title: Liver_ZT23_rep3

hyb_protocol: Following fragmentation, 3.5 microgrammes of ssDNA were hybridized for 16 hr at 45C on MoGene 2.0 Mouse Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36.
MoGene-2_0-st.pgf and MoGene-2_0-st.clf
MoGene-2_0-st-v1.na36.mm10.probeset.csv

growth_protocol: 13 week old C56bl/6J male mice were feed with chow diet during active period (from ZT12 to ZT24) in a fooding cage and transfert into a fasting cage (without any trace of food) everyday at ZT0 until ZT12. Animals were trained to this fooding  protocol during 11 days before starting experiment

value: male

value: 13 week old


title: m3.2

status: Public on May 24 2023

type: SRA

city: Houston

first: Swathi

last: Arur

state: Texas

address: 6767 Bertner Ave,

department: Genetics

country: USA

institute: MD Anderson Cancer Center

library_source: transcriptomic

data_processing:
Trimmed adaptor reads and low quality (Q > 30) base pairs using Cutadapt v1.18
Quality check with FastQC v0.11.5
Read mapping was performed using STAR Alignmer v2.4.0 to the C. elegans reference genome WS259
Mapping results were summarized to counts with featureCount v1.5.3
Differential Expression analysis performed on features with > 2 reads in at least 8 of 12 oocytes using DESeq2 v1.32.0
Assembly: C. elegans WS259
Supplementary files format and content: comma separated file including the counts for each mapped feature per oocyte position, per biological replicate
Supplementary files format and content: comma separated file with DESeq results between the -1 and -5 oocyte
Supplementary files format and content: comma separated file with DESeq results between the -1 and -3 oocyte
Supplementary files format and content: comma separated file with DESeq results between the -3 and -5 oocyte

molecule: total RNA

organism: Caenorhabditis elegans

source_name: Oocyte

extract_protocol:
Freshly collected C. elegans oocytes were lysed in 5.25 µl of lysis buffer with 2 U/µl of RNase inhibitor (Takara Bio) and then promptly frozen at -80 °C.
Libraries were prepared using SMART-seq v4 3’ DE Kit (Takara Bio) following the manufacturer’s manual

tag: cell type

value: Oocyte

tag: position

tag: genotype

value: Wildtype

tag: developmental stage

value: Adult

tag: treatment


title: Liver_ZT20_rep2

type: RNA

city: Lille

first: Alexandre

last: Berthier

address: U1011, Bâtiment J&K, Bd du Pr Leclerc

country: France

institute: Inserm

scan_protocol: GeneChips were scanned using GeneChip Scanner GCS3000.

label: biotin

organism: Mus musculus

source_name: Liver

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 300ng total RNA (GeneChip® WT PLUS Reagent Kit, Affymetrix).

extract_protocol: Total RNA was extracted using Nucleospin RNA kit from Macherey Nagel according to the manufacturer's instructions.

tag: strain

tag: Sex

tag: age

tag: time point

tag: replicate


title: Colonic epithelial cells

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global normalized, background subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: TRABID KI/+

label_protocol: cDNA and Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: Total RNA extracted using RNeasy Mini kit (QIAGEN, 74106) following manufacturer's instructions.

value: colonic epithelial cells

tag: genotype/variation

value: TRABID KI/+

source_name: TRABID KI/KI

value: TRABID KI/KI


title: Liver_ZT23_rep1


title: Liver_ZT20_rep3


title: m3.1


title: Liver_ZT20_rep1


title: Liver_ZT23_rep2


title: m1.4


title: Screening_ATP6_pairID_75 [2E3]

city: Cambridge

first: Lindsey

last: Van Haute

address: Hills Road

department: MRC Mitochondrial Biology Unit

country: United Kingdom

institute: University of Cambridge

library_source: genomic

data_processing:
Quality and 3' end adapter trimming with Trim_Galore!
Reads longer than 20nt were aligned to ChrM (GRCm38)
Samtools mpileup and Cutadapt to count nucleotides surrounding the editing site
Assembly: GRChm38
Supplementary files format and content: xlsx file with off target %, on target % and average coverage

molecule: genomic DNA

source_name: NIH-3T3 cells

growth_protocol: Cells were cultured at 37 °C under 5 % (vol/vol) CO2 in complete Dulbecco's Modified Eagle Medium (DMEM) (4.5 g/L glucose 2 mM glutamine, 110 mg/ml sodium pyruvate), supplemented with 10% calf bovine serum with iron, 5% penicillin/streptomycin (all from Gibco) and 50 µg/ml uridine (Sigma, cn. U3750). The Atp6 animals were maintained in a temperature- and humidity-controlled animal care facility with a 12-h light/12-h dark cycle and free access to water and food, and they were sacrificed by cervical dislocation.

