15 min at 70°C. Second strand synthesis was carried out using second strand synthesis buffer (Invitrogen), dNTPs, DNA polymerase I (New England Biolabs), Escherichia coli ligase (New England Biolabs), and RNase H (Invitrogen). To exchange the buffers and remove enzymes from the previous step, we treated the samples with Pronase (Roche). We introduced a nick at the position of the uridine with RNase HII (New England Biolabs). Then, nick translation was carried out with DNA polymerase I (New England Biolabs) and dNTPs for 8 min at 8°C. The reaction was stopped by the addition of EDTA. At the new position of the nick, we created a blunt end using T7 exonuclease, mung bean nuclease, and Klenow enzyme (New England Biolabs). Previously annealed Illumina TruSeq sequencing adapters (Ad1, 59-AATGATACGGCGACCACCGAGATC TACACTCTTTCCCTACACGACGCTCTTCCGATCT-39;and Ad2, 59-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT AGATCTCGGTGGTCGCCGTAT-39) were then blunt-end-ligated. The magnetic beads were suspended in 39 mLofH2O. Five microliters of beads was used in a PCR reaction. Ten to 13 cycles of PCR were carried out with Phusion polymerase (New England Biolabs), a forward primer (59-AATGATACGGCGACCACCGA GATC-3), and one of the Illumina TruSeq barcode reverse primers. For preparation of the library, six PCR reactions were performed and run on 8% TBE gels (Invitrogen), and the smear between 160 bp and 220 bp was cut out, gel-extracted, ethanol-precipitated, analyzed by Bioanalyzer (Agilent), and sequenced on Illumina HiSeq machines.
3'-seq

treatment_protocol: Heat shock was conducted at 37°C for 20 min. To obtain cells experiencing diauxic shift, the glucose concentration of a culture was determined by Quantichrom glucose assay kit (Bioassay systems) following the manufacturer’s instructions and the culture with diauxic shift was harvested at 2 h after glucose depletion. For DNA damage, a culture was treated with 5 µg/ml 4-nitroquinoline 1-oxide (Sigma) for 2 h. The period of metabolic oscillation was approximately 3.2 h. Cells were harvested at 16, 32, 48, and 60 min from the start of the oxidative phase of each cycle in three consecutive oscillations.

