title: Late resolution ethanol, male 3

city: Chicago

first: Natalia

last: Nieto

address: 909 S. Wolcott Ave

institute: University of Illinois at Chicago

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespce
Differential analysis was performed using RNA-Seq Differential Expression v: 1.0.1 in basespace
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: Liver

extract_protocol:
Illustra RNAspin mini kit (GE Healthcare Life Sciences, Pittsburgh, PA).
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina).

treatment_protocol: Mice were fed the Lieber-DeCarli control or ethanol diet for 6 wk to achive peak injury, then for early resolution mice were fed the Lieber-DeCarli control diet for three days after 6 wk of  Lieber-DeCarli ethanol diet and for late resolution mice were fed the Lieber-DeCarli control diet for 2 wk after 6 wk of  Lieber-DeCarli ethanol diet.

value: Liver

value: Liver tissue lysate

tag: gender

value: Male

value: Ethanol diet

tag: group

value: Late Resolution


title: NS159.A2780.CIS.II

status: Public on Jun 06 2022

type: SRA

city: Saugus

first: Michael

last: Raabe

state: MA

address: 3214 Founders Way

country: USA

institute: Massachusetts General Hospital

library_source: transcriptomic

data_processing:
reads trimmed and quality checked using skewer
aligned to hg38 and repeat elements using STAR
reads assigned to genes and repeats (Gencode and repeat masker) using featureCounts
unassigned reads remapped to Repbase consensus sequence
Assembly: GRCH38; REP
Supplementary files format and content: rawcounts in .tsv format

molecule: total RNA

organism: Homo sapiens

source_name: cell line

growth_protocol: For PDAC and CRC cell lines 3D media contained serum free RPMI supplemented with 20 ul/ml B27 (Invitrogen/Life Technologies), 20 ng/ml EGF (Invitrogen/Life Technologies), 20 ng/ml bFGF (Invitrogen/Life Technologies) and 1% Pen/Strep (Gibco/Life Technologies).  For EOC cell lines, standard growth media (see Supplementary Table 1 of manuscript) was used for 3D cultures in non-adherent tissue culture dishes.

extract_protocol:
RNA was isolated using Trizol reagent (ThermoFisher) or the AllPrep DNA/RNA/protein mini kit (Qiagen #80004) according to manufacturer recommendations.
Clontech/Takara SMARTer Stranded Total RNA-seq PICO v2 kit (Clontech/Takara 634414) for RNA-seq.

treatment_protocol:
OVCAR4, IGROV1, OAW28, and OVSAHO cells were plated at a density of 120,000 cells/well in 6 well tissue culture treated plates (Corning). OVCAR4 and IGROV1 cells were grown in RPMI medium and OAW28 and OVSAHO cells were grown in DMEM/F12, both containing 1% Pen/Strep and 10% FBS. After 2 days, 500 nM Negative control (Scramble) or HSATII custom designed LNA were transfected into the cells with Lipofectamine 2000 (Invitrogen/Life Technologies) following the manufacturer’s recommendations.
IGROV1, OV90, OAW28 and CaOV3 cells were plated at 300,000 cells per well in 6 well ultra-low attachment cell culture dishes (Sigma-Aldrich, Cat #CLS3471) in standard growth media.  Cells were incubated for 48-72 hours to allow tumorsphere formation, then treated with 500 nM 5-azacytidine (Sigma-Aldrich, Cat #A2385), 250 nM Trichostatin A (Sigma-Aldrich, Cat #T1952) or DMSO for vehicle control and incubated for 72 hours.

tag: cell line


title: NS159.A2780.II


title: Lesion_D3_2

city: La Jolla

first: Erna

middle: A

last: van Niekerk

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Reads were aligned to the latest mouse_mm10 reference genome using the STAR spliced read aligner.
No read trimming or filtering was done with this dataset because the quality distribution and variance appear normal.
Assembly: mm10

organism: Mus musculus

source_name: Primary Cortical Neurons isolated from Adult C57/BL6 mice

extract_protocol:
RNA was harvested using Agilent absolute RNA nanoprep kit (catalog #400753)
RNA libraries for RNA-seq were prepared using Nugen RNA Ultra Low Input (500 pg) + Kapa Hyper over 2 lanes by HiSeq4000.

tag: strain

tag: tissue

value: primary cortical culture

tag: cell type

value: Adult Neuron

tag: genotype

value: WT

tag: treatment

value: Conditioning lesion

tag: time

value: Day 3


title: NS159.A2780.CIS


title: Late resolution ethanol, male 2

state: IL

department: Pathology


title: Lesion_D3_1


title: Late resolution ethanol, male 1


title: Naive_D3_3


title: NS159.A2780


title: Late resolution, control, male 4

value: Control diet


title: NS144.Es2


title: NX210d-1

city: changsha

first: LI

last: Biao

address: Nongda South Road

department: College of Animal Science and Technology

country: China

institute: Hunan Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Sus scrofa (pig)

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Ningxiang

value: spleen

tag: developmental stage

value: post natal day 210


title: NX210d-3


title: NX90d-2

value: post natal day 90


title: NX90d-3


title: NS135.SNU8


title: Late resolution, control, male 3


title: Naive_D3_1


title: NS135.SNU119


title: Naive_D3_2


title: NX210d-2


title: NS135.OVCAR3


title: Lesion_D2_2

value: Day 2


title: Lesion_D2_3


title: Late resolution, control, male 1


title: Late resolution, control, male 2


title: Late resolution, ethanol, female 3

value: Female


title: Lesion_D2_1


title: Late resolution, ethanol, female 2

value: Liver


title: Naive_D2_3


title: Late resolution, ethanol, female 1

value: Liver tissue lysate


title: NS135.JHOS2


title: NS135.COV362


title: Lung, 48hr after 4Gy Dose, Sample 24 [miRNA]

type: RNA

city: Northbrook

last: Falduto

address: 1808 Janke, Unit M

institute: GenUs BioSystems, Inc.

description: Lung 4Gy_24

hyb_protocol: 1 µg of purified cRNA was fragmented to uniform size and applied to Agilent Porcine (v2) Gene Expression Microarrays 4x44K Design ID 026440 (Agilent Technologies, Santa Clara, CA) in hybridization buffer. Arrays were hybridized at 65° C for 17 hrs. in a rotating incubator, washed at 37° C for 1 min, and stained with Streptavidin-Alexa555.

scan_protocol: Rinsed and dried arrays were scanned with an Agilent G2505C Microarray Scanner (Agilent Technologies, Santa Clara, CA) at 5 µm resolution.

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

source_name: Lung, 48hr after 4Gy Dose

label_protocol: Labeled cRNA was prepared from total RNA samples. Briefly, the Poly(A)+ RNA population within total RNA was amplified using MessageAMP II (Applied Biosystems, Foster City, CA).  After a second round of reverse transcription, second-strand cDNA synthesis, and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of Biotin-11-UTP.  The quantity and quality of the cRNA was assayed by spectrophotometry and on the Agilent Bioanalyzer.

extract_protocol: Approximately 100 µg of powdered sample was lysed with 700 µl of QIAzol lysis buffer (Cat # 79306, QIAGEN) and homogenized by passing the solution through QIAshredder spin columns (Cat # 79654, QIAGEN). RNA isolation was performed using standard miRNeasy mini kit (Cat # 217004, QIAGEN) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a DeNovix DS-11 nanodrop spectrophotometer (DeNovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Six- to 8-week old female C57BL/6 J mice were given total-body irradiation (TBI) with X-rays using the Small Animal Radiation Research Platform (SARRP Xstrahl Ltd.). Mice were placed in plastic containers and exposed to a single surface dose of 1, 2, 4, 8, or 12 Gy at a dose rate of 1.05 Gy/min. Control mice (0 Gy) were placed in the same type of plastic container and sham irradiated.

value: C57BL/6 J

tag: Sex

value: female

value: Lung

tag: treatment/time point

value: 48hr after 4Gy Dose


title: Lung, 48hr after 4Gy Dose, Sample 14 [miRNA]

description: Lung 4Gy_14


title: NS135.CAOV4


title: Lung, 48hr after 2Gy Dose, Sample 3 [miRNA]

description: Lung 2Gy_3

source_name: Lung, 48hr after 2Gy Dose

value: 48hr after 2Gy Dose


title: Cells transfected with MIR-inihbitor control and treated with DMSO_2

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

hyb_protocol: The labelled cRNAs were hybridized and scanned by the Agilent Scanner G2505C (Agilent Technologies, Santa Clara, California, USA).

scan_protocol: Agilent Feature Extraction software (V.11.0.1.1) was used to analyze the acquired array images.

data_processing: Sample-specific background was calculated and then subtracting this value from the raw values for each gene. Biological normalization was performed to correct for differences in sample abundances. Each sample was normalized according to the quantile normalization method, and the data were log transformed (base 2) for analysis. Cy3 -> Experimental sample RNA. Cy5-> Agilent human reference RNA (cat no 740000)

source_name: MIR inhibitor CTRL DMSO

label_protocol: Each sample was amplified and transcribed into fluorescent cRNA using a random priming method.

extract_protocol: Total RNA has been isolated using TRIZOL reagent (Life technologies) according to manufacture's instructions

value: CCLP

value: cholangiocarcinoma

source_name: reference RNA

tag: sample type


title: Cells transfected with MIR-inihbitor control and treated with cisplatin and gemcitabine_6

source_name: MIR inhibitor CTRL CG

value: Agilent human reference RNA (cat no 740000)


title: Lung, 48hr after 8Gy Dose, Sample 5 [miRNA]

description: Lung 8Gy_5

source_name: Lung, 48hr after 8Gy Dose

value: 48hr after 8Gy Dose


title: Lung, 48hr after 1Gy Dose, Sample 22 [miRNA]

description: Lung 1Gy_22

source_name: Lung, 48hr after 1Gy Dose

value: 48hr after 1Gy Dose


title: Cells transfected with MIR-inihbitor control and treated with cisplatin and gemcitabine_4


title: Lung, 48hr after 1Gy Dose, Sample 12 [miRNA]

description: Lung 1Gy_12


title: NS113.PANC1.VEH.DAY.1.S18

tag: agent


title: Late resolution, control, female 4

value: WT

value: Control diet

value: Late Resolution


title: Naive_D2_2

value: primary cortical culture

value: Adult Neuron

value: Day 2


title: Naive_D2_1


title: Late resolution, control, female 3

value: Liver

value: Liver tissue lysate

value: Female


title: Lesion_D1_3

value: Conditioning lesion

value: Day 1


title: Lung, 48hr after 8Gy Dose, Sample 15 [miRNA]

description: Lung 8Gy_15

value: C57BL/6 J

value: female

value: Lung


title: Lung, 48hr after 8Gy Dose, Sample 25 [miRNA]

description: Lung 8Gy_25


title: Lung, 48hr after 4Gy Dose, Sample 4 [miRNA]

description: Lung 4Gy_4

value: 48hr after 4Gy Dose


title: Late resolution, control, female 2


title: Lung, 48hr after 2Gy Dose, Sample 23 [miRNA]

description: Lung 2Gy_23

value: 48hr after 2Gy Dose


title: Lung, 48hr after 1Gy Dose, Sample 2 [miRNA]

description: Lung 1Gy_2

value: 48hr after 1Gy Dose


title: Lung, 48hr after 0Gy Dose, Sample 21 [miRNA]

description: Lung 0Gy_21

source_name: Lung, 48hr after 0Gy Dose

value: 48hr after 0Gy Dose


title: Cells transfected with MIR-1249 inhibitor and treated with cisplatin and gemcitabine_8

source_name: MIR1249 inhibitor CG

value: CCLP

value: cholangiocarcinoma

value: Agilent human reference RNA (cat no 740000)


title: LS123.3D


title: Cells transfected with MIR-inihbitor control and treated with cisplatin and gemcitabine_5


title: LOVO.3D

value: LOVO


title: Lesion_D1_2

value: primary cortical culture

value: Adult Neuron

value: WT


title: Cells transfected with MIR-inihbitor control and treated with DMSO_3


title: Lesion_D1_1


title: Lung, 48hr after 12Gy Dose, Sample 6 [miRNA]

description: Lung 12Gy_6

source_name: Lung, 48hr after 12Gy Dose

value: 48hr after 12Gy Dose


title: Lung, 48hr after 12Gy Dose, Sample 16 [miRNA]

