title: ST-HSC LowC

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

institute: University Health Network

description: Low-C performed upon ST-HSC

data_processing:
Library strategy: Low-C
Raw reads were aligned to hg19 with Juicer using default parameters (Durand, Shamim, et al. 2016)
3 replicates for each sample were merged
Genome_build: hg19
Supplementary_files_format_and_content: hic format

source_name: Human cord-blood derived ST-HSC

extract_protocol: Low-C was performed using 12k flow sorted cells /rep as previously reported by (Díaz et al. 2018) The following procedural modifications were made: 500U of Hind III-HF (NEB R3104) was used as the restriction enzyme instead of 100U of Mbol. The mock PCR amplification was monitored by qPCR instead of by using an agarose gel. This was done by removing the magnetic beads from, and adding 20x sybr (Biotium 3100) to, a small aliquot of the PCR reaction after two cycles.

tag: cell type

value: cord-blood derived ST-HSC


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H6_ad012

status: Public on Nov 23 2020

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

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

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J P56 Mouse Brain

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

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

treatment_protocol: To label neurons projecting to regions of interest, injections of rAAV2-retro-Cre (produced by Salk Vector Core or Vigene, 2x10^12 to 1x10^13 viral genomes/ml, produced with capsid from Addgene plasmid #81070 packaging pAAV-EF1a-Cre from Addgene plasmid #55636) were made into both hemispheres of the INTACT mice. Animals were anesthetized with either ketamine/xylazine or isoflurane, placed in a stereotaxic frame, and 0.1 to 0.5 microliters of AAV was injected by pressure into stereotaxic coordinates corresponding to the desired projection target.

tag: strain

tag: age

tag: tissue

value: brain

tag: source

value: RSP

tag: target

value: ACA

tag: gender

value: female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H8_ad012


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H6_ad008

value: male


title: 11_moderate_ConvalescenceStage [small_32]

city: Kunming

first: Yong-Gang

last: Yao

state: Yunnan

address: 32 Jiaochang Donglu

department: Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province

country: China

institute: Kunming Institute of Zoology

description:
small_32
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

library_source: transcriptomic

data_processing:
For mRNA and lncRNA, raw RNA-seq reads generated from rRNA-depleted libraries were trimmed to remove sequencing adapters and low quality reads.
The clean reads were then aligned to the primary assembly of the human reference genome, GRCh38, using STAR v2.7.3a (Dobin et al., 2013). StringTie v2.1.2 was used to assemble transcripts in a reference-guided manner for each sample (Pertea et al., 2015). The reference (GENCODE v33) and assembled transcripts for all samples were merged by StringTie (Pertea et al., 2015).
Novel transcripts were obtained by comparing the merged transcripts with the reference transcripts by cuffcompare (code==‘x’ | code == ‘u’ | code==‘i’) (Trapnell et al., 2010). Novel lncRNAs were identified through the following filters: 1) transcript length >200bp and >=2 exons; 2) lack of coding potential predicted by both CPC2 (Kang et al., 2017) and CPAT (Wang et al., 2013); 3) no overlap with known lncRNAs from the RefLnc (http://reflnc.gao-lab.org/) (Jiang et al., 2019) or LNCipedia (https://lncipedia.org/) databases (Volders et al., 2019).
Novel lncRNAs, known lncRNAs from RefLnc (Jiang et al., 2019) and LNCipedia (Volders et al., 2019), and reference transcripts (GENCODE v33) were merged and used for transcript quantification by kallisto v0.46.1 (Bray et al., 2016).
For small RNA-seq analysis, known and novel miRNAs were obtained and quantified by miRdeep2 (Friedlander et al., 2012) using human and chimpanzee miRNA from miRBase v22.1 (http://www.mirbase.org/) (Kozomara et al., 2019) as the references.
Genome_build: GRCh38
Supplementary_files_format_and_content: TPM_matrix_of_lncRNA-mRNA_all_Samples.txt: Tab-delimited text file includes TPM values for each lncRNA-mRNA sample.
Supplementary_files_format_and_content: CPM_matrix_of_miRNA_all_Samples.txt: Tab-delimited text file includes CPM values for each miRNA sample.

molecule: total RNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from the fresh peripheral blood by Ficoll-Paque (GE Healthcare) density gradient centrifugation, and were stored at -80°C until the use for total RNA extraction. Total RNA was extracted by using the RNeasy kit (TianGen, Beijing, China) according to the manufacturer’s instructions.
The purity, concentration, and integrity of total RNA were checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), the Qubit RNA Assay Kit in Qubit 2.0 Fluorometer (Life Technologies, CA, USA), and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 System (Agilent Technologies, CA, USA), respectively. Besides, RNA degradation and contamination was monitored on 1% agarose gels. A total amount of 1μg total RNA per sample was used to prepare for the rRNA-depleted cDNA library. Ribosomal RNA was removed by Epicentre Ribo-zeroTM rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (NEB, USA) and sequenced on an Illumina HiSeq 4000 platform to generate 150bp paired-end reads. For small RNA library, a total amount of 2μg total RNA per sample was used as the input material. Sequencing libraries were generated using NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, USA) following manufacturer’s recommendations. Small RNA libraries were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.

value: peripheral blood mononuclear cells

tag: diagnosis

tag: clinical stage

value: convalescence stage

tag: clinical type

value: moderate

tag: main comorbidities

value: no

tag: patient


title: 8_moderate_RehabilitationStage [small_4]

description:
small_4
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: rehabilitation stage

value: hypertension


title: 202760950152_R04C01_whole blood healthy control

type: genomic

city: Brisbane

first: Marta

middle: Filipa

last: Nabais

state: Queensland

address: 306 Carmody Rd, St. Lucia

department: Institute for Molecular Biosciences

country: Australia

institute: University of Queensland

hyb_protocol: Bisulfite conversions were performed in 96-well plates using the EZ-96 DNA Methylation Kit (Zymo Research, Irvine, CA, USA). Prior to conversion, DNA concentrations were determined by the Take3™ Micro-Volume Plate on the Epoch™ Microplate Spectrophotometer (BioTek Instruments, Inc.) and standardized to include 500 ng. DNA recovery after conversion was quantified using the Take3™ Micro-Volume Plate on the Epoch™ Microplate Spectrophotometer (BioTek Instruments, Inc.). Samples that showed incomplete bisulfite conversion (calculated concentration <25 ng/μl) were not taken forward to the assessment of DNA methylation. Bisulfite converted DNA samples were hybridized to the 8 sample, Illumina Infinium HumanMethylation850 Beadchip (Illumina Inc., San Diego, CA), using Infinium HD Methylation protocol and Tecan robotics.

scan_protocol: HiScan reader, using standard recommended Illumina scanner setting

data_processing:
Illumina GenomeStudio sofwtare and Meffil package
Normalized data: Normalized Average Beta (functional normalization, using Meffil)
Raw data includes Unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: whole blood

label_protocol: Standard Illumina Protocol

growth_protocol: direct ex-vivo analysis

extract_protocol: genomic DNA was extract from whole blood using a standard buffy coat (EDTA) protocol

value: whole blood

value: Male

tag: disease status

value: healthy control


title: 15_serious_RehabilitationStage [small_22]

description:
small_22
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: serious

value: Type II diabetes


title: LT-HSC LowC

city: Toronto

country: Canada

description: Low-C performed upon LT-HSC

source_name: Human cord-blood derived LT-HSC

value: cord-blood derived LT-HSC


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H6_ad004

value: brain

value: SSp


title: 202790040114_R03C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 2_mild_ConvalescenceStage [small_12]

description:
small_12
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: female

value: mild


title: 7_moderate_RehabilitationStage [small_1]

description:
small_1
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: peripheral blood mononuclear cells

value: male


title: 6_mild_TreatmentStage [small_42]

description:
small_42
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: treatment stage


title: 6_mild_ConvalescenceStage [small_43]

description:
small_43
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: convalescence stage

value: no


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H6_ad001

value: RSP


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H6_ad002


title: 7_moderate_ConvalescenceStage [small_3]

description:
small_3
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: moderate


title: 7_moderate_TreatmentStage [small_2]

description:
small_2
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 18_serious_RehabilitationStage [small_28]

description:
small_28
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: rehabilitation stage

value: hypertension


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H5_ad012

value: ACA


title: 202764140090_R03C01_whole blood healthy control

value: whole blood

value: Female

value: healthy control


title: 18_serious_ConvalescenceStage [small_29]

description:
small_29
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: serious


title: 202790040056_R06C01_whole blood healthy control


title: 202760950170_R07C01_whole blood Mild Cognitive Impairment

value: Male

value: Mild Cognitive Impairment


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H5_ad008

value: brain


title: 17_serious_RehabilitationStage [small_39]

description:
small_39
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: peripheral blood mononuclear cells

value: hypertension, myocardial infarction operation


title: 202760950117_R03C01_whole blood healthy control


title: 17_serious_ConvalescenceStage [small_38]

description:
small_38
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: male


title: 202796590025_R06C01_whole blood Mild Cognitive Impairment


title: 16_serious_TreatmentStage [small_36]

description:
small_36
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: treatment stage