tag: strain

value: yeast cell

value: MATa URA3 TRP1 LEU2 HIS3 MAL2-8C SUC2

value: 60 min from the start of oxidative phase


title: mouse choroid plexus from control mouse sacrificed at time 36

value: choroid plexus


title: Sample 28_ago9_cherry_R8


title: Metabolic cycle 4, biol rep 2

description:
ymc4.F.bedgraph
ymc4.R.bedgraph


title: Metabolic cycle 3, biol rep 3

description:
ymc3.F.bedgraph
ymc3.R.bedgraph

value: 48 min from the start of oxidative phase


title: mouse choroid plexus from control mouse sacrificed at time 32

value: tissue


title: Metabolic cycle 3, biol rep 2

description:
ymc3.F.bedgraph
ymc3.R.bedgraph


title: mouse choroid plexus from control mouse sacrificed at time 24

value: adult


title: Metabolic cycle 2, biol rep 3

description:
ymc2.F.bedgraph
ymc2.R.bedgraph

value: 32 min from the start of oxidative phase


title: Sample 26_ago9_cherry_R6


title: Sample 27_ago9_cherry_R7


title: Metabolic cycle 3, biol rep 1

description:
ymc3.F.bedgraph
ymc3.R.bedgraph


title: mouse choroid plexus from control mouse sacrificed at time 28

value: male


title: Metabolic cycle 2, biol rep 2

description:
ymc2.F.bedgraph
ymc2.R.bedgraph


title: Metabolic cycle 2, biol rep 1

description:
ymc2.F.bedgraph
ymc2.R.bedgraph


title: mouse choroid plexus from control mouse sacrificed at time 20


title: Sample 25_ago9_cherry_R5


title: mouse choroid plexus from control mouse sacrificed at time 16


title: Metabolic cycle 1, biol rep 2

description:
ymc1.F.bedgraph
ymc1.R.bedgraph

value: 16 min from the start of oxidative phase


title: Sample 24_ago9_cherry_R4


title: Metabolic cycle 1, biol rep 1

description:
ymc1.F.bedgraph
ymc1.R.bedgraph


title: mouse choroid plexus from control mouse sacrificed at time 12


title: Metabolic cycle 4, biol rep 1

description:
ymc4.F.bedgraph
ymc4.R.bedgraph


title: Heat shock, biol rep 2

description:
hs.F.bedgraph
hs.R.bedgraph

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: log phase, 37℃, 20 min


title: Metabolic cycle 1, biol rep 3

description:
ymc1.F.bedgraph
ymc1.R.bedgraph


title: Heat shock, biol rep 3

description:
hs.F.bedgraph
hs.R.bedgraph


title: mouse choroid plexus from control mouse sacrificed at time 8


title: Heat shock, biol rep 1

description:
hs.F.bedgraph
hs.R.bedgraph


title: Sample 29_ago9_dapi_R1


title: Sample 22_ago9_cherry_R1


title: mouse choroid plexus from control mouse sacrificed at time 4


title: Sample 21_ago5_dapi_R4


title: mouse choroid plexus from control mouse sacrificed at time 0


title: DNA damage, biol rep 3

description:
dna_damage.F.bedgraph
dna_damage.R.bedgraph

value: 5ug/ml 4-nitroquinoline 1-oxide, 2 h


title: DNA damage, biol rep 2


title: Diauxic shift, biol rep 3

description:
diauxic.F.bedgraph
diauxic.R.bedgraph

value: 2h after glucose depletion


title: DNA damage, biol rep 1


title: Sample 20_ago5_dapi_R2

value: 7 days after germination

value: non stem cells


title: Diauxic shift, biol rep 2

description:
diauxic.F.bedgraph
diauxic.R.bedgraph


title: Sample 19_ago5_dapi_R1


title: Heart, rmIL11, 3hr, rep3

city: London

first: Mark

last: Sweeney

address: Du Cane Road

department: London Institute of Medical Science

country: United Kingdom

institute: Imperial College London

data_processing:
Raw reads were aligned to the mouse reference genome GRCm39 (Ensembl release 106) using the STAR16 software v2.7.10a with default parameters.
Aligned reads were assigned to genes to give a gene-level count matrix using the featureCounts tool17 as part of the Rsubread package v2.10.4.
Differential gene expression analysis was performed using the edgeR18 software v3.38.1 following the author's recommended analysis pipeline utilising a quasi-likelihood negative binomial generalized log-linear model.
Assembly: GRCm39
Supplementary files format and content: Count per million data per sample

molecule: polyA RNA

source_name: heart

extract_protocol:
The heart was dissected from the chest and washed in ice-cold PBS and snap-frozen in liquid nitrogen. Total RNA was extracted using TRIzol (Invitrogen, 15596026) in RNeasy columns (Qiagen, 74106).
RNASeq libraries prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module following manufacturer’s instructions.