extract_protocol:
NIH/3T3 mouse cells were collected by trypsinization, washed once in PBS and re-suspended in lysis buffer (1mM EDTA, 1 % Tween20, 50 mM Tris (pH = 8)) with 200 µg/ml of proteinase K. Lysates were incubated at 56 ºC with agitation (300 RPM) for 1 h, and then incubated 95 ºC for 10 min before use in downstream applications. Genomic DNA from mouse ear biopsies was extracted with a Maxwell® 16 Tissue DNA Purification Kit in a Maxwell® 16 Instrument (Promega), according to manufacturer´s instructions.
Illumina NexteraXT

treatment_protocol: NIH/3T3 mouse cells plated in 6-well tissue culture plates at a confluency of 70% were transfected with 3200 ng of each monomer (L and H - see pairID), or 6400 ng of plasmid DNA when using Tandem architectures in a single plasmid (L + H), with 16 µl of FuGENE-HD (Promega), following manufacturer´s guidelines.

tag: ddcbe pair id used

tag: days after transfection

tag: target

value: mtDNA


title: sperm_PANDORAseq-control rep2

city: Riverside

first: Changcheng

last: Zhou

state: California

address: 900 University Avenue

department: Biomedical Sciences

institute: The University of California Riverside

description:
15-50 nt RNA
RNAs were treated with T4PNK, then AlkB before cDNA library construction.

data_processing:
Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) the reads containing “N”; 2) the reads containing more than four bases with quality score <10; 3) the reads containing more than six bases with quality score is <13; 4) the reads with 5’ primer contaminants or without 3’ primer; 5) The reads without the insert tag; 6) the reads with ploy A.; and 7) the reads shorter than 15 nt and longer than 45 nt. The sequencing data analyses were performed upon the clean reads after data filtration.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: sperm

growth_protocol: 8 week old WT male mice were exposed to DCHP for 4 weeks by oral gavage

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen). Then small RNAs sized at 15-50nt were excised from 15% (w/v) urea polyacrylamide gel.
Small RNA libraries were constructed according to NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs).

treatment_protocol: small RNA-seq processed with PANDORA-seq were treated wih AlkB and PNK4

tag: tissue

value: sperm

value: wild type

value: DCHP oral gavage

tag: time

value: 4 weeks


title: Liver_ZT16_rep3


title: sperm_PANDORAseq-control rep1


title: Screening_COIII_pairID_74 [2E2]


title: m1.2


title: m1.3


title: Liver_ZT14_rep2


title: Liver_ZT16_rep1


title: Screening_COIII_pairID_73 [2E1]


title: Liver_ZT16_rep2


title: Liver_ZT14_rep3


title: mtDNAwide_Cytb_T2A_Stable_without HHR_pairID_42 [5E12]


title: m1.1


title: Liver_ZT14_rep1


title: HN2

city: Yangzhou

first: Rugen

last: Xu

address: 88 South Daxue Road, Yangzhou, Jiangsu Province

department: Agricultural College

country: China

institute: Yangzhou university

description:
non-infected leaves, non-diseased field, rep2
HN2

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: Hordeum_vulgare.IBSC_v2.50
Supplementary files format and content: Excel files include FPKM values for all samples

organism: Hordeum vulgare

source_name: non-infected leaves

growth_protocol: Growing under natural conditions in the field

extract_protocol:
Total RNA was extracted using an RNA simple Total RNA Kit (DP441, Tiangen).  A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations
The mRNA was purified from total RNA using poly-T oligo-attached magnetic beads

treatment_protocol: Plant materials are planted in diseased and non-diseased fields respectively