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H5_ad002

value: SSp

value: female


title: 202796590013_R02C01_whole blood Mild Cognitive Impairment


title: 15_serious_TreatmentStage [small_24]

description:
small_24
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: Type II diabetes


title: 14_serious_RehabilitationStage [small_15]

description:
small_15
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: rehabilitation stage


title: 14_serious_ConvalescenceStage [small_13]

description:
small_13
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: convalescence stage

value: hypertension


title: 15_serious_ConvalescenceStage [small_23]

description:
small_23
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H4_ad008

value: RSP

value: ACA


title: 14_serious_TreatmentStage [small_14]

description:
small_14
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H5_ad010


title: 13_moderate_TreatmentStage [small_44]

description:
small_44
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: moderate

value: no


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H4_ad007


title: 18_serious_TreatmentStage [small_30]

description:
small_30
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: serious


title: 12_moderate_ConvalescenceStage [small_34]

description:
small_34
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: Type II diabetes, HCV


title: 202796590039_R07C01_whole blood Alzheimer's disease

value: whole blood

value: Female

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H5_ad007

value: brain

value: male


title: 16_serious_ConvalescenceStage [small_37]

description:
small_37
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 12_moderate_TreatmentStage [small_35]

description:
small_35
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: treatment stage


title: 202790040157_R03C01_whole blood healthy control

value: Male

value: healthy control


title: 11_moderate_RehabilitationStage [small_33]

description:
small_33
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: female

value: rehabilitation stage


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H4_ad002

value: RSP

value: SSp


title: 11_moderate_TreatmentStage [small_31]

description:
small_31
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: moderate


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad012

value: ACA


title: 10_moderate_RehabilitationStage [small_18]

description:
small_18
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: no


title: 202790040050_R02C01_whole blood healthy control


title: 202790040172_R08C01_whole blood healthy control


title: 10_moderate_ConvalescenceStage [small_17]

description:
small_17
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: convalescence stage


title: 202796590033_R04C01_whole blood healthy control

value: whole blood


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H4_ad012


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad008


title: 9_moderate_RehabilitationStage [small_9]

description:
small_9
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 9_moderate_ConvalescenceStage [small_7]

description:
small_7
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 202796590041_R07C01_whole blood healthy control


title: 202796590015_R02C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 13_moderate_ConvalescenceStage [small_45]

description:
small_45
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad007


title: 202790040164_R06C01_whole blood healthy control

value: Female


title: 9_moderate_TreatmentStage [small_8]

description:
small_8
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad006

value: brain


title: 8_moderate_ConvalescenceStage [small_5]

description:
small_5
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: hypertension


title: 8_moderate_TreatmentStage [small_6]

description:
small_6
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 202790040045_R06C01_whole blood healthy control


title: 5_mild_ConvalescenceStage [small_41]

description:
small_41
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: mild


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad004

value: male


title: 202761400001_R01C01_whole blood Alzheimer's disease

value: Male

value: Alzheimer's disease


title: 4_mild_TreatmentStage [small_25]

description:
small_25
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: treatment stage


title: 4_mild_RehabilitationStage [small_27]

description:
small_27
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: rehabilitation stage


title: 3_mild_ConvalescenceStage [small_21]

description:
small_21
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 10_moderate_TreatmentStage [small_16]

description:
small_16
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: female


title: 5_mild_TreatmentStage [small_40]

description:
small_40
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 3_mild_RehabilitationStage [small_20]

description:
small_20
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 4_mild_ConvalescenceStage [small_26]

description:
small_26
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 202790040032_R08C01_whole blood healthy control

value: healthy control


title: 2_mild_RehabilitationStage [small_10]

description:
small_10
small RNA
CPM_matrix_of_miRNA_all_Samples.txt


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad007

value: RSP

value: ACA


title: 2_mild_TreatmentStage [small_11]

description:
small_11
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: no


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad001

value: SSp


title: 202796590015_R01C01_whole blood Mild Cognitive Impairment

value: whole blood

value: Mild Cognitive Impairment


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad008

value: brain


title: 1_mild_ConvalescenceStage [small_47]

description:
small_47
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: convalescence stage


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad006


title: 1_mild_TreatmentStage [small_46]

description:
small_46
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H3_ad002


title: 202790040004_R04C01_whole blood healthy control

value: Female


title: 202790040132_R02C01_whole blood Mild Cognitive Impairment


title: 202796590028_R07C01_whole blood Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad004

value: male


title: 202790040005_R05C01_whole blood Alzheimer's disease


title: 202790040179_R08C01_whole blood Alzheimer's disease

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad001


title: 202760950152_R06C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad012


title: 3_mild_TreatmentStage [small_19]

description:
small_19
small RNA
CPM_matrix_of_miRNA_all_Samples.txt

value: mild


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H2_ad002


title: 202764140144_R06C01_whole blood healthy control


title: 202790040083_R01C01_whole blood healthy control


title: 202760950170_R06C01_whole blood healthy control


title: LT_HSC_shCTCF Rep 3

data_processing:
Tophat (2.0.8b) (Langmead et al. 2009) with Bowtie (2.0.5) (Langmead et al. 2009) was used to align RNA-Seq reads to the human hg19 reference genome using default parameters. Cufflinks (2.1.1) (Trapnell et al. 2012) was used to quantify transcript abundance and call differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: tsv file showing fragments per kilobase mapped per replicate

source_name: cord blood

growth_protocol: Sorted LT-HSC cells were cultivated in 96 well U-bottom plate in 50ul of X-VIVO10 medium (cat. no. 04-380Q, Lonza) supplemented with 1% BSA (cat. No. 10735086001, Roche), L-glutamine, Pen Strep and the following cytokines (all from Miltenyi): SCF (100 ng/ml), Flt3L (100 ng/ml), TPO (50 ng/ml) and IL-7 (10 ng/ml).

extract_protocol:
Total RNA were purified with PicoPure® RNA Isolation Kit (Thermo Fisher Scientific) and RNase-Free DNase Set (QIAGEN). Total RNA integrity and concentration were verified on a Bioanalyzer pico chip (Agilent Technologies). About 1 ng of total RNA was used as input for the cDNA conversion using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). The bulk of the cDNA was around 2-4 Kbp as estimated by a Bioanalyzer DNA high sensitivity chip. About 1 ng of input cDNA as estimated by Qubit DNA HS assay (Invitrogen) was used as input material using the Nextera XT DNA Library Preparation Kit (Iillumina, FC-131-1024). One  ul of the Nextera XT libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip  to check for size; libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems) on a StepOne Plus Real Time PCR System (Thermo Fisher) and were pooled in equimolar quantities. Libraries were sequenced on 4 lanes of a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol  to generate paired-end reads of 126-bases in length and to reach depth of 30 million reads per samples.
About 1 ng of total RNA was used as input for the cDNA conversion using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). The bulk of the cDNA was around 2-4 Kbp as estimated by a Bioanalyzer DNA high sensitivity chip. About 1 ng of input cDNA as estimated by Qubit DNA HS assay (Invitrogen) was used as input material using the Nextera XT DNA Library Preparation Kit (Iillumina, FC-131-1024). One  ul of the Nextera XT libraries was loaded on a Bioanalyzer 2100 DNA High Sensitivity chip  to check for size; libraries were quantified by qPCR using the Kapa Library Quantification Illumina/ABI Prism Kit protocol (KAPA Biosystems) on a StepOne Plus Real Time PCR System (Thermo Fisher) and were pooled in equimolar quantities.
Libraries were sequenced on 4 lanes of a High Throughput Run Mode flowcell with the V4 sequencing chemistry on an Illumina HiSeq 2500 platform following Illumina’s recommended protocol  to generate paired-end reads of 126-bases in length and to reach depth of 30 million reads per samples.

treatment_protocol: Six hours after sorting, lentiviruses (shRNAs) were added in the medium at a multiplicity of infection (MOI) of 30 transforming units per mL.  Next day, 150  μl of same media was added to dilute the virus and cultivated for additional 12 hours.  Medium was replaced with same medium and further cultivated for additional 48 hrs and GFP+ cells were sorted for RNA extraction.

value: LT-HSC

tag: replicate

tag: shRNA

value: shCTCF


title: LT_HSC_Ctrl Rep 1

value: shCtrl


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad007


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad006

value: female


title: LT_HSC_Ctrl Rep 2


title: LT_HSC_Ctrl Rep 3


title: LT_HSC_shCTCF Rep 1


title: 202761400005_R02C01_whole blood healthy control

value: healthy control


title: 202790040056_R04C01_whole blood healthy control


title: OCIAML_2_shCtrl_BR2 CTCF ChIP-Seq

description: CTCF ChIP-Seq in the cell line OCIAML-2 Rep 2

data_processing:
Data was aligned to hg19 using BWA with default parameters
MACS2 was used to call peaks relative to input control.
Genome_build: hg19
Supplementary_files_format_and_content: NarrowPeak files containing genomic location of CTCF-bound regions

growth_protocol: OCIAML-2 were maintained in IMDM supplemented with 10% FCS and Penicillin Streptomycin.

extract_protocol:
Prior to conducting ChIP, 10 μL of Dynabeads protein A and protein G (ThermoFisher Scientific, Cat No. 10002D and 10004D) were prepared for each ChIP. Beads were washed three times in cold PBS/BSA (5mg/mL) and resuspended in 300 μL of cold PBS/BSA. Upon resuspension, 10 μL of CTCF antibody (Cell Signalling Technology, Cat No. 2899) was added. The antibody/beads mixture was incubated at 4°C for 6 hours with rotation.  Approximately five hundred thousand cells collected, pelleted and fixed in 300 μL of 1% formaldehyde in PBS for 10 minutes at room temperature. Then 15 uL of 2.5 M glycine was added to reach 0.125 M final concentration, mixed and left for 5 minutes at room temperature. Cells were then spun down at 3000 RPM for 5 minutes, washed with 300 uL of PBS + protease inhibitor (PI), and spun down again at 3000 RPM for 5 minutes. After wash, cells were lysed with 300 uL of modified RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) + PI. Lysed cells were then sonicated on high setting for 22 cycles at 30 seconds ON and 30 seconds OFF per cycle using the Diagenode Bioruptor Pico sonicator. Insoluble cell debris were removed by centrifugation at 4°C for 15 minutes at 15000 RPM. 15 uL of the sample was set aside as input, 15 uL of the sample was added with 100 uL of decrosslinking buffer (1% SDS, 0.1 M NaHCO3) for shearing efficiency on agarose gel. The rest (270 μL) was added to 1.7 mL of cold modified RIPA buffer + PI. The beads/antibody mixture after 6 hours of incubation is then washed three times with cold PBS/BSA and resuspended in 100 μL of modified RIPA buffer + PI. Subsequently, the beads/antibody mixture was added to the diluted chromatin sample (total 2070 μL), and incubated overnight at 4°C with rotation. The following day, the beads with immunoprecipitated chromatin was washed once with cold modified RIPA buffer (500 μL), once with cold modified RIPA buffer + 500 mM NaCl and once with cold LiCl buffer 10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate), and twice with TE buffer (pH=8). After washes, the beads were resuspended in 100 μL of decrosslinking buffer. Samples were then incubated for ≥ 6 hours at 65°C, and was purified using the Monarch PCR & DNA clean-up kit (New England BioLabs, Cat No. T1030).
The sequencing libraries were prepared using the experimental ChIP or input DNA samples with the manufacturer’s recommended protocol of the ThruPLEX DNA-seq Kit (Rubicon Genomics). The sequencing libraries were then size selected in the range of 240-360 bp using PippinHT 2% Agarose Casette (Sage Science). Size selected libraries were then sequenced on the Illumina HiSeq 2500 machine.