value: heart

value: wild-type

value: rmIL11 - 3hr


title: Diauxic shift, biol rep 1

description:
diauxic.F.bedgraph
diauxic.R.bedgraph

value: yeast cell


title: Sample 23_ago9_cherry_R3

value: stem cells


title: Control2, biol rep2

description:
c2.F.bedgraph
c2.R.bedgraph

value: log phase, 30℃, 2 h


title: Heart, rmIL11, 3hr, rep4


title: Control2, biol rep3

description:
c2.F.bedgraph
c2.R.bedgraph


title: Sample 18_ago5_cherry_R9


title: Sample 17_ago5_cherry_R8


title: Sample 16_ago5_cherry_R7


title: Heart, rmIL11, 3hr, rep2


title: Heart, PBS, baseline, rep4

value: PBS


title: Heart, PBS, baseline, rep3


title: Control2, biol rep1

description:
c2.F.bedgraph
c2.R.bedgraph


title: Sample 15_ago5_cherry_R6


title: Control1, biol rep2

description:
c1.F.bedgraph
c1.R.bedgraph

value: log phase, 30℃, 20 min


title: Control1, biol rep1

description:
c1.F.bedgraph
c1.R.bedgraph


title: Control1, biol rep3

description:
c1.F.bedgraph
c1.R.bedgraph


title: Heart, rmIL11, 6hr, rep4

value: rmIL11 - 6hr


title: DNSupExoQuick2

city: La Jolla

first: Louise

middle: C

last: Laurent

state: CA

address: SCRM, 2880 Torrey Pines Scenic Drive

department: Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

organism: Rattus rattus

source_name: primary culture

extract_protocol:
RNA Isolation kit was miRNeasy (Qiagen).
Library construction kit was NEBNext small RNA library prep (NEB). Samples were multiplexed. Type of Starting Material was total RNA.

tag: condition

value: Healthy Subject

tag: anatomical location

value: Heart part

tag: rna source

value: extracellular vesicle

tag: rna isolation kit

value: SeraMir Kit (System Biosciences)


title: Sample 14_ago5_cherry_R5


title: PNSupUltra1

value: miRNeasy (Qiagen)


title: LNSupExoQuick2


title: DNSupMillipore2


title: LNSupExoRNeasy3


title: Heart, rmIL11, 6hr, rep3


title: PNSupExoRNeasy1


title: DNSupExoRNeasy1


title: Sample 13_ago5_cherry_R4


title: LNSupExoRNeasy2


title: Sample 12_ago5_cherry_R2


title: Heart, rmIL11, 1hr, rep3

value: rmIL11 - 1hr


title: LNSupUltra2


title: LNSupUltra3


title: LNSupExoRNeasy1


title: LNSupMillipore2


title: Sample 10_ago59_dapi_R3

value: 7 days after germination


title: Sample 11_ago5_cherry_R1


title: Heart, rmIL11, 6hr, rep2


title: PNSupMillipore1


title: Heart, PBS, baseline, rep2


title: LNSupUltra1


title: Heart, PBS, baseline, rep1


title: LNSupMillipore3


title: Heart, rmIL11, 1hr, rep2


title: Sample 9_ago59_dapi_R2

value: non stem cells


title: DNSupUltra2


title: Sample 8_ago59_dapi_R1


title: Heart, rmIL11, 1hr, rep1

value: heart


title: LNSupExoQuick3


title: LNSupExoQuick1


title: Heart, rmIL11, 6hr, rep1

value: wild-type


title: Sample 7_ago59_cherry_R8


title: PNSupExoQuick1


title: Heart, rmIL11, 3hr, rep1

value: rmIL11 - 3hr


title: Sample 6_ago59_cherry_R6


title: LNSupMillipore1


title: Sample 5_ago59_cherry_R5


title: Sample 4_ago59_cherry_R4


title: Sample 3_ago59_cherry_R3


title: Wang_ChIP_antiParB_BWX5574

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
For ChIP-seq, we mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0, and exported .csv file.
Assembly: NC_022898.1
Supplementary files format and content: Files ending with .csv: comma-separated values files of ChIP-seq results.

extract_protocol:
ChIP-seq experiments were performed using anti-ParB.
Standard library construction protocol was used for Illumina Nextseq500 sequencing platforms. Illumina Truseq indexes were used.

value: Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature

value: pelB::Psoj ECE spo0J R80A (delta_parS) cat, delta_spo0J spec

value: ChIP using anti-ParB antibodies


title: Wang_ChIP_antiParB_BWX5572

value: pelB::Psoj ECE spo0J (delta_parS) cat, delta_spo0J spec


title: Sample 1_ago59_cherry_R1

value: stem cells


title: 356_RituSE

city: Kobe

first: Yasuyuki

last: Saito

state: Hyogo

address: 7-5-1, Kusunokicho, Chuo-ku

country: Japan

institute: Kobe University Graduate School of Medicine

data_processing:
RNA-seq reads were aligned to the human reference genome (GRCh38) with the STAR aligner.
Raw read counts were obtained with RSEM and were normalized for further analysis with the use of the built-in normalization algorithms of DESeq2.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each sample

