title: N_13

value: Peripheral blood cell (whole blood)

value: Follow-up

value: F


title: Med12 in BMDCs experiment, Med12 KO sample_1

status: Public on Sep 13 2023

type: SRA

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: The Hebrew University of Jerusalem

library_source: transcriptomic

data_processing:
RNA-seq (hMo): Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the hg38 reference by using hisat2 (v2.2.1) with the --very-sensitive option. Transcripts were quantified with stringtie (v2.2.1).
RNA-seq (BMDCs): Raw reads were quality-trimmed using cutadapt (v2.10). Additional quality filtering was performed by the fastx package (v0.0.14). Processed reads were aligned to the mouse genome version GRCm38 (Enembl 99 release) with TopHat (v2.1.1).
ATAC-seq and ChIP-seq: Raw reads quality-trimmed using trim-galore (v0.6.7) and aligned to the mm10 reference using hisat2 (v2.2.1). picard (v2.26.10) MarkDuplicates was used to mark and removed duplicates. Bigwig files were generated using deeptools (v3.5.1), normalizing by RPKM or BPM. Heatmaps were generated using deeptools (v3.5.1). Peaks for each sample were assigned using macs (v2.2.7.1). A union peak set for all samples was constructed by merging the peaks into a set of high-confidence non-overlapping fixed-width (500 bp) peaks.
Assembly: RNA-seq (hMo) - hg38; RNA-seq(BMDCs) - Grcm38 (Ensembl 99); ATAC-seq and ChIP-seq - mm10
Supplementary files format and content: Comma-delimited files listing counts, big-wig files, peak files

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow

growth_protocol: To obtain BMDCs, femurs and tibia were removed, and BM was flushed. Red blood cells were lysed using RBC lysis buffer (e-bioscience). Bone marrow cells were plated in 100 mm diameter dish (Falcon, BD, NJ, USA) at a concentration of 2X105 per ml in 10 ml of medium. The medium included RPMI 1640 (Gibco #21875-034) supplemented with 10% heat-inactivated FBS (Gibco ,#10270106), β-mercaptoethanol (50 µM, Gibco, #31350-010),1% L-glutamine (Gibco, #25030-024), 1% penicillin/streptomycin (Gibco, #15140-122), 1% MEM non-essential amino acids (Gibco, #11140035), 1% HEPES (Gibco, #15630056), 1% sodium pyruvate (Gibco, #11360-039), and murine GM-CSF (20 ng/ml; Peprotech, #315-03). For CRISPR knockout experiments six- to eight-weeks-old constitutive Cas9-expressing mice were used as the source of BMDCs. Cells were maintained at 37°C in a 5% CO2-humidified atmosphere. On day two of culture, 10 ml of fresh medium supplemented with GM-CSF was added. On day five, 10 ml of medium were gently removed and 10 ml of fresh medium with GM-CSF was added. On day seven, 5 ml of fresh medium with GM-CSF was added to the cells and on day eight, floating cells were recovered and used for downstream applications.  Peripheral blood mononuclear cells (PBMCs) were isolated using a density gradient (Lymphoprep, STEMCELL Technologies, #7851) as previously described56. One buffy coat from Hadassah medical hospital was processed for each donor using BSL2* precautions in accordance with institutional safety guidelines. The buffy coat was diluted 1:1 with PBS (BI 02-023-1A), then layered on top of the lymphoprep in a 50 ml tube (Lifegene, LBT50). Isolated PMBCs were then cryopreserved in a mixture containing FBS with 10% DMSO (40X10⁶ cells in 1 ml) and stored in liquid nitrogen, or used directly for monocyte isolation. Monocytes were isolated using the EasySep Human Monocytes Isolation Kit (STEMCELL Technologies, #19359) according to the manufacturer’s instructions. To examine isolation efficiency, fractions of cells before and after separation were stained with human anti-CD14 (1:200) antibody and analyzed with Flow Cytometry.

extract_protocol:
RNA was recovered using RNeasy plus mini kit (Qiagen #74136). Samples for ATAC-seq were prepared with the kit (Active Motif #53150) according to the instruction manual. Samples for Chip-seq were prepared according to the protocol described by Antman et al  with several modifications. We used 30x10^6 BMDCs for each experiment. Quenching of formaldehyde was done at RT on a gently rocking platform. Samples were sonicated for three cycles (30 s on, 30 s off). For immunoprecipitation, 10 µL of Cebpb antibody was added (ab32358) and 30 µL of Protein G magnetic beads. Then, 2.5% of the sample was taken as input. Chromatin was eluted from the beads by shaking them in a heat block at 800 rpm for 30 min at 65 °C and reverse crosslinking was performed at 65 °C overnight.
The libraries for RNA-seq were prepared using KAPA mRNA capture kit (Roche #07962231001) following the manufacturer’s instructions. The libraries for Chip-seq were prepared using   KAPA HyperPrep Kit (Roche #7962347001) according to the instruction manual (1 ng of immunoprecipitated sample and 100 ng of input sample were used for library preparation). The libraried for ATAC-seq were prepared using the kit (Active Motif #53150) according to the instruction manual.

treatment_protocol: For RNA-seq experiment with human monocytes CD14+ cells were electroporated on day zero with RNP complex containing Cas9 portein and gRNA (against Med12 or non-targeting guide). Electroporation was done using Nepa21 machine. For RNA-seq with mouse BMDCs, cells were infected on day two with corresponding lentivirus and on day eight cells were used for RNA extraction. For ATAC-seq experiment, on day two BMDCs were infected with either mCherry lentivirus targeting Cebpb, or BFP lentivirus targeting Med12, or mCherry non-targeting lentivirus. On day eight infected cells were sorted and around 100 000 sortecells were used per sample. For Chip-seq uninfected BMDCs were used on day eight. Around 30x10^6 cells were used per sample.

tag: tissue

value: Bone marrow

tag: cell type

value: BMDCs

tag: genotype

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: Infected with lentivirus that encode gRNA targeting Med12


title: DEGs of Cebpb targeted cells using Cebpb-KO DCs, Low expression expression CD86

description:
CD86 CebpbKO_DCs Secondary.csv
CD86_CebpbKO_DCs_Secondary_L

library_source: genomic

data_processing:
Fastq files were demultiplexed using Bcl2fastq (v2.20.0.422)
The Fastx toolkit (v0.0.13) was used to convert the fastq files to fasta files
Forward and reverse adapters were trimmed using cutadapt (v3.4)
Alignment was performed to the reference library (genome wide or secondary) by using bowtie1 (v 1.3.1)
Assembly: Genome wide - GPP Brie library, Secondary - attached in supplementary material
Supplementary files format and content: Comma-delimited files listing counts for each sgRNA
Library strategy: CRISPR screen

molecule: genomic DNA

source_name: Bone marrow - derived dendritic cells

growth_protocol: Bone marrow - derived dendritic cells were extracted from the femurs and tibia of the mice with constitutively expressed Cas9. Cells were plated at the concentration of 0.2 x 10^6/ml in 10 cm plates (Falcon, nonissue culture treated) in 1640 RPMI media (Gibco) supplemented with 10% heat inactivated FCS (Gibco), β-mercaptoethanol (50μM, Invitrogen), 1% L-glutamine (Gibco), 1% penicillin/streptomycin (Gibco), 1% MEM non-essentialamino acids (Gibco), 1% HEPES (Gibco), 1% sodium pyruvate (Gibco), and GM-CSF (20ng/ml; Peprotech). Cells were fed on D2 (+10 ml of the fresh media and 20 ng/ml of GM-CSF), D5 (-10 ml of the media, +10 ml of the fresh media and 20ng/ml of GM-CSF), and D7 (+ 5ml of the fresh media and 20ng/ml of GM-CSF).

extract_protocol:
Genomic DNA from the sorted cells were extracted using Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions and eluted with 50 ul of water.
Genomic DNA was purified and used for 2 PCR reactions following the protocol that was described in Parnas et al  Cell. 2015 Jul 30;162(3):675-86.

treatment_protocol: Bone marrow - derived dendritic cells were infected with the CRISPR pooled library on Day 2. On Day 5 of the GW CRISPR screen, puromycin selection was applied (because the GW CRISPR library was cloned into Cropseq-Guide-Puro plasmid, Addgene #86708). On Day 5 of the secondary screen, antibiotic selection was not applied since the library was cloned into CRISPRseq - BFP - Backbone plasmid (Addgene #85707). On Day 8, cells were collected and stained with APC anti-mouse CD11c Antibody (BLG-117310) and PE anti-mouse CD86 antibody (BLG-159203) and sorted (CD11c+ cells with 10% highest and 10% lowest expression for GW screens, BFP+ CD11c+ cells with 10% highest and 10% lowest expression for secondary screens).

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9 CD11C-CRE CEBPB (FL/FL)

value: Lentivirus infection with genome - wide CRISPR pooled library


title: 104_Batch2_32_KAA2P06S-01_S40_L003

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

country: USA

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

organism: Homo sapiens

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the baseline and the one month follow-up visit from 188 matched participants (n=376) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl)) and transported to the laboratory within 6 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: visit

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 111_Batch2_39_3872_S47_L004

value: baseline

value: Emavundleni

value: IB

value: Yes


title: DEGs of Cebpb targeted cells using Cebpb-KO DCs, High expression expression CD86

description:
CD86 CebpbKO_DCs Secondary.csv
CD86_CebpbKO_DCs_Secondary_H

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9 CD11C-CRE CEBPB (FL/FL)


title: N_11

city: Houston

first: Shervin

last: Assassi

state: TX

address: 6431 Fannin St

institute: UTHouston

data_processing:
Transcript data were normalized with DESeq2.
Transcripts which had counts per million (CPM) greater than 1 in at least two samples were used for the analysis
Assembly: hg38
Supplementary files format and content: csv file format of DESeq2 normalized and log2 transformed counts.

source_name: Peripheral blood cell (whole blood)

extract_protocol:
PreSSc’s and healthy controls’ whole blood samples were col_x0002_lected in PAX gene tubes and stored at –80_x0002_C. RNA was extracted according to the manufacturer’s protocol and quality was assessed by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Globin genes were depleted using GLOBIN Clear kit. mRNA was enriched from total RNA using oligo(dt) beads (NEB Next Ultra II RNA Kit following the poly(A) enrichment workflow). The mRNA was subsequently fragmented randomly in fragmentation buffer, and reverse transcribed to cDNA. The cDNAs were converted to double stranded cDNAs, then subjected to end-repair, A-tailing and adapter ligation, size selection and PCR enrichment. Library concentration was first quantified using a Qubit 2.0 fluorometer  (Life Technologies, Carlsbad, CA, USA), and then diluted to 1 ng/ul before checking insert size on an Agilent 2100 and quantified to greater accuracy by quantitative PCR (q-PCR) (library activity >2nM). Libraries were pooled into Novaseq6000 machines according to molarity and expected data volume. A paired-end 150 bp sequencing strategy was used to generate an average of 88 million reads per sample.