description: Lung 12Gy_16


title: Lung, 48hr after 12Gy Dose, Sample 26 [miRNA]

description: Lung 12Gy_26


title: Miapaca2.DMSO

value: DMSO


title: Early resolution ethanol, male 4

value: Liver

value: Liver tissue lysate

value: Male

value: Ethanol diet

value: Early Resolution


title: Lung, 48hr after 0Gy Dose, Sample 1 [miRNA]

description: Lung 0Gy_1

value: C57BL/6 J

value: female

value: Lung


title: LL1494.DMSO


title: Cells transfected with MIR-1249 inhibitor and treated with cisplatin and gemcitabine_9

value: CCLP


title: Lung, 48hr after 2Gy Dose, Sample 13 [miRNA]

description: Lung 2Gy_13

value: 48hr after 2Gy Dose


title: Lung, 48hr after 0Gy Dose, Sample 11 [miRNA]

description: Lung 0Gy_11

value: 48hr after 0Gy Dose


title: Liver, 48 hr after 12Gy Dose, Sample 26 [miRNA]

description: Liver 12Gy_26

source_name: Liver, 48 hr after 12Gy Dose

value: 48 hr after 12Gy Dose


title: Cells transfected with MIR-1249 inhibitor and treated with cisplatin and gemcitabine_7

value: cholangiocarcinoma

value: Agilent human reference RNA (cat no 740000)


title: Naive_D1_3

value: primary cortical culture

value: Adult Neuron

value: WT

value: Day 1


title: Cells transfected with MIR-inihbitor control and treated with DMSO_1


title: Early resolution ethanol, male 3

value: Liver

value: Liver tissue lysate


title: Naive_D1_2


title: Late resolution, control, female 1

value: Female

value: Control diet

value: Late Resolution


title: Liver, 48 hr after 12Gy Dose, Sample 16 [miRNA]

description: Liver 12Gy_16

value: C57BL/6 J

value: female


title: Early resolution ethanol, male 2

value: Male

value: Ethanol diet

value: Early Resolution


title: Early resolution ethanol, male 1


title: Naive_D1_1


title: LL.937.VEH.NS71


title: Kuramochi.3D

value: Kuramochi


title: DRG recovery 3 [BE-20]

first: Benayahu

last: Elbaz

state: Illinois

address: 303 E. Chicago Ave. Ward 7-641. Chicago, IL 60611

department: Neurology

institute: Northwestern University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
 Reads were mapped using both STAR v2.6.1a and Kallisto v.0.44.0 using bowtie 2 aligner.
Assembly: mm10
Supplementary files format and content: Counts and Normalized data for all the samples

source_name: Dorsal Root Ganalia L3-L5

extract_protocol:
RNA samples were isolated using RNA extraction kit following the manufacture’s protocol (Bio-Rad, Cat# 732-6820)
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: strain background

value: Dorsal Root Ganalia L3-L5

tag: sample group

value: Recovery


title: Early resolution, control, male 3

tag: gender


title: Liver, 48 hr after 12Gy Dose, Sample 6 [miRNA]

description: Liver 12Gy_6

value: 48 hr after 12Gy Dose


title: Early resolution, control, male 2

tag: group


title: Early resolution, control, male 4


title: IGROV1

tag: cell line


title: DRG no disease-3 [BE-12]

value: No disease


title: DRG recovery 1 [BE-18]


title: DRG recovery 2 [BE-19]


title: LL1222.DMSO

value: DMSO


title: Liver, 48 hr after 8Gy Dose, Sample 15 [miRNA]

description: Liver 8Gy_15

source_name: Liver, 48 hr after 8Gy Dose

tag: strain

value: 48 hr after 8Gy Dose


title: Liver, 48 hr after 8Gy Dose, Sample 25 [miRNA]

description: Liver 8Gy_25

tag: tissue

value: Liver


title: LL1312.DMSO


title: Early resolution, control, male 1

source_name: Liver

tag: cell type

value: Liver tissue lysate

value: WT


title: Liver, 48 hr after 8Gy Dose, Sample 5 [miRNA]

description: Liver 8Gy_5


title: DRG no disease-2 [BE-10]


title: HT29.3D

source_name: cell line


title: Early resolution, ethanol, female 3

tag: genotype

value: Female


title: Liver, 48 hr after 4Gy Dose, Sample 24 [miRNA]

description: Liver 4Gy_24

source_name: Liver, 48 hr after 4Gy Dose

value: 48 hr after 4Gy Dose


title: Liver, 48 hr after 4Gy Dose, Sample 14 [miRNA]

description: Liver 4Gy_14

value: C57BL/6 J


title: DRG no disease-1 [BE-9]


title: Early resolution, ethanol, female 2

tag: treatment


title: Liver, 48 hr after 4Gy Dose, Sample 4 [miRNA]

description: Liver 4Gy_4

value: female


title: Liver, 48 hr after 2Gy Dose, Sample 23 [miRNA]

description: Liver 2Gy_23

source_name: Liver, 48 hr after 2Gy Dose

value: 48 hr after 2Gy Dose


title: HPAFII.DMSO

value: HPAFII


title: HUTU80.3D


title: Early resolution, ethanol, female 1

value: Ethanol diet

value: Early Resolution


title: DRG peak disease-3 [BE-8]

value: Dorsal Root Ganalia L3-L5

value: Peak disease


title: Early resolution, control, female 4

value: Control diet


title: Liver, 48 hr after 2Gy Dose, Sample 13 [miRNA]

description: Liver 2Gy_13


title: HCT116.3D


title: HT115.3D


title: HCT8.3D


title: GP5D.3D


title: HCT15.3D


title: DRG peak disease-1 [BE-6]


title: G.att


title: Early resolution, control, female 1


title: Sciatic nerve recovery-3 [BE-24]

source_name: Sciatic nerve

value: Sciatic nerve

value: Recovery


title: Sciatic nerve recovery-2 [BE-22]


title: Early resolution, control, female 2


title: Peak, ethanol, male 4

value: Male

value: Peak injury


title: Sciatic nerve recovery-1 [BE-21]


title: DLD1.3D


title: Liver, 48 hr after 2Gy Dose, Sample 3 [miRNA]

description: Liver 2Gy_3

value: Liver


title: Liver, 48 hr after 1Gy Dose, Sample 2 [miRNA]

description: Liver 1Gy_2

source_name: Liver, 48 hr after 1Gy Dose

value: 48 hr after 1Gy Dose


title: CX.PDAC2.GFP.VEH.070518


title: Liver, 48 hr after 1Gy Dose, Sample 22 [miRNA]

description: Liver 1Gy_22


title: Peak, ethanol, male 3

value: Liver tissue lysate

value: WT


title: Sciatic nerve no disease-3 [BE-15]

value: No disease


title: Liver, 48 hr after 1Gy Dose, Sample 12 [miRNA]

description: Liver 1Gy_12

value: C57BL/6 J

value: female


title: DRG peak disease-2 [BE-7]


title: Sciatic nerve no disease-2 [BE-14]


title: Liver, 48 hr after 0Gy Dose, Sample 21 [miRNA]

description: Liver 0Gy_21

source_name: Liver, 48 hr after 0Gy Dose

value: 48 hr after 0Gy Dose


title: Liver, 48 hr after 0Gy Dose, Sample 11 [miRNA]

description: Liver 0Gy_11


title: Peak, ethanol, male 2

value: Ethanol diet


title: Sciatic nerve no disease-1 [BE-13]


title: Early resolution, control, female 3

value: Female

value: Early Resolution


title: Peak, ethanol, male 1


title: CL

value: CL


title: Sciatic nerve- peak disease-2 [BE-3]

value: Peak disease


title: Sciatic nerve- peak disease-3 [BE-4]

value: Sciatic nerve


title: Liver, 48 hr after 0Gy Dose, Sample 1 [miRNA]

description: Liver 0Gy_1


title: Sciatic nerve- peak disease-1 [BE-2]


title: CJ

value: CJ


title: Peak, control, male 1

value: Male

value: Control diet


title: Peak, control, male 2

value: Liver

value: Peak injury


title: Capan2.DMSO

value: DMSO


title: CM

value: CM


title: RNA-seq for ATF3-cKO skeletal muscle stem cells 2

city: Hong Kong

first: Feng

last: Yang

address: Room 503, 5/F, Li Ka Shing Medical Sciences Building, Prince of Wales Hospital

department: Chemical Pathology

institute: The Chinese University of Hong Kong

data_processing:
Sequenced fragment were mapped to mouse genome mm9 using TopHat
The abundance levels of transcripts were defined by cufflinks in the form of FPKM
Assembly: mm9

source_name: skeletal muscle

extract_protocol:
Total RNAs from cells or tissues were extracted using TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instructions.
cDNAs were synthesized under the manufacturer’s instructions of HiScript® II Reverse Transcriptase Kit with gDNA wiper (Vazyme, R223-01). Real-time PCR was performed to quantify the expression level of mRNAs by Luna Universal qPCR Master Mix (NEB, M3003E) and LightCycler 480 Real-Time PCR System (Roche). GAPDH (glyceraldehydes 3-phosphate dehydrogenase) or 18s RNA were used as internal controls for normalization.

value: skeletal muscle

value: satellite cell


title: C2C12 cells , ATF3

library_source: genomic

data_processing:
Raw data were first pre-processed by initial quality assessment, adaptors trimming, and low-quality filtering and then mapped to the mouse reference genome (mm9) using bowtie2, and only the non-redundant  reads were kept.
The protein DNA-binding peaks (sites) were identified using MACS2 with input (IgG) sample as the background. During the peak calling, the P‐value cutoff was set to 0.001 for Atf3 ChIP-seq experiment.
Assembly: mm9
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
10 μg of antibodies against Atf3 (Santa Cruz Biotechnology), or normal mouse IgG (Santa Cruz Biotechnology) was used for immunoprecipitation. Immunoprecipitated genomic DNA was resuspended in 20 μl of water.
For DNA library construction，a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB, E7645S) was used according to the manufacturer’s instructions. Bioanalyzer analysis and qPCR were used to measure the quality of DNA libraries including the DNA size and purity. Finally, DNA libraries were sequenced on the Illumina Genome Analyzer II platform.

tag: chip antibody


title: CaOV.3.3D


title: Peak, ethanol, female 4

value: Liver tissue lysate

value: WT


title: Peak, control, male 4


title: Peak, ethanol, female 3

value: Ethanol diet


title: CaOV.3.2D


title: BV

value: BV


title: RNA-seq for WT skeletal muscle stem cells 2


title: RNA-seq for ATF3-iKO skeletal muscle stem cells 1


title: CK

value: CK


title: Peak, control, male 3


title: Peak, ethanol, female 2

value: Female


title: BU.att


title: RNA-seq for WT skeletal muscle stem cells 1


title: Peak, ethanol, female 1


title: BT

value: BT


title: RNA samples from total WBC of healthy control subjects [Control2]

city: Kaohsiung

first: Sung-Chou

last: Li

state: Kaohsiung

address: No.386, Dazhong 1st Rd

department: Department of Medical Education and Research

country: Taiwan

institute: Kaohsiung Veterans General Hospital

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Clariom D Arrays (Affymetrix) and scanned at the Kaohsiung Chang Gung Memorial Hospital Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis was conducted with Partek.
affymetrix-algorithm-name = sst-rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Total WBCs were collected from ADHD patients or healthy control subjects.

extract_protocol: RNA was isolated from cell lysate of total WBC with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. Inclusion of 10 mL/L of the RNase inhibitor NucleoGuard (AmpTec) in the lysis buffer improved RNA yield and recoveries of long transcripts. All samples were treated with TURBO DNA-free (Ambion) to remove trace amounts of genomic DNA. A 2-round amplification was performed with the ExpressArt TRinucleotide mRNA Amplification Kit (AmpTec) according to the manufacturer’s instructions.

