title: 201810150070_R06C01


title: UKN1_SBAD2_Ranitidine_Low_RA [2.DO_216_D51_Ran_1x_(HG-U133_Plus_2).CEL]

status: Public on Nov 03 2022

type: RNA

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

hyb_protocol: The samples were purified using magnetic beads and fragmented. 12,5 μg of fragmented RNA samples were hybridized on Affymetrix Human Genome U133 Plus 2.0 arrays (Affymetrix, Santa Clara, CA, USA). The microarray hybridization step was performed in an Affymetrix GeneChip Hybridization Oven-645 for 16 h at 45 °C and 60 rpm. Washing and staining of the hybridized arrays was completed using the GeneChip HWS Kit (Affymetrix, High Wycombe, United Kingdom) and Affymetrix GeneChip Fluidics Station-450.

scan_protocol: Stained arrays were scanned with Affymetrix Gene-Chip Scanner-3000-7G and evaluated for quality control with Affymetrix GCOS software

data_processing: All analyses were conducted using the statistical software R, version 4.0.5. Pre-processing of the data consists of the three steps background correction, normalization, and summarization, using the frozen robust multi-array average (fRMA) algorithm. This yields expression values for 54675 probe sets. The R-packages affy, frma and hgu133plus2frmavecs were used.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SBAD2 iPS cells

label_protocol: The samples were amplified and labelled with biotin using GeneChip 3′ IVT Express Kit per the manufacturer’s instructions (Affymetrix, High Wycombe, UK).

growth_protocol: The differentiation of SBAD2 hiPSCs to neuroepithelial precursor cells was performed using the UKN1 protocol (Chambers et al. 2009) with minor changes. Briefly, hiPSCs were seeded in 1 ml pluripotent stem cell (PSC) medium (spiked with a Rho-kinase inhibitor (ROCKi)) per well on extracellular matrix protein-coated 12-well-plates at a density of 12,000 - 24,000 cells/cm² on day -3. On day  2 and day  1, the PSC medium was refreshed. On days 0, 1 and 2, medium was changed to differentiation medium, which was spiked with 21.6 µM SB431542, 0.64 µM dorsomorphin, 35 ng/ml noggin and 0.1% DMSO to induce neural differentiation. On day 4, medium was changed to a mixed medium of 75% differentiation medium / 25% N2-S and the same concentrations of SB431542, dorsomorphin and noggin as given above. On day 6, cells were collected for RNA extraction. A more detailed method description is given in the supplemental information.

extract_protocol: Total RNA was isolated from sonicated cell lysates with the ExtractMe Total RNA-Kit (Blirt, Poland). The concentration and purity of the RNA were determined with a NanoDrop2000 (ThermoFisher Scientific, Germany).

treatment_protocol: On days 0, 1 and 2, differentiating cells were incubated (5 % CO2, 37 °C) with the test compounds at 1-fold Cmax and 1.67-, 10- or 20 fold Cmax concentration for a total of 96 h, as well as the vehicle alone (0.1% DMSO). The compounds leflunomide and teriflunomide were tested at a DMSO concentration of 0.5 % and compared to a 0.5% DMSO vehicle control.

tag: gender

value: male

tag: agent


title: 201810150041_R02C01

type: genomic

city: Titusville

first: Qingqin

middle: S

last: Li

state: NJ

address: 1125 Trenton-Harbourton Road

country: USA

institute: Janssen R&D, LLC

hyb_protocol: Infinium® HD Assay Methylation Protocol

scan_protocol: Infinium® HD Assay Methylation Protocol

data_processing:
Illumina® GenomeStudio
normalized (dasen) Average Beta
Unmethylated and methylated signal intensities

label: Cy3 and Cy5

molecule: genomic DNA

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from blood samples

tag: diagnosis

value: MDD

value: M

tag: age

tag: nk

tag: bcell

tag: mono

tag: gran

tag: eos

tag: subject

tag: cohort

value: Cohort 2


title: 201172200021_R07C01


title: UKN1_SBAD2_Magnesium chloride_High_RD [106]

value: Magnesium chloride_High_RD


title: 201810150038_R03C01

value: HC


title: 201810150075_R08C01


title: 201810150057_R08C01


title: UKN1_SBAD2_Methotrexate_High_RC [113]


title: 201800470042_R07C01


title: UKN1_SBAD2_Methicillin_High_RD [104]


title: UKN1_SBAD2_Thalidomide_Low_RD [111]


title: 201172200027_R07C01


title: UKN1_SBAD2_Isotretinoin_Low_RD [109]


title: UKN1_SBAD2_Magnesium chloride_Low_RD [105]

value: Magnesium chloride_Low_RD


title: UKN1_SBAD2_Untreated_Ctrl_RG [107]


title: UKN1_SBAD2_Methicillin_Low_RD [103]


title: 201810150038_R06C01


title: 201502870027_R07C01


title: 201172200025_R06C01


title: UKN1_SBAD2_Ampicillin_High_RD [100]


title: UKN1_SBAD2_Chlorpheniramine_High_RD [98]


title: 201172200055_R03C01


title: UKN1_SBAD2_Ascorbic acid_Low_RD [101]

value: Ascorbic acid_Low_RD


title: UKN1_SBAD2_Ascorbic acid_High_RD [102]

value: Ascorbic acid_High_RD


title: 201172200013_R05C01


title: 201810150068_R07C01


title: 201172200016_R02C01


title: 201800470033_R03C01


title: UKN1_SBAD2_Buspirone_High_RD [96]


title: UKN1_SBAD2_Chlorpheniramine_Low_RD [97]


title: 201800470046_R01C01


title: UKN1_SBAD2_Doxylamine_High_RD [94]


title: 201502870046_R05C01

value: F


title: 201172200025_R07C01


title: UKN1_SBAD2_Methotrexate_Low_RC [91]


title: UKN1_SBAD2_Doxylamine_Low_RD [93]


title: UKN1_SBAD2_Paroxetine_Low_RC [88]


title: UKN1_SBAD2_Thalidomide_High_RC [90]


title: UKN1_SBAD2_Methotrexate_High_RB [92]


title: 201800470052_R05C01


title: 201172200012_R06C01


title: UKN1_SBAD2_Valproic acid_High_RC [86]

value: Valproic acid_High_RC


title: UKN1_SBAD2_Famotidine_High_RD [84]


title: UKN1_SBAD2_Famotidine_Low_RD [83]


title: 201172200051_R02C01


title: UKN1_SBAD2_Valproic acid_Low_RD [85]

value: Valproic acid_Low_RD


title: UKN1_SBAD2_Thalidomide_Low_RC [89]


title: 201810150075_R05C01


title: UKN1_SBAD2_Isotretinoin_Low_RC [87]


title: 201800470046_R02C01


title: 201172200036_R07C01


title: 201172200033_R05C01


title: 201172200058_R03C01


title: 201172200051_R08C01


title: 201172200027_R01C01


title: UKN1_SBAD2_Folic acid_Low_RD [81]

value: Folic acid_Low_RD


title: UKN1_SBAD2_Folic acid_High_RC [77]

value: Folic acid_High_RC


title: UKN1_SBAD2_Folic acid_High_RD [82]

value: Folic acid_High_RD


title: UKN1_SBAD2_Methicillin_Low_RC [78]


title: UKN1_SBAD2_Untreated_Ctrl_RF [80]


title: 201810150040_R08C01


title: UKN1_SBAD2_Ampicillin_Low_RD [99]


title: UKN1_SBAD2_Folic acid_Low_RC [76]

value: Folic acid_Low_RC


title: 201800470030_R02C01


title: UKN1_SBAD2_Methicillin_High_RC [79]


title: 201502870027_R08C01


title: 201172200051_R01C01


title: 201502870046_R08C01


title: 201172200053_R02C01


title: UKN1_SBAD2_Ascorbic acid_Low_RC [72]

value: Ascorbic acid_Low_RC


title: UKN1_SBAD2_Famotidine_Low_RC [74]

value: male


title: 201810150050_R04C01

value: MDD


title: 201172200013_R04C01

value: M


title: 201172200033_R06C01

value: Cohort 2


title: 201810150068_R08C01


title: UKN1_SBAD2_Ampicillin_Low_RC [70]


title: 201502870005_R06C01


title: UKN1_SBAD2_Ampicillin_High_RC [71]


title: UKN1_SBAD2_Chlorpheniramine_High_RC [64]


title: UKN1_SBAD2_Doxylamine_Low_RC [68]


title: UKN1_SBAD2_Magnesium chloride_Low_RC [65]

value: Magnesium chloride_Low_RC


title: UKN1_SBAD2_Doxylamine_High_RC [69]


title: 201810150057_R07C01


title: UKN1_SBAD2_Magnesium chloride_High_RC [66]

value: Magnesium chloride_High_RC


title: 201172200008_R01C01


title: 201172200016_R03C01

value: HC


title: UKN1_SBAD2_Buspirone_High_RC [62]


title: 201172200045_R07C01


title: UKN1_SBAD2_Buspirone_Low_RD [95]


title: UKN1_SBAD2_Untreated_Ctrl_RE [60]


title: UKN1_SBAD2_Buspirone_Low_RC [61]


title: 201800470042_R05C01


title: 201502870048_R08C01


title: 201172200050_R03C01


title: UKN1_SBAD2_Ascorbic acid_High_RC [73]

value: Ascorbic acid_High_RC


title: 201172200050_R06C01


title: 201810150050_R05C01


title: UKN1_SBAD2_Chlorpheniramine_Low_RC [63]


title: UKN1_SBAD2_Ampicillin_High_RB [57]


title: UKN1_SBAD2_Magnesium chloride_High_RB [55]

value: Magnesium chloride_High_RB


title: UKN1_SBAD2_Methicillin_High_RB [59]


title: UKN1_SBAD2_Magnesium chloride_Low_RB [54]

value: Magnesium chloride_Low_RB


title: 201172200050_R02C01


title: 201172200004_R06C01


title: UKN1_SBAD2_Ampicillin_Low_RB [56]


title: 201172200013_R07C01


title: 201172200050_R05C01


title: UKN1_SBAD2_Methicillin_Low_RB [58]


title: 201810150041_R03C01


title: 201800470052_R01C01


title: UKN1_SBAD2_Valproic acid_Low_RC [67]

value: Valproic acid_Low_RC


title: 201502870034_R04C01

value: F


title: 201810150068_R03C01


title: 201800470046_R03C01


title: 201172200003_R06C01


title: 201172200036_R08C01


title: 201502870014_R06C01


title: 201810150072_R07C01


title: 201172200006_R08C01


title: UKN1_SBAD2_Ascorbic acid_High_RB [53]

value: Ascorbic acid_High_RB


title: UKN1_SBAD2_Magnesium chloride_High_RA [46]

value: Magnesium chloride_High_RA


title: UKN1_SBAD2_Ascorbic acid_Low_RB [52]

value: Ascorbic acid_Low_RB


title: 201172200008_R08C01


title: UKN1_SBAD2_Untreated_Ctrl_RC [42]


title: UKN1_SBAD2_Methicillin_High_RA [50]


title: 201172200051_R03C01


title: 201502870018_R03C01


title: UKN1_SBAD2_Untreated_Ctrl_RD [51]


title: UKN1_SBAD2_Ampicillin_High_RA [48]


title: UKN1_SBAD2_Ascorbic acid_High_RA [44]

value: Ascorbic acid_High_RA


title: UKN1_SBAD2_Methicillin_Low_RA [49]


title: UKN1_SBAD2_Ampicillin_Low_RA [47]


title: UKN1_SBAD2_Chlorpheniramine_High_RB [41]


title: UKN1_SBAD2_Magnesium chloride_Low_RA [45]

value: Magnesium chloride_Low_RA


title: UKN1_SBAD2_Chlorpheniramine_Low_RB [40]

value: male


title: 201502870046_R06C01


title: UKN1_SBAD2_Folic acid_Low_RB [38]

value: Folic acid_Low_RB


title: UKN1_SBAD2_Doxylamine_Low_RB [36]


title: 201810150068_R02C01

value: MDD


title: 201810150079_R06C01

value: Cohort 2


title: UKN1_SBAD2_Buspirone_High_RB [33]


title: UKN1_SBAD2_Buspirone_Low_RB [32]