treatment_protocol: OCI-AML2 cells where transduced with shRNA pLKO-GFP-H1 lentiviral vector against LacZ (control). After expansion, GFP positives cells where sorted and amplified up to 10 million. Cells were then pelleted and treated with the lysis buffer for Chip-seq.

tag: line

tag: biomaterial type

value: AML Cell Line

tag: antibody

value: CTCF


title: OCIAML_2_shCtrl_BR1 CTCF ChIP-Seq

description: CTCF ChIP-Seq in the cell line OCIAML-2 Rep1


title: MONO [ATAC-Seq]

description: ATAC-Seq performed on sorted cord blood cells derived from two individual pools, merged and uniformly sampled to 40 million reads

data_processing:
Reads for 2 replicates per cell population were mapped against the hg19 human reference genome using Bowtie (2.0.5) (Langmead et al. 2009) with default parameters and mapped reads merged. All duplicate reads, and reads mapped to mitochondria, chrY, an ENCODE blacklisted region or an unspecified contig were removed (ENCODE Project Consortium 2012).
To ensure even processing, 40 million reads were randomly downsampled from each merged sample. MACS 2.0.10 (Zhang et al. 2008) was used to call peaks in downsampled reads.
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files contain peaks called in each cell population.

source_name: human cord blood cells

growth_protocol: Primary (uncultured) CB cells

extract_protocol:
Library preparation for ATAC-Sec was performed on 30,000 cells with Nextera DNA Sample Preparation kit (FC-121-1030, Iillumina), according to previously reported protocol (Buenrostro et al. 2013).
Libraries for ATAC were sequenced with HiSeq 2500 System (Illumina) to generate single-end 50-bp reads.

treatment_protocol: Primary (uncultured) CB cells

tag: cell type

value: Monocyte

tag: surface markers


title: OCIAML-2_Hi_C

description: Hi-C performed upon the OCIAML-2 Cell Line

data_processing:
Library strategy: HiC-Seq
6 individual replicates of OCIAML-2 Hi-C were  aligned with Juicer using standard parameters
Aligned deduplicated reads were merged and Arrowhead was used to call TADs at a 10kb resolution while HiCCUPS was used to generate loops using the same parameters as Rao et al 2014
Genome_build: hg19
Supplementary_files_format_and_content: bedpe files containing TADs called at 10kb resolution (10000_blocks), and loops (All_Chr_Merged_Loops) as well as hic file encoding interactions

extract_protocol:
HI-C was performed according to the protocol published by (Rao et al 2014) using the restiction enzyme DpnII and including the addition of USER enzyme during adapter ligation.
Library construction included in HI-C protocol


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad004

tag: strain

tag: age

tag: tissue

value: RSP

value: SSp


title: GPA [ATAC-Seq]

value: Erythrocyte


title: 202790040017_R06C01_whole blood healthy control

value: whole blood

tag: gender


title: GRA [ATAC-Seq]

value: Granulocyte


title: LT_HSC_shCTCF Rep 2


title: T [ATAC-Seq]

value: T Cell


title: 202790040048_R08C01_whole blood healthy control

value: Female


title: MEP [ATAC-Seq]

value: MEP


title: 202764140144_R03C01_whole blood healthy control


title: B [ATAC-Seq]

value: B Cell


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad001

value: brain

tag: source

tag: target

value: male


title: DC [ATAC-Seq]

value: Dendritic Cell


title: NK [ATAC-Seq]

value: NK Cell


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad012

value: ACA

value: female


title: 202790040047_R02C01_whole blood healthy control

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad010


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad007


title: ST_HSC [ATAC-Seq]


title: MLP [ATAC-Seq]

value: MLP


title: CMP [ATAC-Seq]

value: CMP


title: 202790040053_R05C01_whole blood healthy control

value: Male


title: 202772890011_R08C01_whole blood healthy control


title: GMP [ATAC-Seq]

value: GMP


title: LT_HSC [ATAC-Seq]


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad002

value: RSP

value: SSp


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H1_ad002


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad001


title: 202760950057_R02C01_whole blood healthy control

value: whole blood


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H12_ad008


title: 202796590040_R08C01_whole blood healthy control


title: 202764140088_R03C01_whole blood healthy control

value: Female


title: 202761400086_R07C01_whole blood healthy control


title: dxo1rdr6_smRNA_rep2 (bud)

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

description:
small RNAs
Arabidopsis thaliana unopened flower bud

data_processing:
All reads (50-nucleotide single-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Arabidopsis protein-coding genes using STAR as above.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
For smRNAs, The reads with length <19, 20-24 and >25 nt from both strands of each endogenous mRNA were counted.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count

organism: Arabidopsis thaliana

source_name: dxo1 rdr6

growth_protocol: Arabidopsis plants were grown under 16hr light 8hr dark days, and buds were harvested at approximately 4 weeks of age

extract_protocol:
Bud tissue was ground with a mortar and pestle. RNA was extracted with Qiazol (Qiagen; Valencia, CA) and then further purified with the Qiagen miRNeasy RNA isolation kit following the included protocol (Qiagen; Valencia, CA).
RNA-seq libraries were prepared with single-end and 50 nt
Illumina Hi-Seq2000 50 nt strand-specific

tag: genotype

value: dxo1 rdr6

value: unopened flower bud


title: P6

type: RNA

city: Bochum

first: Thomas

last: Mika

address: Universitätsstr. 150

country: Germany

institute: Ruhr-University Bochum

description: gene expression

hyb_protocol: Samples were hybridized using Agilent 10x blocking agent and 25x fragmentation buffer, and 2xGEx hybridization buffer according to the manufacturer's instructions  for 17 hours at 65C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting Agilent HD GX 1Color (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE2_107_Sep09 and Grid: 026652_D_F_20100430) to obtain background subtracted and spatially detrended Processed Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: sorted T-cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, using T7 priming and MMLV-RT to generate cDNA. cRNA is then prepared using T7 RNA Polymerase according to the manufacturer's instructions, and labeled with Cy3. RNA was purified by RNAeasy column purification (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Peripheral blood mononuclear cells (PBMC) were collected using standard density centrifugation.  After 24h plastic adherence, cells were counted and adjusted to 1-2 x 106 cells/ml in complete medium (RPMI + 10% FCS + 1% Penicillin/Streptomycin). Cell activation was per-formed with CD3/CD28-nanomatrix (TransAct, Miltenyi Biotec, Bergisch-Gladbach, GER) according to manufacturer’s instructions in presence of interleukin 2 (IL-2).

extract_protocol: RNA was prepared using the Qiagen (Qiagen, Venlo, NED) RNeasy Plus mini kit following the manufacturer's recommendations.  The protocol includes gDNA elimination. RNA was quantified using a NanoDrop (ND-1000, Thermo Fisher) spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: treatment

value: control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H11_ad008

value: brain

value: male


title: P28

description: gene expression

value: high-dose melphalan


title: 202760950174_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H11_ad002


title: Col0_smRNA_rep1 (bud)

value: wildtype


title: dxo1_smRNA_rep1 (bud)


title: Col0_smRNA_rep2 (bud)


title: P1

description: gene expression


title: dxo1_smRNA_rep2 (bud)


title: dxo1_GMUCT_rep2 (bud)

description:
uncapped and cleaved transcripts
Arabidopsis thaliana unopened flower bud