treatment_protocol: Not applicable

tag: subject status

value: healthy control subject

value: living cells


title: RNA samples from total WBC of ADHD patients [Disease3]

value: ADHD patient


title: RNA samples from total WBC of healthy control subjects [Control1]


title: RNA samples from total WBC of healthy control subjects [Control3]


title: RNA samples from total WBC of ADHD patients [Disease2]


title: RNA samples from total WBC of ADHD patients [Disease1]


title: Peak, control, female 4

value: Control diet


title: BP

value: BP


title: D6-500-M_Rep3

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

data_processing:
Data was processed using the nf-core rnaseq pipeline with the following options: --star_index 'star_ercc_mm10_genome' --gtf 'mm10.refGene_wERCC.gtf' --fc_group_features_type gene_id --fc_extra_attributes gene_id -r 1.4.2
Gene counts were obtained from featureCounts with the option ignoreDup=TRUE to try and remove PCR duplicates.
Samples were excluded from downstream analysis based on a number of QC criteria particularly applicable to this type of low input samples from PFA-fixed cells including: too small proportion of the library being of mouse origin (excess spike-in representation), large number of overepresented sequences, and loss of dynamic range in spike-in quantification.
Assembly: mm10

molecule: polyA RNA

growth_protocol: Mouse ES cell lines were maintained in ES cell medium with 1000 U/ml LIF (Chemicon, Int ESG1107) on mitotically inactive primary mouse embryo fibroblasts (feeders) in ES cell medium (Dulbecco’s Modified Eagle Medium (DMEM) Knock Out (Gibco, Cat No. 10829-018) complemented with 10% Foetal Bovine Serum, Penicillin/Streptomycin (Gibco, Cat No. 15140122), 2mM L-Glutamine (Gibco, Cat No. 25030024), 2mM Non-essential amino acids (Gibco, Cat No. 11140-035), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)). For spinal cord neural differentiation, ES cells were dissociated using 0.05% trypsin-EDTA (Gibco, Cat No. 25300054) and then plated onto 0.1% gelatinised (Gibco) tissue culture plates for three successive periods of 15 mins to remove feeders. Differentiations were carried out in N2B27 media (Advanced DMEM - F12 (Gibco, Cat No. 21331-020) and Neurobasal medium (Gibco, Cat No. A35829-01) (1:1), supplemented with 1xN2 (Gibco), 1xB27 (Gibco), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)) with the indicated additives. Cells were plated onto 6-well plates (Corning, Cat. No. 353046) precoated in Matrigel (Corning, Cat. No. 356231) diluted 1/50 and 1/100 in Advanced DMEM - F12 (Gibco, Cat No. 21331-020) at a density of 20,000 cells per 35mm well in 1.5 ml. The media was supplemented on the different days as follows: Day 0 to Day 2, 10ng/ml bFGF (R&D, Cat No. 100-18B) and 5 μM LGK (Cayman Chemical Company, Cat. No. 1.800.364.9897); Day2 to Day 3 for 20 h, 10ng/ml bFGF (R&D, Cat No. 100-18B), 5 μM CHIR99021 (Axon Medchem, Cat. No. 1386), 10 μM SB-431542 (Tocris, Cat. No. S0400), and 2μM  DMH1 (Adooq Bioscience, Cat. No. A12820); from Day 3 onwards, 100 nM RA (Sigma, Cat No. R2625) and either 0 nM, 10 nM, 100 nM or 500 nM SAG (Merck, Cat. No. 566660-5mg).

extract_protocol:
Crosslinked and TF-Sorted RNA-seq was performed as described in the associated manuscript. In brief, cells were PFA fixed, stained with intracellular antibodies and flow sorted. After reverse crosslinking, RNA was extracted using the RecoverAll RNA/DNA Isolation Kit (Thermo Fisher Scientific AM1975)
Libraries were built using SMART-Seq HT kit (Takara Cat no 634437) followed by Nextera XT DNA Library Preparation Kit (Illumina FC-131-1096). Prior to library preparation 1 ul of ERCC spike-ins was added for QC later assessments

treatment_protocol: 0 nM, 10 nM, 100 nM or 500 nM SAG

value: pMN


title: BN

value: BN


title: Peak, control, female 2

value: Liver

value: Peak injury


title: Peak, control, female 1


title: BH

value: BH


title: BG

value: BG


title: Peak, control, female 3

value: Liver tissue lysate

value: WT


title: D6-500-M_Rep1


title: D6-500-3_Rep1


title: D6-500-3_Rep3


title: D6-10-2_Rep3


title: AZ

value: AZ


title: Ver4

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

description: biol rep 1

data_processing:
We first aligned reads to the GRCh38 human reference genome with Cell Ranger 3.1 (10x Genomics) using pre-mRNA gene models and default parameters to produce the cell-by-gene, Unique Molecular Identifier (UMI) count matrix.
The cellranger UMI-count matrices, as used for downstream analysis, are provided as part of the supplementary Seurat object. Reads for the individual organoids used in the analysis were extracted from the multi-sample 10x Genomics possorted_genome_bam.bam, that included other samples not part of this manuscript, using 10XGenomics/subset-bam v1.1.0 and 10XGenomics/bamtofastq v1.4.1.
Assembly: GRCh38
Supplementary files format and content: integration_all_preGruffi.Rds contains all datasets analysed in the study as presented in Fig 1
Supplementary files format and content: integration_all_postGruffi.Rds contains all datasets analysed in the study as presented in Fig 4

source_name: brain organoids

growth_protocol: Cerebral organoids were generated with a modified protocol from (Esk et al. 2020). See methods of the manuscript for details

extract_protocol:
Organoids were cultured to 120 days, then washed in PBS and dissociated using the gentleMACS Dissociator (Miltenyi Biotec) in program NTDK1 using the enzyme mix: Trypsin (Sigma Aldrich)/Accutase (Sigma Aldrich) (1:1) containing 10 U/ml DNaseI (Thermo Fisher Scientific). The washed cell suspension was passed through a 70μm cell strainer.
Cells were counted and the suspension was loaded onto a Chromium Single Cell 3′ B Chip (10x Genomics, PN-1000073) and processed through the Chromium controller to generate single-cell GEMs (Gel Beads in Emulsion). scRNA-seq libraries were prepared with the Chromium Single Cell 3′ Library & Gel Bead Kit v.3 (10x Genomics, PN-1000075).
Ready 10X libraries were sequenced paired end (R1:28, R2: 89 cycles) on NovaSeq (Illumina).

value: brain organoids

value: wild type


title: Ver3

description: biol rep 1


title: D6-10-2_Rep2


title: AT.att


title: D6-10-2_Rep1


title: Ver2

description: biol rep 1


title: AQ

value: AQ


title: Ver1

description: biol rep 1


title: CD4+ T cells_2nd_trimesterpregnant 12

type: genomic

city: Linköping

first: Sandra

last: Hellberg

address: Universitetssjukhuset

country: Sweden

institute: Linköping University

description: methylation expression in isolated blood CD4+ cells from 2nd trimester pregnant woman

hyb_protocol: Bisulfite conversion was performed using the EZ-96 DNA Methylation Gold Kit from Zymo Research. Product No: D5007 with 500 ng of DNA per sample with the exception of the pooled samples were 245.9 ng of DNA per pool were used. The bisulfite converted DNA was eluted in 30μl. For all samples, approximately 200ng of bisulfite converted DNA was used for methylation analysis using the Illumina HumMeth450K array.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Results were analyzed with GenomeStudio Software 2011.1 (Illumina) as per the manufacturer’s instructions.

label: Cy5 and Cy3

source_name: CD4+ T cells, 2nd trimester pregnant 12

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using an organic extraction method. Briefly, isolated CD4+ cells were washed in ice-cold PBS (Medicago) and incubated in digestion buffer consisting of 100 mM NaCl, 10 mM Tris-HCI (pH 8), 25 mM EDTA (pH 8), 0.5% sodium dodecyl sulfate and 0.1 mg/mL proteinase K overnight at 50°C on a shaker. Phenol-Chloroform-Isoamyl alcohol (ratio 25:24:1) was added and the sample centrifuged. The aqueous phase was transferred and mixed with 3M sodium acetate, 100% ethanol and GlycoBlue™ (ThermoFisher Scientific). The pellet was air-dried and then dissolved in Tris-EDTA buffer (10mM Tris-HCI).

treatment_protocol: Venous blood was collected in sodium-heparin tubes (Greiner Bio-One, Kremsmünster, Austria) and peripheral blood mononuclear cells (PBMCs) were isolated by density centrifugation over a Lymphoprep gradient (Axis-Shield, Oslo, Norway) and washed thrice in Hank’s Balanced Salt Solution (Gibco™, Thermo Fisher Scientific, Waltham, MA, USA). The PBMCs were resuspended in MACS buffer (phosphate buffered saline (PBS; Medicago, Uppsala, Sweden) supplemented with 2mM EDTA (Sigma-Aldrich, St Louise, MO, USA) and 5% fetal bovine serum (FBS; Thermo Fisher Scientific) and labelled with anti-CD4-coated microbeads (Miltenyi Biotech, Bergish Gladbach, Germany). The CD4+ cells were isolated by positive immunomagnetic selection using MS columns and a miniMACS separator (Miltenyi Biotec) according to the manufacturer’s instructions provided by the manufacturer.

value: blood

value: isolated CD4+ cells

tag: age

tag: gestational week

value: female


title: D6-10-1_Rep3


title: D6-10-1_Rep2


title: AL

value: AL


title: D6-10-1_Rep1


title: AI

value: AI


title: HEK293T_150_units_RNaseH_Input.rep2

first: Ruitu

last: Lyu

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

description: Input

data_processing:
First, the trim-galore package was used to remove low-qualified bases and adapter-containing reads from raw spKAS-seq data. Trimmed reads shorter than length 30 bp were discarded, and the rest were aligned to the reference genome (hg19) using bowtie2 (v2.3.3.1) under default parameters.
Sam files were subsequently converted and sorted to bam files using samtools (v1.9). Duplicated mapped reads were removed using picard MarkDuplicates (v1.141).
For paired-end spKAS-seq data, SAMtoBED.py was used to combine “properly paired” alignments into a single BED interval. For single-end spKAS-seq data, deduplicated unique mapped reads were extended to 150 bp to match the average length of DNA fragments (awk command).
Bed files were converted to bedGraph files using bedtools. BedGraph files were then converted to bigWig files using bedgraphtobigwig from UCSC pre-compiled utilities.
Assembly: hg19
Supplementary files format and content: bigWig, spKAS-seq density on plus and minus strands.
Library strategy: strand-specific KAS-seq

source_name: Human embryonic kidney cells

growth_protocol: HEK293T were purchased from ATCC (CRL11268 for HEK293T, HB8065 for HepG2) and were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco 10378) and grown at 37 °C with 5% CO2. K562 cells were purchased from ATCC (CCL243) and were cultured in RPMI 1640 (Gibco 11875) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco) and grown at 37 °C with 5% CO2. All cell lines were routinely checked to be free of mycoplasma.

extract_protocol:
After labeling, cells were harvested for genomic DNA isolation by using the PureLink Genomic DNA mini kit (Thermo, K182002). Around 2 µg genomic DNA was then diluted in 100 µL 1× PBS supplemented with 25 mM K3BO3 and 20 mM DBCO-PEG4-biotin (Sigma, 760749). The mixture was gently shacked at 37 °C for 1.5 h, after which 5 µL RNase A (Thermo, 12091039) was added, followed by another 5 min incubation at 37 °C. DNA was then purified from the reaction by using the DNA Clean & Concentrator-5 kit (Zymo, D4013) and was fragmented to 150-350 bp by sonicating 30 cycles at 30s-on/30s-off setting using Diagenode Bioruptor Pico. Save 5% of the sonicated DNA as input and use the rest for enrichment with 10 µL Dynabeads MyOne Streptavidin C1 (Thermo, 65001). The beads were washed by 1× B&W buffer (5 mM Tris-HCl pH 7.4, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 95 µL 2× B&W buffer, and mixed with sonicated DNA. The binding was performed at room temperature for 15 min. The beads were washed once in 1× B&W buffer and then washed twice with 100 mM NaOH solution to denature the dsDNA and remove the DNA strands that are not labeled by N3-kethoxal. A final wash with 1× B&W buffer was followed, and DNA was eluted in 10 µL H2O by heating the beads at 95 °C for 10 min.
Input and enriched DNA were used for library construction by using the Accel-NGS Methyl-seq DNA library kit (Swift, 30024). Libraries were sequenced on Illumina platforms with pair-end more with around 60 million reads per library.

treatment_protocol: Cells were treated with 5 mM N3-kethoxal dissolved in their culture media for 10 min at 37 °C, 5% CO2.