title: UKN1_SBAD2_Untreated_Ctrl_RB [31]


title: UKN1_SBAD2_Methotrexate_High_RA [30]


title: 201502870011_R02C01


title: UKN1_SBAD2_Folic acid_High_RB [39]

value: Folic acid_High_RB


title: 201502870011_R01C01


title: UKN1_SBAD2_Famotidine_Low_RB [34]


title: UKN1_SBAD2_Famotidine_High_RB [35]


title: 201502870027_R01C01


title: 201502870034_R05C01


title: 201172200051_R04C01


title: 201810150048_R02C01


title: 201800470007_R08C01


title: UKN1_SBAD2_Doxylamine_High_RB [37]


title: 201810150048_R05C01


title: 201172200040_R01C01


title: UKN1_SBAD2_Paroxetine_Low_RB [28]


title: UKN1_SBAD2_Methotrexate_Low_RB [29]


title: 201172200012_R01C01


title: 201502870014_R05C01


title: 201172200058_R08C01

value: M


title: 201800470037_R05C01


title: UKN1_SBAD2_Valproic acid_High_RB [27]

value: Valproic acid_High_RB


title: UKN1_SBAD2_Isotretinoin_Low_RB [23]


title: UKN1_SBAD2_Thalidomide_Low_RB [24]


title: 201502870005_R01C01


title: UKN1_SBAD2_Untreated_Ctrl_RB [22]


title: UKN1_SBAD2_Valproic acid_Low_RB [26]

value: Valproic acid_Low_RB


title: UKN1_SBAD2_Chlorpheniramine_Low_RA [19]


title: UKN1_SBAD2_Thalidomide_High_RB [25]


title: 201800470022_R02C01


title: 201810150057_R04C01

value: HC


title: UKN1_SBAD2_Chlorpheniramine_High_RA [20]


title: UKN1_SBAD2_Folic acid_Low_RA [17]

value: Folic acid_Low_RA


title: 201172200045_R08C01


title: UKN1_SBAD2_Doxylamine_High_RA [16]


title: UKN1_SBAD2_Doxylamine_Low_RA [15]


title: UKN1_SBAD2_Folic acid_High_RA [18]

value: Folic acid_High_RA


title: 201502870005_R07C01

value: F


title: 201810150079_R02C01


title: 201172200011_R02C01


title: 201502870034_R06C01


title: 201810150075_R02C01


title: 201172200011_R05C01


title: UKN1_SBAD2_Famotidine_High_RA [14]


title: 201800470029_R03C01


title: 201810150076_R02C01


title: 201172200040_R02C01


title: UKN1_SBAD2_Methotrexate_Low_RA [10]


title: UKN1_SBAD2_Untreated_Ctrl_RA [2]


title: UKN1_SBAD2_Paroxetine_Low_RA [9]


title: UKN1_SBAD2_Valproic acid_Low_RA [7]

value: Valproic acid_Low_RA


title: Embryo, E15.5,  visium

type: SRA

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: spatial transcriptomics

library_source: transcriptomic single cell

data_processing:
Raw data were pre-processed using SpaceRanger’s (v1.3.1)
Using 10X Genomics’ Loupe Browser (v6.0.0), we manually selected barcodes belonging to capture spots overlaying tissue and used these to filter the gene-barcode matrices obtained from SpaceRanger
Data for each section were merged and analyzed with Seurat (v4.1.0).
We normalized data and performed clustering following Signac (v1.6.0) standard workflow.
Assembly: mm10
Supplementary files format and content: h5 (feature-barcode matrix)
Supplementary files format and content: csv (metadata with spatial coordinates, sample, and clustering)
Supplementary files format and content: png/jpg (picture of the tissue section)

organism: Mus musculus

source_name: Embryo

extract_protocol:
Libraries were prepared according to Visium Spatial Gene Expression Slide and Reagents kit.
Libraries were dual indexed using Dual Index Kit TT Set A
Libraries were sequenced on Illumina NextSeq 550/2000 platform

tag: tissue

value: Embryo

tag: strain

tag: genotype

value: WT


title: UKN1_SBAD2_Valproic acid_High_RA [8]

value: Valproic acid_High_RA


title: 201502870018_R04C01


title: Embryo, E13.5,  visium

description: spatial transcriptomics


title: 201502870015_R06C01


title: 201172200001_R04C01


title: 201502870018_R05C01


title: A549_sgMEN1_xeno_1

city: Shanghai

first: Yin

last: Liu

state: Shanghai

address: Building #2, 507 Zhengmin Road

department: Department of Laboratory Medicine

country: China

institute: Shanghai Pulmonary Hospital, Tongji University School of Medicine

library_source: transcriptomic

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 hg38 whole genome using STAR/2.4.2a with parameters --clip3pNbases 0       --clip5pNbases 0 --outFilterMultimapNmax 2    --outFilterMismatchNoverReadLmax 0.04  --outSAMmapqUnique 255 --outSAMtype BAM SortedByCoordinate  --outSAMattributes All
The number of reads falling in the exons were calculated using HTSeq/0.11.0.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 xenograft

growth_protocol: A549 cells were cultured in RPMI-1640 and supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MEN1 was knockout by lenti-guide virus.

tag: cell type

value: lung

tag: growth

value: in vivo

value: NOD/SCID


title: UKN1_SBAD2_Untreated_Ctrl_RA [1]

value: male


title: 201810150071_R06C01

value: MDD

value: Cohort 2


title: 201502870034_R02C01


title: A549_sgMEN1_xeno_2


title: 201172200053_R05C01


title: 201172200005_R04C01


title: A549_sgLacZ_xeno_2


title: UKN1_SBAD2_Buspirone_Low_RA [11]


title: UKN1_SBAD2_Thalidomide_Low_RA [5]


title: UKN1_SBAD2_Thalidomide_High_RA [6]


title: 201172200050_R07C01

value: M


title: 201810150022_R03C01


title: 201172200036_R04C01


title: Inoculated root 2

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The integration of the replicates and the processing of the data was generated in Seurat.
Assembly: Medicago truncatula reference genome and genome annotation (https://medicago.toulouse.inra.fr/MtrunA17r5.0-ANR/)
Supplementary files format and content: Tab-separated values files and matrix files

organism: Medicago truncatula

source_name: root

extract_protocol:
Roots were chopped and passed through a 30µm cell strainer. The filtered nuclei were purified by cell sorting using FACSAria II™ cell sorter (BD Biosciences). An average of 80-100,000 nuclei were collected for each sample, centrifuged, and re-suspended in phosphate buffered saline-bovine serum albumin 0.5%-RNA-inhibitor solution.
Libraries were performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10x Genomics).
sNucRNA-seq

value: root cells

value: root

value: 6 day-old

tag: infection

value: rhizobia


title: 201502870015_R05C01

tag: gender


title: Inoculated root 3

description: 10x Genomics


title: 201172200022_R02C01


title: 201800470037_R06C01


title: UKN1_SBAD2_Isotretinoin_Low_RA [4]

tag: agent


title: Mock root 3

description: 10x Genomics

value: mock


title: UKN1_SBAD2_Famotidine_Low_RA [13]


title: Inoculated root 1

description: 10x Genomics


title: 201502870018_R02C01

tag: diagnosis

value: F


title: 201502870058_R03C01

tag: age


title: 201502870055_R06C01

value: HC

tag: nk


title: Mock root 2

description: 10x Genomics


title: 201502870014_R04C01

tag: bcell


title: A549_sgMEN1_cell_line_1

source_name: A549 cell line

value: in vitro


title: A549_sgLacZ_cell_line_2


title: 201502870015_R01C01

tag: mono


title: A549_sgLacZ_xeno_1


title: A549_sgMEN1_cell_line_2


title: A549_sgLacZ_cell_line_1


title: HeLa_TRP24_3

city: New Haven

first: Eduardo

middle: A

last: Groisman

state: Connecticut

address: Boyer Center for Molecular Medicine, 295 Congress Ave

department: Department of Microbial Pathogenesis

institute: Yale School of Medicine

data_processing:
sequencing files from a given replicate were concatenated (usegalaxy.org)
fastp: filter low quality reads, trim reads, cut adaptors (usegalaxy.org)
HISAT2: alignment to reference genome (usegalaxy.org)
htseq-count: count reads aligned to features (usegalaxy.org)
DESeq2: differential gene expression analysis (R)
Genome_build: Chlamydia trachomatis L2 434/Bu ASM6858v1; Homo sapiens GRCh38
Supplementary_files_format_and_content: Normalized count values for each feature output by DESeq2

organism:
Homo sapiens
Chlamydia trachomatis L2/434/Bu

source_name: C. trachomatis-infected HeLa

growth_protocol: Cells were cultured in DMEM + 10% FBS + 2 mM L-Gln + 10 µg/mL gentamicin until treatments were applied

extract_protocol:
Total RNA was collected from cultured cells in Trizol, vortexed with zirconia beads, and phenol-chloroform extracted prior to isolation through a PureLink RNA Mini Kit with two on-column DNA digestion steps. To remove rRNA, 10 µg of total RNA was run in 5 µg parallel samples through the RiboMinus Transcriptome Isolation kit with 3 µL of pan-prokaryotic rRNA probe and 4 µL eukaryotic rRNA probe. Depleted RNA was subsequently concentrated in an RNA Clean and Concentrator Kit from Zymo.
TruSeq Stranded Total RNA library preparation kit (Illumina, San Diego, CA, USA) was used to generate RNA-sequencing libraries following manufacturer protocols with a starting amount of 100 ng rRNA-depleted RNA. Depletion of rRNA in the TruSeq kit was performed by the addition of 2.5 µL each of standard rRNA Removal Mix (RRM) or Prokaryotic RRM.

treatment_protocol: 100 µM 2,2-bipyridyl was added to complete medium as described above; complete media was replaced with defined tryptophan-depleted media: DMEM-F12 w/o L-Trp + 10% dialyzed FBS + 2 mM L-Gln + 10 µg/mL gentamicin

value: C. trachomatis-infected HeLa

tag: treatment

value: Tryptophan-depleted


title: 201810150068_R04C01

tag: gran

tag: eos


title: HeLa_TRP24_2


title: 201172200027_R05C01

tag: subject

tag: cohort


title: 201502870011_R08C01


title: 201502870014_R01C01


title: 201502870034_R01C01


title: 201502870011_R03C01


title: HeLa_BPD24_3

tag: tissue

value: Bipyridyl


title: C6 input  C57BL/6 mice , m6A RNA

city: Jinan City

first: song

last: han

state: ShanDong province

address: Tianqiao District

institute: The Second Hospital of Shandong University， Cheeloo College of Medicine，Shandong University

description: both the input samples without immunoprecipitation and the m6A IP samples were submitted to 153-bp paired-end sequencing

data_processing:
library strategy:circRNA-seq
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3).
First, clean reads of input libraries were aligned to reference genome (UCSC MM10) by STAR software.
Reverse transcription (RT)-qPCR was used to evaluate eight genes with differentially methylated sites according to circRNA m6A-seq
Then circRNAs were identified by DCC software using the STAR alignment results
After that, clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4).
Methylated sites on RNAs (peaks) were identified by MACS software. Differentially methylated sites were identified by diffReps
These peaks identified by both softwares overlapping with exons of mRNA, LncRNA and circRNA were figured out and choosed by home-made scripts
GO and Pathway enrichment analysis were performed by the differentially methylated protein coding genes, the associated genes of differentially methylated LncRNAs and the source genes of differentially methylated circRNAs separately.
Assembly: MM10
Supplementary files format and content: xlsx  files BED  files

source_name: cortex, hippocampus and cerebellum

extract_protocol:
m6A RNA-Seq service was provided by Cloudseq Biotech Inc. (Shanghai, China). Briefly, m6A RNA immunoprecipitation was performed with the GenSeqTM m6A RNA IP Kit (GenSeq Inc., China) by following the manufacturer's instructions.
Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra II Directional RNA Library Prep Kit (New England Biolabs, Inc., USA). The library quality was evaluated with BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired-end reads.