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Follow-up

tag: pair

tag: gender

value: F


title: DEGs of Cebpb targeted cells using WT DCs, Low expression expression CD86

description:
CD86 WT_DCs Secondary.csv
CD86_WT_DCs_Secondary_L

tag: cell type

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: rat#12-control_hippocampus_14d

type: RNA

city: Moscow

first: Diana

last: Salikhova

address: Miklukho-Maklaya, 8

department: Institute of molecular and cellular medecine

country: Russia

institute: RUDN University

description:
control
SAMPLE 44

data_processing:
For the normalization it uses the average of housekeeping genes: GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)
Fold Change worksheet reports control/test (median all samples PBS treatment/ median all samples EV treatment) ratios at 7 and 14 days for brain regions (cortex, striatum, hippocampus).
Genes that did not show expression were excluded.

label: SYBR Green

organism: Rattus norvegicus

source_name: brain tissue

label_protocol: cDNA was synthesized using RevertAid First Strand cDNA Synthesis Kit (TermoFisher) by corresponding standard protocol. The PCRs set with qPCRmix-HS SYBR master mixes (Evrogen, Russia) were carried out in a Bio-Rad cfx96 (BioRad, USA) in the following mode: primary denaturation 95 °C for 5 min; denaturation 95 °C 20 s, annealing 56–63 °C 20 s, elongation 72 °C 20 s (40 cycles).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

tag: tissue

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: PBS treatment

tag: time

value: 14 days


title: DEGs of Cebpb targeted cells using WT DCs, High expression expression CD86

description:
CD86 WT_DCs Secondary.csv
CD86_WT_DCs_Secondary_H

tag: genotype

tag: treatment


title: rat#7-control_hippocampus_14d

description:
control
SAMPLE 42


title: rat#16-control_hippocampus_14d

description:
control
SAMPLE 43


title: rat#1-control_striatum_14d

description:
control
SAMPLE 41

value: striatum


title: Neural tube MOXD1 KO, replicate 12

city: Lund

first: Stina

last: Andersson

address: Sölvegatan 19

country: Sweden

institute: Lund University

data_processing:
Demultiplexing: organizing the FASTQ files based on the sample index information, and generating the statistics and reporting files. This task was performed using the bcl2fastq2 software with –no-lane-splitting tag, and using the provided SampleSheet.csv for demultiplexing files on samples.
Raw Quality Control (QC): FastQC provides quality control analyses and checks on raw sequence data coming from the above Demultiplexing step of the pipeline. For each analysis it provides a graphical plot and a suggestive warning if the data has any problems.
Read Mapping: alignment of reads to a specified reference genome. This task was performed using the STAR software, and the reference genome sequence was from the Ensemble database, the Gallus Gallus GRCg6a assembly, and the annotation (GTF) from ensemble GRCg6a release 101. Data is sorted by genomic coordinate.
Expression counts: Quantification of the expression levels of each gene. This task was performed using the featureCounts software, with the following settings: Paired-end mode (-p), strand specific (-s 2), no multimapping counted, counting exonic reads.
MultiQC: Summarizing statistics from demultiplexing, fastQC, alignment and quantification: multiQC.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Assembly: Ensemble database (Gallus Gallus GRCg6a, release 101)
Supplementary files format and content: 2020_75_R2_gene_id.featureCounts.txt contains the featureCount output.

organism: Gallus gallus

source_name: Trunk portion of neural tubes

growth_protocol: Chick embryos were acquired from commercially purchased fertilized eggs and incubated at 37.5°C until desired developmental Hamburger Hamilton (HH) (Hamburger and Hamilton, 1951) stages were reached. Optimal conditions for high transfection efficiency applying one-sided electroporation in ovo were determined to 5 pulses of 30ms each at 22V. Ringer’s balanced salt solution (Solution-1: 144g NaCl, 4.5g CaCl•2H2O, 7.4g KCl, ddH2O to 500ml; Solution-2: 4.35g Na2HPO4•7H2O, 0.4g KH2PO4, ddH2O to 500ml (adjust final pH to 7.4)) containing 1% penicillin/streptomycin was used in all experiments. All constructs were injected at HH stage 10+/11 into the lumen of the neural tube from the posterior end. Embryos were electroporated in ovo in a one-sided fashion. Embryos injected with CRISPR/Cas9 constructs were allowed to sit at room temperature for 6 – 10 hours before further incubation of the embryos at 37.5°C in order to allow the Cas9 protein to fold.

extract_protocol:
Total RNA was extracted using RNAqueous Micro Kit (Ambion RNAqueous™-Micro Kit, ThermoFisher, #AM1931). The total RNA input to library preparation was 50 ng
The library preparation was performed with Illumina Stranded mRNA Prep Ligation (#1000000124518 v00) with 14 cycles under final PCR amplification.

value: Trunk portion of neural tubes

value: MOXD1 KO


title: Neural tube MOXD1 KO, replicate 11


title: B_9

value: Baseline


title: Neural tube MOXD1 KO, replicate 10


title: 112_Batch2_40_8270_S48_L004

tag: visit

tag: site

value: Emavundleni

tag: rin

value: IVB

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: Neural tube MOXD1 KO, replicate 9


title: Genome wide screen on Cebpb-KO DCs, Low expression expression CD86

description:
CD86 CebpbKO_DCs GW.csv
CD86_CebpbKO_DCs_GW_L

tag: cell type

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9 CD11C-CRE CEBPB (FL/FL)

value: Lentivirus infection with genome - wide CRISPR pooled library


title: rat#12-control_striatum_14d

description:
control
SAMPLE 40

tag: animal

tag: Sex

value: male

value: Wistar

value: TBI

value: brain

value: striatum

value: PBS treatment

value: 14 days


title: rat#16-control_striatum_14d

description:
control
SAMPLE 39

tag: strain

tag: tissue


title: B_8

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: F


title: Neural tube MOXD1 KO, replicate 8

value: Trunk portion of neural tubes

tag: genotype

value: MOXD1 KO


title: rat#7-control_striatum_14d

description:
control
SAMPLE 38

tag: treatment

tag: brain region

tag: activation agent

tag: time


title: N_12

value: Follow-up

value: M


title: Genome wide screen on Cebpb-KO DCs, High expression CD86

description:
CD86 CebpbKO_DCs GW.csv
CD86_CebpbKO_DCs_GW_H

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9 CD11C-CRE CEBPB (FL/FL)


title: B_7


title: Neural tube MOXD1 KO, replicate 7


title: B_5

value: Evolving PreSSc


title: 5xFAD, expr 3, scRNAseq

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description:
inDrops
5xFAD_hippocampus_5m

library_source: transcriptomic single cell

data_processing:
Sequencing results were first processed through pipeline for processing inDrop sequencing data (https://github.com/indrops/indrops) based on Python 2.7 with default parameters, aligned to a mouse genome GRCm38 (release 102). The datasets were imported via indRop (https://github.com/caleblareau/indRop) into R environments and used for subsequent bioinformatic analysis with Seurat v4.2.
The initial dataset contained 147,371 barcoded beads with more than 1,000 reads. Cells with fewer than 500 unique molecular identifiers filtered mapped (UMIFM) counts and genes with fewer than 10 cells were excluded, as low UMIFM indicates dead or dying cells. The R package, scDblFinder, was employed to identify and eliminate probable doublets. We further filtered cells whose nFeature_RNA and nCount_RNA was more than five standard deviations from the median value, because a high nCount_RNA or a nFeature_RNA implies that the cell may be a doublet or multiplet. In addition, cells with mitochondrial genes whose expression was more than two standard deviations above the median value of their total transcripts were excluded from further analysis.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Comma-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Brain tissue was harvested and dissociated in less than an hour. Briefly, mice (12 ~ 24-week-old) were quickly decapitated after being CO2 anesthetized. The brain was cut into 1mm slices, and the hippocampus then was extracted. The samples were dissociated enzymatically to obtain a single-cell suspension with 0.05% papain and DNase 1 (DN25, Sigma-Aldrich, USA) in neurobasal media (Gibco, USA) at 37 °C for 30 min. After the enzymatic reaction was stopped by the addition of OIA, the cell suspension was passed through a 40-μm filter and washed by differential centrifugation to remove debris. The dissociated cells were put in Hank’s balanced salt solution containing 0.04% bovine serum albumin and diluted to 100 cells/μl.
Directly after cell counting, a cell suspension volume equivalent to 5000 target cells was used for further processing. Preparation of gel beads in emulsion and libraries were performed with the custom-made microfluidic device and inDropTM chemistry, according to the inDrop™ Library Preparation, Version 2.1 provided by the manufacturer. Libraries’ quality and quantity were verified with a High-Sensitivity DNA Kit (Agilent Technologies, USA) on a 2100 Bioanalyzer (Agilent Technologies, USA). Next, sequencing was run in the rapid run flow cell and paired-end sequenced on a NovaSeq6000 (Illumina, USA).