value: Human embryonic kidney cells

value: RNaseH


title: HEK293T_150_units_RNaseH_Input.rep1

description: Input


title: CD4+ T cells_2nd_trimesterpregnant 11

source_name: CD4+ T cells, 2nd trimester pregnant 11


title: HEK293T_150_units_RNaseH_spKAS-seq.rep2

description: strand-specific KAS-seq(spKAS-seq)


title: AB.att


title: D6-100-M_Rep2

value: pMN


title: HEK293T_150_units_RNaseH_spKAS-seq.rep1

description: strand-specific KAS-seq(spKAS-seq)


title: D6-100-M_Rep3


title: donor_35_DMSO

city: New York

first: Robert

last: Sebra

state: New York

address: 1 Gustave L. Levy Place

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Transcript expression was quantified from RNA-Seq data using Salmon 1.2.1 against an index built from the Ensembl GRCh38 v99 transcriptome model with default parameters.
Pseudocounts were imported into an R 4.0.3 environment and summarized to the gene level using tximeta 1.8.2.
Assembly: hg38
Supplementary files format and content: Tab-separated text file containing estimated gene counts from Salmon for each sample.

source_name: whole blood

extract_protocol:
Whole blood was treated with ACK lysis buffer for 15 minutes at RT to remove red blood cells. Cells were resuspended in Trizol (300µL) and RNA was extracted using Zymo’s Direct-zol extraction kit as per the manufacturer’s instructions.
Sequencing libraries were prepared from the eluted RNA using the Ovation Ultralow V2 DNA-Seq Library Preparation Kit following the manufacturer’s instruction (NuGEN) at the Mount Sinai Oncological Sciences Sequencing Facility. Sequencing was performed on an Illumina NextSeq 500 instrument to produce 75-bp single-end reads.

treatment_protocol: 320 μl of whole blood drawn on the same day were mixed with 80 μl RPMI and stimulated with pools of SARS-CoV-2 peptides (S or NP; 2 μg/ml) or DMSO control at 37ºC.

tag: donor id

tag: donor covid_status

value: DMSO

value: vaccinated

tag: cohort


title: donor_35_SpG

value: SpG


title: AP.SPH


title: CD4+ T cells_2nd_trimesterpregnant 10

source_name: CD4+ T cells, 2nd trimester pregnant 10


title: donor_34_SpG


title: D6-100-3_Rep3


title: HEK293T_100_units_RNaseH_Input.rep2

description: Input


title: D6-100-3_Rep2


title: donor_34_DMSO


title: HEK293T_100_units_RNaseH_spKAS-seq.rep2

description: strand-specific KAS-seq(spKAS-seq)


title: D6-100-3_Rep1


title: donor_33_SpG

value: naive


title: HEK293T_100_units_RNaseH_spKAS-seq.rep1

description: strand-specific KAS-seq(spKAS-seq)


title: CD4+ T cells_2nd_trimesterpregnant 6

source_name: CD4+ T cells, 2nd trimester pregnant 6


title: HEK293T_100_units_RNaseH_Input.rep1

description: Input


title: D6-100-M_Rep1


title: D6-100-2_Rep3


title: CD4+ T cells_2nd_trimesterpregnant 7

source_name: CD4+ T cells, 2nd trimester pregnant 7


title: CD4+ T cells_2nd_trimesterpregnant 9

source_name: CD4+ T cells, 2nd trimester pregnant 9


title: CD4+ T cells_2nd_trimesterpregnant 4

source_name: CD4+ T cells, 2nd trimester pregnant 4


title: donor_33_DMSO


title: HEK293T_50_units_RNaseH_Input.rep2

description: Input


title: D6-100-2_Rep2


title: HEK293T_50_units_RNaseH_Input.rep1

description: Input


title: donor_32_SpG


title: CD4+ T cells_2nd_trimesterpregnant 5

source_name: CD4+ T cells, 2nd trimester pregnant 5


title: CD4+ T cells_1st_trimesterpregnant 11

description: methylation expression in isolated blood CD4+ cells from 1st trimester pregnant woman

source_name: CD4+ T cells, 1st trimester pregnant 11


title: CD4+ T cells_1st_trimesterpregnant 10

source_name: CD4+ T cells, 1st trimester pregnant 10


title: D6-100-2_Rep1


title: donor_32_DMSO


title: CD4+ T cells_2nd_trimesterpregnant 8

source_name: CD4+ T cells, 2nd trimester pregnant 8


title: donor_31_SpG


title: HEK293T_50_units_RNaseH_spKAS-seq.rep1

description: strand-specific KAS-seq(spKAS-seq)


title: CD4+ T cells_2nd_trimesterpregnant 2

source_name: CD4+ T cells, 2nd trimester pregnant 2


title: D6-0-1_Rep2


title: HEK293T_50_units_RNaseH_spKAS-seq.rep2

description: strand-specific KAS-seq(spKAS-seq)


title: CD4+ T cells_2nd_trimesterpregnant 1

source_name: CD4+ T cells, 2nd trimester pregnant 1


title: donor_31_DMSO


title: CD4+ T cells_2nd_trimesterpregnant 3

source_name: CD4+ T cells, 2nd trimester pregnant 3


title: CD4+ T cells_1st_trimesterpregnant 8

source_name: CD4+ T cells, 1st trimester pregnant 8


title: RM9

city: Stanford

first: Andrew

last: Gentles

address: 291 Campus Drive

institute: Stanford University

description: Random Mix

data_processing:
Estimated transcript read counts and transcripts per million (tpm) were generated via pseudo-alignment with Kallisto v0.46.0 using Homo_sapiens.GRCh38.cdna.all.idx.
A translation table of Ensembl transcript ID to Ensembl gene ID and gene symbol was derived using biomaRt and stored on the Synapse platform at syn21574276.
Estimated gene read counts and counts per million were calculated as the sum of transcript counts and tpms, respectively, associated with the gene via the translation table.
Assembly: hg38
Supplementary files format and content: Matrix table with Kallisto-estimated counts for every Ensembl transcript ID and every sample
Supplementary files format and content: Matrix table with Kallisto-estimated tpms for every Ensembl transcript ID and every sample
Supplementary files format and content: Matrix table with Kallisto-estimated counts for every Ensembl gene ID and every sample
Supplementary files format and content: Matrix table with Kallisto-estimated cpms for every Ensembl gene ID and every sample
Supplementary files format and content: Matrix table with Kallisto-estimated counts for every gene symbol and every sample
Supplementary files format and content: Matrix table with Kallisto-estimated cpms for every gene symbol and every sample

extract_protocol: We generated in vitro and in silico admixtures of tumor, immune, and stromal cells and sequenced them along with the purified populations from which they were derived. We used the admixtures as ground truth in a community-wide DREAM Challenge aimed at providing an objective, unbiased assessment of published deconvolution methods and at promoting development of new approaches.

value: Random Mix


title: D6-0-1_Rep1


title: donor_30_SpG


title: RM8

description: Random Mix


title: donor_30_DMSO


title: CD4+ T cells_1st_trimesterpregnant 7

source_name: CD4+ T cells, 1st trimester pregnant 7


title: donor_29_SpG


title: D5-500-M_Rep2


title: RM5

description: Random Mix


title: RM7

description: Random Mix


title: RM6

description: Random Mix


title: CD4+ T cells_1st_trimesterpregnant 5

source_name: CD4+ T cells, 1st trimester pregnant 5


title: CD4+ T cells_1st_trimesterpregnant 6

source_name: CD4+ T cells, 1st trimester pregnant 6


title: donor_29_DMSO

source_name: whole blood


title: D5-500-M_Rep1


title: donor_28_SpG


title: D5-500-3_Rep3


title: RM4

description: Random Mix


title: CD4+ T cells_1st_trimesterpregnant 9

source_name: CD4+ T cells, 1st trimester pregnant 9


title: CD4+ T cells_1st_trimesterpregnant 4

source_name: CD4+ T cells, 1st trimester pregnant 4


title: D6-0-1_Rep3


title: RM36

description: Random Mix


title: D5-500-3_Rep1


title: RM35

description: Random Mix


title: donor_27_SpG


title: donor_28_DMSO


title: D5-10-2_Rep3


title: RM34

description: Random Mix


title: donor_27_DMSO


title: D5-10-2_Rep2


title: CD4+ T cells_1st_trimesterpregnant 2

source_name: CD4+ T cells, 1st trimester pregnant 2


title: CD4+ T cells_1st_trimesterpregnant 1

source_name: CD4+ T cells, 1st trimester pregnant 1


title: donor_26_SpG


title: CD4+ T cells_nonpregnant 12

description: methylation expression in isolated blood CD4+ cells from non-pregnant woman

source_name: CD4+ T cells, nonpregnant 12


title: RM33

description: Random Mix


title: CD4+ T cells_1st_trimesterpregnant 3

source_name: CD4+ T cells, 1st trimester pregnant 3


title: donor_26_DMSO


title: D5-500-3_Rep2


title: D5-10-2_Rep1


title: RM32

description: Random Mix


title: donor_25_SpG


title: D5-10-1_Rep3


title: RM31

description: Random Mix


title: CD4+ T cells_nonpregnant 10

source_name: CD4+ T cells, nonpregnant 10


title: D5-10-1_Rep2


title: donor_25_DMSO


title: donor_24_SpG


title: RM3

description: Random Mix


title: D5-10-1_Rep1


title: D6_500_3,Replicate3

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10 --macs_fdr 0.00001 --skip_diff_analysis --min_reps_consensus 2 -r 1.2.0
Peaks were further filtered out if they didn't pass qval < 0.00001 in at least 1 sample. The qval comes from MACS peak calling in each sample.
Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file
Assembly: mm10
Supplementary files format and content: consensus_peaks.mLb.vsd.csv provides variant stabilised data obtained with DESeq2 from the read count across the consensus chromatin accessibility regions
Supplementary files format and content: consensus_peaks.mLb.clN.annotatePeaks.txt provides annotation for all the intervals in consensus_peaks.mLb.vsd.csv

extract_protocol:
Crosslinked and TF-Sorted ATAC-seq (CaTS-ATAC) was performed as described in the associated manuscript. In brief, cells were PFA fixed, subject to Tn5 transposition for ATAC-seq, stained with intracellular antibodies and flow sorted. After overnight reverse crosslinking, DNA was extracted using Zymo DNA concentrator kit.
Transposed DNA was first amplified as described in Corces et al (2017) and Ma et al (2020)