value: frozen mouse brain

value: cortex, hippocampus and cerebellum

value: nerve cell

tag: genotype

value: m6A RNA


title: C6 IP  C57BL/6 mice , m6A RNA

description: both the input samples without immunoprecipitation and the m6A IP samples were submitted to 152-bp paired-end sequencing

tag: cell type


title: 201172200044_R06C01

value: MDD

value: Cohort 2


title: HeLa_BPD24_2


title: Mock root 1

description: 10x Genomics

value: root cells

tag: strain


title: 201172200022_R03C01


title: C3 input C57BL/6 mice ,m6A RNA

description: both the input samples without immunoprecipitation and the m6A IP samples were submitted to 151-bp paired-end sequencing


title: 201502870055_R07C01


title: C3 IP  C57BL/6 mice ,m6A RNA

description: both the input samples without immunoprecipitation and the m6A IP samples were submitted to 150-bp paired-end sequencing


title: 201800470042_R02C01


title: A9 input  APP/PS1 AD mice , m6A RNA

value: APP/PS1 AD mice


title: 201172200059_R05C01


title: 201810150076_R03C01


title: HeLa_TRP16_2


title: HeLa_TRP16_3


title: 201502870046_R01C01


title: HeLa_BPD16_3


title: 201172200036_R03C01


title: A6 input  APP/PS1 AD mice , m6A RNA


title: 201172200011_R04C01


title: HeLa_BPD16_2


title: A9 IP  APP/PS1 AD mice , m6A RNA


title: A6 IP  APP/PS1 AD mice , m6A RNA


title: 201172200028_R07C01

value: M


title: 201502870005_R03C01


title: HeLa_UTD24_3

value: Untreated


title: 201172200022_R04C01


title: HeLa_UTD24_2


title: 201172200044_R07C01


title: 201502870015_R02C01


title: MOLM-13 cells sh-c-Myc and sh-Bcl2

city: Hangzhou

first: ping

last: wang

address: 88th Jiefang Road

department: School of Medicine

institute: Zhejiang University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.annotation.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and  FPKM values for each sample

growth_protocol: MOLM-13 cell lines were cultured in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS) and 1% Pen/Strep at 37°C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: MOLM-13 cells were collected and resuspended in fresh RPMI-1640 medium, infected with lentiviruses, and selected in medium containing 0.5 μg/ml puromycinor medium containing 600 μg/ml G418 Sulfate.Gene expression knock-down was confirmed by Western Blot after doxycycline introduction for 72 h.

value: blood

tag: cell line

value: MOLM-13 cells

value: c-Myc knockdown and Bcl-2 knockdown

value: Doxycycline induction


title: 201172200019_R04C01

tag: gender

value: F


title: HeLa_Mock_3

source_name: HeLa

value: Mock-infected HeLa


title: MOLM-13 cells sh-c-Myc

value: c-Myc knockdown


title: MOLM-13 cells sh-Bcl2

value: Bcl-2 knockdown


title: 201502870011_R04C01


title: 201172200006_R03C01


title: 201502870058_R05C01


title: HeLa_Mock_2


title: 3610, treatment 2

city: Malaga

first: Carlos

middle: Molina

last: Santiago

state: Malaga

address: Bulevar Louis Pasteur 49

department: MIcrobiology

country: Spain

institute: UMA

data_processing:
The raw reads were pre-processed with SeqTrimNext using the specific NGS technology configuration parameters (Falgueras et al., 2010). This pre-processing removes low quality, ambiguous and low complexity stretches, linkers, adapters, vector fragments, and contaminated sequences while keeping the longest informative parts of the reads. SeqTrimNext also discarded sequences below 25 bp. Subsequently, clean reads were aligned and annotated using the Cucumis melo genome as the reference with Bowtie2 (Langmead and Salzberg, 2012) in BAM files, which were then sorted and indexed using SAMtools v1.484110 (Li et al., 2009).
Uniquely localized reads were used to calculate the read number value for each gene via Sam2counts (https://github.com/vsbuffalo/sam2counts). Differentially expressed genes (DEGs) between treatments were analyzed via DEgenes Hunter, which provides a combined p value calculated (based on Fisher’s method) using the nominal p values provided by from edgeR113 (Robinson et al., 2010) and DEseq2114 (Anders and Huber, 2010).
Genome_build: ASM34474v1 (B. subtilis)
Supplementary_files_format_and_content: Excel files include raw counts, Log2FC of the comparison between treated and non-treated seeds and leaves, with p-value, gene names and descriptions

organism: Bacillus subtilis subsp. subtilis NCIB 3610 = ATCC 6051 = DSM 10

source_name: 3610, treatment

extract_protocol:
Liquid growth cultures of B. subtilis were grown overnight in Luria–Bertani (LB) medium at 30°C. Overnight cultures were diluted and, after 3-4 hours (exponential phase), B. subtilis cells were treated with Tse1 or with control buffer. Cultures were grown for 3 h.  Cells were harvested by centrifugation at 8000 g for 10 min and suspended immediately in stop solution (95% (v/v) ethanol, 5% (v/v) phenol) and pelleted by centrifugation. After that, total RNA was extracted with Trizol (Invitrogen). Removal of DNA was carried out by treatment with Nucleo-Spin RNA Plant (Macherey–Nagel) kit. The integrity and quality of total RNA was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 3h after exponential phase

value: B. subtilis cells


title: 201800470052_R06C01

tag: diagnosis


title: 201810150070_R07C01

tag: age


title: 201810150025_R02C01

tag: nk


title: 201800470019_R06C01

tag: bcell


title: 201172200003_R02C01

tag: mono


title: 201502870034_R03C01


title: 3610, treatment 1

tag: treatment


title: Lis46_late_primed_rep2_small

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description: small RNA-seq

data_processing:
The data were trimmed and mapped to GRCh38 using the exceRpt Small RNA-seq Pipeline Workflow implemented in the Genboree Workbench (Rozowsky et al., 2019).
Micro RNAs were filtered such that at least five reads in at least two samples were retained, resulting in 1035 pass-filter miRNAs.
Differential expression was carried out in DESeq2 (v.1.26.0) (Love, Huber and Anders, 2014) requiring an adjusted p-value < 0.05 and log2 FoldChange > 1 considered differentially expressed unless otherwise noted.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads per million normalized counts for each sample, processed reads include all miRNAs (unfiltered)

growth_protocol: Naïve conditions included culture on MEFs in a modification of the naïve human stem cell medium (NHSM) developed by the Hanna laboratory (Gafni et al., 2013), consisting of: 1:1 Neurobasal medium and DMEM/F-12 (Gibco); 1X Pen/Strep (Biological industries); 2 mM L-Glutamine (Biological industries); 1% non-essential amino acids (Biological industries); 0.7 mM sodium pyruvate (Biological industries); 2% ml B27 supplement (in house produced); 0.2% ml defined lipid concentrate (Gibco); 0.05 mM β-ME (Gibco); 12.5 µg/ml insulin (Sigma-Aldrich); 100 µg/ml apo-transferrin (Sigma-Aldrich); 0.02 µg/ml progesterone (Sigma-Aldrich); 16 µg/ml putrescine (Sigma-Aldrich); 30 µM sodium selenite (Sigma-Aldrich); 50 µg/ml L-ascorbic acid 2-phosphate (Sigma-Aldrich); 0.07% BSA (Gibco); 20 ng/ml human LIF (Peprotech); 5 µM IWR1 (Biotest); 20 ng/ml human activin A (Peprotech); 1.7 ng/ml FGF2 (Peprotech); 0.2 µM Chir99021 (Axon Medchem); 1 µM PD0325901 (Axon Medchem); 0.2 µM BIRB796 (Axon Medchem); 2 µM SP600125 (Tocris); 2 µM PKCi (Tocris); 0.4 µM Thiazovivin (Peprotech); and 1.5 µM CGP77675 (Axon Medchem). Primed conditions included culturing on mitotically inactivated mouse embryo fibroblast (MEF) feeder layers in primed hESC culture medium, consisting of: DMEM/F-12 with 20% Knockout Serum Replacement (Gibco); 2 mM L-glutamine (Biological industries); 0.1 mM β-ME (Gibco); 1% non-essential amino acids (Biological industries); 1X Pen/Strep (Biological industries) and 8 ng/ml FGF2 (Peprotech). For both naïve and primed cultures, the medium was changed daily, passaging was performed every 3-5 days using 0.05% trypsin + EDTA (Biological industries), and 5 μM of Y27632 ROCK inhibitor (Axon Medchem) were used for 24 hr before and after passaging. Both naïve and primed cultures were grown without MEFs for two passages prior to collection of cells for molecular analysis.

extract_protocol:
RNA was extracted using mirVana miRNA Isolation Kit (Life Technologies, Inc.), following the manufacturers' instructions. RNA quality was assessed using a BioAnalyzer 2100 (Agilent Technologies, Inc.). All samples had a RIN greater than 8.5.
Small RNA-seq libraries were constructed using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (New England Biolabs, Inc., Ipswich, MA). The libraries were pooled, size-selected for products that were 120-135 nucleotides in length using a Pippin Prep with a 3% agarose gel cassette (Sage Science, Beverly, Massachusetts), and run on a MiSeq instrument (Illumina, San Diego, California) at the UC San Diego UCSD Institute for Genomic Medicine (IGM) Genomics Core. Samples that produced adequate numbers of miRNA read counts were then rebalanced to produce similar numbers of miRNA reads and sequenced on a HiSeq 4000 instrument using 1x75 bp reads (Illumina, San Diego, California) at the UC San Diego IGM Genomics Core.

value: human embryonic stem cell

tag: Sex

value: male

tag: culture conditions

value: primed

tag: timepoint

value: late


title: 3610, control 2

source_name: 3610, control

value: control


title: Lis46_late_primed_rep3_small

description: small RNA-seq


title: Lis46_late_primed_rep1_small

description: small RNA-seq


title: 201172200011_R03C01

value: MDD

tag: gran

tag: eos

tag: subject

tag: cohort

value: Cohort 2


title: 201810150022_R04C01


title: 201502870027_R05C01


title: HS3 input

city: Qingdao

first: Dongxue

last: Xu

address: Changcheng road No.700

institute: Qingdao Agricultural University

library_source: genomic

data_processing:
After trimming and filtering the reads, clean reads were analyzed and mapped in A. japonicus genome using BWA software.
Samtools (version 1.3.1) was used to remove potential PCR duplicates.
MACS2 software (version 2.1.1.20160309) was used to call peaks by default parameters.
If the summit of a peak located closest to the transcription start site (TSS) of one gene, the peak will be assigned to that gene.
Genome_build: GenBank assembly accession: GCA_002754855.1
Supplementary_files_format_and_content: clean reads files

organism: Apostichopus japonicus

source_name: intestine tissue

growth_protocol: Sea cucumbers in the heat stress (HS) group went through a temperature-rise process from 18 °C to 26 °C, with a rate of 2 °C per hour with a heating rod. The moment when the temperature just reached 26 °C was regarded as initial time. Then the temperature of HS group were kept at 26 °C since. After the 48 h from initial time, the sea cucumbers from control group and HS group were sampled with intestine tissue respectively, and then frozen in the liquid nitrogen. All the samples were stored at -80 °C freezer until the next processing.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Immunoprecipitated DNA was used to construct sequencing libraries following the protocol provided by the I NEXTFLEX® ChIP-Seq Library Prep Kit for Illumina® Sequencing（NOVA-5143-02，Bioo Scientific） and sequenced on Illumina Xten with PE 150 method (Illumina, San Diego, CA, USA).

treatment_protocol: Samples were washed twice in cold PBS buffer and cross-linked with 1% formaldehyde for 10 minutes at room temperature and then quenched by addition of 0.125 M glycine. Afterwards, samples were lysed and chromatins were obtained on ice. Chromatins were sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp).20ul chromatin was saved at –20 °C for input DNA, and was then immunoprecipitated with the antibody anti-Acetyl-Histone 3 Lysine 9 (#9649, Cell signaling technology) overnight at 4 °C, after saving 2% of the chromatin as input. The next day, 30 μL of protein beads was added and the samples were further incubated for 3 h.