value: Brain cells

value: hippocampus

tag: age

value: 20 weeks old


title: N_10


title: rat#1-control_cortex_14d

description:
control
SAMPLE 37

value: male

value: Wistar

value: TBI

value: brain

value: cortex


title: Neural tube MOXD1 KO, replicate 6


title: WT, ctrl 2, scRNAseq

description:
inDrops
WT_hippocampus_5m-a

value: 12 weeks old


title: WT, ctrl 3, scRNAseq

description:
inDrops
WT_hippocampus_5m-b


title: B_55

value: Peripheral blood cell (whole blood)

value: Baseline

value: F


title: Genome wide screen on Cebpb-KO DCs, Unsorted cells

description:
CD86 CebpbKO_DCs GW.csv
CD86_CebpbKO_DCs_GW_US

value: Lentivirus infection with genome - wide CRISPR pooled library


title: B_54


title: Neural tube MOXD1 KO, replicate 4

value: Trunk portion of neural tubes

value: MOXD1 KO


title: Neural tube MOXD1 KO, replicate 5


title: rat#16-control_cortex_14d

description:
control
SAMPLE 35

value: PBS treatment

value: 14 days


title: 180d Male Heart FXNG127V 3

city: New York

first: Nicole

last: Sayles

address: 407 East 61st Street

institute: Weill Cornell

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw sequence reads were procewssed using the BBDuk program in the BBMap package
Trimmed readsd were aligned to the mouse genome assembly GRCm38.p6 using the STAR aligner (version2.5.0a).
SAM files were converted to BAM to read overlapping reads per gene using HTseq-count (version 0.6.1)

source_name: Heart

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and Qiagen RNeasy Mini Kit (Cat# 74104). The Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina was used with 500 ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: post natal day 180


title: rat#7-control_cortex_14d

description:
control
SAMPLE 34


title: Neural tube MOXD1 KO, replicate 3


title: 180d Male Heart FXNG127V 2


title: B_4

value: Evolving PreSSc


title: rat#16-EV _hippocampus7d

description:
Test
SAMPLE 33

value: male

value: hippocampus

value: EV treatment

value: 7 days


title: 180d Male Heart FXNG127V 1


title: Neural tube MOXD1 KO, replicate 2


title: rat#12-EV _hippocampus_7d

description:
Test
SAMPLE 32

value: Wistar

value: TBI

value: brain


title: B_3

value: Peripheral blood cell (whole blood)

value: Baseline


title: B_35

value: Stable PreSSc

value: F


title: Neural tube MOXD1 KO, replicate 1

value: Trunk portion of neural tubes

value: MOXD1 KO


title: 180d Female Heart FXNG127V 3


title: rat#10-EV _hippocampus_7d

description:
Test
SAMPLE 31


title: 180d Female Heart FXNG127V 2


title: rat#12-control_cortex_14d

description:
control
SAMPLE 36

value: cortex

value: PBS treatment

value: 14 days


title: rat#4-EV _hippocampus_7d

description:
Test
SAMPLE 30


title: B_34

value: Evolving PreSSc


title: Neural tube, CTRL, replicate 8

value: WT


title: Neural tube, CTRL, replicate 9


title: B_52

value: M


title: 180d Male Heart KIKO-700 3

value: Heart

value: post natal day 180


title: Neural tube, CTRL, replicate 6


title: B_32


title: B_33


title: rat#9-EV _hippocampus_7d

description:
Test
SAMPLE 29

value: male

value: Wistar

value: hippocampus

value: EV treatment

value: 7 days


title: Neural tube, CTRL, replicate 7


title: 180d Female Heart FXNG127V 1


title: B_31

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

value: Baseline


title: 180d Male Heart KIKO-700 2


title: rat#16-EV_striatum_7d

description:
Test
SAMPLE 27

value: TBI

value: brain

value: striatum


title: Neural tube, CTRL, replicate 5

value: Trunk portion of neural tubes


title: 180d Male Heart KIKO-700 1


title: B_30

value: F


title: rat#1-EV _hippocampus_7d

description:
Test
SAMPLE 28


title: B_2


title: Neural tube, CTRL, replicate 4

value: WT


title: 180d Female Heart KIKO-700 2


title: B_29


title: Neural tube, CTRL, replicate 3


title: 180d Female Heart KIKO-700 1


title: Neural tube, CTRL, replicate 2


title: B_28

value: Evolving PreSSc


title: rat#4-EV _striatum_7d

description:
Test
SAMPLE 24


title: rat#12-EV_striatum_7d

description:
Test
SAMPLE 26


title: B_27


title: 180d Male Heart WT (for KIKO-700 and FXNG127V) 3

value: Heart

value: wild type


title: Neural tube, CTRL, replicate 1


title: B_25


title: 103_Batch2_31_KAA2NL6Z-01_S39_L003

tag: visit

value: baseline

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: yeasts

value: Obs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 98_Batch2_26_CAA2PK8B-01_S34_L003

tag: mobilincus

value: Nobs

value: Checked


title: rat#9-EV _striatum_7d

description:
Test
SAMPLE 23

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

tag: tissue

value: brain

value: striatum

value: EV treatment

value: 7 days


title: B_23

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: F


title: 180d Male Heart WT (for KIKO-700 and FXNG127V) 1

value: Heart

tag: age

value: post natal day 180

tag: genotype

value: wild type


title: 180d Female Heart KIKO-700 3


title: 180d Female Heart WT (for KIKO-700 and FXNG127V) 3


title: rat#16-EV _cortex_7d

description:
Test
SAMPLE 21

tag: treatment

tag: brain region

value: cortex

tag: activation agent

tag: time


title: rat#10-EV_striatum_7d

description:
Test
SAMPLE 25


title: 97_Batch2_25_BAA2NZLB-01_S33_L003

tag: visit

value: baseline

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: yeasts

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No


title: rat#1-EV_striatum_7d

description:
Test
SAMPLE 22

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

tag: tissue

value: brain

value: striatum

value: EV treatment

value: 7 days


title: rat#4-EV _cortex_7d

description:
Test
SAMPLE 18

tag: treatment

value: cortex


title: B_22

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: F


title: 94_Batch2_22_560243136601_S30_L002

tag: visit

tag: site

value: KEMRI

tag: rin

value: IB

value: LD

value: TRUE

value: Negative

value: Positive

value: Abs

tag: mobilincus

value: Primary school, some or complete

value: Unchecked


title: 180d Female Heart WT (for KIKO-700 and FXNG127V) 2

value: Heart

tag: age

value: post natal day 180

tag: genotype

value: wild type


title: 93_Batch2_21_560234166601_S29_L002

value: baseline

value: IIIA

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

tag: yeasts

value: Nobs

tag: maritalstatus

value: Never married

value: No


title: B_20

tag: cell type

value: Peripheral blood cell (whole blood)

value: Stable PreSSc

value: Baseline

value: F


title: 88_Batch2_16_EAA2P9GW-01_S24_L002

value: WRHI

value: IB

value: LD

value: TRUE

value: Negative

value: Secondary school, some or complete


title: 180d Female Heart WT (for KIKO-700 and FXNG127V) 1

tag: strain

tag: tissue

value: Heart

value: post natal day 180


title: rat#9-EV_cortex_7d

description:
Test
SAMPLE 17

tag: animal

tag: Sex

value: male

value: Wistar

tag: treatment

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: EV treatment

tag: time

value: 7 days


title: 87_Batch2_15_KAA2P16H-01_S23_L002

tag: visit

value: baseline

tag: site

tag: rin

value: IIIA

value: Abs

tag: mobilincus

value: Nobs

value: Never married

value: No

value: Unchecked


title: 180d Heart YG8-800 4

tag: age

tag: genotype


title: rat#1-EV _cortex_7d

description:
Test
SAMPLE 16


title: B_19

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: M


title: 180d Heart YG8-800 3

tag: strain

tag: tissue

value: Heart

value: post natal day 180


title: rat#12-EV_cortex_7d

description:
Test
SAMPLE 20

tag: animal

tag: Sex

value: male

value: Wistar

value: TBI

value: brain


title: 70_Batch1_70_6592_S7_L001

value: Emavundleni

value: IB

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Positive

tag: chlamydiatrachomatis

tag: lactobacilli

value: Negative

tag: yeasts

value: Obs

tag: maritalstatus

value: Secondary school, some or complete


title: 180d Male Heart WT (for KIKO-700 and FXNG127V) 2

value: wild type


title: 69_Batch1_69_4912_S6_L001

tag: visit

value: baseline

tag: site

tag: rin

value: Abs

tag: mobilincus

value: Nobs

value: Never married

value: Unchecked


title: 180d Heart YG8-800 2

value: Heart

tag: age

value: post natal day 180

tag: genotype


title: rat#13-control_hippocampus_7d

description:
control
SAMPLE 14

value: male

value: Wistar

tag: treatment

value: TBI

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: PBS treatment

tag: time

value: 7 days


title: 180d Heart YG8-800 1

tag: strain

tag: tissue


title: rat#10-EV_cortex_7d

description:
Test
SAMPLE 19

tag: animal

tag: Sex

value: cortex

value: EV treatment


title: B_16

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: F


title: B_15

value: Evolving PreSSc


title: 66_Batch1_66_560245396601_S3_L001

tag: visit

tag: site

value: KEMRI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: yeasts

value: Nobs

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: No

value: Unchecked


title: 180d Heart WT (for YG8-800) 4

tag: strain

tag: tissue

value: Heart

tag: age

value: post natal day 180

tag: genotype

value: wild type


title: B_18

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Baseline


title: rat#15-control_hippocampus_7d

description:
control
SAMPLE 15

tag: animal

tag: Sex

value: male

value: Wistar

tag: treatment

value: TBI

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: PBS treatment

tag: time

value: 7 days


title: rat#2-control_hippocampus_7d

description:
control
SAMPLE 13


title: B_21

value: Stable PreSSc

tag: time point

tag: pair

tag: gender

value: F


title: 65_Batch1_65_560234146601_S2_L001

tag: visit

value: baseline

tag: site

value: KEMRI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

value: Married

value: Primary school, some or complete


title: rat#5-control_hippocampus_7d

description:
control
SAMPLE 11

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

tag: tissue


title: 180d Heart WT (for YG8-800) 3

value: Heart

tag: age

value: post natal day 180

tag: genotype

value: wild type


title: B_1

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Evolving PreSSc

tag: time point

value: Baseline

tag: pair

value: F


title: 46_Batch1_46_6544_S46_L007

tag: visit

tag: site

value: Emavundleni

tag: rin

value: IVA

value: nonLD

value: BV

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: 180d Heart WT (for YG8-800) 2


title: B_13

tag: gender


title: 45_Batch1_45_3888_S45_L007

value: baseline

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: Nobs


title: B_12

value: Stable PreSSc

value: M


title: 180d Heart WT (for YG8-800) 1

tag: strain

tag: tissue

value: Heart

value: post natal day 180

value: wild type


title: B_11

value: Peripheral blood cell (whole blood)