title: D6_500_M,Replicate2


title: CD4+ T cells_nonpregnant 6

source_name: CD4+ T cells, nonpregnant 6


title: D5-100-M_Rep3


title: D5-500-M_Rep3


title: RM30

description: Random Mix


title: RM29

description: Random Mix


title: CD4+ T cells_nonpregnant 11

source_name: CD4+ T cells, nonpregnant 11


title: CD4+ T cells_nonpregnant 9

source_name: CD4+ T cells, nonpregnant 9


title: donor_24_DMSO


title: CD4+ T cells_nonpregnant 7

source_name: CD4+ T cells, nonpregnant 7


title: D5-100-M_Rep2


title: donor_23_SpG


title: D6_500_3,Replicate2


title: D6_10_2,Replicate3


title: D5-100-M_Rep1


title: CD4+ T cells_nonpregnant 5

source_name: CD4+ T cells, nonpregnant 5


title: CD4+ T cells_nonpregnant 8

source_name: CD4+ T cells, nonpregnant 8


title: CD4+ T cells_nonpregnant 4

source_name: CD4+ T cells, nonpregnant 4


title: D6_500_M,Replicate3


title: donor_23_DMSO


title: RM27

description: Random Mix


title: D6_10_2,Replicate2


title: donor_22_SpG


title: CD4+ T cells_nonpregnant 3

source_name: CD4+ T cells, nonpregnant 3


title: RM25

description: Random Mix


title: D5-100-3_Rep2


title: D5-100-3_Rep3


title: RM26

description: Random Mix


title: D5-100-3_Rep1


title: D6_10_2,Replicate1


title: D6_10_1,Replicate3


title: RM24

description: Random Mix


title: D5-100-2_Rep3


title: CD4+ T cells_nonpregnant 2

source_name: CD4+ T cells, nonpregnant 2


title: RM23

description: Random Mix


title: D6_10_1,Replicate2


title: donor_21_SpG

source_name: whole blood


title: donor_21_DMSO


title: D6_10_1,Replicate1


title: D5-100-2_Rep2


title: donor_22_DMSO


title: donor_20_SpG


title: D6_100_M,Replicate3


title: RM21

description: Random Mix


title: donor_20_DMSO


title: D5-100-2_Rep1


title: D6_100_M,Replicate2


title: donor_19_SpG


title: RM20

description: Random Mix


title: D5-0-1_Rep3


title: D6_100_3,Replicate3


title: D5-0-1_Rep2


title: D6_100_3,Replicate2


title: donor_19_DMSO


title: RM2

description: Random Mix


title: RM19

description: Random Mix


title: donor_18_SpG


title: D5-0-1_Rep1


title: D6_100_2,Replicate3


title: D4-500-M_Rep3


title: donor_18_DMSO


title: D6_100_2,Replicate2


title: RM22

description: Random Mix


title: RM17

description: Random Mix


title: RM18

description: Random Mix


title: donor_17_DMSO


title: donor_17_SpG


title: D4-500-3_Rep3


title: RM16

description: Random Mix


title: RM15

description: Random Mix


title: D4-500-3_Rep2


title: donor_16_SpG


title: D6_0_1,Replicate3


title: donor_16_DMSO


title: D4-10-2_Rep3


title: D5_500_M,Replicate3


title: D4-500-M_Rep2


title: D5_500_M,Replicate2


title: D4-10-1_Rep3


title: RM12

description: Random Mix


title: D6_100_2,Replicate1


title: donor_15_DMSO


title: RM11

description: Random Mix


title: donor_14_SpG


title: D5_500_3,Replicate3


title: D5_500_3,Replicate2


title: donor_14_DMSO


title: RM10

description: Random Mix


title: D4-10-1_Rep2


title: D4-10-1_Rep1


title: D6_0_1,Replicate2


title: RM1

description: Random Mix


title: D5_10_2,Replicate3


title: donor_13_SpG


title: D5_10_2,Replicate2


title: D4-100-M_Rep2


title: D4-100-M_Rep3


title: RM14

description: Random Mix


title: donor_15_SpG


title: RM13

description: Random Mix


title: BM9

description: Biological Mix

value: Biological Mix


title: D5_10_2,Replicate1


title: D4-100-3_Rep3


title: donor_13_DMSO


title: BM8

description: Biological Mix


title: donor_12_SpG


title: D4-100-2_Rep3


title: D5_10_1,Replicate3


title: D4-100-2_Rep2


title: BM60

description: Biological Mix


title: donor_11_SpG


title: D4-0-1_Rep3


title: donor_11_DMSO


title: BM6

description: Biological Mix


title: BM59

description: Biological Mix


title: donor_10_SpG


title: D4-0-1_Rep2


title: donor_10_DMSO


title: D5_100_M,Replicate2


title: BM58

description: Biological Mix


title: D5_100_M,Replicate1


title: D5_100_M,Replicate3


title: D3-0-NMP_Rep2

value: NMP


title: BM57

description: Biological Mix


title: donor_09_SpG


title: BM7

description: Biological Mix


title: donor_12_DMSO


title: D5_10_1,Replicate1


title: D5_100_3,Replicate3


title: donor_09_DMSO


title: BM56

description: Biological Mix


title: D3-0-NMP_Rep1


title: D3-0-NMP_Rep3


title: BM55

description: Biological Mix


title: donor_08_SpG

value: convalescent


title: BM54

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT22 - rep2

first: Katya

last: Frazier

address: 900 E. 57th Street

data_processing:
RNA quality and quantity was assessed using the Agilent bio-analyzer. RNA-SEQ libraries were generated using the Illumina stranded mRNA library making kit. Sequencing was performed on the HiSEQ4000 with Illumina reagents and protocols. Data was demultiplexed using the Illumina bcl2fastq software.
Quality control was confirmed by FastQC and MultiQC
Sequenced reads were mapped to mm10 whole genome using STAR 2.6.1b
Featurecounts matrix generated using featureCounts v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Liver

extract_protocol:
Livers were removed via dissection, flash frozen in liquid nitrogen, and RNA was harvested using TRIzol and chloroform as previously described (Leone et al, 2015).
RNA quality and quantity was assessed using the Agilent bio-analyzer. RNA-SEQ libraries were generated using the Illumina stranded mRNA library making kit.

value: Liver

tag: Sex

value: male

value: Bmal1 fl/fl Albumin-Cre

tag: microbial status

value: GF

tag: timepoint

value: ZT 22


title: Liver L-Bmal1-KO GF ZT22 - rep3


title: donor_08_DMSO


title: Liver L-Bmal1-KO GF ZT22 - rep1


title: BM53

description: Biological Mix

tag: group


title: D5_100_3,Replicate2

tag: cell line


title: Liver L-Bmal1-KO GF ZT18 - rep3

tag: strain

value: ZT 18


title: BM52

description: Biological Mix


title: donor_07_SpG


title: CD4+ T cells_nonpregnant 1

source_name: CD4+ T cells, nonpregnant 1

tag: tissue

value: blood

value: isolated CD4+ cells

tag: gender

value: female


title: donor_07_DMSO

value: DMSO


title: donor_06_SpG


title: D5_100_2,Replicate2

tag: cell type


title: D5_100_2,Replicate1

tag: treatment


title: Liver L-Bmal1-KO GF ZT18 - rep2

tag: genotype


title: BM51

description: Biological Mix


title: BM50

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT18 - rep1


title: donor_06_DMSO


title: D5_0_1,Replicate3


title: D5_100_3,Replicate1


title: donor_05_SpG


title: Liver L-Bmal1-KO GF ZT14 - rep3

value: ZT 14


title: D5_100_2,Replicate3


title: D5_0_1,Replicate2


title: D5_10_1,Replicate2


title: BM5

description: Biological Mix


title: donor_05_DMSO


title: D4_500_M,Replicate3

value: pMN


title: Liver L-Bmal1-KO GF ZT14 - rep2


title: BM49

description: Biological Mix


title: BM48

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT14 - rep1


title: donor_04_SpG

value: SpG


title: RM28

description: Random Mix

value: Random Mix


title: Liver L-Bmal1-KO GF ZT10 - rep3

value: ZT 10


title: BM47

description: Biological Mix

value: Biological Mix


title: D4_500_M,Replicate2


title: Liver L-Bmal1-KO GF ZT10 - rep2


title: D4_500_M,Replicate1


title: donor_04_DMSO

value: convalescent


title: donor_03_SpG


title: Liver L-Bmal1-KO GF ZT10 - rep1

value: Liver


title: BM46

description: Biological Mix


title: donor_03_DMSO


title: D4_500_3,Replicate3


title: BM45

description: Biological Mix


title: D4_500_3,Replicate1


title: D5_0_1,Replicate1


title: donor_02_SpG


title: D4_10_2,Replicate3


title: Liver L-Bmal1-KO GF ZT6 - rep2

value: male

value: ZT 6


title: donor_02_DMSO


title: Liver L-Bmal1-KO GF ZT6 - rep1

value: Bmal1 fl/fl Albumin-Cre

value: GF


title: BM43

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT6 - rep3


title: BM42

description: Biological Mix


title: D4_10_2,Replicate1


title: donor_01_DMSO


title: Liver L-Bmal1-KO GF ZT2 - rep3

value: ZT 2


title: D4_10_2,Replicate2


title: BM41

description: Biological Mix


title: donor_01_SpG


title: D4_10_1,Replicate3


title: BM40

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT2 - rep2


title: D4_10_1,Replicate2


title: BM44

description: Biological Mix


title: BM4

description: Biological Mix


title: PACJ17_Null

city: Atlanta

first: Greg

last: Gibson

state: GA

address: North Ave NW

institute: Georgia Institute of Technology

library_source: transcriptomic single cell

data_processing:
Cellranger software was used process base call files, generate count matrices, map reads to the genome and conduct initial QC and filtering
Each sample was further filtered and processed using Seurat package in R® statistical software and futher analyses were conducted using JMP statistical software.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell
Supplementary files format and content: Tab-separated values file with the list of cell barcodes for the sample, corresponding to column indices in the matrix file
Supplementary files format and content: Tab-separated values file with the list of features for the sample, corresponding to row indices in the matrix file
Supplementary files format and content: Tab-delimited text files include subject assignment for each cell barcode in the case of multiplexed samples (Lneg, Lpos, Nneg, Npos)

source_name: Peripheral blood

growth_protocol: Whole blood collected from patients was transferred via syringe needle into two 1mL TruCulture whole-blood  culture tubes.

extract_protocol:
500uL of whole blood pellet was aliquoted for PBMC isolation by negative selection using Stem Cell Technology EasySep Direct Human PBMC isolation kit (catalog #19654). PBMCs were filtered, washed and resuspended. Single cell suspensions were loaded into a Chromium Single-cell Controller (P/N 110211) in accordance with 10X Genomics recommendations for a target cell recovery of 3000 cells per sample.
Single-cell RNA libraries were prepared using Chromium™ Single Cell 3' Library & Gel Bead Kit v2 following manufacturer’s specifications. Batches 1 and 2 were run on a Flowcell  v2.0 while batches 3 and 4 were run on a Flowcell v2.5.

treatment_protocol: Of the two 1mL TruCulture whole-blood culture tubes, one was supplemented with tumor necrosis factor alpha (TNF-α, 10 ng/ml) and one null. Cells were allowed 24hr ex-vivo stimulation at 37°F.

tag: batch

tag: disease status

value: JIA

tag: subjects


title: PACJ17_TNF

value: TNF


title: BM39

description: Biological Mix


title: Liver WT GF ZT22 - rep3

value: Bmal1 fl/fl

value: ZT 22


title: PACJ15_TNF


title: BM38

description: Biological Mix


title: Liver WT GF ZT22 - rep2


title: PACJ15_Null


title: D4_100_M,Replicate3


title: Liver WT GF ZT22 - rep1


title: BM37

description: Biological Mix


title: BM36

description: Biological Mix


title: D4_100_M,Replicate1


title: PACJ14_TNF


title: D4_100_3,Replicate3


title: PACJ14_Null


title: Liver WT GF ZT18 - rep3

value: ZT 18


title: Liver WT GF ZT18 - rep2


title: BM35

description: Biological Mix


title: D4_100_3,Replicate2


title: BM34

description: Biological Mix


title: Liver L-Bmal1-KO GF ZT2 - rep1


title: D4_10_1,Replicate1


title: Liver WT GF ZT14 - rep3

value: ZT 14


title: BM33

description: Biological Mix


title: D4_100_3,Replicate1


title: PACJ13_Null


title: D4_100_M,Replicate2

value: pMN


title: D4_100_2,Replicate3


title: PACJ12_TNF


title: D4_100_2,Replicate2


title: Liver WT GF ZT14 - rep1


title: PACJ12_Null


title: BM31

description: Biological Mix


title: PACH14_TNF

value: Healthy


title: Liver WT GF ZT18 - rep1


title: PACJ13_TNF


title: D4_100_2,Replicate1


title: Liver WT GF ZT10 - rep2

value: ZT 10


title: PACH14_Null


title: BM30

description: Biological Mix

value: Biological Mix


title: Liver WT GF ZT10 - rep3


title: BM3

description: Biological Mix


title: BM29

description: Biological Mix


title: D4_0_1,Replicate1


title: PACJ11_TNF


title: D4_0_1,Replicate3


title: D4_0_1,Replicate2


title: Liver WT GF ZT14 - rep2


title: PACJ11_Null


title: BM28

description: Biological Mix


title: Liver WT GF ZT10 - rep1


title: Liver WT GF ZT6 - rep3


title: D3_0_NMP,Replicate3

value: NMP


title: PACH22_TNF


title: BM32

description: Biological Mix


title: BM27

description: Biological Mix


title: Liver WT GF ZT6 - rep2

value: Liver


title: D3_0_NMP,Replicate2


title: PACH22_Null


title: Liver WT GF ZT6 - rep1

value: male


title: BM26

description: Biological Mix


title: Liver WT GF ZT2 - rep3


title: BM25

description: Biological Mix


title: Liver WT GF ZT2 - rep2


title: mCh-Foxa2,Rep3

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10 --macs_fdr 0.00001 --skip_diff_analysis --min_reps_consensus 2 -r 1.2.0
Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file
Assembly: mm10
Supplementary files format and content: coverage bigwig files for each sample