tag: tissue

value: intestine

tag: chip-antibody

value: heat stress-treatment


title: 201810150048_R03C01

value: HC

tag: gender


title: 201172200012_R03C01


title: Lis46_early_primed_rep3_small

description: small RNA-seq

tag: cell line

tag: cell type

value: early


title: 3610, control 1

tag: time


title: MOLM-13 cells shControl

value: blood

value: MOLM-13 cells

tag: genotype

value: negative control

value: Doxycycline induction


title: Lis46_early_primed_rep2_small

description: small RNA-seq


title: Lis46_early_primed_rep1_small

description: small RNA-seq


title: HS2 input


title: 201172200011_R07C01

tag: diagnosis

value: F

tag: age

tag: nk

tag: bcell


title: 201810150071_R05C01

tag: mono


title: 201800470042_R03C01


title: 201502870055_R05C01


title: 201810150057_R02C01


title: HS3

value: H3K9ac (#9649, Cell signaling technology)

tag: treatment


title: HS2


title: 201810150057_R05C01

tag: gran


title: 201172200027_R04C01

tag: eos


title: UKN1_SBAD2_Buspirone_High_RA [12]

tag: agent


title: Lis46_late_naive_rep3_small

description: small RNA-seq

value: human embryonic stem cell

tag: Sex

tag: culture conditions

value: naive

tag: timepoint


title: Lis46_late_naive_rep2_small

description: small RNA-seq

value: male


title: HS1 input

tag: tissue

tag: chip-antibody


title: HS1


title: 201502870027_R03C01

tag: gender

tag: subject

tag: cohort


title: 201502870046_R04C01

tag: diagnosis


title: 201800470030_R06C01

tag: age


title: Lis46_early_naive_rep3_small

description: small RNA-seq

tag: cell line

tag: cell type


title: 201172200024_R04C01

tag: nk

tag: bcell

tag: mono


title: 201800470030_R04C01

tag: gran

tag: eos


title: Lis46_early_naive_rep2_small

description: small RNA-seq

tag: Sex


title: Contol3

tag: treatment

value: non-treatment


title: Contol3 input


title: 201172200012_R02C01


title: Lis46_late_naive_rep1_small

description: small RNA-seq

tag: culture conditions

tag: timepoint

value: late


title: Contol2 input

tag: tissue

tag: chip-antibody


title: 201810150025_R03C01

tag: gender

tag: subject


title: 201800470017_R05C01

tag: diagnosis

tag: cohort


title: 201172200003_R01C01

value: MDD

tag: age


title: 201800470037_R02C01

value: Cohort 2


title: 201800470007_R05C01


title: 201800470007_R01C01


title: Lis46_virgin_rep3_small

description: small RNA-seq

tag: cell line

tag: cell type

value: virgin


title: Lis46_early_naive_rep1_small

description: small RNA-seq


title: Lis46_virgin_rep2_small

description: small RNA-seq


title: 201502870048_R07C01

tag: nk

tag: bcell


title: Contol1

value: intestine


title: Contol1 input


title: Lis46_virgin_rep1_small

description: small RNA-seq


title: UKN1_SBAD2_Ascorbic acid_Low_RA [43]

tag: agent

value: Ascorbic acid_Low_RA


title: Lis45_late_primed_rep3_small

description: small RNA-seq

value: female

value: primed


title: Contol2


title: 201800470037_R04C01

tag: mono

tag: gran

tag: eos


title: 201172200045_R04C01

value: M


title: 201810150040_R01C01


title: 201800470029_R04C01


title: 201800470008_R04C01


title: 201502870018_R01C01


title: Scr3-RAD21

city: Philadelphia

first: Jennifer

middle: Mary

last: Luppino

state: Pennsylvania

address: 415 Curie Blvd., Room: 570

department: Genetics

institute: University of Pennsylvania

description:
Scr3-RAD21
Scr2-RAD21.bed

data_processing:
ChIP-seq: Sequencing quality was examined using FASTQC to ensure that the library GC% and duplication rate were within expected range (v0.11.5). Reads were aligned against the hg38 reference genome using Bowtie2 (v2.2.5) allowing 1 mismatch in seed alignment ("-N 1") and soft clipping ("--local"). For single-end libraries, the primary alignment of each read with a MAPQ score higher than 10 was retained using SAMtools (v0.1.19). For paired-end reads, only properly paired primary alignment were retained and the maximum fragment size was set to be 2kb. Alignments were then filtered for PCR duplicates using SAMtools. Alignments that mapped to mitochondria, random contigs and ENCODE blacklisted regions were also removed for downstream analysis using BEDtools (v2.27.1).
ChIP-seq:Visualization tracks were generated using BEDtools, in which process, samples were normalized to 1M reads per library and corresponding input controls were subtracted from IP. Peaks were called for IP libraries against their corresponding input controls using MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff. Finally, a non-overlapping union set of peaks was created by merging peaks in all samples using BEDtools such that all peaks that overlap by at least 1bp were merged. The union peaks were annotated to nearest genes using HOMER tools. ChIP-seq signal was quantified in each sample over each of the union peaks using Bwtools.
Assembly: hg38
Supplementary files format and content: ChIP-seq: Bigwig files were generated using BEDtools (v2.27.1) on each biological replicate; bed files of peaks for each biological replicate were called with MACS2 (v2.1.1), with default parameters and a 0.01 q-value cutoff

growth_protocol: We obtained the HCT-116 cell line from ATCC (RRID:CVCL_0291). All cells were cultured in McCoy’s 5A medium supplemented with 10% fetal bovine serum, 2 mM l-glutamine, 100 U ml−1 penicillin, and 100 μg ml−1 streptomycin at 37 °C with 5% CO2.

extract_protocol:
ChIP-seq: ChIP was performed based on (Shah et al., Dev Cell 2021). HCT-116 cells were cross-linked in culture medium by addition of methanol-free formaldehyde (ThermoFisher, final 1% v/v) and incubated at room temperature for 10 minutes with gentle nutation. Crosslinking was quenched by addition of glycine (final 125 mM) and incubated at room temperature for 5 minutes with gentle nutation. Media was aspirated and replaced with cold DPBS. Cells were scraped and transferred to conical tubes, then pelleted by centrifugation (1500 rpm, 3 minutes, room temperature). Pellets were flash frozen on liquid nitrogen and stored at -80C. For ChIP, 30 uL protein G magnetic beads (per sample; ThermoFisher) were washed three times in blocking solution (0.5% BSA in DPBS). Beads were then resuspended in 250 uL blocking solution and 2 ug antibody (RAD21, Abcam ab992; CTCF, Cell Signaling Technology 3418) was added. Beads and antibody were rotated at 4C for at least six hours. Nuclei were isolated from frozen cell pellets as follows: pellet was resuspended in 10 mL cold lysis buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100, and protease inhibitors) and rotated at 4C for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was aspirated and the pellet was resuspended in 10 mL cold lysis buffer 2 (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors) and rotated at room temperature for 10 minutes, followed by centrifugation (1500 rpm, 3 minutes, 4C). Supernatant was discarded and nuclei were resuspended in 1 mL cold lysis buffer 3 (10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris). Nuclei were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Sonicated chromatin was transferred to 1.5mL microcentrifuge tubes and Triton-X 100 was added (1% final v/v) followed by centrifugation (top speed, 10 minutes, 4C). Supernatant was transferred to a new tube. Antibody-conjugated protein G beads were washed three times in blocking solution, resuspended in 50 ul blocking buffer, and added to 500 ug sonicated chromatin. Chromatin was rotated overnight at 4C. 50 ug lysate was reserved in a separate tube at -20C for input.   On day 2, beads were washed five times in 1 mL RIPA buffer (50mM HEPES-KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate). Beads were then washed in 1 mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes. Beads were finally resuspended in 210 uL elution buffer (50mM Tris-HCl pH 8.0, 10mM EDTA, 1% SDS), and chromatin was eluted from beads by agitation at 65 °C for 30 minutes. 200 uL eluate was transferred to a new tube, and all samples (ChIP and input) were reverse cross-linked overnight at 65 °C with agitation for between 12 and 18 hours. 200 uL 1xTE was added to all samples, and samples were treated with RNase A (final 0.2mg/mL RNase; 37 °C for 2 hours) and proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours). DNA was purified using phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.
ChIP-seq: ChIP and input DNA were quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for either single or dual-index sequencing. Library quality was assessed on Bioanalyzer (Agilent) and quantified by qPCR (Kapa Biosystems).
ChIP-seq: Quantified libraries were sequenced via Illumina sequencing using the NextSeq500 (single end, 75bp) platform. Data from the same libraries were merged for final analysis.

treatment_protocol: RNAiMAX transfection reagent (Thermo Fisher Scientific) was diluted in Opti-MEM reduced serum medium (Thermo Fisher Scientific), and pipetted onto siRNA. Plates were incubated at room temperature for 20 minutes. HCT-116 cells were trypsinized and resuspended in antibiotic-free medium, then plated on siRNA duplexes to obtain a final siRNA concentration of 25 nM. After 72 h of RNAi treatment, cells were collected for experiments.

tag: genotype

value: Parental

tag: treatment

value: Control siRNA

tag: chip antibody

value: RAD21, Abcam ab992


title: Lis45_late_primed_rep2_small

description: small RNA-seq

tag: Sex

tag: culture conditions

tag: timepoint


title: 201172200024_R03C01

tag: diagnosis

tag: gender

value: F

tag: subject


title: Lis45_late_primed_rep1_small

description: small RNA-seq

tag: cell line

value: human embryonic stem cell


title: Scr2-Input

description:
Scr2-Input
Scr2-RAD21.subtract.bw
Scr2-RAD21.bed
Scr3-CTCF.subtract.bw
Scr3-CTCF.bed
Scr2-RAD21.subtract.bw
Scr2-RAD21.bed

value: none; input


title: Lis45_early_primed_rep3_small

description: small RNA-seq

tag: cell type

value: early


title: 201172200053_R07C01

tag: age

tag: nk

tag: cohort


title: Scr2-RAD21


title: 201172200044_R05C01

tag: bcell

tag: mono


title: 201800470037_R01C01

tag: gran

tag: eos


title: 201172200003_R03C01


title: Lis45_early_primed_rep2_small

description: small RNA-seq


title: Lis45_early_primed_rep1_small

description: small RNA-seq


title: 201172200001_R03C01


title: 201810150048_R01C01


title: donor 10 - 7

city: Seoul

first: Dae Yong

last: Yi

address: Heukseok-ro 102

country: South Korea

institute: Chung-Ang University

data_processing:
RNA QC, cDNA Library, Sequencing, Trimming, Mapping, Normalization, Comparison
Assembly: hg19
Supplementary files format and content: processed data files
Library strategy: Exosomal RNA-Seq

source_name: human breast milk

extract_protocol:
Human breast milk fractionation and miRNA isolation, Library preparation and sequencing
For control and test RNAs, the  construction of library w as performed using NEBNext Multiplex Small  RNA Library Prep kit New England BioLabs, Inc. USA according to the manufacturer’ instructions