value: Baseline

value: F


title: rat#13-control_striatum_7d

description:
control
SAMPLE 9

tag: animal

tag: Sex

value: male

value: Wistar

tag: treatment

value: TBI

value: brain

tag: brain region

value: striatum

tag: activation agent

value: PBS treatment

tag: time

value: 7 days


title: rat#2-control_striatum_7d

description:
control
SAMPLE 8


title: rat#15-control_striatum_7d

description:
control
SAMPLE 10


title: 44_Batch1_44_560250826601_S44_L007

tag: visit

tag: site

value: KEMRI

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Abs

value: BV

tag: yeasts

value: Married

value: Primary school, some or complete

value: Yes

value: Checked


title: B_10

tag: cell type

value: Peripheral blood cell (whole blood)

tag: group

value: Stable PreSSc

tag: time point

value: Baseline

tag: pair

tag: gender

value: F


title: 37_Batch1_37_5248_S37_L007

value: baseline

value: Emavundleni

tag: rin

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: rat#7-control_hippocampus_7d

description:
control
SAMPLE 12

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

tag: treatment

value: TBI

tag: tissue

value: brain

tag: brain region

value: hippocampus

tag: activation agent

value: PBS treatment

value: 7 days


title: rat#7-control_striatum_7d

description:
control
SAMPLE 7

value: striatum

tag: time


title: DOK-SI_PGC1a-3

city: chengdu

first: Liu

last: Yunkun

address: Sichuan

country: China

institute: sichuan university

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.The clean reads were mapped to the reference genome  using HISAT2 . FPKM  of each gene was calculated and the read counts of each gene were obtained by HTSeq-count . PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Differential expression analysis was performed using the DESeq2 . Q value < 0.05 and foldchange > 2 or foldchange < 0.5 was set as the threshold for significantly differential expression gene (DEGs)
Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software. The analysis was used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples.
Assembly: hg38
Supplementary files format and content: tab-delimited text files included PFKM value for each samples
Supplementary files format and content: tab-delimited text files included counts value for each samples

source_name: PGC1α knockdown

extract_protocol:
Total RNA was extracted using the TRIzol reagent  (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

tag: cell line

value: DOK

tag: cell type

value: human dysplastic oral keratinocyte

tag: genotype

value: PGC1{alpha} knockdown


title: DOK-SI_PGC1a-1


title: 18_Batch1_18_GAA2P377-01_S18_L006

tag: visit

tag: site

value: WRHI

tag: rin

value: IIIA

value: LD

value: TRUE

tag: bmi

value: Negative

value: Abs

tag: yeasts

value: No


title: HTO_Tumor-infiltrating neutrophils (TINs)

city: Notre Dame

first: Yun

last: Zhao

state: Indiana

address: 100 Galvin Life Science Center

institute: University of Notre Dame

description: Drop-seq

data_processing:
Raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline. Briefly, reads were mapped to the mouse mm10 reference genome.
A digital gene expression data matrix was generated with counts of unique molecular identifiers (UMIs) for every detected gene (row) per cell barcode (column).
We applied the knee plot method as recommended by the Drop-seq core computational protocol, which utilize the cumulative distribution of reads and identify an inflection point in the plot, to determine the number of cells (cell barcodes) represented in the expression matrix.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Py7160 cells (10^6 cells in 100uL) were injected into FVB mice.  About 2-3 weeks post injection, the diameter of tumor reach about 1cm. Tumors were harvested  (n=3) and enzymatically processed into single cell suspension. Blood cells were harvested from the same mice (n=3) and treated with RBC buffer. Neutrophils were enriched to reach ~90% purity with MojoSort™ Mouse Ly-6G Selection Kit (Cat# 480124).  Enriched cells were stained with hashtag antibodies (Cat#1 55811; 155813; 155815) to enable sample multiplexing. Cells from biological repeats were pooled into two groups (Blood NFs and TINs) and subsequently labelled with flow cytometry antibodies followed by sorting neutrophils (CD11b+ Ly6G+) to achieve the maximal purity (>99%) of neutrophils. The samples are subsequently ready for sequencing.
Samples prepared above were loaded on the microfluidic device (fabricated in-house, CAD file from McCarroll Lab website: http://mccarrolllab.org/dropseq/) at ~100 cells/µl. Blood NFs and TINs were loaded at ~200 cells/µl. Single-cell suspension and uniquely barcoded microbeads (Chemgenes, MACOSKO201110) suspended in lysis buffer were co-encapsulated in droplets by the microfluidic device. The droplets serve as compartmentalizing chambers for RNA capture. Once droplet generation was complete, collected droplets were disrupted and RNA-hybridized beads were harvested. Reverse transcription was performed using Maxima H Minus Reverse Transcriptase (Thermo Fisher Scientific, EP0752) with template switching oligo. cDNA was amplified and PCR products were then purified using AMpure Beads (Beckman Coulter). After quantification on a BioAnalazyer High Sensitivity Chip (Agilent), samples were fragmented and amplified for sequencing with the Nextera XT DNA sample prep kit (Illumina). The libraries were purified, quantified, and then sequenced on the NextSeq 500.

value: Tumor

tag: injected cell_line

value: neutrophils

value: FVB

value: no treatment


title: GEX_Tumor-infiltrating neutrophils (TINs)

description: Drop-seq


title: rat#5-control_striatum_7d

description:
control
SAMPLE 6

tag: animal

value: male

value: Wistar

value: TBI

value: brain

value: PBS treatment


title: Experiment2, Cebpb KO + Nr4a3 KO sample 3

description:
Exp2_Cebpb_Nr4a3_3
Exp2_DEseq.csv

data_processing:
Experiment1:
Raw reads were quality-trimmed with TrimGalore (v0.6.4).
Processed reads were aligned to the mouse genome version GRCm38 (Ensembl release 89) with the STAR70 (v2.7.3) aligner and quantified using Salmon (v0.14.0).
Experiment2 + Human monocytes experiment:
Raw reads were quality-trimmed and the remaining adapter sequences were removed using cutadapt (v2.10).
Processed reads were aligned to the mouse genome version GRCm38 (with genome annotations of Ensembl release 99) with TopHat66 (v2.1.1).
Assembly: Ensembl 89 (Experiment 1), Ensembl 99 (Experiment 2 + Human monocytes experiment)
Supplementary files format and content: Comma-delimited files listing counts for each biologic triplicate

growth_protocol: To obtain BMDCs, femurs and tibia were removed, and BM was flushed. Red blood cells were lysed using RBC lysis buffer (e-bioscience). Bone marrow cells were plated in 100 mm diameter dish (Falcon, BD, NJ, USA) at a concentration of 2X105 per ml in 10 ml of medium. The medium included RPMI 1640 (Gibco #21875-034) supplemented with 10% heat-inactivated FBS (Gibco ,#10270106), β-mercaptoethanol (50 µM, Gibco, #31350-010),1% L-glutamine (Gibco, #25030-024), 1% penicillin/streptomycin (Gibco, #15140-122), 1% MEM non-essential amino acids (Gibco, #11140035), 1% HEPES (Gibco, #15630056), 1% sodium pyruvate (Gibco, #11360-039), and murine GM-CSF (20 ng/ml; Peprotech, #315-03). For CRISPR knockout experiments six- to eight-weeks-old constitutive Cas9-expressing mice were used as the source of BMDCs. Cells were maintained at 37°C in a 5% CO2-humidified atmosphere. On day two of culture, 10 ml of fresh medium supplemented with GM-SCF was added. On day five, 10 ml of medium were gently removed and 10 ml of fresh medium with GM-CSF was added. On day seven, 5 ml of fresh medium with GM-CSF was added to the cells and on day eight, floating cells were recovered and used for downstream applications.  Peripheral blood mononuclear cells (PBMCs) were isolated using a density gradient (Lymphoprep, STEMCELL Technologies, #7851) as previously described56. One buffy coat from Hadassah medical hospital was processed for each donor using BSL2* precautions in accordance with institutional safety guidelines. The buffy coat was diluted 1:1 with PBS (BI 02-023-1A), then layered on top of the lymphoprep in a 50 ml tube (Lifegene, LBT50). Isolated PMBCs were then cryopreserved in a mixture containing FBS with 10% DMSO (40X10⁶ cells in 1 ml) and stored in liquid nitrogen, or used directly for monocyte isolation. Monocytes were isolated using the EasySep Human Monocytes Isolation Kit (STEMCELL Technologies, #19359) according to the manufacturer’s instructions. To examine isolation efficiency, fractions of cells before and after separation were stained with human anti-CD14 (1:200) antibody and analyzed with Flow Cytometry.

extract_protocol:
RNA was recovered using RNeasy plus mini kit (Qiagen #74136).
The libraries were prepared using KAPA mRNA capture kit (Roche #07962231001) following the manufacturer’s instructions.

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Cebpb + Nr4a5


title: DOK-SH-3

source_name: WT

value: DOK

value: human dysplastic oral keratinocyte

value: WT


title: 17_Batch1_17_CAA2NPPY-01_S17_L006

value: baseline

value: WRHI

value: IIIA

value: LD

value: TRUE

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 12_Batch1_12_4112_S12_L005

value: Emavundleni

value: IVD

value: nonLD

value: Positive

value: BV


title: HTO_Blood neutrophils

description: Drop-seq

source_name: Blood

tag: tissue

value: Blood

value: neutrophils

value: FVB

tag: treatment

value: no treatment


title: Experiment2, Cebpb KO + Nr4a3 KO sample 2

description:
Exp2_Cebpb_Nr4a3_2
Exp2_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Cebpb + Nr4a4


title: rat#2-control_cortex_7d

description:
control
SAMPLE 3

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: PBS treatment

tag: time

value: 7 days


title: DOK-SH-2

tag: cell line

value: DOK

tag: cell type

value: human dysplastic oral keratinocyte

tag: genotype

value: WT


title: DOK-SH-1


title: 11_Batch1_11_2416_S11_L005

tag: visit

value: baseline

tag: site

value: Emavundleni

tag: rin

value: IVD

value: nonLD

value: TRUE

tag: bmi

value: Negative

value: Positive

value: Abs

value: BV

tag: yeasts

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 38_Batch1_38_7376_S38_L007

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus


title: 6_Batch1_6_BAA2NTTD-01_S6_L005

value: WRHI

value: IIIA

value: LD

tag: maritalstatus


title: Experiment2, Cebpb KO + Nr4a3 KO sample 1

description:
Exp2_Cebpb_Nr4a3_1
Exp2_DEseq.csv

tag: tissue

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

tag: treatment

value: Infected with lentivirus that encode gRNA targeting Cebpb + Nr4a3


title: DOK-SI_PGC1a-2

value: DOK

value: human dysplastic oral keratinocyte

value: PGC1{alpha} knockdown


title: RNAseq_PF-502_rep3

city: Chengdu, Cihna

first: Xaingyu

last: Pan

state: Sichuan

address: No.17 Renming road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University.