growth_protocol: Mouse ES cell lines were maintained in ES cell medium with 1000 U/ml LIF (Chemicon, Int ESG1107) on mitotically inactive primary mouse embryo fibroblasts (feeders) in ES cell medium (Dulbecco’s Modified Eagle Medium (DMEM) Knock Out (Gibco, Cat No. 10829-018) complemented with 10% Foetal Bovine Serum, Penicillin/Streptomycin (Gibco, Cat No. 15140122), 2mM L-Glutamine (Gibco, Cat No. 25030024), 2mM Non-essential amino acids (Gibco, Cat No. 11140-035), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)). For spinal cord neural differentiation, ES cells were dissociated using 0.05% trypsin-EDTA (Gibco, Cat No. 25300054) and then plated onto 0.1% gelatinised (Gibco) tissue culture plates for three successive periods of 15 mins to remove feeders. Differentiations were carried out in N2B27 media (Advanced DMEM - F12 (Gibco, Cat No. 21331-020) and Neurobasal medium (Gibco, Cat No. A35829-01) (1:1), supplemented with 1xN2 (Gibco), 1xB27 (Gibco), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)) with the indicated additives. Cells were plated onto 6-well plates (Corning, Cat. No. 353046) precoated in Matrigel (Corning, Cat. No. 356231) diluted 1/50 and 1/100 in Advanced DMEM - F12 (Gibco, Cat No. 21331-020) at a density of 20,000 cells per 35mm well in 1.5 ml. The media was supplemented on the different days as follows: Day 0 to Day 2, 10ng/ml bFGF (R&D, Cat No. 100-18B) and 5 μM LGK (Cayman Chemical Company, Cat. No. 1.800.364.9897); Day2 to Day 3 for 20 h, 10ng/ml bFGF (R&D, Cat No. 100-18B), 5 μM CHIR99021 (Axon Medchem, Cat. No. 1386), 10 μM SB-431542 (Tocris, Cat. No. S0400), and 2μM  DMH1 (Adooq Bioscience, Cat. No. A12820); from Day 3 to D4, 100 nM RA (Sigma, Cat No. R2625), 0 nM SAG (Merck, Cat. No. 566660-5mg) and 1μg/ml Doxycycline (Sigma-Aldrich D9891) for the second 12h.

extract_protocol:
Trasposition was performed as previously described with 50,000 cells.
Transposed DNA was first amplified as described in Corces et al (2017) and Ma et al (2020)

treatment_protocol: 12h overexpression of tetON-mCherry or tetON-Foxa2-mCherry

value: NPs


title: mCh-Foxa2,Rep2


title: BM24

description: Biological Mix


title: BM22

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT22 - rep3

value: Bmal1 fl/fl Albumin-Cre

value: SPF


title: mCh-Foxa2,Rep1


title: Liver L-Bmal1-KO SPF ZT22 - rep1


title: BM23

description: Biological Mix


title: mCh-Ctrl,Rep3

value: tetON-Control


title: mCh-Ctrl,Rep2


title: BM21

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT18 - rep3


title: D3_0_NMP,Replicate1


title: mCh-Ctrl,Rep1


title: 3T3-CA77

city: Bronx

first: Mericka

last: McCabe

state: NY

address: 1300 Morris Park Avenue

institute: Albert Einstein College of Medicine

description: NIH3T3 treated with 20 µM CA77

hyb_protocol: Agilent Hybridization Protocol

scan_protocol: Scanned with Agilent Technologies Scanner G2505C US11263920 using one color scan. 2 microns per pixel

data_processing: Data were processed using the oligo package and normalized using Robust Multiarray Average (RMA) method

source_name: NIH-3T3 fibroblasts

label_protocol: Amount used was 0.6 μg Cyanine-3(Cy3)-labeled RNA.

growth_protocol: NIH3T3s were grown in DMEM supplemented with 10% fetal bovine serum and 1% antibiotics. The cultures were maintained at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen) and purified with RNeasy chromatography (Qiagen). according to manufacturer’s instructions. RNA was quantified using a NanoDrop ND-1000 and quality was monitored with Agilent RNA 6000 Nano Assay Bioanalyzer.

treatment_protocol: NIH3T3s were cultured to confluency in DMEM supplemented with 10% fetal bovine serum and 1% antibiotics and treated with indicated compound solubilized in DMSO. The cultures were maintained at 37 ºC in a humidified incubator with 5% CO2. Cells were collected 24 hours after treatment

value: WT

value: 20 µM CA77


title: BM20

description: Biological Mix


title: BM2

description: Biological Mix


title: 3T3-CA39

description: NIH3T3 treated with 20 µM CA39

value: 20 µM CA39


title: Liver WT GF ZT2 - rep1

value: Bmal1 fl/fl

value: GF

value: ZT 2


title: BMS614 Treatment

description: NIH3T3 cells treated with 20 µM BMS614

value: 20 µM BMS614


title: 3T3-AR7

description: NIH3T3 treated with 20 µM AR7

value: 20 µM AR7


title: Liver L-Bmal1-KO SPF ZT18 - rep2

value: ZT 18


title: BM19

description: Biological Mix

value: Biological Mix


title: No Treament

description: Untreated NIH3T3 cells


title: Liver L-Bmal1-KO SPF ZT22 - rep2

value: ZT 22


title: Liver L-Bmal1-KO SPF ZT18 - rep1

value: Liver


title: RGP, GSK, rep2

city: Beijing

first: Xiaoxiang

last: Dong

address: Shuangqing Road, Haidian District, Beijing

institute: TSINGHUA UNIVERSITY

data_processing:
Sequence reads were mapped to GrCM38/mm10 using STAR software with default parameters
Read count extraction and normalization were porformed with DEseq package in R
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: neocortex

growth_protocol: E10.5 neocortices were dissected and enzymatically dissociated to generate single-cell suspension, and 1×10^5 cells were cultured in the culture medium DMEM++ per well using 96-well plate

extract_protocol:
After ~24 hours, the cell cultures were collected and resuspended with DPBS containing CD133-APCand DAPI for 15 min, and used for FACS sorting. About 1000 CD133+;DAPI－ cells were sorted per sample for bulk RNA-seq
Bulk RNA-seq libraries were prepared using Smart-seq2 protocol with minor modification

treatment_protocol: About 2 hours later, 100 mM LDH inhibitor GSK2837808A was added in the medium, and an equal volume of DMSO was used as a control.

value: neocortex

value: Radial glial progenitor (RGP)

tag: developmental stage

value: GSK

tag: time


title: RGP, GSK, rep3


title: RGP, GSK, rep1


title: BM18

description: Biological Mix


title: AR7 Treatment

description: NIH3T3 cells treated with 20 µM AR7


title: RGP, DMSO, rep3

value: DMSO


title: BM17

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT14 - rep2

value: male

value: Bmal1 fl/fl Albumin-Cre

value: SPF

value: ZT 14


title: Liver L-Bmal1-KO SPF ZT14 - rep3


title: Lung, 48hr after 12Gy Dose, Sample 26

first: Michael

description: Lung 12Gy_26

data_processing: Agilent Feature Extraction software was used to process the scanned images from arrays (gridding and feature intensity extraction) and the data generated for each probe on the array was analyzed with GeneSpring GX v7.3.1 software (Agilent Technologies, Santa Clara, CA).

label: Alexa 555

source_name: Lung, 48hr after 12Gy Dose

extract_protocol: Approximately 100 µg of powdered sample was lysed with 700 µl of QIAzol lysis buffer (Cat # 79306, QIAGEN) and homogenized by passing the solution through QIAshredder spin columns (Cat # 79654, QIAGEN). RNA isolation was performed using standard miRNeasy mini kit (Cat # 217004, QIAGEN) according to the manufacturer’s protocol. Quality and quantity of the RNA samples were assessed using a DeNovix DS-11 nanodrop spectrophotometer (DeNovix, DE, US) and Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA).

value: C57BL/6 J

value: female

value: Lung

tag: treatment/time point

value: 48hr after 12Gy Dose


title: 3T3-control

description: Untreated NIH3T3 cells

value: WT


title: Lung, 48hr after 12Gy Dose, Sample 16

description: Lung 12Gy_16

tag: Sex


title: BM16

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT14 - rep1

tag: microbial status


title: RGP, DMSO, rep2


title: Lung, 48hr after 12Gy Dose, Sample 6

description: Lung 12Gy_6


title: BM15

description: Biological Mix


title: RGP, DMSO, rep1


title: Liver L-Bmal1-KO SPF ZT10 - rep3

tag: timepoint

value: ZT 10


title: Liver L-Bmal1-KO SPF ZT10 - rep2


title: BM13

description: Biological Mix

tag: group

value: Biological Mix


title: P90 OMPCreR26AP2e Double Heterozygous VNO

city: Albany

first: Paolo

middle: E

last: Forni

address: 1400 Washington Avenue

institute: University at Albany

description: Sample 3 - VNO_029

data_processing:
Singulomics generated fastq files from two libraries using Illumina's bcl2fastq
Our lab used cellranger count (4.0.0) to perform alignment, filtering, barcode counting, and UMI counting on the fastq files.
We used aggregated filtered processed files as input and Seurat 3.2.3 package in R studio to do quality control and downstream cell clustering analysis.
Genome_build: mm10-2020-A
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes and gene count matrix

source_name: Vomeronasal Organ

extract_protocol:
Vomeronasal organs of postnatal day 10 and 3mo OMPCre and OMPCreR26AP2e mice were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate. The single cell suspension was sent to SingulOmics for high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cells suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 2 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

tag: strain background

value: C57 BL/6J 129P2/OlaHsd Mixed Background

value: Male

tag: age

value: 3mo Adult

tag: genotype/variation

value: OMPCreR26AP2e Double Heterozygous

value: Vomeronasal Organ


title: Lung, 48hr after 8Gy Dose, Sample 25

description: Lung 8Gy_25

source_name: Lung, 48hr after 8Gy Dose

tag: strain

tag: tissue

value: 48hr after 8Gy Dose


title: BM14

description: Biological Mix


title: P10 OMPCreR26AP2e Double Heterozygous VNO

description: Sample 2 - Mutant

value: Postnatal day 10


title: Liver L-Bmal1-KO SPF ZT10 - rep1

city: Chicago

value: Liver

value: male

value: Bmal1 fl/fl Albumin-Cre


title: Lung, 48hr after 8Gy Dose, Sample 15

description: Lung 8Gy_15

value: C57BL/6 J


title: BM11

description: Biological Mix


title: Lung, 48hr after 8Gy Dose, Sample 5

description: Lung 8Gy_5

value: female


title: P10 OMPCre Heterozygous VNO

description: Sample 1 - Control

value: OMPCre Heterozygous


title: Liver L-Bmal1-KO SPF ZT6 - rep3

value: SPF

value: ZT 6


title: BM12

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT6 - rep2


title: P60 wild-type VNO_2

department: Department of Biological Sciences

description: Sample 2 - Forni01b (Library2)

data_processing:
Singulomics generated fastq files from two libraries using Illumina's bcl2fastq
Our lab used cellranger count (version4) to perform alignment, filtering, barcode counting, and UMI counting on the fastq files of 2 separate libraries.
We used cellranger aggr to aggregate outputs from two libraries (Forni01a and Forni01b) of cellranger count, normalizing those runs to the same sequencing depth.
We used aggregated filtered processed files as input and Seurat 3.2.3 package in R studio to do quality control and downstream cell clustering analysis. Cells with mitochondrial read rate >5% and expressed < 200 genes were  filtered out from our data set.
Genome_build: mm10
Supplementary_files_format_and_content: tsv and mtx files containing cell barcodes and gene count matrix

extract_protocol:
5 Vomeronasal organs of postnatal day 60 C57BL/6J male mice were isolated and dissociated into single-cell suspension using neural isolation enzyme/papain (NIE/Papain in Neurobasal Medium with 0.5mg/mL Collagenase A, 1.5mM L-cysteine and 100U/mL DNAse I) incubated at 37ºC. The dissociated cells were then washed with HBSS and reconstituted in cell freezing medium (90% FBS, 10% DMSO). Cells were frozen from room temperature to -80ºC at a -1°C/min freeze rate. The single cell suspension was sent to SingulOmics for high-throughput single-cell gene expression profiling using the 10x Genomics Chromium Platform.
Single cell library preparation and sequencing were conducted by Singulomics Corporation (https://singulomics.com/, Bronx, NY). Cryopreserved, viable single cell suspensions were thawed, washed, resuspended in cell culture media with 0.04% BSA, and counted. Viable cell suspensions were then loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEM) with each GEM containing a single cell as well as barcoded oligonucleotides. We targeted 10,000 cells to be captured per sample for a total of 2 samples. Next, the GEMs were placed in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scentific, Wilmington, DE) and reverse transcription was performed in each GEM (GEM-RT). After the reaction, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10X Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). Amplified full-length cDNAs from poly-adenylated mRNA were then used to generate 3ʹ Gene Expression library (Chromium Next GEM 3’ Single Cell Reagent kits v3.1, dual index), following the manufacturer’s instructions (10x Genomics, Pleasanton, CA). Amplified cDNAs and the libraries were measured by Qubit dsDNA HS assay (Thermo Fisher Scientific, Wilmington, DE) and quality assessed by BioAnalyzer (Agilent Technologies, Santa Clara, CA).