tag: tissue

value: human breast milk

value: milk cell

tag: protocol

value: frozen, 1week , microwave

tag: treatment

value: not applicable


title: donor 10 - 8

value: frozen, 4week , bottle warmer


title: 201172200008_R03C01

value: MDD

value: Cohort 2


title: 201172200053_R06C01


title: donor 10 - 6

value: frozen, 1week , bottle warmer


title: 201502870018_R08C01


title: Lis45_late_naive_rep2_small

description: small RNA-seq

tag: Sex

value: female

tag: culture conditions

value: naive

value: late


title: 201800470007_R02C01

tag: diagnosis


title: Lis45_late_naive_rep3_small

description: small RNA-seq

tag: timepoint


title: 201172200004_R07C01

tag: gender

value: M

tag: subject


title: 201810150038_R04C01


title: donor 10 - 3

tag: cell type

value: room temperature, 1week


title: 201800470037_R07C01

value: HC

value: F

tag: age


title: 201172200008_R04C01

tag: nk


title: donor 9 - 8


title: 201172200012_R04C01

tag: cohort


title: 201800470030_R05C01

tag: bcell


title: Lis45_early_naive_rep1_small

description: small RNA-seq

tag: cell line

value: human embryonic stem cell


title: 201172200004_R03C01

tag: mono

tag: gran


title: Lis45_early_naive_rep2_small

description: small RNA-seq

value: early


title: donor 10 - 2

tag: tissue

value: human breast milk

value: microwave


title: 201800470037_R03C01

tag: eos


title: Scr3-CTCF

tag: genotype

value: Parental

tag: treatment

value: Control siRNA

tag: chip antibody

value: CTCF, Cell Signaling Technology 3418


title: 201172200040_R05C01

tag: diagnosis

value: MDD


title: 201502870058_R02C01

value: Cohort 2


title: donor 9 - 7

value: milk cell

tag: protocol

value: frozen, 1week , microwave

value: not applicable


title: donor 10 - 4

value: refrigerator, 1week,


title: 201172200019_R08C01

tag: gender


title: Lis45_virgin_rep1_small

description: small RNA-seq

tag: Sex

value: female

tag: culture conditions

value: naive

tag: timepoint

value: virgin


title: 201172200055_R05C01

value: M

tag: age

tag: nk

tag: subject


title: Lis45_late_naive_rep1_small

description: small RNA-seq

tag: cell line

tag: cell type

value: human embryonic stem cell

value: late


title: Lis45_early_naive_rep3_small

description: small RNA-seq

value: early


title: Lis45_virgin_rep3_small

description: small RNA-seq


title: donor 9 - 4

value: human breast milk


title: 201800470021_R02C01

tag: bcell

tag: mono

tag: gran

tag: cohort


title: 201172200036_R05C01

value: F

tag: eos


title: donor 10 - 1

tag: tissue

value: control, fresh sample

tag: treatment


title: 201172200058_R02C01

tag: diagnosis


title: donor 9 - 3

tag: protocol

value: room temperature, 1week


title: 201810150076_R07C01

value: MDD

tag: gender


title: Lis39_late_primed_rep2_small

description: small RNA-seq

tag: Sex

tag: culture conditions

value: primed


title: 201172200027_R08C01

tag: age

value: Cohort 2


title: donor 9 - 6

value: milk cell

value: frozen, 1week , bottle warmer


title: 201800470052_R03C01

tag: nk


title: donor 9 - 2

value: microwave

value: not applicable


title: 201502870027_R02C01

tag: subject


title: 201172200040_R04C01


title: 201172200001_R02C01


title: 201502870046_R02C01


title: Lis39_late_primed_rep1_small

description: small RNA-seq

tag: cell line

value: female

tag: timepoint


title: Lis45_virgin_rep2_small

description: small RNA-seq

tag: cell type

value: naive

value: virgin


title: Lis39_early_primed_rep3_small

description: small RNA-seq

value: human embryonic stem cell


title: donor 9 - 1


title: 201502860016_R02C01

tag: bcell

tag: mono


title: 201172200040_R03C01

tag: gran

tag: cohort


title: Lis39_early_primed_rep2_small

description: small RNA-seq


title: donor 8 - 7

tag: tissue

value: frozen, 1week , microwave


title: 201800470008_R03C01

tag: eos


title: Lis39_late_primed_rep3_small

description: small RNA-seq

value: late


title: donor 8 - 4

value: human breast milk

value: refrigerator, 1week,

tag: treatment


title: 201502870005_R02C01

tag: diagnosis

value: F


title: Lis39_late_naive_rep3_small

description: small RNA-seq


title: 201502870046_R03C01

tag: gender


title: 201800470020_R05C01

value: M


title: 201172200051_R05C01

value: MDD


title: Lis39_late_naive_rep2_small

description: small RNA-seq

tag: Sex


title: donor 8 - 8

tag: protocol

value: frozen, 4week , bottle warmer


title: Lis39_late_naive_rep1_small

description: small RNA-seq

tag: culture conditions


title: donor 8 - 6


title: 201172200006_R05C01

tag: age

tag: nk

value: Cohort 2


title: Lis39_early_primed_rep1_small

description: small RNA-seq

tag: cell line

value: primed

value: early


title: 201172200036_R02C01

tag: subject


title: 201810150025_R06C01


title: 201810150022_R06C01


title: 201172200006_R01C01


title: 201810150038_R05C01


title: 201172200003_R04C01


title: Lis39_early_naive_rep2_small

description: small RNA-seq

tag: cell type

tag: timepoint


title: 201810150079_R01C01

tag: bcell

tag: mono


title: Lis39_early_naive_rep1_small

description: small RNA-seq


title: 201172200059_R06C01

tag: gran

tag: cohort


title: 201172200027_R03C01

tag: eos


title: Lis39_virgin_rep3_small

description: small RNA-seq


title: donor 7 - 7

tag: tissue

value: milk cell

tag: treatment


title: Lis39_virgin_rep2_small

description: small RNA-seq


title: 201172200028_R01C01

tag: diagnosis

tag: gender


title: 201172200001_R05C01


title: 201172200003_R05C01


title: donor 8 - 3

tag: protocol

value: room temperature, 1week

value: not applicable


title: donor 7 - 4


title: Lis39_early_naive_rep3_small

description: small RNA-seq

tag: Sex

value: female

tag: culture conditions

value: naive


title: donor 8 - 2

value: microwave


title: 201172200025_R08C01

value: Not depressed

tag: age

tag: nk


title: donor 8 - 1

value: control, fresh sample


title: 201810150040_R05C01

tag: subject


title: donor 7 - 8

value: human breast milk

tag: cell type


title: 201172200022_R01C01


title: Lis38_late_primed_rep3_small

description: small RNA-seq

tag: cell line

value: human embryonic stem cell

value: male

tag: timepoint

value: late


title: donor 7 - 2


title: 201172200001_R07C01

value: HC

value: F

tag: bcell

tag: mono


title: donor 7 - 6

value: frozen, 1week , bottle warmer


title: 201172200006_R02C01

value: MDD

tag: gran

tag: cohort

value: Cohort 2


title: donor 6 - 8

tag: tissue

value: milk cell

value: frozen, 4week , bottle warmer


title: Lis39_virgin_rep1_small

description: small RNA-seq

value: virgin


title: donor 7 - 1

tag: treatment

value: not applicable


title: 201502870055_R03C01

tag: diagnosis

tag: eos


title: 201172200024_R01C01

tag: gender


title: 201172200005_R06C01


title: 201810150041_R05C01


title: donor 6 - 7

tag: protocol

value: frozen, 1week , microwave


title: Lis38_late_primed_rep2_small

description: small RNA-seq

tag: Sex

tag: culture conditions

value: primed


title: Lis38_early_primed_rep3_small

description: small RNA-seq

value: early


title: 201810150040_R04C01

tag: age

tag: nk


title: Lis38_early_primed_rep2_small

description: small RNA-seq

tag: cell type


title: 201172200019_R06C01

tag: subject


title: donor 6 - 6


title: donor 7 - 3

value: room temperature, 1week


title: 201172200059_R04C01


title: 201172200021_R06C01

value: M


title: donor 6 - 4

value: human breast milk

value: refrigerator, 1week,


title: Lis38_early_primed_rep1_small

description: small RNA-seq

tag: cell line

value: human embryonic stem cell

value: male

tag: timepoint


title: 201800470033_R01C01

value: F

tag: bcell

tag: mono


title: Lis38_late_primed_rep1_small

description: small RNA-seq

value: late


title: Lis38_late_naive_rep3_small

description: small RNA-seq

value: naive


title: 201172200019_R07C01

value: HC

tag: gran

tag: cohort

value: Cohort 2


title: 201172200053_R08C01

value: MDD


title: donor 6 - 3

tag: tissue

value: milk cell

tag: treatment


title: 201800470022_R04C01

tag: diagnosis

tag: eos


title: Lis38_late_naive_rep2_small

description: small RNA-seq


title: 201800470022_R06C01

tag: gender


title: 201172200028_R03C01


title: Lis38_late_naive_rep1_small

description: small RNA-seq

tag: Sex


title: 201502870027_R04C01


title: 201810150022_R07C01


title: 201502870058_R04C01


title: 201172200055_R02C01


title: donor 5 - 8

tag: protocol

value: frozen, 4week , bottle warmer

value: not applicable


title: Lis38_early_naive_rep3_small

description: small RNA-seq

tag: culture conditions


title: 201172200040_R07C01

tag: age

tag: nk


title: 201810150041_R08C01

tag: subject


title: 201172200019_R05C01


title: 201172200004_R05C01


title: donor 5 - 6

tag: cell type

value: frozen, 1week , bottle warmer


title: Lis38_early_naive_rep1_small

description: small RNA-seq

tag: cell line

tag: timepoint

value: early


title: donor 5 - 3

value: room temperature, 1week


title: 201810150050_R03C01

tag: bcell

tag: mono


title: 201800470037_R08C01

tag: gran

tag: cohort


title: Lis38_virgin_rep2_small

description: small RNA-seq

value: virgin


title: 201172200004_R04C01


title: 201810150025_R05C01


title: donor 6 - 1

tag: tissue

value: human breast milk

value: control, fresh sample

tag: treatment


title: 201810150025_R08C01

tag: diagnosis

tag: eos


title: Lis38_virgin_rep1_small

description: small RNA-seq

value: human embryonic stem cell

tag: Sex


title: donor 6 - 2

tag: protocol

value: microwave


title: donor 5 - 2


title: donor 5 - 1


title: donor 5 - 7

value: frozen, 1week , microwave


title: Lis38_early_naive_rep2_small

description: small RNA-seq

value: male

tag: culture conditions


title: Lis46_late_primed_rep3

data_processing:
Reads were mapped to GRCh38.p10 (GENCODE release 26) using STAR (v. 2.7.3a)
Reads were annotated using featureCounts (subread v.1.6.3, GENCODE release 26 primary assembly annotation)
The STAR parameters used were: --runMode alignReads --outSAMmode Full --outSAMattributes Standard --genomeLoad LoadAndKeep --clip3pAdapterSeq AGATCGGAAGAGC --clip3pAdapterMMp 1. The featureCounts parameters were: -s 2 -p -t exon -T 13 -g gene_id.
Ensembl genes without at least three samples with more than 10 reads were removed from the analysis leaving about 20k genes. BiomaRt (v. 2.42.1) was used to convert Ensembl gene ID’s to HUGO gene names.
The R (v. 3.6.3) package DESeq2 (v.1.26.0) (Love, Huber and Anders, 2014), using a multifactor design formula to account for experimental design variables, was used to perform differential expression analysis and normalize the count matrix.
Assembly: GRCh38.p10 (GENCODE release 26)
Supplementary files format and content: tab-delimited text files include DESeq2 normalized counts for each sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using mirVana miRNA Isolation Kit (Life Technologies, Inc.), following the manufacturers' instructions. RNA quality was assessed using a BioAnalyzer 2100 (Agilent Technologies, Inc.). All samples had a RIN greater than 8.5.
RNA-seq libraries were constructed in triplicate using the KAPA mRNA HyperPrep Kit (Roche) with 500 ng of input RNA according to the manufacturers instructions.