source_name: Tumor

growth_protocol: Single-cell suspensions isolated from Raji-bearing HIS-MITRG mice at day 24 were incubated with biotin-labeled human CD19 and mouse CD45 antibodies, followed by anti-streptavidin microbeads. Biotin-labeled cells were depleted by autoMACS Pro Separator (Miltenyi Biotech). The remained cells were further stained, and tumor-infiltrating macrophages were sorted as hCD45+HLA-DR+hCD14+hCD1c– cells with the use of the FACSAriaIII instrument. The purity of the isolated cells was >98%, as determined by flow cytometry.

extract_protocol: Total RNA was extracted from sorted hCD14+ macrophages from Raji-inoculated HIS-MITRG mice with the use of RNeasy Micro Kit (QIAGEN). The cDNA was synthesized from total RNA and amplified using the SMART-Seq V4 Ultra Low Input RNA Kit for Sequencing (Clontech). RNA-seq libraries were prepared via the Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: RajiGFP/Luc cells (5×105 cells in 100 μL PBS) were injected subcutaneously into the flank of HIS-MITRG and non-HIS-MITRG mice at 6-8 weeks of age. The mice were injected intraperitoneally either with normal mouse IgG (200 μg), rituximab (200 μg), or rituximab with SE12C3 (200 μg), three times per week beginning after tumor volume had achieved an average of 60 mm3 in each treatment group. Tumor tissues were harvested 14 days after the first treatment

value: Tumor

value: Macrophages


title: Sample 2_ago59_cherry_R2


title: blood_healthy_CA0120_timepoint 1

type: RNA

city: Seattle

first: Fang Yun

last: Lim

state: WA

address: 1100 Eastlake Ave E

department: Vaccine and Infectious Disease Division

institute: Fred Hutchinson Cancer Center

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0120

data_processing: nCounter RCC files of all samples were pre-processed on the nSolverTM software (nanoString) to obtain normalized expression counts. Quality control (QC) measures were applied to all participant samples.  Imaging QC was assessed by measuring the percent field of view (FOV) successfully scanned within each sample. Samples with scanned FOV < 75% were flagged for removal. Binding density QC was assessed by measuring the density of the reporter probe on the cartridge surface within each sample. Samples with binding density outside of 0.1 - 2.25 spots/square micron were flagged for removal. The correlations between the observed counts for all six positive ERCC control probes (Positives A – F) and their spike-in synthetic nucleic acids (0.125 fM – 128 fM) were used to determine a sample’s positive control linearity. Samples with positive control linearity of < 0.95 were flagged for removal. Gene expression count normalization was performed on all samples that passed the QC metrics above. For normalization, all samples were subjected to i) positive control normalization, ii) codeset content normalization, and iii) panel standard normalization. Nine reference genes (ABCF1, GUSB, HRPT1, MRPS7, NMT1, NRDE2, PGK1, SDHA, TBP) were used in codeset content normalization.

label: Molecular barcode with using 4 fluorophores (Alexa 488, Alexa 594, Alexa 647, Cy3) in 7 positions: https://www.nature.com/articles/nbt1385

source_name: healthy uninfected participants-single timepoint

label_protocol: color-coded reporter and capture probes from manufacturer (nCounter codeset chemistry): https://nanostring.com/wp-content/uploads/MAN-10056-05-Gene-Expression-Hybridization-Protocol.pdf

growth_protocol: Capillary blood was self-collected and immediately stabilized using a home-use blood collection kit (homeRNA). Stabilized blood were mailed back to the lab and samples stored at -80ºC until ready for RNA extraction.