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H11_ad010

value: ACA

value: female


title: 202790040044_R02C01_whole blood healthy control

value: healthy control


title: dxo1rdr6_smRNA_rep1 (bud)


title: dxo1_GMUCT_rep1 (bud)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H10_ad012


title: dxo1_mRNA_rep2 (bud)

description: Arabidopsis thaliana unopened flower bud

molecule: polyA RNA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H10_ad010


title: dxo1_mRNA_rep1 (bud)


title: 202790040005_R02C01_whole blood healthy control


title: Col0_mRNArep2_ (bud)


title: 202760950102_R07C01_whole blood healthy control


title: Col0_mRNA_rep1 (bud)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H11_ad007


title: 202796590044_R04C01_whole blood healthy control


title: dxo1_total_RNA_rep2 (bud)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H10_ad008


title: 202790040055_R08C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 202796590019_R07C01_whole blood healthy control

value: Male


title: 202790040005_R04C01_whole blood Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_H10_ad007


title: 202764140088_R08C01_whole blood Alzheimer's disease


title: Col0_total_RNA_rep2 (bud)


title: Col0_NAD_RNA_rep2 (bud)

description:
NAD capped RNA
Arabidopsis thaliana unopened flower bud

data_processing:
Library strategy: NAD-seq
All reads (50-nucleotide single-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Arabidopsis protein-coding genes using STAR as above.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
For smRNAs, The reads with length <19, 20-24 and >25 nt from both strands of each endogenous mRNA were counted.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count


title: Col0_NAD_RNA_rep1 (bud)


title: dxo1_total_RNA_rep1 (bud)


title: Col0_total_RNA_rep1 (bud)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G9_ad007


title: dxo1_NAD_RNA_rep2 (bud)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G9_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G8_ad012


title: Col0_ABA_total_rep2 (ABA)

description:
total RNA
12-day-old seedling under ABA treatment

data_processing:
All reads (50-nucleotide single-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Arabidopsis protein-coding genes using STAR as above.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count

growth_protocol: Arabidopsis plants were grown in 1/2 MS under 16hr light 8hr dark days under normal and ABA condition, and seedlings were harvested at 12-day-old

value: ABA treatment

value: 12-day-old seedling

value: Bud tissue


title: 202796590036_R08C01_whole blood healthy control

value: whole blood


title: dxo1_NAD_RNA_rep1 (bud)


title: dxo1_ABA_total_rep2 (ABA)


title: dxo1_ABA_total_rep1 (ABA)


title: 202764140088_R04C01_whole blood healthy control

value: Female


title: P27

description: gene expression


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G8_ad010

value: RSP


title: Col0_ABA_total_rep1 (ABA)


title: dxo1_NT_total_rep2 (ABA)

description:
total RNA
12-day-old seedling under normal condition

value: normal condition


title: 202796590034_R05C01_whole blood healthy control


title: 202790040032_R07C01_whole blood healthy control


title: Col0_NT_total_rep2 (ABA)


title: dxo1_NT_total_rep1 (ABA)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G8_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G9_ad012


title: 202761400022_R03C01_whole blood healthy control


title: dxo1_ABA_NAD_rep1 (ABA)

description:
NAD capped RNA
12-day-old seedling under ABA treatment

data_processing:
Library strategy: NAD-seq
All reads (50-nucleotide single-end sequences) were trimmed to remove the adapter sequences using cutadapt with default parameter
Trimmed reads were aligned to the Arabidopsis genome (TAIR10) using STAR (version 2.4.2a with parameters “—outFilterMultimapNmax 10 –outFilterMismatchNmax 10 –outFilterMismatchNoverLmax 0.10”); for small RNAs, the reads were also aligned to full-length mature mRNAs of all Arabidopsis protein-coding genes using STAR as above.
HTSeq was used to calculate the raw reads mapping to given genes in strand-specific manner.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files, count


title: 202796590034_R01C01_whole blood healthy control


title: Col0_ABA_NAD_rep2 (ABA)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G8_ad001

value: SSp


title: Col0_ABA_NAD_rep1 (ABA)


title: dxo1_NT_NAD_rep2 (ABA)

description:
NAD capped RNA
12-day-old seedling under normal condition


title: dxo1_NT_NAD_rep1 (ABA)


title: dxo1_ABA_NAD_rep2 (ABA)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G7_ad010

value: brain


title: Col0_NT_NAD_rep2 (ABA)


title: Col0_NT_NAD_rep1 (ABA)


title: 202761400086_R04C01_whole blood Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G7_ad012


title: 202790040143_R02C01_whole blood healthy control


title: dxo1_ABA_GMUCT_rep2 (ABA)

description:
Uncapped and cleaved transcripts
12-day-old seedling under ABA treatment


title: 202796590043_R06C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 202796590037_R07C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G7_ad007

value: male


title: dxo1_NT_GMUCT_rep2 (ABA)

description:
Uncapped and cleaved transcripts
12-day-old seedling under normal condition


title: dxo1_ABA_GMUCT_rep1 (ABA)


title: dxo1_NT_GMUCT_rep1 (ABA)


title: Col0_NT_total_rep1 (ABA)

value: wildtype


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G7_ad002


title: 202796590004_R04C01_whole blood healthy control


title: Col0_ABA_GMUCT_rep2 (ABA)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G8_ad007

value: ACA


title: Col0_ABA_GMUCT_rep1 (ABA)


title: Col0_NT_GMUCT_rep2 (ABA)


title: Col0_NT_GMUCT_rep1 (ABA)


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G6_ad012

value: female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G6_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G6_ad010


title: 202790040073_R02C01_whole blood healthy control

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G6_ad007


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G7_ad008


title: 202796590034_R03C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 202790040052_R05C01_whole blood healthy control


title: Ribo-seq-SARS2-highMOI-24hpi-HT-rep2

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: MO

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
Library strategy: Ribo-seq
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots
Supplementary_files_format_and_content: For reads that map to host mRNAs, counts files are provided.

organism: Chlorocebus sabaeus

source_name: Vero E6

growth_protocol: Vero E6 cells were grown in DMEM-10%FBS media. Isolation and growth of primary human bronchial epithelial cells is explained elsewhere. Primary CD4+ T-cells were isolated from PBMCs of deidentified blood donors using negative selection kit from StemCell Technologies and grown in RPMI media supplemented with 10%FBS, IL-2 and activated with CD3/CD28 conjugated Dynabeads.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Infected cells were lysed and two aliquots were processed in parallel for ribo-seq and RNA-seq. For RNA-seq, total RNA was isolated using ZymoClean RNA-Clean and Concentrator kit and subjected to Illumina stranded mRNA prep. Ribo-seq libraries were prepared in house following published protocols. Both libraries were sequenced using Illumina NextSeq following the manufacturer's protocols.

treatment_protocol: Cells were infected with SARS-CoV-2 at an MOI of 0.1 pfu/cell (low MOI) and 2 pfu/cell (high MOI) for Vero E6 cells, or MOI of 0.5 pfu/cell (low) and 1 pfu/cell (high) for primary human bronchial epithelial cells. Primary activated CD4+ T-cells were infected with HIV-1 at an MOI of 2

value: Cycloheximide+Harringtonine

tag: agent

tag: time point


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G5_ad012


title: Ribo-seq-SARS2-highMOI-48hpi-HT-rep2


title: Ribo-seq-SARS2-highMOI-12hpi-HT-rep2


title: 202761400001_R08C01_whole blood healthy control

tag: disease status


title: 202790040075_R03C01_whole blood healthy control

value: Male


title: 202790040085_R04C01_whole blood Alzheimer's disease


title: Ribo-seq-SARS2-highMOI-6hpi-HT-rep2


title: Ribo-seq-mock-highMOI-HT-rep2

value: mock-highMOI-HT


title: 202790040008_R02C01_whole blood healthy control


title: 202790040043_R07C01_whole blood Alzheimer's disease


title: 202790040005_R06C01_whole blood healthy control


title: Ribo-seq-SARS2-highMOI-2hpi-HT-rep2


title: 202790040089_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G5_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G5_ad001


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G5_ad006


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G6_ad002


title: 202796590009_R08C01_whole blood healthy control


title: 18_serious_ConvalescenceStage [lnc_29]

description:
lnc_29
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells

tag: diagnosis

tag: clinical stage

value: convalescence stage

tag: clinical type

value: serious

tag: main comorbidities

value: hypertension

tag: patient


title: 18_serious_RehabilitationStage [lnc_28]

description:
lnc_28
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

tag: cell type

value: rehabilitation stage


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G4_ad012

tag: strain

value: RSP


title: Ribo-seq-SARS2-highMOI-48hpi-HT-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G5_ad007

tag: age

value: brain


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G4_ad010

tag: tissue


title: Ribo-seq-SARS2-highMOI-24hpi-HT-rep1


title: 202790040086_R05C01_whole blood healthy control

value: whole blood

tag: gender


title: 18_serious_TreatmentStage [lnc_30]

description:
lnc_30
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: male

value: treatment stage


title: Ribo-seq-SARS2-highMOI-12hpi-HT-rep1


title: 202796590015_R06C01_whole blood healthy control


title: Ribo-seq-SARS2-highMOI-2hpi-HT-rep1


title: 202796590026_R03C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G4_ad006

tag: source

value: SSp


title: Ribo-seq-SARS2-highMOI-6hpi-HT-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G4_ad008

tag: target

value: ACA


title: Ribo-seq-mock-highMOI-HT-rep1


title: 17_serious_ConvalescenceStage [lnc_38]

description:
lnc_38
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: hypertension, myocardial infarction operation


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G4_ad004


title: 202790040056_R08C01_whole blood healthy control

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G3_ad012

value: female


title: 16_serious_ConvalescenceStage [lnc_37]

description:
lnc_37
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: 16_serious_TreatmentStage [lnc_36]

description:
lnc_36
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: 15_serious_ConvalescenceStage [lnc_23]

description:
lnc_23
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: Type II diabetes


title: 202764140044_R05C01_whole blood healthy control

value: Male


title: RNA-seq-SARS2-highMOI-48hpi-HT-rep2

data_processing:
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots
Supplementary_files_format_and_content: For reads that map to host mRNAs, counts files are provided.