value: primed

value: late


title: 201502860016_R04C01

tag: gender

value: F

tag: age

value: Cohort 2


title: 201172200027_R06C01

value: MDD

tag: nk

tag: subject


title: 201172200028_R02C01


title: Lis46_late_primed_rep2

tag: cell line

tag: cell type


title: 201172200028_R08C01

value: M

tag: bcell


title: Lis46_late_primed_rep1

tag: timepoint


title: 201800470022_R08C01

value: HC

tag: mono

tag: gran


title: Lis38_virgin_rep3_small

description: small RNA-seq

value: naive


title: 201810150071_R04C01

tag: cohort


title: 201810150041_R06C01


title: 201172200021_R03C01


title: donor 4 - 6

tag: tissue

value: milk cell

value: frozen, 1week , bottle warmer

tag: treatment

value: not applicable


title: 201810150050_R02C01

tag: diagnosis

tag: eos


title: 201800470019_R05C01


title: Lis46_early_primed_rep2

tag: Sex

value: early


title: donor 4 - 2

value: human breast milk

tag: protocol


title: 201502870011_R07C01

tag: gender


title: Lis46_late_naive_rep3

value: human embryonic stem cell

tag: culture conditions


title: Lis46_early_primed_rep1


title: 201172200006_R06C01

tag: age

tag: nk


title: donor 4 - 8

value: frozen, 4week , bottle warmer


title: 201502860016_R05C01

tag: subject


title: 201800470036_R04C01


title: Lis46_late_naive_rep2

tag: cell line

tag: cell type


title: donor 4 - 7

value: frozen, 1week , microwave


title: 201172200028_R06C01

tag: bcell


title: Lis46_late_naive_rep1

value: male

tag: timepoint


title: donor 3 - 7


title: donor 3 - 8


title: donor 3 - 6


title: 201800470036_R08C01

tag: mono

tag: gran


title: 201810150038_R07C01

tag: cohort


title: 201810150041_R07C01


title: donor 4 - 1

tag: tissue

value: control, fresh sample

tag: treatment


title: Lis46_early_naive_rep3


title: Lis46_early_primed_rep3

value: primed


title: donor 4 - 3

value: room temperature, 1week


title: 201810150050_R01C01

tag: diagnosis

tag: eos

value: Cohort 2


title: 201172200013_R02C01

value: MDD

value: F


title: 201172200024_R02C01


title: donor 3 - 4

tag: protocol

value: refrigerator, 1week,


title: Lis46_early_naive_rep2

tag: Sex

value: naive


title: donor 3 - 3

value: milk cell


title: 201810150070_R08C01

tag: gender


title: 201502870055_R01C01

tag: age


title: 201172200001_R06C01

value: HC

tag: nk


title: 201172200045_R03C01

tag: subject


title: 201502860016_R03C01


title: donor 3 - 2

value: microwave

value: not applicable


title: Lis46_early_naive_rep1

tag: cell line

tag: culture conditions

value: early


title: Lis46_virgin_rep3

tag: cell type

value: human embryonic stem cell

value: virgin


title: 201800470030_R01C01

tag: bcell


title: donor 3 - 1

value: human breast milk


title: 201502860016_R06C01

tag: mono


title: donor 2 - 8

value: frozen, 4week , bottle warmer


title: 201172200059_R07C01

tag: gran


title: Lis45_late_primed_rep3

value: female

tag: timepoint

value: late


title: 201502860016_R07C01

tag: cohort


title: Lis45_late_primed_rep2

value: primed


title: 201172200021_R05C01

value: Cohort 2


title: 201172200024_R05C01

value: MDD


title: donor 2 - 7

tag: tissue

value: frozen, 1week , microwave

tag: treatment


title: donor 2 - 6

value: frozen, 1week , bottle warmer


title: 201172200006_R04C01

tag: diagnosis

value: F

tag: eos


title: Lis46_virgin_rep2

tag: Sex

value: male

value: naive


title: 201172200028_R04C01

tag: gender


title: donor 2 - 4

value: milk cell

tag: protocol

value: refrigerator, 1week,


title: 201800470008_R02C01

tag: age

tag: nk


title: Lis45_late_primed_rep1

tag: cell line


title: 201810150022_R05C01

tag: subject


title: donor 2 - 3

tag: cell type

value: room temperature, 1week

value: not applicable


title: Lis45_early_primed_rep3

value: human embryonic stem cell

tag: culture conditions

value: early


title: 201172200025_R01C01

tag: bcell

tag: mono


title: 201800470033_R02C01

tag: gran


title: donor 2 - 2

value: human breast milk

value: microwave


title: 201172200004_R08C01

value: Excluded

value: M

tag: cohort


title: Lis45_early_primed_rep2

value: female

value: primed

tag: timepoint


title: 201172200055_R01C01

value: MDD

value: Cohort 2


title: 201172200016_R04C01

value: F


title: Lis46_virgin_rep1

value: male

value: virgin


title: donor 2 - 1

tag: tissue

value: milk cell

value: control, fresh sample

tag: treatment


title: donor 1 - 8

value: frozen, 4week , bottle warmer


title: 201800470020_R04C01

tag: diagnosis

tag: eos


title: Lis45_late_naive_rep3

tag: Sex

value: naive

value: late


title: 201172200013_R01C01

tag: gender


title: 201172200025_R02C01

tag: age


title: donor 1 - 7

tag: protocol

value: frozen, 1week , microwave

value: not applicable


title: 201800470036_R06C01

tag: nk


title: 201172200005_R07C01

value: HC

tag: subject


title: 201172200050_R08C01


title: 201172200004_R02C01


title: Lis45_early_naive_rep3

tag: cell line

tag: cell type

value: human embryonic stem cell

value: early


title: Lis45_late_naive_rep2

value: female

tag: culture conditions


title: donor 1 - 3

value: human breast milk

value: room temperature, 1week


title: donor 1 - 4

value: refrigerator, 1week,


title: 201800470008_R01C01

value: MDD

value: F

tag: bcell

tag: mono

value: Cohort 2


title: Lis45_late_naive_rep1


title: 201810150072_R01C01

tag: gran

tag: cohort


title: 201800470036_R05C01


title: donor 1 - 6

tag: tissue

value: milk cell

value: frozen, 1week , bottle warmer


title: 201172200028_R05C01


title: Lis45_early_naive_rep2

tag: timepoint


title: Lis45_early_primed_rep1

value: primed


title: 201172200021_R01C01

tag: diagnosis


title: donor 1 - 2

value: microwave

tag: treatment


title: donor 1 - 1

value: control, fresh sample


title: 201800470021_R06C01

value: M

tag: eos


title: Lis45_early_naive_rep1

tag: Sex

value: naive


title: Lis45_virgin_rep3

value: virgin


title: 201810150038_R08C01

tag: gender

tag: age


title: 201502860016_R08C01

tag: nk


title: 201502870055_R02C01

tag: subject


title: Lis45_virgin_rep2

tag: cell line

value: human embryonic stem cell


title: 201172200016_R08C01


title: Lis45_virgin_rep1

tag: cell type


title: 201172200004_R01C01


title: AD3, Alzheimer's disease, monocytes

city: Sherbrooke

first: Mariano

last: Avino

address: 3201 Jean Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Sherbrooke University

data_processing:
Quality control of RNA-seq data was performed using FastQC (version 0.11.5) with default parameters.
Trimming of the reads was achieved using TrimGalore (version 0.6.6) with default parameters.
Reads were mapped to the mouse genome (GRCh38, GCF_000001405.39_GRCh38.p13_genomic, primary assembly) with Rsubread (version 2.10.4) function Align. Align was used with default parameters except for –sortReadsByCoordinates = TRUE.
The evaluation of gene expression of raw counts was done using with Rsubread (version 2.10.4) function featureCounts. featureCounts was used with default parameters except for: isPairedEnd = F, isGTFAnnotationFile = T, GTF.attrType = "gene_name".
The evaluation of gene expression of TMM was done using with edgeR (version 3.38.2) function cpm. cpm was used with default parameters except for: normalized.lib.sizes=FALSE.
Supplementary files format and content: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts and TMM values for each sample

source_name: Monocytes

extract_protocol:
Monocytes were first homogenized in 500µL of cold TRIzol and then 500µL of chloroform:isoamyl alcohol 24:1 (Sigma Aldrich) were added. Samples were vortexed for 20 seconds and incubated 2 min at room temperature. The samples were then centrifuged at 10,000g for 18 min at 4°C. The aqueous phase, that contains RNAs, was transferred in a new Eppendorf tube. An equal volume of ethanol 100% was added and the mixture was then loaded into a Zymo-Spin™ IIICG Column from the Quick-RNA™ Miniprep Kit. Further steps were conducted according to the manufacturer’s protocol. The RNA concentration in ng/µL was determined using a Nanodrop system (Thermo Fisher Sscientific).
Library preparation was initiated with 10ng of total RNA.
RNA-seq libraries were prepared using NEBNext® single cell/low input RNA library preparation Kit (New England Biolabs).

value: Monocytes

tag: age of_individual_(years)

value: male

tag: subject status

value: Alzheimer's disease


title: AD2, Alzheimer's disease, monocytes


title: 201172200003_R07C01

tag: bcell

tag: mono


title: 201172200024_R06C01

tag: gran

tag: cohort


title: Lis39_late_primed_rep3

value: female

tag: culture conditions

tag: timepoint

value: late


title: 201810150068_R01C01

tag: diagnosis

value: MDD


title: MCI5, Mild Cognitive Impairment, monocytes

value: Mild Cognitive Impairment


title: 201800470021_R03C01

tag: eos

value: Cohort 2


title: Lis39_late_primed_rep2

tag: Sex


title: 201810150022_R02C01

tag: gender

value: F


title: MCI3, Mild Cognitive Impairment, monocytes


title: 201800470034_R06C01

value: HC

tag: age


title: Lis39_late_primed_rep1

value: primed


title: 201172200055_R08C01

tag: nk


title: 201172200044_R03C01

tag: subject


title: 201800470021_R07C01


title: H3B, Healthy, monocytes

value: Healthy


title: Lis39_early_primed_rep3

tag: cell line

value: early


title: H4B, Healthy, monocytes

tag: cell type


title: Lis39_early_primed_rep2


title: 201172200001_R08C01


title: Lis39_early_primed_rep1


title: HHEX_shRNA_rep1_2

first: Zhongyun

address: 1665 Kongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific), Agilent 2100 Bioanalyzer and 2100 RNA nano 6000 assay kit (Agilent Technologies)  were used to quantify and qulify RNA sample
The RNA with poly-A in eukaryotic total RNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN) and TIANSeq  Fast RNA Library Kit (Illumina) was used to construct the transcriptome sequencing libraries.
Library concentration was first quantified using Qubit 2.0 fluorometer (Life Technologies), and checking insert size on an Agilent 2100 and quantifying to greater accuracy by quantitative PCR (Q-PCR) (library activity >2 nM).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions
Assembly: three biological replicates per cell infection HHEX/CTRL shRNA virus
Supplementary files format and content: tab-delimited text files include log2 counts per million (CPM) values for each Sample

source_name: Thyroid

growth_protocol: 1x106 cells/well were plated in 6-well plate and placed in a 5% CO2 37 °C incubator for 24 hours

extract_protocol:
RNA was isolated by Trizol.
libraries were prepared using the TIANSeq mRNA Capture Kit (TIANGEN) and TIANSeq Fast RNA Library Kit (Illumina), according to the manufacturer’s instructions.

treatment_protocol: Not applicable

value: human thyroid cancer cells

tag: tissue

value: Thyroid

tag: genotype

value: HHEX KD

tag: treatment

value: untreated


title: HHEX_shRNA_rep1_1


title: 201172200040_R06C01

tag: bcell

tag: mono


title: HHEX_shRNA_rep2_1


title: 201800470019_R07C01

value: M

tag: gran

tag: cohort


title: 201172200044_R02C01


title: 201172200012_R07C01


title: 201172200025_R05C01


title: 201800470034_R03C01


title: Lis39_late_naive_rep2

value: human embryonic stem cell

tag: culture conditions

value: naive

tag: timepoint


title: 201172200025_R03C01

tag: diagnosis

tag: eos


title: CTRL_shRNA_rep2_1

value: wild-type


title: Lis39_late_naive_rep3

tag: Sex

value: female

value: late


title: CTRL_shRNA_rep1_2


title: 201172200040_R08C01

value: MDD

tag: gender

tag: age


title: CTRL_shRNA_rep1_1


title: 201800470034_R08C01

tag: nk

tag: subject

value: Cohort 2


title: 201800470034_R05C01

value: F


title: Lis39_early_naive_rep3

tag: cell line

tag: cell type


title: 201172200044_R08C01

value: Excluded


title: Lis39_late_naive_rep1


title: 201172200021_R08C01

value: HC


title: S21, CVID_N, rep 5

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

country: Norway

institute: Oslo University Hospital

data_processing:
The clean reads were aligned to reference human genome GRCh38 by HISAT.
The transcripts from all samples were futher assembled and merged using StringTie.  The  rows with MSTRG* geneIDs represent the novel assembling transcripts, which are not found in reference human genome annotation.  These IDs name were generated  automatically by software StringTie,  please refer the weblink for this software: https://ccb.jhu.edu/software/stringtie/.
The DESeq2 tool was used to normalize counts and identify the differentially expressed genes.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: duodenal biopsies

extract_protocol:
RNA extracted by AllPrep DNA/RNA/Protein mini-Kit.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Nondirectioanl RNA library kit with PolyA selection following manufacturer's protocols.