institute: Sichuan University

data_processing:
RNA libraries were sequenced on an Illumina NovaSeq 6000 sequencing machine with 150-base pair (bp) paired-end reads.
Transcript abundance was normalized and measured by FPKM.
DESeq2 (v.1.26.0, RRID:SCR_000154) was used to identify differentially expressed genes
Assembly: hg19
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: HUVECs

growth_protocol: Primary human umbilical vein endothelial cells (HUVECs) were isolated from donors(West China Hospital). The endothelial cells were cultured with endothelial cell medium (Catalog#1001, Sciencell) containing endothelial growth factors. Primary human umbilical vein endothelial cells (HUVECs) were isolated from donors(West China Hospital). The endothelial cells were cultured with endothelial cell medium (Catalog#1001, Sciencell) containing endothelial growth factors.

extract_protocol:
The HUVEC cells were seeded in 6-well plate about 105 cells per well and treated the following day with either vehicle(DMSO) or PF-502(0.15μM) for 12hrs. And then, the cells were harvested to extract total RNA and reverse transcribed into cDNA(operate as described above). Three independent experiments were performed. RNA-seq analysis then was performed. The NEBNext® Ultra™ RNA Library Prep Kit for Illumina® was used to prepare the RNA-seq libraries.
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kit (NEB, E7770) according to the manufacturer’s protocol.

treatment_protocol: The HUVEC cells were seeded in 96-well plate about 104 cells per well and treated the following day with either vehicle(DMSO) or PF-502(0-2μM) for 24hrs. Cells were washed in PBS and then incubated with 10μL of CCK-8 reagent(CK12, 500T, DOJINDO) for 2hrs, and the absorbance at 450nm was measured. The assay was performed in six replicate wells.

value: HUVECs

value: WT


title: 5_Batch1_5_EAA2NNZ2-01_S5_L005

value: baseline

value: TRUE

value: Negative

value: Abs

value: Nobs


title: Experiment2, Nr4a3 KO sample 3

description:
Exp2_Nr4a3_3
Exp2_DEseq.csv

value: Infected with lentivirus that encode gRNA targeting Nr4a5


title: Candida glabrata, treatment,rep3

city: guangzhou

first: Wu

last: Shuo

state: Guangdong

address: wushan

institute: South China Agricultural University

data_processing:
The library  was  sequenced on Illumina sequencing platform.
Low quality reads were trimmed by using Trimmomatic (version 0.38)(parameter settings :HEADCROP:8 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Quality control of raw reads was performed using FastQC (version 0.11.5).
Assembly: GCF_013267435.1,GCF_000002545.3,GCA_001576635.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Nakaseomyces glabratus

source_name: Candida glabrata

growth_protocol: Bacterial suspension culture at 37℃;Fungus suspension culture at 28℃

extract_protocol:
RNA was extracted using Invitrogen TRIzol® Reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
The fragmented mRNA was reverse transcripted with SuperScript II and then converted to double-stranded cDNA using RNaseH and DNA Pol I by random priming. After purification, the double-stranded cDNA was subjected to blunt-ending, dA addition to 3’-end and adapter ligation. Finally, PCR was carried out to enrich the adapter ligated cDNA and the libraries were analyzed by Agilent Bioanalyzer 2100 and quantified by qPCR before sequenced by the Illumina sequencing platform.

treatment_protocol: Microorganisms in logarithmic growth phase were cultured for 4 hours after adding MIC values essential oil or not.

value: Candida glabrata

value: treated with Neolamarckia cadamba essential oil for four hours


title: rat#5-control_cortex_7d

description:
control
SAMPLE 1

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

value: brain

tag: brain region

value: cortex

tag: activation agent

value: PBS treatment

value: 7 days


title: RNAseq_PF-502_rep2

value: HUVECs

tag: cell type

value: Primary human umbilical vein endothelial cells

tag: genotype


title: rat#13-control_cortex_7d

description:
control
SAMPLE 4

tag: time


title: Candida glabrata, treatment,rep2


title: 2_Batch1_2_5056_S2_L005

tag: visit

tag: site

value: Emavundleni

tag: rin

value: IVA

value: nonLD

tag: bmi

value: BV

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: Candida glabrata, treatment,rep1

value: Candida glabrata

value: treated with Neolamarckia cadamba essential oil for four hours


title: rat#15-control_cortex_7d

description:
control
SAMPLE 5

value: male

value: Wistar

value: TBI


title: RNAseq_PF-502_rep1

value: WT


title: Experiment2, Nr4a3 KO sample 1

description:
Exp2_Nr4a3_1
Exp2_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Nr4a3


title: GEX_Blood neutrophils

description: Drop-seq

value: Blood

tag: injected cell_line

value: neutrophils

value: FVB

value: no treatment


title: 1_Batch1_1_3408_S1_L005

value: baseline

value: Emavundleni

value: IVA

value: nonLD

value: TRUE

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: BV

tag: yeasts

value: Nobs

value: Never married

value: Secondary school, some or complete


title: Candida glabrata, control,rep3

value: Candida glabrata

tag: treatment

value: control


title: rat#7-control_cortex_7d

description:
control
SAMPLE 2

tag: animal

tag: Sex

value: male

tag: strain

value: Wistar

value: TBI

tag: tissue

value: brain

value: cortex

value: PBS treatment

value: 7 days


title: RNAseq_ctrl_rep3

value: HUVECs

tag: cell type

value: Primary human umbilical vein endothelial cells

tag: genotype

value: WT

value: Control


title: Experiment2, Cebpb KO sample 3

description:
Exp2_Cebpb_3
Exp2_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: 384_Batch6_25_560244386601_S105_L007

tag: visit

value: KEMRI

value: IIIA

value: LD

value: nonLD

value: FALSE

value: Negative

value: Abs

value: Nobs

tag: maritalstatus

value: Never married

value: Primary school, some or complete

value: No

value: Unchecked


title: Experiment2, Cebpb KO sample 2

description:
Exp2_Cebpb_2
Exp2_DEseq.csv


title: RNAseq_ctrl_rep2

value: HUVECs

value: Primary human umbilical vein endothelial cells

value: WT

value: Control


title: RNAseq_ctrl_rep1


title: Experiment2, Cebpb KO sample 1

description:
Exp2_Cebpb_1
Exp2_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: Experiment2, Nr4a3 KO sample 2

description:
Exp2_Nr4a3_2
Exp2_DEseq.csv

value: Infected with lentivirus that encode gRNA targeting Nr4a4


title: 371_Batch6_12_560226536601_S92_L006

value: baseline

tag: site

value: KEMRI

tag: rin

value: nonLD

value: FALSE

value: Married

value: Yes


title: Candida glabrata, control,rep2

value: Candida glabrata

value: control


title: Experiment2, NT sample 3

description:
Exp2_NT_3
Exp2_DEseq.csv

value: Infected with lentivirus that encode non-targeting gRNA


title: Human embryonic brain cortical tissue, gestational week 22

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description: HN 2-3

data_processing:
spaceranger-1.3.1
Assembly: GRCh38-2020-A
Supplementary files format and content: Loupe Browser File (extention .cloupe)

source_name: Brain (cortex)

extract_protocol:
Donated human brain tissues with consent was fresh-frozen, sectioned at 10um thickiness, and mounted on the gene expression slide provided in the 10X Visium kit
Spatial 3' v1
10X Library & Gel Bead Kit v3.1

value: Brain (cortex)

value: Gestational week 22

value: healthy, no known abnormality


title: 356_Batch5_69_6032_S77_L005

value: Emavundleni

tag: bmi

value: Negative

value: Intermediate

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: BJAB, Lyn, biol rep 2

city: Patras

first: Athanasios

middle: Nasir

last: Shaukat

state: Western Greece

address: Asklipiou 1

department: Department of Biochemistry

country: Greece

institute: University of Patras

data_processing:
Basecalling, de-multiplexing and filtering of low quality reads was performed within the Torrent Suite 5.12.3
Reads were trimmed with trimmomatic (Version 0.38) with the following parameters SLIDINGWINDOW:30:15 MINLEN:25
The trimmed files were initially aligned with the STAR aligner (v2.7.8a) with default parametes except the following: --sjdbOverhang 75 --outSAMmapqUnique 255 --chimSegmentMin 18 --chimScoreMin 12 --outFilterType BySJout
The unmapped reads were subsequently aligned to hg38 using bowtie2 (v2.4.5) using the --very-sensitive-local preset
The generated alignment files were then merged using picard MergeSamFiles (v2.18.2.1)
The unmapped reads were filtered out using samtools view (v1.15.1)
Read counts and differential gene expression analysis was performed with featureCounts (v2.0.1) and limma-voom (v3.50.1) respectively
Assembly: hg38
Supplementary files format and content: Normalized count matrix

source_name: BJAB

extract_protocol:
Cells in suspension from studied experimental conditions were isolated via centrifugation and lysed directly with TRIzol reagent (Invitrogen).
Total RNA extraction from 2 independent BJAB-Lck, BJAB-Lyn and BJAB/-Dox cell cultures was performed using TRIzol (ThermoFischer Scientific Inc.) according to the manufacturer’s protocol and was followed by DNase I (NEB) treatment. The quality of the RNA was visualized using agarose gel electrophoresis. Before the preparation of the RNA libraries the ribosomal RNA was depleted using the RiboMinusTM Eukaryote Kit v2 (ThermoFisher Scientific Inc.). Quantification of the RNAs was done using the Qubit RNA HS (High Sensitivity) Assay Kit (ThermoFisher Scientific Inc.) with the Qubit Fluorometer. The cDNA libraries were prepared from 100 ng of rRNA-depleted total RNA using the Ion Total RNA-Seq v2 Kit (ThermoFisher Scientific Inc.) according to the manufacturer’s instructions. In brief, the digestion of RNAs with RNase III to produce 200nt RNA fragments was followed by adapter ligation, reverse transcription, and 14 cycles of PCR amplification using the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (ThermoFisher Scientific Inc.). The quantity of the libraries was measured with the Qubit 1x dsDNA HS Assay Kit (ThermoFisher Scientific Inc.) and their quality was assessed using the Agilent High Sensitivity DNA Kit on the Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Template preparation and chip loading were performed on the Ion Chef system using the Ion 540™ Chef kit and an Ion 540™ chip. The single-end sequencing was carried out on an Ion GeneStudio S5 sequencer.