tag: disease status

value: Healthy uninfected

tag: participant id

value: male

tag: age

tag: covid-19 vaccination history

value: vaccinated

tag: study day

tag: ncounter host response codeset


title: blood_healthy_HC0105_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-05

value: female


title: blood_healthy_CA0119_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0119

value: unvaccinated


title: blood_healthy_CA0113_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0113


title: 431_RituSE

tag: tissue

tag: cell type


title: blood_healthy_HC0105_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-07


title: blood_healthy_HC0105_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-04


title: blood_healthy_CA0108_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0108


title: blood_healthy_CA0112_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0112


title: blood_healthy_CA0101_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CA-0101


title: blood_healthy_HC0105_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-03


title: LhSupExoRNeasy3

source_name: embryonic stem cell

value: Healthy Subject

value: Entire embryo

value: extracellular vesicle

value: miRNeasy (Qiagen)


title: blood_healthy_HC0105_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-06


title: 438_Ritu

value: Rituximab


title: 295_Ritu


title: blood_healthy_HC0105_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-02


title: DhSupExoRNeasy1


title: blood_healthy_HC0104_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0104-07


title: blood_healthy_HC0105_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0105-01


title: 368_IgG

value: Control IgG


title: LhSupExoRNeasy2


title: 316_IgG


title: blood_healthy_HC0104_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0104-05


title: PhSupExoRNeasy1


title: LhSupUltra3


title: blood_healthy_HC0104_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0104-04


title: N1-3

city: Ningbo

first: liyun

last: fu

state: Zhejiang

address: ningbo xibei street No.41, zhejiang province

department: Department of Hepatology

institute: HwaMei Hospital, University of Chinese Academy of Sciences (Ningbo No.2 hospital)

data_processing:
For circRNA expression analysis, the reads were to mapped genome using the STAR (58) and DCC (59) was used to identify the circRNA and to estimate the circRNA expression
TMM (trimmed mean of M-values) was used to normalize the gene expression
Genome_build: hg19
Supplementary_files_format_and_content: TMM_normalized_reads_count_per_million

source_name: Plasma

extract_protocol:
Total RNA of plasma exosome  was isolated using Magen Hipure Total RNA Mini Kit(Magen,Guangzhou,China) according to the protocol
RNA-seq library was prepared with approximately 100ng of total RNA using KAPA RNA HyperPrep Kit with RiboErase (HMR) for Illumina® (Kapa Biosystems, Inc., Woburn, MA).The RNA was purified with VAHTS RNA Clean Beads. The RNAs was fragmented and then first strand and directional second strand synthesis were performed. Then the A tailing and adapter ligation

tag: disease state

value: Healthy

value: Plasma


title: cutaneous neurofibroma

city: Suita

first: Wei-Ning

state: Osaka

address: 2-2 Yamadaoka

department: Dermatology

institute: Osaka University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: human skin

extract_protocol:
Single-cell suspensions of cNF and pNF were obtained from NF1 patient. Samples were mechanically dissociated and enzymatically digested in 0.5% collagenase type I and 2% FBS in PBS at 37℃ for 3 hours. The cell suspension was filtered and washed. Erythrocytes were removed by adding ACK Lysing Buffer to the remaining pellet. Live cells were sorted by excluding 7-aminoactinomycin D-positive cells using Cell Sorter SH800.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, cell suspension was resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane Dynabeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: neurofibromatosis 1

value: epithelial tissue

value: cutaneous neurofibroma


title: PKSupExoRNeasy1

source_name: neoplastic cell

value: Cholangiocarcinoma

value: Bile duct structure


title: LKSupMillipore3


title: N1-2


title: plexiform neurofibroma

description: 10x Genomics

value: plexiform neurofibroma


title: blood_healthy_HC0103_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-07

value: Healthy uninfected

value: vaccinated


title: LKSupMillipore1


title: blood_healthy_HC0103_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-05

value: female


title: blood_healthy_HC0103_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-04


title: blood_healthy_HC0104_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0104-02


title: blood_healthy_HC0103_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-06


title: DhSupUltra2

value: Healthy Subject


title: JS1-3

value: Hepatocellular carcinoma


title: blood_healthy_HC0102_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0102-07


title: blood_healthy_HC0103_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-03


title: blood_healthy_HC0104_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0104-06


title: blood_healthy_HC0103_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-01


title: blood_healthy_HC0103_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0103-02


title: blood_healthy_HC0102_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0102-06


title: N1-1


title: LhSupUltra2

value: Entire embryo

value: extracellular vesicle


title: JS1-2


title: blood_healthy_HC0102_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0102-05


title: blood_healthy_HC0102_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0102-04


title: DKSupMillipore2

value: miRNeasy (Qiagen)


title: JS1-1


title: blood_healthy_HC0101_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-04