tag: tissue

value: duodenal biopsies

tag: disease state


title: S20, CVID_N, rep 4


title: 201800470034_R02C01

tag: bcell


title: 201800470020_R01C01

tag: mono


title: Lis39_early_naive_rep1

value: early


title: Lis39_early_naive_rep2


title: 201800470020_R02C01

tag: gran


title: 201800470034_R04C01

tag: cohort


title: S18, control, rep 4

value: control


title: 201800470020_R08C01


title: Lis39_virgin_rep2

tag: culture conditions

value: virgin


title: 201800470034_R07C01


title: Lis39_virgin_rep3

tag: timepoint


title: S19, control, rep 5


title: 201172200055_R06C01

tag: diagnosis


title: S17, control, rep 3


title: Lis39_virgin_rep1


title: S16, control, rep 2


title: 201172200060_R08C01

tag: eos


title: 201810150072_R03C01


title: Lis38_late_primed_rep3

tag: Sex

value: male

value: primed


title: Lis38_late_primed_rep2


title: S15, control, rep 1


title: S14, celiac, rep 4

value: celiac


title: Scr4-CTCF

description:
Scr4-CTCF
Scr3-CTCF.subtract.bw

tag: genotype

value: Parental

tag: treatment

value: Control siRNA

tag: chip antibody

value: RAD21, Abcam ab992


title: Lis38_late_primed_rep1

value: human embryonic stem cell


title: S12, celiac, rep 2


title: 201172200012_R08C01

tag: gender

tag: age

tag: nk

tag: subject


title: Lis38_early_primed_rep2

tag: cell line

tag: cell type


title: Day28,ReprogIII

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

data_processing:
Libraries were sequenced on the NovaSeq-S2 platform following the manufacturer’s protocols. Sequencing data were aligned to the Hg38 genome using BSMAP. Adapters were trimmed from FASTQ sequences (trimglore) and mapped to the hg38 genome using the BSMAP v. 2.74 software.
CpGs were extracted by the methratio.py in the BSMAP package.
Assembly: hg38
Supplementary files format and content: methylated ratios for all detected cpgs

source_name: Cord blood

growth_protocol: Human cord blood mononuclear cells (CBMCs) were isolated and CD8+ T cells were expanded in vitro by TCR stimulation (soluble anti-CD3) from day 0-7 (acute) or day 0-28 (chronic).

extract_protocol:
Human CD8+ T cells were sorted on days 0 (naïve), 7, and 28, and genomic DNA was extracted and bisulfite-treated to convert unmethylated cytosine to uracil residues using the EZ DNA Methylation-Direct Kit (Zymo).
DNA libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer’s protocol. The libraries were purified by the AMPureXP Beads followed by QC using Qubit method, and the purified DNA was captured on an Illumina flow cell for cluster generation.

treatment_protocol: CD8+ T cells under chronic stimulation were treated with TGFB1 (5 ng/ml) starting from day 7. Reprogrammed treatments were added to TGFB1 treated cells starting from day 14 as follows: TGFR1i (Reprog.I), TGFBR1i+BMPa (Reprog.II), TGFBR1i+BMPa+Vitamin C (starting from day 21) (Reprog.III).

tag: tissue

value: Cord blood


title: Day28,ReprogII


title: S11, celiac, rep 1

tag: disease state


title: Day0,Naïve

value: No treatment


title: Day7,Effector

value: Acute TCR


title: Day28,ReprogI


title: Day28,ChronicTCR

value: Chronic TCR


title: Lis38_early_primed_rep1


title: S10, CVID_IEL, rep 7


title: S09, CVID_IEL, rep 6


title: Day28,AcuteTCR


title: Lis38_late_naive_rep3

value: naive

value: late


title: Day28,Dysf


title: Scr4-Input

description:
Scr4-Input
Scr4-CTCF.subtract.bw
Scr4-CTCF.bed

value: none; input


title: S07, CVID_IEL, rep 4

value: duodenal biopsies


title: Lis38_early_primed_rep3

value: early


title: S13, celiac, rep 3


title: Lis38_late_naive_rep1


title: Lis38_early_naive_rep3


title: Lis38_late_naive_rep2


title: Lis38_early_naive_rep2


title: Lis38_early_naive_rep1


title: S06, CVID_IEL, rep 3


title: S08, CVID_IEL, rep 5


title: Lis38_virgin_rep3

value: virgin


title: S04, CVID_N, rep 2


title: S03, CVID_IEL, rep 2


title: Lis38_virgin_rep2

value: male


title: S02, CVID_IEL, rep 1


title: S05, CVID_N, rep 3


title: 3D-Plasma-V1-309

city: Chicoutimi

first: Luigi

last: Bouchard

state: Quebec

address: 305 rue Saint-Vallier, Pavillon des Augustines

department: Biochimie et génomique fonctionnelle

institute: Université de Sherbrooke

description:
309
3D-Plasma-V1-309

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with FASTX-Toolkit. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using STAR. As rRNA contamination was almost inexistant in our samples (average of 1.04±0.90% of total mapped reads based on metrics from STAR), the mapping step to the rRNA was removed to speed tup the process.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple sample (PMID : 30956140).
Samples with < 1M miRNAs reads were considered outliers and removed from the downstream analysis (differential analysis using DESeq2 package).
DESeq2 function collapseReplicates was used to combined technical replicates in the analysis for data that were extracted and sequenced twice. Technical replicate have the same ID and fastq files contains either "pilote" or "projet". Technical replicate are identified in the technical replicates column (N = 12 originally, 9 gave consent for genetic data sharing)
Assembly: GRCh37
Supplementary files format and content: tab-seperated value files include raw read counts (non-normalized) for each Sample
Supplementary files format and content: 3D_Plasma_miRNA_v1_geo_rawcounts.txt

source_name: Plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from either 500μl of plasma kept at −80 °C until extraction. Seventy-five μl of nuclease-free water was used to eluate total RNA which was then precipitated following the method described by Burgos et al. (PMID: 23525801). Briefly, 35 μl of cold (4°C) 7 M ammonium acetate solution (ThermoFisher Scientific, catalogue # 02002268) were added to 70μl of total RNA. This was followed by the addition of 420μl of chilled (−20°C) absolute ethanol (Commercial Alcohols, ON, Canada; catalogue # P006EAAN) and overnight precipitation at −20°C. The mix was then centrifuged at 16 000g at 4°C for 30 min. RNA pellets were then washed twice with 200 μl of cold 80% ethanol followed by centrifugation at 16 000g at 4°C for 5min. It was then dried for 30min at room temperature and 5μl of nuclease-free water was added. The total volume was used for library preparation.
Samples were randomized before library preparation. An adapted version of the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) protocol from Burgos et al. (PMID: 23525801) was used to manage low concentrated miRNA samples. In this protocol, half of the standard volumes were used for ligation (3′ and 5′ ends) of RNA sample (5μl), reverse transcription, barcoding (index 1-20: one index per sample) and PCR amplification (15 cycles) to preserve the ratio between RNA amount (which is lower in plasma samples) and the reagents. Purification and size-selection (145-160bp) of the libraries were done by migration on a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, catalogue # EC6265BOX) followed by elution in 300 μl of nuclease-free water and overnight incubation at 500 RPM at room temperature on an incubating microplate shaker (VWR, ON, Canada, catalogue #12620-930). The libraries were then precipitated according to the manufacturer's instructions (including incubation of the precipitation mix at −80°C for 30min) and were resuspended in 25 μl of 10 mM Tris-HCI pH 8.5 buffer. Library sequencing, including quality control and sample pooling, was performed at the McGill University and Génome Québec Innovation Centre (Québec, Canada). Libraries were first quantified using the Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) and the average size fragment was determined using a LabChip GX II (PerkinElmer) instrument. The libraries were normalized and pooled before being denatured in 0.05N NaOH and neutralized using HT1 buffer. The pool was loaded at 225pM on an Illumina NovaSeq S1 lane using Xp protocol as per the manufacturer’s recommendations. The run was performed for 1x100 cycles (single-end mode). A phiX library was used as a control and mixed with libraries at 1% level. Base calling was performed with RTA v3. Program bcl2fastq2 v2.20 was then used to demultiplex samples and generate fastq reads. Ten samples were extracted and sequenced twice to account for batch preparation and to confirm standardization.

value: Plasma

value: female

tag: pregnancy status_1

value: Other pregnancy complications


title: 3D-Plasma-V1-321

description:
321
3D-Plasma-V1-321


title: 3D-Plasma-V1-313

description:
313
3D-Plasma-V1-313


title: 3D-Plasma-V1-316

description:
316
3D-Plasma-V1-316

value: Normal


title: 3D-Plasma-V1-323

description:
323
3D-Plasma-V1-323


title: 3D-Plasma-V1-311

description:
311
3D-Plasma-V1-311


title: 3D-Plasma-V1-322

description:
322
3D-Plasma-V1-322


title: 3D-Plasma-V1-315

description:
315
3D-Plasma-V1-315


title: 3D-Plasma-V1-308

description:
308
3D-Plasma-V1-308


title: 3D-Plasma-V1-318

description:
318
3D-Plasma-V1-318


title: 3D-Plasma-V1-319

description:
319
3D-Plasma-V1-319


title: 3D-Plasma-V1-324

description:
324
3D-Plasma-V1-324


title: 3D-Plasma-V1-325

description:
325
3D-Plasma-V1-325


title: 3D-Plasma-V1-320

description:
320
3D-Plasma-V1-320


title: 3D-Plasma-V1-314

description:
314
3D-Plasma-V1-314


title: 3D-Plasma-V1-312

description:
312
3D-Plasma-V1-312


title: 3D-Plasma-V1-317

description:
317
3D-Plasma-V1-317


title: S01, CVID_N, rep 1


title: 2 Whole Cell Extract

city: Rehovot

first: Idit

last: Shachar

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19)
Bound regions were detected using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS2 peaks

source_name: Human Primary Periphheral Blood B Cells

growth_protocol: Primary B cells were isolated from freshly received blood donations.

extract_protocol: In-house ChIP-Seq protocol, Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of y samples on one lane.

treatment_protocol: anti-CD74 activating antibody was added to 10^7 cells for 1 hour. Then samples 1 Vehicle, 1 CD74 activated, 2 Vehicle and 2 CD74 activated underwent IP with anti-H3K4me2 antibody (ab-32356 ).

value: B cells

tag: activating antibody

value: No Treatment


title: 3D-Plasma-V1-310

description:
310
3D-Plasma-V1-310


title: 3D-Plasma-V1-305

description:
305
3D-Plasma-V1-305

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-306

description:
306
3D-Plasma-V1-306


title: 3D-Plasma-V1-307

description:
307
3D-Plasma-V1-307


title: 2 CD74 activated

value: Human Recombinant MIF (100 ng/ml)

value: 8 hours activation


title: Lis38_virgin_rep1

value: human embryonic stem cell

tag: culture conditions

tag: timepoint


title: 3D-Plasma-V1-303

description:
303
3D-Plasma-V1-303


title: 2 Vehicle

value: Vehicle

value: 8 hours incubation


title: 3D-Plasma-V1-302

description:
302
3D-Plasma-V1-302


title: L1C5c_t20_B10

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
library strategy: Exome-seq
Illumina BCL files were processed using bcl2fastq v2.20.0.422
alignment, SNV/indel and CNV analysis were run using nfcore/sarek pipeline (v2.6.1)
Reads were trimmed using TrimGalore
Reads were aligned using BWA mem
Treatment specfic SNVs/Indels were called using Mutect2 and Strelka
CNVkit was used to identify CNV
SNVs/Indels were annotated using SNPEff
Genome_build: GRCh38
Supplementary_files_format_and_content: VCF files containing annotated treatment specfic SNVs/Indels
Supplementary_files_format_and_content: tbi VCF index files
Supplementary_files_format_and_content: CNS files containing segmented copy number regions

source_name: NSCLC cells LXFL 1674

growth_protocol: PDX MeA5a and L1C5c cells were grown in RPMI medium containing 15% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Genomic DNA was extracted with a kit-free protocol based on cell lysis followed by ethanol extraction (see paper for a detailed version)
For whole exome sequencing, Genomic DNA (gDNA) samples were quantified using the Promega QuantiFluor dsDNA system on the GloMax Multi Detection System following the manufacturer’s guidelines. Samples were qualified using the Agilent Genomic DNA ScreenTape System run on the TapeStation 4200 according to the manufacturer’s instructions. Subsequently, gDNA was fragmented using Covaris LE220-plus focused ultrasonicator and then prepared into libraries using the NEBNext Ultra II DNA library prep kit according to manufacturer’s instructions.  Libraries were then combined in 8-plex and exonic regions enriched via hybridisation using the Twist Human Core Exon kit according to the manufacurer’s instructions.  Libraries were sequenced on the HiSeq 4000 using paired end 100 bp reads.