value: Cycloheximide+Harringtonine


title: RNA-seq-SARS2-highMOI-24hpi-HT-rep2


title: 202790040009_R05C01_whole blood Mild Cognitive Impairment

value: Female

value: Mild Cognitive Impairment


title: RNA-seq-SARS2-highMOI-12hpi-HT-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G3_ad010


title: 202790040162_R02C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G3_ad008


title: 17_serious_RehabilitationStage [lnc_39]

description:
lnc_39
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells

value: serious


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G3_ad007

value: RSP


title: 15_serious_TreatmentStage [lnc_24]

description:
lnc_24
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: RNA-seq-SARS2-highMOI-6hpi-HT-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G2_ad012

value: brain


title: RNA-seq-SARS2-highMOI-2hpi-HT-rep2


title: 202772890011_R04C01_whole blood healthy control

value: whole blood


title: 14_serious_ConvalescenceStage [lnc_13]

description:
lnc_13
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: convalescence stage

value: hypertension


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G2_ad010


title: 202790040018_R03C01_whole blood healthy control


title: RNA-seq-mock-highMOI-HT-rep2

value: mock-highMOI


title: 202790040115_R04C01_whole blood healthy control


title: 14_serious_TreatmentStage [lnc_14]

description:
lnc_14
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: treatment stage


title: RNA-seq-SARS2-highMOI-48hpi-HT-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G2_ad008

value: ACA

value: male


title: 202796590033_R07C01_whole blood healthy control

value: healthy control


title: 13_moderate_ConvalescenceStage [lnc_45]

description:
lnc_45
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: moderate

value: no


title: 14_serious_RehabilitationStage [lnc_15]

description:
lnc_15
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: female

value: rehabilitation stage


title: RNA-seq-SARS2-highMOI-24hpi-HT-rep1

value: Cycloheximide+Harringtonine


title: 13_moderate_TreatmentStage [lnc_44]

description:
lnc_44
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G2_ad006

value: SSp


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G2_ad001

value: RSP


title: RNA-seq-SARS2-highMOI-12hpi-HT-rep1


title: RNA-seq-SARS2-highMOI-6hpi-HT-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad010

value: brain


title: 12_moderate_TreatmentStage [lnc_35]

description:
lnc_35
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: Type II diabetes, HCV


title: RNA-seq-SARS2-highMOI-2hpi-HT-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad008


title: 12_moderate_ConvalescenceStage [lnc_34]

description:
lnc_34
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: convalescence stage


title: RNA-seq-mock-highMOI-HT-rep1

value: mock-highMOI-HT


title: 11_moderate_RehabilitationStage [lnc_33]

description:
lnc_33
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: 202761400004_R01C01_whole blood healthy control

value: whole blood

value: Male


title: 202790040085_R03C01_whole blood healthy control


title: 202790040039_R08C01_whole blood healthy control

value: Female


title: 202796590044_R02C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad007

value: ACA

value: male


title: 202760950057_R08C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: Ribo-seq-SARS2-highMOI-48hpi-CHX-rep2

value: Cycloheximide


title: 202790040068_R06C01_whole blood healthy control

value: healthy control


title: 202760950170_R04C01_whole blood Alzheimer's disease


title: 10_moderate_RehabilitationStage [lnc_18]

description:
lnc_18
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: female

value: rehabilitation stage

value: moderate

value: no


title: Ribo-seq-SARS2-highMOI-24hpi-CHX-rep2


title: 10_moderate_ConvalescenceStage [lnc_17]

description:
lnc_17
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad004

value: brain

value: RSP

value: SSp


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad012


title: 202790040088_R04C01_whole blood healthy control

value: whole blood


title: 10_moderate_TreatmentStage [lnc_16]

description:
lnc_16
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: treatment stage


title: Ribo-seq-SARS2-highMOI-12hpi-CHX-rep2


title: Ribo-seq-SARS2-highMOI-6hpi-CHX-rep2


title: Ribo-seq-SARS2-highMOI-2hpi-CHX-rep2


title: 202796590041_R05C01_whole blood healthy control

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad001


title: 11_moderate_TreatmentStage [lnc_31]

description:
lnc_31
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: 9_moderate_ConvalescenceStage [lnc_7]

description:
lnc_7
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: convalescence stage


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad012

value: ACA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad010


title: Ribo-seq-SARS2-highMOI-48hpi-CHX-rep1


title: 8_moderate_ConvalescenceStage [lnc_5]

description:
lnc_5
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: hypertension


title: 9_moderate_TreatmentStage [lnc_8]

description:
lnc_8
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: Ribo-seq-mock-highMOI-CHX-rep2

value: mock-highMOI


title: 202760950055_R03C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad007

value: male


title: Ribo-seq-SARS2-highMOI-24hpi-CHX-rep1

value: Cycloheximide


title: 202790040172_R01C01_whole blood Alzheimer's disease

value: Female


title: Ribo-seq-SARS2-highMOI-12hpi-CHX-rep1


title: 202790040162_R08C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 202764140038_R01C01_whole blood Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad002

value: female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad006


title: 5_mild_ConvalescenceStage [lnc_41]

description:
lnc_41
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells

value: mild

value: no


title: Ribo-seq-SARS2-highMOI-6hpi-CHX-rep1


title: 9_moderate_RehabilitationStage [lnc_9]

description:
lnc_9
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: rehabilitation stage

value: moderate


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G1_ad002

value: brain

value: RSP

value: SSp


title: 5_mild_TreatmentStage [lnc_40]

description:
lnc_40
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: treatment stage


title: 202796590038_R04C01_whole blood Alzheimer's disease

value: whole blood

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad001


title: 202790040083_R02C01_whole blood healthy control

value: healthy control


title: 4_mild_RehabilitationStage [lnc_27]

description:
lnc_27
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: male


title: Ribo-seq-SARS2-highMOI-2hpi-CHX-rep1

value: Cycloheximide


title: 202790040153_R07C01_whole blood Alzheimer's disease

value: Female

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G12_ad008

value: ACA


title: 202790040004_R07C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G11_ad008


title: 8_moderate_TreatmentStage [lnc_6]

description:
lnc_6
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells

value: female

value: hypertension


title: RNA-seq-SARS2-highMOI-48hpi-CHX-rep2


title: 202790040159_R06C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 4_mild_TreatmentStage [lnc_25]

description:
lnc_25
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: mild

value: no


title: 4_mild_ConvalescenceStage [lnc_26]

description:
lnc_26
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: convalescence stage


title: RNA-seq-SARS2-highMOI-24hpi-CHX-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G11_ad007

value: brain

value: RSP


title: 202790040131_R05C01_whole blood healthy control

value: whole blood


title: 3_mild_RehabilitationStage [lnc_20]

description:
lnc_20
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: rehabilitation stage


title: 202760950112_R02C01_whole blood Alzheimer's disease

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G11_ad002

value: SSp


title: RNA-seq-SARS2-highMOI-12hpi-CHX-rep2

value: Cycloheximide


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G10_ad012


title: RNA-seq-SARS2-highMOI-6hpi-CHX-rep2


title: 202790040008_R04C01_whole blood Mild Cognitive Impairment

value: Female


title: 3_mild_ConvalescenceStage [lnc_21]

description:
lnc_21
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: male


title: 3_mild_TreatmentStage [lnc_19]

description:
lnc_19
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: treatment stage


title: RNA-seq-SARS2-highMOI-2hpi-CHX-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G10_ad007

value: ACA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G11_ad010

value: female


title: 2_mild_RehabilitationStage [lnc_10]

description:
lnc_10
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: peripheral blood mononuclear cells


title: 202796590039_R08C01_whole blood healthy control

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G10_ad004


title: Ribo-seq-mock-highMOI-CHX-rep1

value: mock-highMOI


title: RNA-seq-mock-highMOI-CHX-rep2


title: 202796590029_R07C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G10_ad002


title: 202760950057_R04C01_whole blood healthy control


title: 2_mild_TreatmentStage [lnc_11]

description:
lnc_11
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: mild

value: no


title: RNA-seq-SARS2-highMOI-48hpi-CHX-rep1


title: 1_mild_TreatmentStage [lnc_46]

description:
lnc_46
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt


title: RNA-seq-SARS2-highMOI-24hpi-CHX-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad012

value: brain

value: RSP


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_G10_ad001


title: 202790040068_R08C01_whole blood healthy control

value: whole blood


title: RNA-seq-SARS2-highMOI-12hpi-CHX-rep1


title: 202760950123_R01C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad010


title: RNA-seq-SARS2-highMOI-6hpi-CHX-rep1


title: 3E (miRNA)

city: Shenyang

first: Mingzhu

last: Jin

address: 155N Nanjing Street, Heping District

institute: The First Hospital of China Medical University

description:
sample biological material as in 3E (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression

data_processing:
[CircRNA, lncRNA, mRNA]  High-quality reads were aligned to the human reference genome (UCSC HG19) using hisat2 software (v2.0.4). Then, the fragments per kilobase of exon per million fragments mapped (FPKM) values of the lncRNA and mRNA expression profiles were obtained under the guidance of the gtf gene annotation file using Cuffdiff software (v2.2.1, part of Cufflinks) was used to.
[CircRNA, lncRNA, mRNA]  The fold change and p values of the EF and control groups were calculated and compared to screen for differentially expressed lncRNAs and mRNAs. Fold change ≥ 2.0 (i.e., log 2(FC) ≥ 1.0, p value < 0.05) and FPKM value of ≥ 0.1 in at least one sample were used as the threshold values when screening of differential expression.
[CircRNA, lncRNA, mRNA]  High-quality reads were aligned to the reference genome/transcriptome using STAR software (v2.5.1b). CircRNAs were detected and identified with DCC software (v0.4.4). CircBase and Circ2Traits were used to annotate the identified circRNAs. Then, edgeR (v3.16.5) was used for data standardization and differential expression of circRNAs. Differential expression of circRNA was determined as a fold change of ≥ 2.0 and a p value < 0.05.
[miRNA]  After sequencing, image analysis, and base recognition, raw data were generated after quality control using Q30. Cutadapt software (v1.9.3) and miRDeep2 software (v2.0.0.5) were used. The trimmed reads were aligned to the merged human pre-miRNA databases (miRBase and the newly predicted pre-miRNAs) using Novoalign software (v3.02.12) with at most one mismatch. The numbers of mature miRNA mapped tags were defined as the raw expression levels of the miRNA. The raw counts were normalized by edgeR, and filtered to find differentially expressed miRNAs with a fold change of ≥1.5 and a p value of <0.05.
Genome_build: HG19
Supplementary_files_format_and_content: circRNA: ID, junction reads, logCPM by edgeR, the coordinates of circRNA, circBaseID, source, best_transcript, GeneName, Catalog, predicted_sequence_length. lncRNA: transcript_id, the gene name, gene_id, biotype, strand, transcription direction, locus, length, FPKM values, counts. mRNA: gene name, gene_id, biotype, strand, transcription direction, genomic locus, length, FPKM values, counts, annotation information. miRNA: mature miRNA name, pre-miRNA name, sequence, raw tag counts, edgeR normalized counts.