value: C57 BL/6J wild-type

value: Postnatal day 60


title: Liver WT SPF ZT22 - rep2

value: Bmal1 fl/fl

value: ZT 22


title: Tissue_Peri-implantitis site3

first: Shasha

last: Yuan

address: No.22, Zhongguancun Nandajie, Haidian District

department: Department of Periodontology

institute: Peking University School and Hospital of Stomatology

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 (GRCm38.p6) whole genome using bowtie version 2.4.1.
Transcripts Per Million reads (TPM) were calculated using RSEM version 1.3.3.
Genome_build: mm39
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.
Supplementary_files_format_and_content: Matrix table with TPM values for every gene and every sample

source_name: Gingival tissues

extract_protocol:
Gingival tissues around ligatured implants and corresponding ligatured tooth were regarded as peri-implantitis sites and periodontitis sites respectively, while tissues around the third molars were collected as healthy controls, total RNA from the gingival tissues was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The left maxillary first molars were extracted in all mice under general anesthesia. After healing, a screw-shaped titanium implant (1 mm in length and 0.5 mm in diameter; D. P. Machining Inc) was screwed clockwise into the maxillary bone until torque can be achieved. After implant osseointegration, experimental peri-implantitis and periodontitis were induced. Silk ligature (5-0, Roboz Surgical Instrument Co., MD, USA ) was placed subgingivally around each implant apical to the implant head on the left side of the maxilla, while the rightl maxillary first molars were tied with a 5-0 silk ligature subgingivally. Two weeks after the ligature placement, all mice were killed by CO2 inhalation and gingival tissue were harvested.

value: gingiva

tag: diasease state

value: peri-implantitis site


title: BM1

description: Biological Mix

value: Biological Mix


title: BM10

description: Biological Mix


title: Liver L-Bmal1-KO SPF ZT6 - rep1

tag: genotype


title: P60 wild-type VNO_1

description: Sample 1 - Forni01a (Library1)

value: Vomeronasal Organ

value: Male


title: Lung, 48hr after 4Gy Dose, Sample 14

last: Falduto

address: 1808 Janke, Unit M

description: Lung 4Gy_14

source_name: Lung, 48hr after 4Gy Dose

value: Lung

value: 48hr after 4Gy Dose


title: Tissue_Peri-implantitis site2


title: NK_cells_2

description: Purified Cell

source_name: NK cells, healthy

value: PBMC

value: NK cells

value: healthy

tag: vendor

value: All Cells

value: Untouched NPB-CD56+ Natural Killer (NK) cells are negatively selected from mononuclear cells using an indirect immunomagnetic NK cell labeling system to deplete the non-CD56+ NK cells.

value: Purified Cell


title: Lung, 48hr after 4Gy Dose, Sample 4

description: Lung 4Gy_4

value: C57BL/6 J

value: female


title: Lung, 48hr after 2Gy Dose, Sample 23

description: Lung 2Gy_23

source_name: Lung, 48hr after 2Gy Dose

value: 48hr after 2Gy Dose


title: Tissue_Peri-implantitis site1


title: NK_cells_1

description: Purified Cell

value: Stem Express

value: Human peripheral blood CD56+ natural killer cells are enriched by means of negative selection. Cells expressing CD3, CD4, CD14, CD19, CD20, CD36, CD66b, CD123, HLA-DR, and CD235a are depleted from the mononuclear cell fraction by using immunomagnetic particles leaving purified, untouched CD56+ natural killer cells. Isolated cells are characterized by flow cytometry to ensure a highly pure and viable cell population.


title: Lung, 48hr after 4Gy Dose, Sample 24

description: Lung 4Gy_24


title: Lung, 48hr after 2Gy Dose, Sample 13

description: Lung 2Gy_13


title: Liver L-Bmal1-KO SPF ZT2 - rep2

value: Liver

value: male

value: Bmal1 fl/fl Albumin-Cre

value: SPF

value: ZT 2


title: Liver L-Bmal1-KO SPF ZT2 - rep1


title: Lung, 48hr after 2Gy Dose, Sample 3

description: Lung 2Gy_3

value: Lung


title: Tregs

description: Purified Cell

source_name: Tregs, healthy

value: PBMC

value: Tregs

value: Human Peripheral Blood CD4+CD25+ Tregs are enriched in a multi-step process. First, peripheral blood mononuclear cells (PBMCs) are isolated by means of apheresis. Next, cells expressing CD8, CD14, CD16, CD19, CD20, CD36, CD56, CD66b, CD123, TCR?/?, and CD235a are depleted from the PBMC population using immunomagnetic particles leaving purified, untouched CD4+ T cells. Then, enriched CD4+ T cells are selected for CD25+ cells by positive selection using anti-CD25 immunomagnetic particles allowing for the enrichment of CD4+CD25+ regulatory T cells. Isolated cells are characterized by flow cytometry before cryopreservation to ensure a highly pure and viable cell population.


title: Tissue_Periodontitis site3

value: gingiva

value: periodontitis site


title: Liver WT SPF ZT22 - rep3

value: Bmal1 fl/fl

value: ZT 22


title: Neutrophils_2

description: Purified Cell

source_name: Neutrophils, healthy

value: Peripheral blood

value: Neutrophils

value: healthy

value: Stanford HIMC

value: Human whole blood samples were collected under informed consent in EDTA-coated tubes. After 2h resting, whole blood samples were split for neutrophils and CD8 memory T cell isolation. Neutrophils isolation were performed with MACSxpress® Whole Blood Neutrophil Isolation Kit (Miltenyi Biotec) according to manufacturer’s indications. Briefly, the whole blood samples were mix with the appropriate amount of isolation mix buffer consisting in magnetically-coated beads conjugated to antibodies targeting all the immune populations in the peripheral blood except for the neutrophils. The cell suspension containing the isolation mix was incubated for 5 min at room temperature on a low-speed rotator. Then we proceeded to the magnetic separation for 15 minutes prior to collect the untouched neutrophils in a clean tube. Finally, isolated neutrophils were resuspended in RNAprotect Cell Reagent (Qiagen) for RNA extraction.

value: Purified Cell


title: Lung, 48hr after 1Gy Dose, Sample 22

description: Lung 1Gy_22

source_name: Lung, 48hr after 1Gy Dose

value: C57BL/6 J

value: female

value: 48hr after 1Gy Dose


title: Tissue_Periodontitis site2


title: Liver L-Bmal1-KO SPF ZT2 - rep3

value: Liver

value: male

value: Bmal1 fl/fl Albumin-Cre

value: SPF

value: ZT 2


title: Lung, 48hr after 1Gy Dose, Sample 12

description: Lung 1Gy_12

value: Lung


title: Liver WT SPF ZT22 - rep1

value: Bmal1 fl/fl


title: Tissue_Periodontitis site1

value: gingiva

value: periodontitis site


title: Monocytes_1

description: Purified Cell

source_name: Monocytes, healthy

value: PBMC

value: Monocytes

value: Stem Express

value: Human peripheral blood CD14+ monocytes are isolated from the mononuclear cell fraction by means of negative selection. Cells expressing CD2, CD3, CD16, CD19, CD20, CD56, CD66b, CD123, and CD235a are depleted from the mononuclear cell population using immunomagnetic particles leaving purified, untouched CD14+ monocytes. Isolated cells are characterized by flow cytometry before cryopreservation to ensure a highly pure and viable cell population.


title: Tissue_Healthy site3

value: healthy site


title: Macrophages_2

description: Purified Cell

source_name: Macrophages, healthy

value: Macrophages

value: healthy

value: The isolation of mature macrophages from tissue can be difficult, therefore the use of monocyte-derived macrophages (MDM) for functional studies is a very attractive alternative. Non-monocytes are depleted from the mononuclear cell population using immunomagnetic particles leaving purified, untouched CD14+ monocytes. The untouched monocytes are cultured for 4-5 days with 10% FBS in the presence of M-CSF and IL-4. After culture, cells are checked for the expression of CD11b, CD18, CD68, and HLA-DR by flow cytometry.

value: Purified Cell


title: Liver WT SPF ZT18 - rep3

source_name: Liver

value: Liver

value: male

value: ZT 18


title: Lung, 48hr after 0Gy Dose, Sample 21

description: Lung 0Gy_21

source_name: Lung, 48hr after 0Gy Dose

value: C57BL/6 J

value: female

value: 48hr after 0Gy Dose


title: Tissue_Healthy site2

value: gingiva


title: Lung, 48hr after 1Gy Dose, Sample 2

description: Lung 1Gy_2

value: Lung

value: 48hr after 1Gy Dose


title: Liver WT SPF ZT18 - rep1

value: Bmal1 fl/fl

value: SPF


title: Liver WT SPF ZT18 - rep2


title: Tissue_Healthy site1


title: Macrophages_1

description: Purified Cell

value: PBMC

value: Stem Express


title: Monocytes_2

description: Purified Cell

value: Monocytes

value: All Cells

value: Untouched NPB-CD14+ Monocytes are indirectly isolated from mononuclear cells using an immunomagnetic labeling system.


title: Fibroblasts

description: Purified Cell

source_name: Fibroblasts, healthy

value: skin

value: Fibroblasts

value: healthy

value: ATCC

value: Normal dermal fibroblasts (PCS-201-012)

value: Purified Cell


title: Lung, 48hr after 0Gy Dose, Sample 11

description: Lung 0Gy_11

value: C57BL/6 J

value: female

value: 48hr after 0Gy Dose


title: Liver WT SPF ZT14 - rep3

value: Liver

value: male

value: ZT 14


title: Dendritic_cells_2

description: Purified Cell

source_name: Dendritic cells, healthy

value: PBMC

value: Dendritic cells

value: NPB-Monocyte Derived Myeloid Dendritic Cells (MoDC) are derived from highly purified monocytes. For seven days, the highly purified monocytes are cultured with 10% Fetal Bovine Serum in the presence of GM-CSF and IL-4. These cells express the following markers:CD11c, CD40, and CD86. These cells lack the expression of CD14.


title: Endothelial_cells

description: Purified Cell

source_name: Endothelial cells, healthy

value: heart

value: Endothelial cells

value: Primary aortic endothelial cells (PCS-100-11)


title: Lung, 48hr after 0Gy Dose, Sample 1

description: Lung 0Gy_1

value: Lung


title: Liver WT SPF ZT14 - rep2

value: Bmal1 fl/fl

value: SPF


title: CspE non-crosslinked replicate 2

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
CLIP-seq
789_CspE_R2_NXL

data_processing:
Reads were trimmed for adaptors and a minimum read quality of 20 using cutadapt 1.15
Reads were mapped to O78-9 genome and plasmids p789-1, p789-2 and p789-3 (CP010315.1, CP010316 (p789-1), CP010317, and CP010318, respectively) obtained from NCBI using READemption version 0.3.7
Only uniquely mapping reads were retained, and used as input for PEAKachu in adaptive peak calling mode using the default DESeq normalization between conditions.
Assembly: CP010315.1, CP010316, CP010317, CP010318
Supplementary files format and content: csv, called peaks for CspC
Supplementary files format and content: csv, called peaks for CspE

organism: Escherichia coli

source_name: bacteria

growth_protocol: Bacteria were grown up to OD600 of 1.2-1.4 and processed.