treatment_protocol: During nutrient starvation cells were washed from L-glut rich media and cultured  for 20 days in RPMI without glutamine (ThermoFisher Scientific #21870076). Media wash refreshed every 3 days.

value: NSCLC cells LXFL 1674

value: Glutamine deprivation

tag: time point

value: DAY 20


title: 1 Whole Cell Extract


title: L1C5c_t20_C5


title: 4 Control

data_processing:
Reads were trimmed using cutadapt
After trimming the reads were mapped to the human genome
Deduplication was carried out by flagging all reads that were mapped to the same gene and had the same UMI
Counting proceeded over genes (1000 bases of the 3’ UTR) using htseq-count
Normalization and differential expression was performed using DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes the normalized counts and DESeq2 output

extract_protocol:
total RNA was extracted using Quiagen's RNAeasy mini kit.
Bulk MARS-Seq protocol
RNA-Seq (3') UMI appears in Read2

treatment_protocol: 10^7 cells were activatied/incubated for 8 hours either with hrMIF or with vehicle.

tag: activating molecule


title: 3D-Plasma-V1-304

description:
304
3D-Plasma-V1-304

tag: Sex


title: 1 CD74 activated

tag: treatment


title: L1C5c_t0

value: No treatment

value: DAY 0


title: MeA5a_t20_F8

source_name: Melanoma cells MEXF 2090

value: Melanoma cells MEXF 2090


title: L1C5c_t20_B8


title: MeA5a_t20_F3


title: MeA5a_t20_E6


title: 3 Control


title: 4 Activated

value: Human Recombinant MIF (100ng/ml)


title: 1 Vehicle


title: 3D-Plasma-V1-291

description:
291
3D-Plasma-V1-291

value: Plasma

value: female


title: 3D-Plasma-V1-293

description:
293
3D-Plasma-V1-293

value: Normal


title: 3D-Plasma-V1-299

description:
299
3D-Plasma-V1-299


title: 3D-Plasma-V1-290

description:
290
3D-Plasma-V1-290


title: 3D-Plasma-V1-298

description:
298
3D-Plasma-V1-298


title: 3D-Plasma-V1-297

description:
297
3D-Plasma-V1-297


title: MeA5a_t20_B2


title: 3D-Plasma-V1-300

description:
300
3D-Plasma-V1-300

tag: pregnancy status_2

value: Other pregnancy complications


title: 3D-Plasma-V1-292

description:
292
3D-Plasma-V1-292


title: 3D-Plasma-V1-294

description:
294
3D-Plasma-V1-294

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-295

description:
295
3D-Plasma-V1-295


title: 3D-Plasma-V1-296

description:
296
3D-Plasma-V1-296


title: 3D-Plasma-V1-301

description:
301
3D-Plasma-V1-301


title: MeA5a_t0


title: 3 Activated

value: B cells


title: 3D-Plasma-V1-285

description:
285
3D-Plasma-V1-285


title: 3D-Plasma-V1-286

description:
286
3D-Plasma-V1-286


title: 3D-Plasma-V1-288

description:
288
3D-Plasma-V1-288


title: Multiplexed_sample_crispr_Day12 [LOU523A8]

description:
LOU523A8_S14
processed data file: LOU523A4_LOU523A8.tar.gz

data_processing:
Sequencing libraries were sequenced on Illumina HiSeq4000.
CellRanger 3.0.2 was used to convert BCL to fastq, quantify both transcriptome and CRISPR libraries and call usable cells.
sgRNA demultiplexing: We used the 6 CRISPR guide counts to assign the cell type label to all cells. All cells from the four time points were analysed together.  Only the counts of the 6 CRISPR guide genes were used to assign the cell type to each cell.  Firstly, we removed all cells with empty CRISPR guide genes (all zeros) because they could not be assigned.  We applied a multinomial logistic regression model to assign cell labels. The cells with only one CRISPR gene counts different from zero were assigned to the corresponding cell type, and used to fit the logistic regression model. CRISPR gene counts were normalised by dividing by the total counts of the gene across all cells. The model, fitted using caret1 package for R, was used to predict the assignment probability of cells with two or more non-zeros CRISPR gene counts. Cells with a predicted probability greater than 95% were assigned to the corresponding label. The other cells were considered ambiguous and therefore removed from the dataset.
Filtering of low-quality cells: We applied an iterative procedure to identify and remove low-quality cells and noise genes from the gene counts of the labelled cells of the four time points.  At each iteration, the procedure:  1. removed genes detected in less than 20 cells (across all time points)  2. removed cells with small total counts and a small number of detected genes  3. removed cells with a high percentage of Mitochondrial genes counts2  The three steps were repeated until no further cell or gene was removed from the dataset.  For each filter, we used the median absolute deviation (MAD) to identify the threshold. A value greater (resp. smaller) than 3 MADs from the median was considered an outlier and added to the filtered set.
Normalization: The filtered dataset consisting of the four time-points cells was normalised using the scran3 package for R.  The scaling factors were firstly estimated on clusters identified by the function quickCluster, and then deconvoluted using the function calculateSumFactors. The same results were obtained by using the function computeSumFactors.
Genome_build: GRCh38
Supplementary_files_format_and_content: per-sample tar file containing cellranger matrix, feature and barcode data
Supplementary_files_format_and_content: new_raw_full.rds ; R rds file containing transcriptome UMI count matrix
Supplementary_files_format_and_content: new_scran_full.rds ; R rds file containing scran normalised transcriptome UMI count matrix
Supplementary_files_format_and_content: scale_data_cell_cycle_corrected_global.rds ; matrix with cell-cycle correccted normalised transcriptome UMI counts
Supplementary_files_format_and_content: cell_labels.rds ; R rds file containing cell labels after sgRNA demultiplexing

growth_protocol: Cells were grown in RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Single cell mRNA-Seq with Feature Barcoding was carried out using the 10x Single Cell Gene Expression kit v3.1 according to the manufacturer’s instructions. Briefly, cell suspension was counted and assessed for viability using an EVE automated cell counter (NanoEntek).  Approximately 10,000 cells were loaded into the 10x Chromium chip and loaded into the 10x.  GEM generation, barcoding, cDNA synesis and clean-up was carried out as per the 10x protocol.  Subsequently, the gene expression and feature barcoding libraries were separated by size selection and sequenced on the HiSeq 4000 according to the 10x guidelines.
As per 10X Genomics' instructions
10X Genomics scRNAseq with sgRNA Feature barcoding

treatment_protocol: Cells were grown in the absence of glutamine (RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2) for 1d, 2d or 12d

tag: genotype

value: sgRNA multiplexed sample

value: Glutamine starvation (d12)

tag: gex-crispr pairing

tag: molecule subtype

value: CRISPR guides


title: 2 Control

value: Vehicle

value: 8 hours incubation


title: 2 Activated

value: 8 hours activation


title: 3D-Plasma-V1-289

description:
289
3D-Plasma-V1-289


title: 1 Control


title: Multiplexed_sample_crispr_Day1 [LOU523A6]

description:
LOU523A6_S12
processed data file: LOU523A2_LOU523A6.tar.gz

value: Glutamine starvation (d1)


title: Multiplexed_sample_gex_Day2 [LOU523A3]

description:
LOU523A3_S10_S9
processed data file: LOU523A3_LOU523A7.tar.gz

value: Glutamine starvation (d2)

value: polyadenylated RNA


title: 1 Activated


title: Multiplexed_sample_gex_Day12 [LOU523A4]

description:
LOU523A4_S10
processed data file: LOU523A4_LOU523A8.tar.gz

value: Melanoma cells MEXF 2090


title: Multiplexed_sample_gex_Day1 [LOU523A2]

description:
LOU523A2_S23
processed data file: LOU523A2_LOU523A6.tar.gz


title: Multiplexed_sample_crispr_Day0 [LOU523A5]

description:
LOU523A5_S11
processed data file: LOU523A1_LOU523A5.tar.gz

value: No treatnent


title: Multiplexed_sample_crispr_Day2 [LOU523A7]

description:
LOU523A7_S13
processed data file: LOU523A3_LOU523A7.tar.gz


title: Multiplexed_sample_gex_Day0 [LOU523A1]

description:
LOU523A1_S1_S1
processed data file: LOU523A1_LOU523A5.tar.gz


title: TNP2 KO DAY12 LGLUT biological replicate 3, technical replicate 3

description: RNA-Seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.2.31) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 1”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
3’ mRNA-Seq libraries were prepared with the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit.  Total RNA was quantified using via the RNA QuantiFluor RNA system E3310 on the GloMax (Promega) Multi Detection system following the maufacturer's guidelines.  RNA quality was checked via the High Sensitivity RNA ScreenTape using the TapeStation 4200 (Agilent).  RNA was normalised to 30 ng and used for cDNA synthesis and library preparation using the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit according to the manufacturer’s instructions.  Libraries were sequenced on the Illumina HiSeq 4000 with single ended reads

treatment_protocol: Cells were grown in the absence of glutamine (RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2) for 12d

value: TNP2 KO

value: DAY 12

value: L-GLUT


title: L1C5c_t20_C4

value: NSCLC cells LXFL 1674

value: Glutamine deprivation

value: DAY 20


title: KrasFVB_replicate2

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Eight mRNA-seq libraries were sequenced with Illumina chemistry.
Samples were trimmed for adapters and low quality bases using Cutadapt 1.18 software and aligned with reference mouse mm10 genome using STAR 2.7.6a software.
Quantification was carried out with RSEM 1.3.0 using the transcriptome bam file created by STAR.
Basecalling was performed by RTA.
Demultiplexing and FASTQ generation was performed using bcl2fastq.
Trimming of adapters and low-quality bases was performed using Trimmomatic (version 0.36).
First pass alignment of reads to the mm10 reference genome was performed using STAR (version 2.5.1) with parameters: STAR --genomeDir $star_genome --readFilesIn R1_trimmed.fastq R2_trimmed.fastq --outTmpDir /logs/star --outSAMunmapped Within -- outFilterType BySJout --outFilterMultimapNmax 20 -- outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 -- alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 -- sjdbScore 1 --runThreadN 8 --genomeLoad NoSharedMemory -- outSAMtype BAM Unsorted --quantMode TranscriptomeSAM
Gene-level expression quantificiation and library size normalization in counts-per-million was performed using RSEM (version 1.2.22).
Quantile-normalization and differential expression was performed using limma-voom (version 3.34.5).
Assembly: mm10
Supplementary files format and content: Comma-Separated Values (.csv) file containing filtered raw counts produced by RSEM

source_name: mouse primary keratinocytes

growth_protocol: Primary mouse keratinocytes and hair follicle buds were isolated from newborn pups and cultured in modified Eagle's medium (EMEM, Lonza 06-174G), 8% Chelex-treated FBS (Gemini Bio Products 100-106), and 0.05 mmol/L calcium unless otherwise indicated.

extract_protocol:
mRNA was extracted by Psomogen using standard protocols.
TruSeq Stranded mRNA LT Sample Prep Kit/TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: The Cre recombinase (Cre) was introduced into primary keratinocytes using an adenoviral construct driven by a cytomegalovirus promoter.

tag: background strain

tag: genotype/variation

value: LSL-KrasG12D mice


title: KrasFVB_replicate3


title: KrasFVB_replicate1


title: KrasFVB_replicate4


title: KrasC57_replicate4


title: 3D-Plasma-V1-271

description:
271
3D-Plasma-V1-271

value: Plasma

value: female

value: Normal


title: 3D-Plasma-V1-269

description:
269
3D-Plasma-V1-269

value: Other pregnancy complications


title: 3D-Plasma-V1-270

description:
270
3D-Plasma-V1-270


title: 3D-Plasma-V1-273

description:
273
3D-Plasma-V1-273

value: Gestational diabetes mellitus


title: 3D-Plasma-V1-283

description:
283
3D-Plasma-V1-283


title: 3D-Plasma-V1-284

description:
284
3D-Plasma-V1-284


title: 3D-Plasma-V1-280

description:
280
3D-Plasma-V1-280


title: 3D-Plasma-V1-278

description:
278
3D-Plasma-V1-278