source_name: Adipose-derived stem cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (Thermo Scientific, MA, USA).
After removing the rRNAs with an NEBNext rRNA Depletion Kit (New England Biolabs, Inc., MA, USA), RNA libraries were constructed from total RNA using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc.). The quality of the library was controlled and quantified using a BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an Illumina Hiseq instrument with 150-bp paired-end reads.Paired-end reads were harvested from the Illumina HiSeq 4000 sequencer. High-quality trimmed reads were acquired after quality control by Q30, and 3ʹ-adaptor-trimming together with removal of low-quality reads by cutadapt (v1.9.3).
Total RNA was used to prepare the miRNA sequencing library, including 3ʹ-adaptor ligation, 5ʹ-adaptor ligation, cDNA synthesis, PCR amplification, and retrieving of approximately 150-bp PCR amplicons (corresponding to approximately 22-nt miRNAs). The libraries were denatured as single-stranded DNA molecules, captured on an Illumina flow cell, amplified as clusters in situ, and then sequenced for 50 cycles on an Illumina HiSeq sequencer in accordance with the manufacturer’s instructions.

value: Adipose-derived stem cells

tag: passage

value: in 300mV/mm direct-current electric field for 6 hours


title: 2E (miRNA)

description:
sample biological material as in 2E (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression

tag: treatment


title: RNA-seq-SARS2-highMOI-2hpi-CHX-rep1

value: Cycloheximide

tag: agent


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad008


title: 202790040032_R05C01_whole blood healthy control

value: Female


title: 1E (miRNA)

description:
sample biological material as in 1E (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression


title: 202790040117_R08C01_whole blood healthy control


title: RNA-seq-mock-highMOI-CHX-rep1


title: 3C (miRNA)

description:
sample biological material as in 3C (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression

value: in 0 electric field for 6 hours


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad002

value: SSp


title: 1_mild_ConvalescenceStage [lnc_47]

description:
lnc_47
TPM_matrix_of_lncRNA-mRNA_all_Samples.txt

value: male

value: convalescence stage


title: Ribo-seq-SARS2-lowMOI-72hpi-rep2

tag: time point


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad007

value: ACA


title: 2C (miRNA)

description:
sample biological material as in 2C (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression


title: Ribo-seq-SARS2-lowMOI-48hpi-rep2


title: 202790040058_R06C01_whole blood Mild Cognitive Impairment

value: Male

tag: disease status

value: Mild Cognitive Impairment


title: 202790040047_R06C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F9_ad001


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F8_ad010

value: female


title: 1C (miRNA)

description:
sample biological material as in 1C (CircRNA, lncRNA, mRNA-seq)
miRNA_Expression


title: Ribo-seq-SARS2-lowMOI-24hpi-rep2


title: 3E (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 3E (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F8_ad008


title: Ribo-seq-mock-lowMOI-72hpi-rep2

value: mock-lowMOI


title: 2E (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 2E (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F8_ad007

value: brain


title: Ribo-seq-mock-lowMOI-48hpi-rep2


title: 202761400010_R04C01_whole blood healthy control

value: healthy control


title: 1E (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 1E (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling


title: 202790040056_R01C01_whole blood healthy control

value: whole blood


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F8_ad001

value: RSP


title: 202760950117_R07C01_whole blood healthy control


title: Ribo-seq-mock-lowMOI-24hpi-rep2


title: 202796590025_R03C01_whole blood healthy control


title: 3C (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 3C (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling

value: Adipose-derived stem cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F7_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F7_ad007


title: Ribo-seq-SARS2-lowMOI-48hpi-rep1

value: Cycloheximide


title: 2C (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 2C (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling


title: 202790040088_R01C01_whole blood healthy control

value: Female


title: 1C (CircRNA, lncRNA, mRNA)

description:
sample biological material as in 1C (miRNA-seq)
CircRNA Expression Profiling
LncRNA Expression Profiling
mRNA Expression Profiling

value: in 0 electric field for 6 hours


title: 202764140005_R07C01_whole blood healthy control


title: 202760950123_R06C01_whole blood healthy control


title: 202796590004_R02C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F7_ad002

value: SSp


title: Ribo-seq-SARS2-lowMOI-24hpi-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad012


title: 202790040051_R01C01_whole blood healthy control


title: Ribo-seq-mock-lowMOI-72hpi-rep1


title: G1-phase cytoplasmic extract, poly(A)+ selected RNA

city: Oxford

first: Esther

last: Griesbach

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: RNA-Seq

data_processing:
Adapter trimming with Cutadapt v. 1.8.3 in paired end mode with minimum-length 10
Alignment with Tophat v. 2.0.13 and the parameters -g 1 -r 3000 --no-coverage-search to hg38
Extraction of properly paired, properly mapped reads (samflags 0x63, 0x93, 0x53, 0xA3) with SAMtools v. 0.1.19
Data was visualized with Bedtools v. 2.23.0 (genomeCoverageBed).
Genome_build: hg38
Supplementary_files_format_and_content: bedgraph files: genome-coverage files for all samples

source_name: HeLa cells

growth_protocol: Cells were grown in DMEM medium 10% FBS and 1x penicillin/streptomycin

extract_protocol:
Cytoplasmic lysates were obtained by lysing the cells in HLB+N buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 2.5 M MgCl2 and 0.5% NP-40). RNA was extracted using Tri-Reagent. Nuclei were direclty lysed in Tri-Reagent. Poly(A)+ mRNA was selected, poly(A)- mRNA was ribodepleted (Ribo-Zero Magnetic Kit (Human/Mouse/Rat) from Illumina (#MRZH116)). Poly(A)+ and poly(A)- mRNA was used for library preparation.
500 ng poly(A)+ or ribo-depleted poly(A)- RNA was employed for library preparation with the NEBNext Ultra Directional RNA Library Prep Kit (Illumina, #E7420S)

treatment_protocol: For S-phase synchronisation, cells were treated with 4 μg/mL Aphidicolin for 24 hr. Cells were harvested 6 hr after block release. For G1, cells were treated with 200 ng/mL nocodazole for 18-20 hr and harvested 6 hr after block release.

value: Cytoplasmic Extract

tag: sample type

value: Poly(A)+ selected RNA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad010

value: ACA


title: 202796590026_R04C01_whole blood healthy control


title: Ribo-seq-mock-lowMOI-48hpi-rep1


title: Ribo-seq-mock-lowMOI-24hpi-rep1


title: S-phase cytoplasmic extract, ribo-depleted poly(A)- RNA

description: RNA-Seq

value: Ribo-depleted poly(A)- RNA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad008

value: male


title: RNA-seq-SARS2-lowMOI-72hpi-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad007


title: 202790040048_R07C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad002


title: Ribo-seq-SARS2-lowMOI-72hpi-rep1


title: 202790040018_R07C01_whole blood healthy control


title: 202790040115_R08C01_whole blood healthy control

value: Male


title: S-phase nuclear extract,  poly(A)+ selected RNA

description: RNA-Seq

value: Nuclear Extract


title: G1-phase nuclear extract, poly(A)+ selected RNA

description: RNA-Seq


title: RNA-seq-SARS2-lowMOI-48hpi-rep2


title: RNA-seq-SARS2-lowMOI-24hpi-rep2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F6_ad001


title: G1-phase nuclear extract, ribo-depleted poly(A)- RNA

description: RNA-Seq


title: 202796590031_R01C01_whole blood healthy control


title: S-phase cytoplasmic extract,  poly(A)+ selected RNA

description: RNA-Seq


title: 202760950131_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F5_ad008


title: RNA-seq-mock-lowMOI-72hpi-rep2

value: mock-lowMOI


title: 202790040054_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F5_ad007

value: brain


title: RNA-seq-mock-lowMOI-48hpi-rep2


title: G1-phase cytoplasmic extract, ribo-depleted poly(A)- RNA

description: RNA-Seq


title: RNA-seq-mock-lowMOI-24hpi-rep2


title: 99_S17_L003_R1_001

city: New York

first: Ana

last: Pavel

state: NY

address: One Gustave L. Levy Place

department: Dermatology

institute: Icahn School of Medicine at Mount Sinai

description:
sample name:
99

data_processing:
RNA-seq sample quality was assessed using FastQC and MultiQC.
Samples were aligned to human reference genome based on STAR RNA-sequencing aligner and sequencing reads were assigned to genomic features by featureCounts.
Genomic features with 0 counts in more than 20% of the samples were filtered out.
Data was then transfromed to log2-counts per million by voom-transform.
Fold changes (FCHs) vs. baseline were estimated and hypothesis testing was conducted with contrasts under the general framework for linear models in limma package. P-values were adjusted using the Benjamini-Hochberg procedure, which controls False Discovery Rate (FDR).
Genome_build: GRCh38
Supplementary_files_format_and_content: log2-counts per million

source_name: Skin biopsy

extract_protocol:
Total RNA was extracted from skin biopsy samples using Qiagen miRNeasy Mini kit.
The libraries were generated using TruSeq Stranded mRNA Library Prep kit following manufactory protocol. Briefly, mRNA was first extracted from 240ng of total RNA using oligo-dT magnetic beads and fragmented at high temperature. A cDNA library was then prepared from the fragemented mRNA by revervse transcription, second strand synthesis and ligation of specific adapters.
Next generation sequencing was performed on Illumina Hiseq 4000 with single-ended 100 red cycles. Image analysis and bases calling was conducted in real-time by the Illumina analysis pipeline.