tag: cell line

value: BJAB

value: Human Burkitt lymphoma B cell line

value: Dox-induced Lyn overexpression

tag: time


title: BJAB, Lck, biol rep 2

value: Dox-induced Lck overexpression


title: BJAB, Lyn, biol rep 1


title: Experiment2, NT sample 1

description:
Exp2_NT_1
Exp2_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)


title: 348_Batch5_61_560236296601_S69_L005

value: baseline

value: KEMRI

value: nonLD

value: FALSE

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

value: Yes


title: 361_Batch6_2_KAA2PG4Q-01_S82_L006

value: WRHI

value: IIIA

value: LD

value: Negative

tag: mobilincus

tag: yeasts

value: Nobs

value: Married


title: Human embryonic brain cortical tissue, gestational week 24

description: HN 2-4

value: Brain (cortex)

value: Gestational week 24

value: healthy, no known abnormality


title: Experiment1, Cebpb KO sample 3

description:
Exp1_Cebpb_3
Exp1_DEseq.csv

value: Bone marrow

value: BMDCs

tag: treatment

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: Human embryonic brain cortical tissue, gestational week 20

description: HN 2-1

value: Gestational week 20


title: Human embryonic brain cortical tissue, gestational week 21

description: HN 2-2

value: Gestational week 21


title: BJAB, Lck, biol rep 1

value: BJAB

value: Human Burkitt lymphoma B cell line

value: Dox-induced Lck overexpression


title: Experiment1, Cebpb KO sample 2

description:
Exp1_Cebpb_2
Exp1_DEseq.csv

value: Cas9 expressing mice (JAX#026556)


title: Human embryonic brain cortical tissue, gestational week 15

description: HN 1-3

value: Gestational week 15


title: 327_Batch5_40_7168_S48_L004

value: Emavundleni

value: nonLD

value: FALSE

value: BV

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: Human embryonic brain cortical tissue, gestational week 17

description: HN 1-4

value: Brain (cortex)

value: Gestational week 17

value: healthy, no known abnormality


title: BJAB, -Dox, biol rep 2

value: no Dox


title: Experiment1, Cebpb KO sample 1

description:
Exp1_Cebpb_1
Exp1_DEseq.csv

value: Bone marrow

value: BMDCs

value: Infected with lentivirus that encode gRNA targeting Cebpb


title: Candida glabrata, control,rep1

value: Candida glabrata

value: control


title: 313_Batch5_26_560236366601_S34_L003

value: KEMRI

value: Negative

value: Abs

value: Intermediate

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes

value: Checked


title: 312_Batch5_25_560232256601_S33_L003

value: baseline

value: IB

value: LD

value: nonLD

value: FALSE


title: Experiment1, NT sample 3

description:
Exp1_NT_3
Exp1_DEseq.csv

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode non-targeting gRNA


title: 365_Batch6_6_560240746601_S86_L006

value: KEMRI

value: Negative

value: Unchecked


title: Experiment2, NT sample 2

description:
Exp2_NT_2
Exp2_DEseq.csv


title: Human embryonic brain cortical tissue, gestational week 13

description: HN 1-2

value: Brain (cortex)

value: Gestational week 13

value: healthy, no known abnormality


title: Experiment1, NT sample 2

description:
Exp1_NT_2
Exp1_DEseq.csv


title: Hippocampus, GSDMD knockout, room air exposure [GSD496]

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

data_processing:
Alignment with mm.GRCM39.104 genome build with Kallisto
Gene summarization and feature counts with tximport
Differental expression with DESeq2
Assembly: mm.GRCM39.104

molecule: polyA RNA

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from tissue homogenates with QIAGEN Rneasy kit per manufacturer's intructions
Afer polyA selection, paired-end RNA-sequencing with 150bp was done with a depth of 30M reads.
Library was generated at BGI Genomics

tag: breed

value: GSDMD knockout

value: Hippocampus

tag: developmental stage

value: postnatal day 15

value: room air


title: Human embryonic brain cortical tissue, gestational week 10

description: HN 1-1

tag: tissue

tag: cell type

value: Gestational week 10


title: 305_Batch5_18_4384_S26_L002

tag: visit

value: Emavundleni

value: IIIA

value: LD

value: nonLD

value: Abs

value: Nobs

value: Never married

value: Secondary school, some or complete

value: No


title: 295_Batch5_8_8254_S16_L001

value: IVD

value: FALSE

value: Negative

value: Positive

value: BV

tag: maritalstatus

value: Unchecked


title: Hippocampus, GSDMD knockout, hyperoxia exposure [GSD495]

tag: genotype

value: GSDMD knockout

value: Hippocampus

value: postnatal day 15

value: hyperoxia (85%)


title: Hippocampus, GSDMD knockout, hyperoxia exposure [GSD494]


title: Hippocampus, GSDMD knockout, hyperoxia exposure [GSD491]


title: Secondary PDL1 screen, Repeat 2, High expression [PDL1_Secondary_2_H]

description: PDL1 Secondary Screen.csv

data_processing:
Fastq files were demultiplexed using Bcl2fastq (v2.20.0.422)
The Fastx toolkit (v0.0.13) was used to convert the fastq files to fasta files
Forward and reverse adapters were trimmed using cutadapt (v3.4)
Alignment was performed to the reference library (genome wide or secondary) by using bowtie1 (v 1.3.1)
Assembly: Genome wide - GPP library, Secondary - attached in supplementary material
Supplementary files format and content: Comma-delimited files listing counts for each sgRNA

source_name: Primary cells

value: Primary cells

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: RS4;11 co-cultured with MSCs-LV-IFI6 _rep3

city: Guiyang

first: Chengyun

state: Guizhou

address: No. 28, Guiyi Street, Yunyan District

institute: Affiliated Hospital of Guizhou Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of P value below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: RS4;11 co-cultured with MSCs-LV-IFI6

growth_protocol: The human ALL cell lines RS4;11 were cultured in an RPMI-1640 medium supplemented with 10% fetal bovine serum, 100 mg/mL streptomycin and 100 units/mL penicillin under 37 °C and 5% CO2 conditions.BM-MSCs were cultured in the complete medium of adult BM-MSCs (Saiye, Shanghai, China).

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

treatment_protocol: RS4;11 cell lines (n=3) co-cultured with MSCs transfected with empty vector (EV) or MSCs transfected with IFI6 overexpress clone lentiviral particle (LV-IFI6) for 72 h.

value: RS4;11 + MSCs-LV-IFI6

value: Overexpression of IFI6

value: RS4;11 cell lines co-cultured with MSCs-LV-IFI6


title: Secondary PDL1 screen, Repeat 2, Low expression [PDL1_Secondary_2_L]

description: PDL1 Secondary Screen.csv


title: Experiment1, NT sample 1

description:
Exp1_NT_1
Exp1_DEseq.csv

source_name: Bone marrow

value: Bone marrow

value: BMDCs

value: Cas9 expressing mice (JAX#026556)

value: Infected with lentivirus that encode non-targeting gRNA


title: 288_Batch5_1_FAA2NVZH-01_S9_L001

source_name: endocervical cells

value: baseline

tag: site

value: WRHI

tag: rin

value: LD

value: FALSE

value: Negative

value: Abs

value: Nobs

value: Married

value: Secondary school, some or complete

value: No


title: RS4;11 co-cultured with MSCs-LV-IFI6 _rep1

tag: cell line

value: RS4;11 + MSCs-LV-IFI6


title: BJAB, -Dox, biol rep 1

value: BJAB

value: Human Burkitt lymphoma B cell line

value: no Dox

tag: time


title: Hippocampus, GSDMD knockout, room air exposure [GSD490]

value: GSDMD knockout

value: Hippocampus

value: postnatal day 15

value: room air


title: 245_Batch4_30_BAA2PDWS-01_S88_L006

value: WRHI

value: nonLD

tag: bmi

tag: ngonorrhoeae

value: BV

value: Unchecked


title: 217_Batch4_2_JAA2NSWZ-01_S60_L004

value: IIIA

value: LD

value: FALSE

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

value: Never married

value: Yes


title: Secondary PDL1 screen, Repeat 1, High expression [PDL1_Secondary_1_H]

description: PDL1 Secondary Screen.csv

value: Primary cells

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: Hippocampus, wild-type, hyperoxia exposure [GSD408]

value: wild-type

value: Hippocampus

value: postnatal day 15


title: Secondary PDL1 screen, Repeat 1, Low expression [PDL1_Secondary_1_L]

description: PDL1 Secondary Screen.csv


title: RS4;11 co-cultured with MSCs-EV _rep3

source_name: RS4;11 co-cultured with MSCs-EV

value: RS4;11 + MSCs-EV

value: WT

value: RS4;11 cell lines co-cultured with MSCs-EV


title: RS4;11 co-cultured with MSCs-EV _rep2


title: Genome wide PDL1 screen, Low expression [PDL1_GW_L]

description: PDL1 GW Screen.csv


title: RS4;11 co-cultured with MSCs-EV _rep1


title: 208_Batch3_65_560233946601_S51_L004

value: baseline

value: KEMRI

value: nonLD

tag: mobilincus

tag: yeasts

value: Nobs

value: Post-secondary school

value: No

value: Unchecked


title: Hippocampus, wild-type, hyperoxia exposure [GSD406]

tag: breed

tag: treatment

value: hyperoxia (85%)


title: 203_Batch3_60_560243366601_S46_L003

value: FALSE

value: Negative

value: Abs

value: Intermediate

value: Never married

value: Secondary school, some or complete

value: Yes

value: Checked


title: MSCs co-culture with Nalm-6 cell lines-3

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
Hisat2 2.0.4 mapping to reference genome
count counting
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: bone marrow

growth_protocol: BM-MSCs were cultured in the complete medium of adult BM-MSCs (Saiye, Shanghai, China)

extract_protocol:
The total RNA of HeLs cells was extracted with Trizol (Invitrogen) under the manufacturer’s guiding.
The cDNA libraries were constructed for each pooled RNA sample using the NEBNext® UltraTM Directional RNA library Prep Kit for Illumina according to the manufacturer’s instructions.