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 8 rep3

city: Istanbul

first: Halil

last: Kavakli

address: Rumelifeneri Yolu, Sariyer

department: Chemical and Biological Engineering

country: Turkey

institute: Koc University

data_processing:
Quality of sequencing reads was evaluated by using FastQC (Babraham Bioinformatics, UK) program. Trimmomatic (v0.35) was used to clean low-quality bases and adaptor contaminations
Star aligner program (v2.5.3) was used to align clean reads to reference mouse genome (GRCm39). To determine differentially expressed genes (DEGs) among genetically different mice and time points, DESeq2 function (adjusted p value < 0.05 ) in R was used
Sorted reads by the STAR aligner were counted by using HTSeq (htseq-count v. 1.99.2)
DEGs were calculated by using DESeq2 to construct distance-distance matrix and to perform principle component analysis (PCA).
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes read counts
Supplementary files format and content: normalized reads obtained from deseq2

source_name: Liver

growth_protocol: All mice received a standard diet, and food and water were provided ad libitum.

extract_protocol:
Total RNA from liver samples (WT and CRYDKO mice treated with oxaliplatin at CT8 and CT16) were isolated by using RNeasy Mini Kit (QIAGEN, Germany). Quality of amount of RNA were assessed by using Qubit (Thermo Fisher Scientific, USA).
High quality RNA samples (OD260/280 1.8-2.0) were used to prepare library for RNA Sequencing analysis. Briefly, adenylated mRNAs were isolated by using Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, US). Then mRNAs were fragmented, converted to cDNA and second strand synthesis was performed.

treatment_protocol: Oxaliplatin (Alfa Aesar, Germany) was diluted in 5% dextrose solution to a final concentration of 12 mg/kg before each injection. Oxaliplatin (12 mg/kg, i.p.) was given to wild-type and Cry DKO male mice at two circadian times (CT8, CT16) for three consecutive days.

value: Liver

tag: genotype

tag: treatment

value: Oxaliplatin


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 16 rep3


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 8 rep4


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 16 rep2


title: blood_healthy_HC0102_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0102-01

tag: Sex


title: blood_healthy_HC0101_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-03


title: blood_healthy_HC0101_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-01


title: LKSupExoQuick1

value: SeraMir Kit (System Biosciences)


title: DKSupExoQuick2


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 16 rep4


title: blood_covid+_CB0139_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-02

source_name: acute phase COVID-19+ participants-longitudinal

value: male

tag: day post symptom onset


title: blood_covid+_CB0139_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-07


title: blood_covid+_CB0139_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-06


title: blood_healthy_HC0101_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-05


title: blood_covid+_CB0139_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-04


title: blood_covid+_CB0139_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-05


title: PhSupUltra1

tag: condition


title: blood_covid+_CB0139_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-03


title: blood_covid+_CB0139_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0139-01


title: LhSupExoRNeasy1

tag: anatomical location


title: PKSupUltra1

tag: rna source


title: blood_healthy_HC0101_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-02


title: blood_healthy_HC0101_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-07


title: blood_healthy_HC0101_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
HC-0101-06


title: LKSupExoQuick3

tag: rna isolation kit


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 16 rep1


title: blood_covid+_CB0138_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-07

tag: disease status


title: LhSupMillipore2


title: blood_covid+_CB0138_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-06

tag: participant id


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 8 rep2


title: LhSupMillipore3


title: Cry1-/- Cry2-/- C57BL/6J Circadian Time 8 rep1


title: WT C57BL/6J Circadian Time 16 rep4

value: Wild Type


title: LKSupExoRNeasy3


title: blood_covid+_CB0138_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-04