tag: patient diagnosis

value: Atopic Dermatitis

tag: ptid

tag: timepoint

value: Placebo

value: skin

tag: tissue disease state

value: Les


title: 202790040017_R03C01_whole blood healthy control

value: whole blood

value: healthy control


title: 98_S48_L007_R1_001

description:
sample name:
98

value: Baseline

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F5_ad001

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

value: RSP

value: SSp


title: 202796590005_R03C01_whole blood healthy control

value: Female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F5_ad002

value: female


title: RNA-seq-SARS2-lowMOI-72hpi-rep1

value: Cycloheximide


title: 97_S16_L002_R1_001

description:
sample name:
97


title: 202760950119_R02C01_whole blood healthy control


title: 95_S15_L002_R1_001

description:
sample name:
95


title: S-phase nuclear extract, ribo-depleted poly(A)- RNA

description: RNA-Seq

value: Ribo-depleted poly(A)- RNA


title: RNA-seq-SARS2-lowMOI-48hpi-rep1


title: RNA-seq-SARS2-lowMOI-24hpi-rep1


title: 94_S14_L002_R1_001

description:
sample name:
94


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad008

value: ACA

value: male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad012

value: brain


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad010


title: 202790040152_R01C01_whole blood healthy control


title: 202790040159_R01C01_whole blood healthy control


title: 92_S12_L002_R1_001

description:
sample name:
92

value: Atopic Dermatitis


title: 202796590029_R02C01_whole blood healthy control

value: Male


title: 93_S13_L002_R1_001

description:
sample name:
93

value: Placebo

value: skin


title: 91_S11_L002_R1_001

description:
sample name:
91

value: Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad002


title: RNA-seq-mock-lowMOI-48hpi-rep1

value: mock-lowMOI


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad004


title: 202760950102_R08C01_whole blood healthy control

value: whole blood

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad006

value: RSP


title: NP6_Ep

city: Heidelberg

first: Elisa

last: Espinet

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

data_processing:
The human reference genome (hg19) was in silico transformed for both the top strand (C to T) and bottom strand (G to A) using MethylCtools. Before alignment, trimming of adaptor sequences was performed using SeqPrep (https://github.com/jstjohn/SeqPrep). The first read in each read pair was then C to T converted and the second read in the pair was G to A converted. The converted reads were aligned to a combined reference of the transformed top strands (C to T) and bottom strands (G to A) using BWA (bwa-0.6.2-tpx) with default parameters but with disabling the quality threshold parameter for read trimming (-q) of 20 and the Smith-Waterman for the unmapped mate (-s).
After alignment, reads were converted back to the original states, and reads mapping to the antisense strand of the respective reference were removed. Duplicate reads were marked, and the complexity was determined using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Reads with alignment scores of less than 1 were filtered before subsequent analysis.
Only bases with Phred-scaled quality score of ≥ 20 were considered
The raw counts of methylated and unmethylated reads for each CpG site from different libraries were merged for each sample
Genome_build: Genome_build: hg19
Supplementary_files_format_and_content: bed file containing all seen CpGs within this library. The number of methylated reads/number of total reads per CpG is given as raw counts and as a ratio.

source_name: EPCAM+/CD45- epithelial cells isolated from human histologically normal pancreas

extract_protocol:
Genomic DNA from sorted cells was isolated using the QIAamp DNA Micro Kit (Qiagen) according to the manufacturer’s instructions
Four tagmentation based sequencing libraries with different barcodes were generated per sample as previously described (Weichenhan et al. DNA Methylation Protoc. 2018)

tag: material

value: Epithelial cells isolated by flow cytometry

value: normal pancreas

tag: cell type

value: EPCAM+/CD45- epithelial cells


title: 202790040032_R06C01_whole blood healthy control

data_processing:
Illumina GenomeStudio sofwtare and Meffil package
Normalized data: Normalized Average Beta (functional normalization, using Meffil)
Raw data includes Unmethylated and methylated signal intensities

value: Female


title: RNA-seq-mock-lowMOI-24hpi-rep1

value: Cycloheximide


title: 90_S10_L002_R1_001

description:
sample name:
90


title: 202796590039_R01C01_whole blood healthy control


title: 89_S9_L002_R1_001

description:
sample name:
89

value: Baseline

value: Non-Les


title: 202790040172_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F3_ad008

tag: strain

tag: age

value: brain

value: ACA

value: male


title: 88_S8_L001_R1_001

description:
sample name:
88

value: Atopic Dermatitis

tag: tissue


title: NP3_Ep


title: 9_S36_L005_R1_001

description:
sample name:
9

value: skin


title: RNA-seq-mock-lowMOI-72hpi-rep1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F4_ad001

tag: source

value: SSp

tag: gender


title: 202760950117_R04C01_whole blood Mild Cognitive Impairment

value: Male

value: Mild Cognitive Impairment


title: NP2_Ep


title: 202790040056_R05C01_whole blood healthy control

value: whole blood

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F3_ad007

value: RSP

tag: target


title: 87_S47_L007_R1_001

description:
sample name:
87

tag: treatment

value: Placebo


title: NP1_Ep

value: Epithelial cells isolated by flow cytometry

value: normal pancreas

value: EPCAM+/CD45- epithelial cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F3_ad004


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F3_ad006

value: female


title: 202796590027_R08C01_whole blood healthy control

value: Female


title: 84_S7_L001_R1_001

description:
sample name:
84

value: Baseline

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F3_ad001

value: brain

value: male


title: 202796590037_R05C01_whole blood healthy control


title: 82_S46_L007_R1_001

description:
sample name:
82

value: Atopic Dermatitis

value: skin


title: PDAC6_Ep

source_name: EPCAM+/CD45- epithelial cells isolated from human PDAC sample

value: PDAC


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad012

value: ACA


title: 202790040055_R05C01_whole blood healthy control

value: whole blood


title: NP5_Ep


title: NP4_Ep


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad010


title: PDAC4_Ep


title: PDAC5_Ep


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad007


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad006

value: SSp


title: 80_S43_L007_R1_001

description:
sample name:
80


title: 202790040085_R05C01_whole blood Alzheimer's disease

value: Alzheimer's disease


title: PDAC3_Ep


title: 202796590035_R05C01_whole blood healthy control

value: healthy control


title: 81_S45_L007_R1_001

description:
sample name:
81

value: Les


title: 202790040018_R02C01_whole blood healthy control


title: 8_S2_L002_R1_001

description:
sample name:
8

value: Placebo


title: 79_S42_L007_R1_001

description:
sample name:
79


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad004

value: RSP


title: 202760950052_R05C01_whole blood healthy control


title: PDAC1_Ep

value: Epithelial cells isolated by flow cytometry

value: EPCAM+/CD45- epithelial cells


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad002

value: female


title: PDAC2_EP


title: 202796590028_R01C01_whole blood healthy control

value: Male


title: PDAC7_Ep


title: 78_S6_L001_R1_001

description:
sample name:
78


title: 202790040086_R03C01_whole blood healthy control

value: Female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F1_ad008

value: brain

value: male


title: Ribo-seq-CD4-Donor1-HIV-rep2

source_name: Primary CD4+ T-cells

value: Cycloheximide

tag: agent

value: HIV


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F2_ad001


title: 202772890012_R08C01_whole blood healthy control


title: 76_S5_L001_R1_001

description:
sample name:
76

value: Atopic Dermatitis

value: Baseline

value: skin


title: 80A_S44_L007_R1_001

description:
sample name:
80A


title: 75_S4_L001_R1_001

description:
sample name:
75


title: Ribo-seq-CD4-Donor2-HIV-rep1


title: 202790040048_R01C01_whole blood healthy control

value: whole blood


title: 74_S41_L007_R1_001

description:
sample name:
74

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F1_ad007

value: ACA


title: Ribo-seq-CD4-Donor2-mock-rep1

value: mock


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F1_ad004

value: RSP

value: SSp


title: 202796590039_R06C01_whole blood healthy control

value: healthy control


title: 202796590043_R03C01_whole blood healthy control


title: Ribo-seq-CD4-Donor1-mock-rep2


title: RNA-seq-CD4-Donor2-HIV


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F1_ad001


title: 202790040016_R04C01_whole blood Mild Cognitive Impairment

value: Mild Cognitive Impairment


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F12_ad010

value: female


title: 72_S2_L001_R1_001

description:
sample name:
72

value: Placebo


title: RNA-seq-CD4-Donor1-HIV


title: 71_S1_L001_R1_001

description:
sample name:
71

value: Les


title: 202790040056_R02C01_whole blood healthy control

value: Female


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F12_ad002

value: brain


title: RNA-seq-CD4-Donor1-mock

value: Cycloheximide


title: 202790040039_R07C01_whole blood Mild Cognitive Impairment

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F12_ad001

value: male


title: 69_S55_L008_R1_001

description:
sample name:
69

value: Atopic Dermatitis

value: Baseline

value: skin


title: 70_S56_L008_R1_001

description:
sample name:
70


title: 202760950112_R04C01_whole blood healthy control

value: whole blood


title: K2

city: Changchun

first: zhenhua

last: zhu

address: Xinmin  Street 71#

institute: The First Hospital of Jilin 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 UCSC-hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Read counts data of each sample were calculated using featurecounts model of subread software (V1.6.5). Counts data of each sample were normalized using R package DESeq2.
Genome_build: UCSC-hg38
Supplementary_files_format_and_content: Read counts data for each sample; normalized expression data

source_name: HT-1080_KIF20A knockdown

extract_protocol:
RNA was harvested using Trizol reagent. Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for Illumina® was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: Fibrosarcoma cell line