treatment_protocol: MSCs cultured alone for 72 h and MSCs co-cultured with Nalm-6 cell lines for 72 h

tag: tissue

value: bone marrow

value: mesenchymal stem cells

value: BM-MSCs+Nalm-6 cell lines

value: MSCs co-culture with Nalm-6 cell lines


title: Genome wide PDL1 screen, High expression [PDL1_GW_H]

description: PDL1 GW Screen.csv

extract_protocol:
Genomic DNA from the sorted cells were extracted using Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions and eluted with 50 ul of water.
Genomic DNA was purified and used for 2 PCR reactions following the protocol that was described in Parnas et al  Cell. 2015 Jul 30;162(3):675-86.

value: Primary cells

tag: cell type

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: RS4;11 co-cultured with MSCs-LV-IFI6 _rep2

value: RS4;11 + MSCs-LV-IFI6

value: Overexpression of IFI6

value: RS4;11 cell lines co-cultured with MSCs-LV-IFI6


title: Hippocampus, wild-type, hyperoxia exposure [GSD405]

value: wild-type

value: Hippocampus

tag: developmental stage

value: postnatal day 15

value: hyperoxia (85%)


title: MSCs co-culture with Nalm-6 cell lines-2


title: Hippocampus, wild-type, hyperoxia exposure [GSD404]


title: 264_Batch4_49_4064_S107_L007

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

tag: visit

value: baseline

value: Emavundleni

value: IIIA

value: LD

value: nonLD

value: FALSE

value: Negative

value: Positive

value: Abs

value: Nobs

tag: maritalstatus

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: Secondary CD86 screen, Low expression [CD86_Secondary_L]

description: CD86 Secondary Screen.csv

value: Primary cells

value: Bone marrow - derived dendritic cells

tag: genotype

value: constitutively expressed Cas9

value: Lentivirus infection with secondary CRISPR pooled library


title: 178_Batch3_35_CAA2P38C-01_S21_L002

value: baseline

tag: site

value: WRHI

tag: rin

value: BV


title: Hippocampus, wild-type, room air exposure [GSD401]

value: wild-type

value: Hippocampus

value: postnatal day 15

value: room air


title: Secondary CD86 screen, High expression [CD86_Secondary_H]

description: CD86 Secondary Screen.csv

tag: cell line


title: 174_Batch3_31_3280_S17_L002

value: Emavundleni

value: nonLD

value: FALSE

tag: bmi

value: Negative

value: Positive

value: Abs

value: Intermediate


title: 133_Batch2_61_7200_S69_L005

value: LD

tag: ngonorrhoeae

value: Obs

value: Never married

value: Secondary school, some or complete

value: Unchecked


title: MSCs culture alone-3

value: bone marrow

value: mesenchymal stem cells

value: BM-MSCs

value: MSCs culture alone


title: Hippocampus, GSDMD knockout, room air exposure [GSD489]

value: GSDMD knockout

value: Hippocampus

value: postnatal day 15

value: room air


title: Hippocampus, wild-type, room air exposure [GSD400]

value: wild-type


title: 126_Batch2_54_FAA2NS6H-01_S62_L005

value: baseline

value: WRHI

value: IIIA

value: nonLD

value: FALSE

value: Negative

tag: chlamydiatrachomatis

value: Nobs

value: Yes


title: Genome wide CD86 screen, Repeat 2, High expression [CD86_GW_2_H]

description: CD86 GW Screen.csv

value: Primary cells

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: Hippocampus, wild-type, room air exposure [GSD399]


title: MSCs culture alone-2

value: bone marrow

value: mesenchymal stem cells

value: BM-MSCs

value: MSCs culture alone


title: 43_Batch1_43_560244166601_S43_L007

value: KEMRI

tag: lactobacilli

value: Abs

value: BV

value: Married

value: Primary school, some or complete

value: Checked


title: MSCs culture alone-1


title: Genome wide CD86 screen, Repeat 1, Low expression [CD86_GW_1_L]

description: CD86 GW Screen.csv


title: Hippocampus, wild-type, room air exposure [GSD398]

value: wild-type

value: Hippocampus

value: postnatal day 15

value: room air


title: Kaede-green and Kaede-red (from colon) CD45+ splenocytes, 7-wk-old Kaede.B6 mice (12 samples)

city: Boston

first: Silvia

last: Galvan-Pena

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Immunology

institute: Harvard Medical School

description: 12 samples (6  Kaede-green and 6 Kaede-red CD45+ splenocytes) were hashed together into a single 10X scRNA-seq run

data_processing:
Sequenced reads were demultiplexed, aligned, assigned to cells, and output as count matrices using Cell Ranger (10x Genomics).
Hash-by-cell matrices were computed using CITE-seq-count.
Cells with no or multiple hashes, high mitochondrial content, low gene number, low UMI number, or lineage markers of contaminants were filtered out in Seurat
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Spleen

extract_protocol:
Immunocytes were released by mechanical disruption followed by filtering and washed in RPMI containing 5% fetal calf serum (FCS). Red blood cells were lysed prior to filtering using ACK lysing buffer Cells were then purified by fluorescence-activated cell sorting. Single cells were then sent to the Broad Institute Genomics Platform, which performed encapsulation following 10x Genomics protocols.
10x Genomics library prep, 3' v3 chemistry

value: Spleen

value: CD45+ immune cells

tag: strain

tag: age

tag: Sex

value: Female

value: Colon photoconversion


title: MSCs co-culture with Nalm-6 cell lines-1

value: bone marrow

value: mesenchymal stem cells

value: BM-MSCs+Nalm-6 cell lines

tag: treatment

value: MSCs co-culture with Nalm-6 cell lines


title: B-NC L1 134A34

status: Public on Sep 12 2023

city: Shenzhen

first: Yue

last: Liu

address: No. 3004, Longgang Section, Longgang Avenue, Longgang District

institute: Longgang E.N.T Hospital & Shenzhen Key Laboratory of E.N.T, Institute of E.N.T

description: OC1 cells, siControl NC

data_processing:
Base-calling was done by  Illumina’s Real Time Analysis (RTA) software (Version 3.0) to generate the bcl files, then followed by bcl2fastq (Version 2.20) to transfer the bcl files to fastq format. For both steps the default parameters were adopted.
Quality control and data filtering was performed by fastp software (Version 0.21.0) with default parameters.
Raw counts matrix was generated by the salmon software (Version 1.4.0), wherein an alignment-free algorithm was used to quantify reads (transcripts). The salmon-used index was generated from cDNA data of Rattus_norvegicus (mRatBN7.2). Raw counts of transcripts were mapped to genes by the R package of tximport (version 1.12.3) based on the annotation information from mRatBN7.2.110.
Raw counts normalization was done by DESeq2 software (version 1.24.0) with default parameters.
Assembly: mRatBN7.2.110.
Supplementary files format and content: Two processed files were generated. The first is named as gene_count.csv, containing gene-level raw counts for each sample. The rows are gene IDs, while the columns are sample IDs.
Supplementary files format and content: The second processed file is named as DEseq_norm.Rdata, containing the normalized counts calculated by DESeq2 software. It can be directly loaded by R language.

growth_protocol: OC1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
OC1 cells were placed into 6-well plates (3.0 × 105/mL) containing with 1ml culture medium and 15 µl siRNA in Opti medium were used to transfected cells with 2μl Lipo3000 per well
RNA library for Strand-specific RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA was synthesised using DNA polymerase I and dNTPs (dATP, dUTP, dCTP and dGTP). Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template without U was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: Transfected cells were collected via 0.25% Trypsin-EDTA （Thermo Fisher Scientific）

value: cochlear sensory epithelial cells

value: WT

value: plasmid transfection


title: D-1928 L1 139A39

description: OC1 cells, siBcl-2 1928

value: Bcl-2 knowdown


title: A-1423 L1 129A29

description: OC1 cells, siBcl-2 1423


title: B-1928 L1 133A33

description: OC1 cells, siBcl-2 1928


title: Genome wide CD86 screen, Repeat 2, Low expression [CD86_GW_2_L]

city: Jerusalem

first: Oren

address: Faculty of Medicine, Ein-Kerem medical center

institute: The Hebrew University of Jerusalem

description: CD86 GW Screen.csv

value: Primary cells

value: Bone marrow - derived dendritic cells

value: constitutively expressed Cas9

value: Lentivirus infection with genome - wide CRISPR pooled library


title: C-NC L1 137A37

description: OC1 cells, siControl


title: A-1928 L1 130A30

description: OC1 cells, siBcl-2 1928


title: D-NC L1 140A40

description: OC1 cells, siControl


title: C-1928 L1 136A36

description: OC1 cells, siBcl-2 1928


title: B-1423 L1 132A32

description: OC1 cells, siBcl-2 1423


title: D-1423 L1 138A38

description: OC1 cells, siBcl-2 1423


title: C-1423 L1 135A35

description: OC1 cells, siBcl-2 1423


title: A-NC L1 131A31

description: OC1 cells, siControl


title: Genome wide CD86 screen, Repeat 1, High expression [CD86_GW_1_H]

description: CD86 GW Screen.csv


title: WholeRoot, 0.55mMN, 4d, rep3

city: Seeland

first: Anja

last: Hartmann

state: Saxony-Anhalt

address: Corrensstraße 3

department: PZB

country: Germany

institute: IPK Gatersleben

description: Gene expression after 4 days of 0.55 mM nitrogen treatment

hyb_protocol: RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 021169_D_F_20140929) to obtain background subtracted and spatially detrended Processed Signal intensities. Analysis of microarray data was performed with the R package limma. Raw feature intensities were background corrected using “normexp”, and “quantile” normalization method was used to normalize between arrays.

organism: Arabidopsis thaliana

source_name: Whole root, 0.55 mM N, 4 days

growth_protocol: Plants were pre-cultured for seven days on 0.5 MS Difco agar and then transferred grown on 0.5 MS Difco agar using 11.4 and 0.55 mM nitrogen for control and N-deficient conditions, respectively.

extract_protocol: RNA was extracted from root material using an RNeasy plant mini kit (Qiagen) with on-column DNase treatment according to the manufacturer’s instructions. cDNA was prepared using  random hexamer primers and SuperScript II reverse transcriptase (Life Technologies)  according to the manufacturer’s protocol.

treatment_protocol: Plants were grown on 0.5 MS Difco agar using 11.4 and 0.55 mM nitrogen for control and N-deficient conditions, respectively.