tag: age


title: WT C57BL/6J Circadian Time 16 rep3


title: LhSupUltra1


title: blood_covid+_CB0138_timepoint 2

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-02

tag: covid-19 vaccination history


title: blood_covid+_CB0138_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-05

tag: study day


title: PhSupMillipore1


title: WT C57BL/6J Circadian Time 16 rep2


title: LhSupExoQuick2


title: LKSupExoRNeasy2


title: blood_covid+_CB0136_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0136-07

tag: ncounter host response codeset


title: WT C57BL/6J Circadian Time 16 rep1

tag: tissue


title: blood_covid+_CB0138_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-01


title: blood_covid+_CB0135_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-06


title: WT C57BL/6J Circadian Time 8 rep4


title: blood_covid+_CB0136_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0136-06


title: blood_covid+_CB0136_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0136-05


title: blood_covid+_CB0135_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-07


title: LKSupUltra3


title: blood_covid+_CB0138_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0138-03


title: WT C57BL/6J Circadian Time 8 rep2


title: WT C57BL/6J Circadian Time 8 rep1


title: NC.D0_Plate1.B6

city: Sendai

first: Kota

last: Sato

state: Miyagi

address: 1-1, Seiryo-machi, Aoba-ku

department: Ophthalmology

institute: Tohoku University

data_processing:
Obtained raw reads were trimmed and quality-filtered using the Trim Galore! (version 0.4.4), Trimmomatic (version 0.36), and cutadapt (version 1.16) software. Trimmed reads were then mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads on annotated genes were counted using featureCounts (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: retina

extract_protocol:
Total RNA were directly extracted with lysis buffer inculding Rnase inhibitor from single cell sorted with FACS.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology (GO) enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). cDNA synthesis and amplification of RNA derived from lysed cell was sequentially conducted in a same PCR tube. After purification, amplified cDNA was validated and quantified. Following tagmentation of cDNA, adapter addition and PCR amplification were conducted using Nextera XT DNA Library Prep Kit (Illumina).

tag: cell type

value: microglia

value: retina

tag: strain

value: 16 weeks old

value: no treatment


title: LhSupMillipore1


title: PhSupExoquick1


title: blood_covid+_CB0135_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-01


title: blood_covid+_CB0135_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-05


title: blood_covid+_CB0134_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-07


title: blood_covid+_CB0134_timepoint 6

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-06


title: D7_M.ONC.D7.4.200124

data_processing:
RNA-seq libraries were sequenced using paired end reads (50 nt for read 1 and 25 nt for read 2) on a NextSeq 500 instrument (Illumina). The obtained reads were mapped to the mouse GRCm38.p6 (mm10) genome with STAR software (version 2.7.2b). Reads of annotated genes were counted using featureCounts software (version 1.6.1). FPKM values were calculated from mapped reads by normalizing to total counts and the transcript.
Assembly: GRCm38.p6
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

value: optic nerve crush day 7


title: D7_M.ONC.D7.3.200124


title: blood_covid+_CB0134_timepoint 5

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-05

value: vaccinated


title: DhSupMillipore2


title: blood_covid+_CB0134_timepoint 1

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-01


title: LKSupUltra2

value: Cholangiocarcinoma

value: Bile duct structure


title: blood_covid+_CB0133_timepoint 7

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-07


title: DKSupExoRNeasy1


title: blood_covid+_CB0136_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0136-04


title: blood_covid+_CB0135_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0135-03

value: female


title: D7_M.ONC.D7.2.191127


title: blood_covid+_CB0134_timepoint 4

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0134-04


title: blood_covid+_CB0133_timepoint 3

description:
nCounter host response codeset comprising 773 immune/host response genes, 12 reference genes. Assay included addition of the coronovirus panel plus codeset. Panel plus codeset were not included in the analysis.
CB-0133-03


title: D7_M.ONC.D7.1.191127