tag: genotype/variation

value: KIF20A knockdown


title: K3


title: 68_S54_L008_R1_001

description:
sample name:
68


title: 202760950170_R08C01_whole blood Alzheimer's disease

tag: disease status

value: Alzheimer's disease


title: 73_S3_L001_R1_001

description:
sample name:
73

tag: patient diagnosis


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F11_ad012

value: RSP

value: ACA


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F11_ad008


title: 67_S53_L008_R1_001

description:
sample name:
67

tag: ptid


title: K1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F12_ad008


title: 202790040045_R03C01_whole blood Alzheimer's disease


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F11_ad007


title: 202790040060_R03C01_whole blood healthy control

value: healthy control


title: C3

value: Control


title: RNA-seq-CD4-Donor2-mock

value: mock


title: 65_S51_L008_R1_001

description:
sample name:
65

tag: timepoint

value: Les


title: C2


title: 66_S52_L008_R1_001

description:
sample name:
66

tag: tissue disease state

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F11_ad002

value: brain

value: SSp

value: female


title: 202761400001_R03C01_whole blood healthy control

value: Male


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F11_ad001

value: male


title: 64_S50_L008_R1_001

description:
sample name:
64

value: Atopic Dermatitis

value: Placebo

value: skin


title: C1

value: Fibrosarcoma cell line


title: 202796590004_R05C01_whole blood healthy control

value: whole blood

value: Female


title: 63_S49_L008_R1_001

description:
sample name:
63

value: Baseline


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad012

value: RSP

value: ACA


title: 62_S8_L002_R1_001

description:
sample name:
62


title: 202790040090_R08C01_whole blood healthy control

value: healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad008


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad010


title: 202790040115_R07C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad007


title: 60_S39_L006_R1_001

description:
sample name:
60


title: 6_S11_L003_R1_001

description:
sample name:
6

value: Les


title: 61_S40_L006_R1_001

description:
sample name:
61


title: 202772890011_R07C01_whole blood healthy control


title: 202790040127_R04C01_whole blood healthy control


title: 202790040151_R05C01_whole blood healthy control


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad001


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E9_ad012


title: RNA-P17-KO-2

city: Dallas

first: Andres

last: Ramirez-Martinez

state: TX

address: 6000 Harry Hines Blvd.

department: Molecular Biology

institute: UTSW Medical Center

data_processing:
Single-end raw reads with more than 30% nucleotide with phred quality scores less than 20 were filtered from further analysis.
Quality-filtered reads were then aligned to the mouse reference genome (version GRCm38.mm10) using the HISAT2 aligner (v2.1.0).
Aligned reads were then counted using featurecount (v 1.6.2) which assign read counts to each annotation gene id.
DESeq2 R Bioconductor package (REFERENCE_22, 23) was used to normalize read counts and identify differentially expressed (DE) genes.
Genome_build: GRCm38.mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample for each timepoint

source_name: Quadriceps muscle

extract_protocol:
RNA was harvested using Trizol reagent. Total RNA was extracted using QIAGEN Rneasy mini kit
Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.

tag: genotype

value: Net39 KO

value: 17 days old


title: RNA-P17-KO-3


title: RNA-P17-KO-1


title: 202796590014_R07C01_whole blood healthy control


title: RNA-P17-WT-3

value: WT


title: 56_S36_L006_R1_001

description:
sample name:
56


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E9_ad010

source_name: C57BL/6J P56 Mouse Brain

value: brain

value: female


title: 202796590029_R05C01_whole blood healthy control


title: 55_S35_L006_R1_001

description:
sample name:
55


title: 57_S37_L006_R1_001

description:
sample name:
57

value: Non-Les


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E9_ad008

value: male


title: RNA-P17-WT-2


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_F10_ad002

value: SSp


title: 58_S38_L006_R1_001

description:
sample name:
58

value: Atopic Dermatitis

value: Placebo

value: skin


title: 202796590009_R06C01_whole blood healthy control

value: whole blood

value: Female


title: RNA-P17-WT-1


title: 53_S33_L006_R1_001

description:
sample name:
53

value: Baseline


title: 54_S34_L006_R1_001

description:
sample name:
54


title: 202796590035_R08C01_whole blood healthy control


title: naïve T cells, WT biological replicate 2

city: Singapore

first: Alison

middle: P

last: Lee

address: 20 Biopolis Way

country: Singapore

institute: Bioprocessing Technology Institute

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

data_processing: Raw data from CEL files was RMA-normalized and summarized to transcript clusters using Partek Genomics Suite.

label: biotin

source_name: pooled spleen and lymph nodes, WT genotype

label_protocol: Expression profiling was carried out on Affymetrix GeneChip Mouse Gene 2.0 ST Array according to manufacturer's protocol.

extract_protocol: CD4+ CD62Lhigh CD44low CD25- naïve T cells were FACS-sorted from spleens and lymph nodes of TACI-/- and WT mice (n = 2 each). Total RNA was isolated using TRIzol and purified using RNeasy MinElute Cleanup Kit with DNase I digestion according to manufacturer's protocol.

tag: cell type

value: Naive CD4+ T cells


title: naïve T cells, TACI-/- biological replicate 2

source_name: pooled spleen and lymph nodes, TACI-/- genotype

tag: strain

value: TACI-/-


title: 202790040179_R07C01_whole blood healthy control

source_name: whole blood

value: healthy control


title: naïve T cells, WT biological replicate 1


title: 202760950112_R07C01_whole blood healthy control


title: 51_S31_L005_R1_001

description:
sample name:
51


title: 52_S32_L005_R1_001

description:
sample name:
52

value: ET

value: Les


title: naïve T cells, TACI-/- biological replicate 1


title: RNA-P9-KO-2

value: Net39 KO

tag: age

value: 9 days old


title: 202790040009_R07C01_whole blood Alzheimer's disease

tag: tissue

value: Alzheimer's disease


title: RNA-P9-KO-1


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E8_ad008

extract_protocol:
Approximately two weeks after the AAVretro injection, brains were extracted from the 56-63 day old INTACT mice, immediately submerged in ice-cold slicing buffer (2.5mM KCl, 0.5mM CaCl2, 7mM MgCl2, 1.25mM NaH2PO4, 110mM sucrose, 10mM glucose and 25mM NaHCO3) that was bubbled with carbogen, and sliced into 0.6 mm coronal sections starting from the frontal pole. From each AAVretro-injected brain, the slices were kept in the ice-cold dissection buffer from which selected brain regions (Supplementary Table 1) were manually dissected under a fluorescent dissecting microscope (Olympus SZX16), following the Allen Mouse Common Coordinate Framework (CCF), Reference Atlas, Version 3 (2015) (Extended Data Fig. 1). The dissected brain tissues were transferred to prelabeled microcentrifuge tubes, immediately frozen in dry ice, and subsequently stored at -80oC.   For each dissected brain region, samples from 2 males and 2 females were pooled separately as biological replicates for nuclei preparation. The 2-mL glass tissue dounce homogenizer and pestles (Sigma-Aldrich D8938-1SET) were pre-chilled on ice. Nuclei were prepared using a modified protocol as reported by Lacar et al., 201622. In summary, the frozen brain tissues were transferred to the dounce homogenizer with 1 mL ice-cold NIM buffer (0.25M sucrose, 25mM KCl, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT (Sigma 646563), 10μl of protease inhibitor (Sigma P8340)), with 0.1% Triton X-100 and 5μM Hoechst 33342 (Invitrogen H3570), and gently homogenized on ice with the pestle 10-15 times. The homogenate was transferred to pre-chilled microcentrifuge tubes and centrifuged at 1000 rcf for 8 min at 4oC to pellet the nuclei. The pellet was resuspended in 1 mL ice-cold NIM buffer, and again centrifuged at 1000 rcf for 8 min at 4oC. The pellet was then resuspended in 450 μL of ice-cold NSB buffer (0.25M sucrose, 5mM MgCl2, 10mM Tris-HCl (pH7.4), 1mM DTT, 9ul of Protease inhibitor), and filtered through 40μM cell strainer. The filtered nuclei suspension was incubated on ice for at least 30 minutes with 50μl of nuclease-free BSA for at least 10 minutes, then incubated with GFP antibody, Alexa Fluor 488 (Invitrogen, A-21311) and anti-NeuN antibody (EMD Millipore MAB377) conjugated with Alexa Fluor 647 (Invitrogen A20173). GFP+/NeuN+ single nuclei were isolated using fluorescence-activated nuclei sorting (FANS) on a BD Influx sorter with 100μm nozzle, and sorted into 384-well plates preloaded with 2μl of digestion buffer for snmC-seq215 (20 mL digestion buffer consists of 10 mL M-digestion buffer (2×, Zymo D5021-9), 1 ml Proteinase K (20 mg, Zymo D3001-2-20), 9 mL water, and 10 µL unmethylated lambda DNA (100 pg/µL, Promega, D1521)). The collected plates were incubated at 50oC for 20 minutes then stored at -20 oC.
The bisulfite conversion and library preparation were performed following the detailed snmC-seq2 protocol as previously described (Luo, C. et al., Nat. Commun. 2018, 9(1):3824.). The snmC-Seq2 libraries were sequenced on Illumina Novaseq 6000 using the S4 flow cell 2 x 150 bp mode.

value: brain

tag: source

value: RSP

value: ACA


title: 50_S30_L005_R1_001

description:
sample name:
50

value: Atopic Dermatitis


title: RNA-P9-WT-3

value: WT


title: 180508_CEMBA_mm_P56_P63_RS2_Pool21_P1_Pool21_P2_E8_ad007

tag: gender

value: male


title: 202790040083_R08C01_whole blood healthy control

value: whole blood


title: 202790040046_R02C01_whole blood healthy control

value: Male