tag: tissue

value: whole root

tag: time after treatment

value: 4 days


title: WholeRoot, 11.4mMN, 4d, rep3

description: Gene expression after 4 days of 11.4 mM nitrogen treatment

source_name: Whole root, 11.4 mM N, 4 days

label_protocol: RNA amplification, labeling and hybridization to Agilent microarrays (Arabidopsis (V4, 021169) Gene Expression Microarray) were conducted following the manufacturer’s protocol (Agilent Technologies).


title: WholeRoot, 0.55mMN, 4d, rep1


title: endometrium, seminal vesicle-deficient mated mated, rep4

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Sequences were assessed for quality using FastQC, sequencing adapters trimmed using AdapterRemoval version 2 and aligned to the GRCm38/mm10 mouse reference genome sequence (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/) using STAR [27]
Gene counts were identified using featureCounts [28], which were then transferred to R for downstream analysis
All downstream differential expression analyses were carried out using R/Bioconductor packages limma-voom [29] and edgeR [30, 31]
Assembly: GRCm38/mm10 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.20/)

source_name: endometrium

growth_protocol: C57Bl/6 females were provided food and water ad libitum and housed under controlled temperature and a 12h light/12h dark cycle in a pathogen-free facility.

extract_protocol:
Total RNA was extracted using Trizol and the isopropanol protocol, followed by Dnase treatment using TURBO DNA-free kit
TruSeq Stranded total RNA Library Prep Kit

treatment_protocol: Females were mated with Balb/c males (intact, vasectomised, seminal vesicle-deficient or seminal vesicle-deficient/vasectomised), and tissues were collected 3.5 days after mating. Estrous females were used controls.

value: endometrium

value: mated with seminal vesicle-deficient male


title: endometrium, seminal vesicle-deficient/vasectomised mated, rep2

value: mated with seminal vesicle-deficient/vasectomised male


title: endometrium, seminal vesicle-deficient/vasectomised mated, rep3


title: endometrium, seminal vesicle-deficient/vasectomised mated, rep1


title: endometrium, seminal vesicle-deficient/vasectomised mated, rep4


title: WholeRoot, 11.4mMN, 2d, rep3

description: Gene expression after 2 days of 11.4 mM nitrogen treatment

source_name: Whole root, 11.4 mM N, 2 days

value: 2 days


title: WholeRoot, 0.55mMN, 2d, rep2

description: Gene expression after 2 days of 0.55 mM nitrogen treatment

source_name: Whole root, 0.55 mM N, 2 days


title: endometrium, seminal vesicle-deficient mated mated, rep2


title: WholeRoot, 0.55mMN, 1d, rep2

description: Gene expression after 1 day of 0.55 mM nitrogen treatment

source_name: Whole root, 0.55 mM N, 1 days

value: 1 day


title: WholeRoot, 0.55mMN, 2d, rep3


title: WholeRoot, 11.4mMN, 4d, rep1


title: WholeRoot, 11.4mMN, 4d, rep2


title: WholeRoot, 11.4mMN, 2d, rep2


title: WholeRoot, 0.55mMN, 1d, rep3


title: endometrium, seminal vesicle-deficient mated mated, rep3


title: WholeRoot, 11.4mMN, 2d, rep1


title: WholeRoot, 0.55mMN, 4d, rep2


title: WholeRoot, 0.55mMN, 1d, rep1


title: endometrium, seminal vesicle-deficient mated, rep1


title: endometrium, vasectomised mated, rep4

value: mated with vasectomised male


title: WholeRoot, 11.4mMN, 1d, rep2

description: Gene expression after 1 day of 11.4 mM nitrogen treatment

source_name: Whole root, 11.4 mM N, 1 days


title: endometrium, vasectomised mated, rep3


title: WholeRoot, 11.4mMN, 1d, rep3


title: WholeRoot, 11.4mMN, 0d, rep2

description: Gene expression after 0 days of 11.4 mM nitrogen treatment

source_name: Whole root, 11.4 mM N, 0 days

value: 0 days


title: WholeRoot, 11.4mMN, 1d, rep1


title: WholeRoot, 0.55mMN, 2d, rep1


title: WholeRoot, 11.4mMN, 0d, rep1


title: WholeRoot, 11.4mMN, 0d, rep3


title: endometrium, vasectomised mated, rep2


title: endometrium, vasectomised mated, rep1


title: endometrium, intact mated, rep4

value: mated with Intact male


title: endometrium, intact mated, rep3

value: WT


title: endometrium, intact mated, rep1


title: endometrium, intact mated, rep2


title: endometrium, estus, rep1

value: estrous female, no treatment


title: endometrium, estus, rep2


title: N2, kin-19 RNAi, rep 3

city: Québec

first: VIVEK

middle: NILESH

last: SHAH

state: Québec

address: 9 Rue McMahon

department: Département de biologie moléculaire, de biochimie médicale et de pathologie

country: Canada

institute: Université Laval

description: small RNA analysis

data_processing:
The samples are debarcoded using the 8 nt barcodes
The 3' AGATCGGAA and beyond are removed and only reads of size >16 are kept
Small RNAs are mapped to genome and cDNA using Bowtie 0.12.7 and at most 3 mismatches are considered
The samples were normalized to the total small RNAs including miRNAs, 22G-RNAs, and 21U-RNAs.
Assembly: C. elegans WS215
Supplementary files format and content: tab-delimited text files includes normalized RPM for each sample

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Worms were grown on NGM IPTG plates with OP50 expressing ds RNAi against control or kinase RNAi at 20 °C.

extract_protocol:
RNA isolation by TRIzol reagent
Small RNA cloning was performed with the NEBNext multiplex small RNA library kit and according to the manufacturer’s protocol.

value: whole worm

tag: developmental stage

value: Young adults

value: N2 (Bristol)

value: kin-19 RNAi


title: N2, kin-3 RNAi, rep 4

description: small RNA analysis

value: kin-3 RNAi


title: N2, kin-3 RNAi, rep 3

description: small RNA analysis


title: N2, control RNAi, rep 3

description: small RNA analysis

value: control RNAi


title: N2, control RNAi, rep 4

description: small RNA analysis


title: N2, kin-19 RNAi, rep 4

description: small RNA analysis


title: N2, kin-10 RNAi, rep 2

description: small RNA analysis

value: kin-10 RNAi


title: N2, kin-3 RNAi, rep 2

description: small RNA analysis


title: N2, kin-19 RNAi, rep 2

description: small RNA analysis


title: N2, control RNAi, rep 2

description: small RNA analysis


title: N2, kin-10 RNAi, rep 1

description: small RNA analysis


title: N2, kin-19 RNAi, rep 1

description: small RNA analysis


title: N2, kin-3 RNAi, rep 1

description: small RNA analysis


title: endometrium, estus, rep4

value: endometrium


title: N2, control RNAi, rep 1

description: small RNA analysis


title: C. elegans sorted oocyte P-bodies Rep2

city: Nice

first: Arnaud

last: Hubstenberger

address: 28 avenue Valrose

department: IBV

country: France

institute: Université Côte D'Azur

data_processing:
Demultiplexing was performed by bcl2fastq application, sequencing reads were checked for quality by FastQC and 4 bases of the 5’-end, and 1 base of the 3’-end were trimmed. Read mapping was then performed on a local Galaxy server.
Reads were aligned to the C. elegans genome (WBcel235.96) using HISAT2 v2.1.0. For the alignment, the following stranded revers-forward design parameters were used: function governing the maximum number of ambiguous characters was allowed, maximum mismatch penalty = 6, minimum mismatch penalty = 2, maximum soft clipping penalty = 2, minimum soft clipping penalty = 1, ambiguous read penalty = 1, read gap open penalty = 5, read gap extend penalty = 3, reference gap open penalty = 5, reference gap extend penalty = 3, penalty for canonical splice sites = 0, penalty for non-canonical splice sites = 12, minimum intron length = 20, maximum intron length = 140000
To estimate relative RNA abundance for each transcript species, FPKM (Fragments Per Kilobase Million) and TPM (Transcripts Per Kilobase Million) were computed with StringTie using default parameters.
Raw read counts were determined for each annotated gene by HTseq-count using default stranded parameters.
DESeq2 Bioconductor package was used to detect fold-change differences between groups taking into account internal normalization with correction for library size and RNA composition bias.
Assembly: WBcel235.96
Supplementary files format and content: Gene_abundances_StringTie (samples in columns, replicates numbered1-3)
Supplementary files format and content: Raw_reads_HTSeqCounts (samples in columns, replicates numbered1-3)

source_name: germline

extract_protocol:
Total RNA was extracted using a miRNeasy FFPE kit (Qiagen) with adaptations: i) deparaffinization step was skipped, and ii) since sorted oocyte P-bodies were subcellular fractions, the separation of cell debris by centrifugation was omitted for these samples.  The subsequent steps followed the recommendations of the supplier. the process included DNase-I treatment and revers crosslink of fixed fractions.
Ten ng of total RNA were used. Briefly, paired-end RNA-seq libraries with barcodes were generated using SMARTer Stranded Total RNA-Seq Kit v2 - Pico (Takara). The quality and average size of the libraries were confirmed with Agilent High Sensitivity DNA Chips (Agilent 2100 BioAnalyser), and the concentration was measured with dsDNA HS Assay Kit (Invitrogen) using a Qubit 4.0. For RNA-seq, libraries were pooled in equimolar concentrations of 4 nM.

tag: strain -_flourescent_labelling

value: fog2; car1:GFP, pgl1:RFP

value: female

value: oocyte arrest

tag: time

value: Day 3

tag: selection

value: sorting by FAPS

tag: cell type

value: germline


title: C. elegans sorted oocyte P-bodies Rep1


title: C. elegans sorted oocyte P-bodies Rep3


title: C. elegans whole animal extracts Rep-2

source_name: somatic and germline

value: no dissection, no FAPS

value: somatic and germline


title: C. elegans whole animal extracts Rep-1


title: N2, kin-10 RNAi, rep 3

description: small RNA analysis

tag: genotype


title: C. elegans whole animal extracts Rep-3


title: N2, kin-10 RNAi, rep 4

description: small RNA analysis


title: C. elegans whole oocytes Rep-3

value: dissected


title: PC3_5_0_Era_1

city: nan ning

first: 周

last: 青鸟

address: shaungyonglu street num 22

institute: Guangxi Medical University

description:
treatment
PC3_group_gene_fpkm.txt

data_processing:
Illumina Casava2.19 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 hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Prostate

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

value: Prostate

tag: cell line

value: Prostate cancer cells

value: WT