extract_protocol:
phenol chloroform isoamyl alcohol (PCI) RNA extraction on the eluted samples
NEBNext Multiplex Small RNA Library Prep Set for Illumina

treatment_protocol: For each biological replicate, 200 mL bacterial culture were grown to OD600 of 2.0. Half of the culture was treated directly and half was irradiated with UV-C light at 800 mJ/cm2.

tag: cell type

value: bacteria

value: CspE-FLAG

tag: treatment


title: CspE non-crosslinked replicate 3

description:
CLIP-seq
789_CspE_R3_NXL


title: CspE crosslinked replicate 3

description:
CLIP-seq
789_CspE_R3_XL

value: UV cross-linked


title: Liver WT SPF ZT14 - rep1


title: CRC

description: Purified Cell

source_name: CRC, cancer

value: colon

value: CRC

value: cancer

value: ATCC

value: HT-29 colon adenocarcinoma (HTB-38)

value: Purified Cell


title: Liver, 48 hr after 8Gy Dose, Sample 25

institute: GenUs BioSystems, Inc.

description: Liver 8Gy_25

source_name: Liver, 48 hr after 8Gy Dose

value: C57BL/6 J

value: female

value: Liver

value: 48 hr after 8Gy Dose


title: Liver, 48 hr after 8Gy Dose, Sample 15

description: Liver 8Gy_15


title: Liver, 48 hr after 12Gy Dose, Sample 26

description: Liver 12Gy_26

source_name: Liver, 48 hr after 12Gy Dose

value: 48 hr after 12Gy Dose


title: Liver, 48 hr after 12Gy Dose, Sample 6

description: Liver 12Gy_6


title: Naive_CD8_T_cells_2

description: Purified Cell

source_name: Naive CD8 T cells, healthy

value: PBMC

value: Naive CD8 T cells

value: healthy

value: All Cells

value: Negatively isolated from mononuclear cells using an indirect immunomagnetic CD8+/CD45RA+ T Cell labeling system.


title: Liver WT SPF ZT10 - rep2

value: male

value: Bmal1 fl/fl

value: SPF

value: ZT 10


title: Liver, 48 hr after 8Gy Dose, Sample 5

description: Liver 8Gy_5


title: Liver, 48 hr after 4Gy Dose, Sample 24

description: Liver 4Gy_24

source_name: Liver, 48 hr after 4Gy Dose

value: 48 hr after 4Gy Dose


title: Liver, 48 hr after 12Gy Dose, Sample 16

description: Liver 12Gy_16


title: Liver WT SPF ZT6 - rep3

value: ZT 6


title: Memory_CD8_T_cells_2

description: Purified Cell

source_name: Memory CD8 T cells, healthy

value: Memory CD8 T cells

value: Stanford HIMC

value: Human whole blood samples were collected under informed consent in EDTA-coated tubes. After 2h resting, whole blood samples were split for neutrophils and CD8 memory T cell isolation. For CD8+ memory T cells isolation, PBMCs were first isolated by density gradient centrifugation using Ficoll-Paque™ Plus (Cytiva). After washes, cell counts were obtained using a Vi-Cell XR cell viability analyzer (Beckman Coulter). Then we proceeded to CD8+ memory T cell isolation using the CD8+ Memory T Cell Isolation Kit (Miltenyi Biotec) per the manufacturer’s indications. First, PBMCs were incubated at 4°C for 10 min with a cocktail of biotin-conjugated monoclonal antibodies against CD4, CD11c, CD14, CD15, CD16, CD19, CD34, CD36, CD45RA, CD56, CD57, CD61, CD123, CD141, TCRgd and CD235a. After wash, cells were resuspended with a solution of anti-biotin magnetic microbeads and incubated for 15 min at 4°C. After another wash, we proceeded to magnetic separation using LS columns (Miltenyi Biotec) and we collected the cell fraction corresponding to CD45RO+CD45RA-CD56-CD57‑CD8+ T cells. Finally, isolated CD8+ memory T cells were resuspended in RNAprotect Cell Reagent (Qiagen) for RNA extraction.

value: Purified Cell


title: CspE non-crosslinked replicate 1

description:
CLIP-seq
789_CspE_R1_NXL

value: bacteria

value: CspE-FLAG


title: CspC non-crosslinked replicate 3

description:
CLIP-seq
789_CspC_R3_NXL

value: CspC-FLAG


title: Liver WT SPF ZT10 - rep1

value: Liver


title: Liver, 48 hr after 4Gy Dose, Sample 14

description: Liver 4Gy_14

value: C57BL/6 J

value: female


title: Liver WT SPF ZT6 - rep2


title: CspE crosslinked replicate 2

description:
CLIP-seq
789_CspE_R2_XL

value: UV cross-linked


title: Liver WT SPF ZT10 - rep3

value: male


title: Dendritic_cells_1

description: Purified Cell

value: PBMC

value: Dendritic cells

value: healthy

value: All Cells

value: NPB-Monocyte Derived Myeloid Dendritic Cells (MoDC) are derived from highly purified monocytes. For seven days, the highly purified monocytes are cultured with 10% Fetal Bovine Serum in the presence of GM-CSF and IL-4. These cells express the following markers:CD11c, CD40, and CD86. These cells lack the expression of CD14.


title: Naive_CD4_T_cells_2

description: Purified Cell

source_name: Naive CD4 T cells, healthy

value: Naive CD4 T cells

value: First, NPB-CD4+ T Cells are negatively isolated using immunomagnetic CD4+ isolation kit from mononuclear cells. Next, CD45RO MicroBeads are used to deplete the CD45RO+ cell population, leaving an untouched, purified CD4+/CD45RA+ Naïve T Cell population.


title: Liver WT SPF ZT6 - rep1

value: Bmal1 fl/fl

value: SPF

value: ZT 6


title: Memory_CD8_T_cells_1

description: Purified Cell

value: Memory CD8 T cells

value: Stanford HIMC

value: Human whole blood samples were collected under informed consent in EDTA-coated tubes. After 2h resting, whole blood samples were split for neutrophils and CD8 memory T cell isolation. For CD8+ memory T cells isolation, PBMCs were first isolated by density gradient centrifugation using Ficoll-Paque™ Plus (Cytiva). After washes, cell counts were obtained using a Vi-Cell XR cell viability analyzer (Beckman Coulter). Then we proceeded to CD8+ memory T cell isolation using the CD8+ Memory T Cell Isolation Kit (Miltenyi Biotec) per the manufacturer’s indications. First, PBMCs were incubated at 4°C for 10 min with a cocktail of biotin-conjugated monoclonal antibodies against CD4, CD11c, CD14, CD15, CD16, CD19, CD34, CD36, CD45RA, CD56, CD57, CD61, CD123, CD141, TCRgd and CD235a. After wash, cells were resuspended with a solution of anti-biotin magnetic microbeads and incubated for 15 min at 4°C. After another wash, we proceeded to magnetic separation using LS columns (Miltenyi Biotec) and we collected the cell fraction corresponding to CD45RO+CD45RA-CD56-CD57‑CD8+ T cells. Finally, isolated CD8+ memory T cells were resuspended in RNAprotect Cell Reagent (Qiagen) for RNA extraction.

value: Purified Cell


title: Naive_CD4_T_cells_1

description: Purified Cell

value: Stem Express

value: Human peripheral blood CD4+CD45RA+ naïve helper T cells are enriched by depleting cells expressing CD8, CD14, CD16, CD19, CD20, CD36, CD56, CD66b, CD123, CD45RO, TCRγ/δ, and CD235a from the mononuclear cell population using immunomagnetic particles leaving purified, untouched CD4+CD45RA+ naïve helper T cells. Isolated cells are characterized by flow cytometry before cryopreservation to ensure a highly pure and viable cell population.


title: CspC non-crosslinked replicate 1

description:
CLIP-seq
789_CspC_R1_NXL

value: bacteria

value: CspC-FLAG


title: Liver WT SPF ZT2 - rep3

value: Liver

value: male

value: ZT 2


title: Memory_CD4_T_cells_2

description: Purified Cell

source_name: Memory CD4 T cells, healthy

value: PBMC

value: Memory CD4 T cells

value: healthy

value: All Cells

value: Negatively isolated from mononuclear cells using an indirect immunomagnetic CD4+/CD45RO+ labeling system


title: CspC non-crosslinked replicate 2

description:
CLIP-seq
789_CspC_R2_NXL


title: CspC crosslinked replicate 3

description:
CLIP-seq
789_CspC_R3_XL

value: UV cross-linked


title: CspC crosslinked replicate 2

description:
CLIP-seq
789_CspC_R2_XL


title: Liver, 48 hr after 2Gy Dose, Sample 13

description: Liver 2Gy_13

source_name: Liver, 48 hr after 2Gy Dose

value: C57BL/6 J

value: female

value: 48 hr after 2Gy Dose


title: Liver, 48 hr after 2Gy Dose, Sample 23

description: Liver 2Gy_23


title: Liver, 48 hr after 4Gy Dose, Sample 4

description: Liver 4Gy_4

value: 48 hr after 4Gy Dose


title: Breast

description: Purified Cell

source_name: Breast, cancer

value: breast

value: Breast

value: cancer

value: ATCC

value: BT-483 breast ductal carcinoma (HTB-121)

value: Purified Cell


title: Liver WT SPF ZT2 - rep2

value: Liver

value: male

value: Bmal1 fl/fl

value: SPF

value: ZT 2


title: Liver WT SPF ZT2 - rep1


title: Memory_CD4_T_cells_1

description: Purified Cell

value: PBMC

value: Memory CD4 T cells

value: healthy

value: Stem Express

value: Human CD4+CD45RO+ memory T cells are isolated from peripheral blood mononuclear cells by depleting cells expressing CD8, CD14, CD16, CD19, CD36, CD45RA, CD56, CD123, TCRγ/δ, and CD235a using immunomagnetic particles leaving purified, untouched CD4+CD45RO+ memory T cells. Isolated cells are characterized by flow cytometry before cryopreservation to ensure a highly pure and viable cell population.


title: CspC crosslinked replicate 1

description:
CLIP-seq
789_CspC_R1_XL

value: bacteria

value: CspC-FLAG

value: UV cross-linked


title: Naive_B_cells_1

description: Purified Cell

source_name: Naive B cells, healthy

value: Naive B cells

value: Human CD19+CD27– naïve B cells are isolated from peripheral blood mononuclear cells by means of negative selection. Cells expressing CD2, CD14, CD16, CD27, CD36, CD43, and CD235a are depleted from the mononuclear cell population using immunomagnetic particles leaving purified, untouched CD19+CD27– naïve B cells. Isolated cells are characterized by flow cytometry before cryopreservation to ensure a highly pure and viable cell population.


title: mr_012_post

city: Worcester

first: Jing

last: Wang

address: 100 Research Drive

institute: AbbVie

data_processing:
RNA-seq reads were aligned to the Ensembl release 76 top-level assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Assembly: GRCh38.85
Supplementary files format and content: Raw count

source_name: Synovial Tissue

extract_protocol: Total RNA was extracted from synovial tissue using Trizol and Chloroform (ThermoFisher Scientific, Invitrogen Division, UK)

treatment_protocol: anti-TNF treatment (19 etanercept, 27 certolizumab pegol)

value: Post

tag: pathotype

value: Lymphoid

tag: biologic

value: Etanercept

tag: status

value: Mod-Responder

tag: bx rna conc. (ng/ul)

tag: bx rna volume (ul)

tag: bx rna yield (ng)

tag: rin

tag: ethnicity

value: Caucasian

tag: gender

value: F

tag: smoking status (prev)

value: No

tag: smoking status (curr)

tag: diagnosis

value: RA

tag: duration of disease (yrs)

tag: steroids (medication)

value: Yes

tag: location of joint biopsy

value: Wrist

tag: aggregational histological score

value: Grade 1

tag: inflammatory score

tag: swollen joint count (28)

tag: tender joint count (28)

tag: das28 score

tag: delta das28

tag: patient global assessment of pain (vas)

tag: patient global assessment of disease activity (vas)

tag: physician global assessment of disease activity (vas)

tag: haq-di score

tag: crp

tag: esr

tag: rf

tag: acpa (ccp)

tag: radiographic erosion