value: non-infected leaves

tag: cell line

value: barley

value: leaves

value: non-diseased field


title: sperm_PANDORAseq-treated rep1


title: HN3

description:
non-infected leaves, non-diseased field, rep3
HN3

tag: cell type


title: HN1

description:
non-infected leaves, non-diseased field, rep1
HN1


title: mtDNAwide_WT_T2A_Stable_without HHR_pairID_ [5E10]

value: empty


title: mtDNAwide_Nd3_T2A_Stable_without HHR_pairID_32 [5E11]


title: UN3

description:
resistant leaves, diseased field, , rep3
UN3

source_name: resistant leaves

value: resistant leaves

value: diseased field


title: STB-Kr Rep3

city: Paris

first: Mickael

last: Orgeur

address: 25-28 rue du Docteur Roux

institute: Institut Pasteur

data_processing:
Reads were mapped against the reference genome of M. tuberculosis H37Rv using BWA-MEM v0.7.17-r1188 (parameters: -M; -h 1000).
Uniquely-mapped reads were extracted from the alignment maps according to the XA tag using the Python wrapper pysam v0.20.0 of SAMtools.
Reads mapped on gene features were counted using featureCounts v2.0.4 (parameters: -s 2; --primary).
Read counts were normalized and transformed by regularized logarithm using DESeq2 v1.38.3, and differential expression analysis was performed using a FDR of 0.05.
Assembly: Mycobacterium tuberculosis H37Rv AL123456.3
Supplementary files format and content: Tab-delimited matrix file containing the raw read counts for each gene (rows) for all samples (columns) determined by featureCounts

organism: Mycobacterium canetti

source_name: STB-K

growth_protocol: Bacterial strains were cultured in triplicate in 30 mL of Middlebrook 7H9 liquid medium (Difco) containing ADC (0.2% dextrose, 0.5% BSA fraction V, 0.0003% beef catalase) and 0.05% Tween 80 at 37°C without agitation. Cultures were harvested when reaching the exponential phase of growth with a final OD at 600nm between 0.5 and 0.8.

extract_protocol:
RNA extraction was performed using a Trizol RNA isolation protocol (Invitrogen) and a mechanical lysis in Lysing Matrix B tubes (MP Biomedicals, Fisher Scientific) via rapid agitation in a Bead Mill 24 Homogenizer (Fisherbrand, Thermo Fisher Scientific). RNA extracts were then treated with the Turbo DNase (Ambion) and cleaned up using the RNeasy mini kit (Qiagen). RNA integrity and quality was monitored with a Bioanalyzer RNA nano assay (Agilent Technologies) to ensure that the RNA Integrity Number (RIN) was greater than 9.
RNA-seq libraries were prepared using the Stranded Total RNA Prep and Ligation with Ribo-Zero Plus kit (Illumina) and sequenced using a NextSeq 2000 device (Illumina).

value: STB-K

tag: morphotype

value: rough


title: STB-Kr Rep2

tag: genotype


title: STB-Kr Rep1


title: UN2

description:
resistant leaves, diseased field, , rep2
UN2


title: mtDNAwide_Atp6_T2A_Stable_with HHR_pairID_50 [5E9]


title: STB-Ks Rep3

value: smooth


title: mtDNAwide_CoII_T2A_Stable_with HHR_pairID_46 [5E8]


title: STB-Ks Rep2


title: Liver_ZT13_rep3

value: male

value: 13 week old


title: mtDNAwide_Cytb_T2A_Stable_with HHR_pairID_42 [5E7]

value: mtDNA


title: HD3

description:
non-infected leaves, non-diseased field, rep3
HD3

value: Dan 2


title: Liver_ZT13_rep2


title: mtDNAwide_Nd3_T2A_Stable_with HHR_pairID_32 [5E6]


title: HD2

description:
non-infected leaves, non-diseased field, rep2
HD2


title: mtDNAwide_Atp6_T2A_Stable_without HHR_pairID_50 [5E5]


title: 630CMOBSuccinate_4

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

description: 633 C. difficile strains in MOB medium with Succinate

data_processing:
The RNA‐seq analysis was performed with the Sequana framework (Cokelaer et al, 2017 doi:10.21105/joss.00352)
Version used: RNA‐seq pipeline (v0.13.0)
Reads were trimmed from adapters using Cutadapt 2.10
Then mapped to the Clostridium difficile 630 genome using Bowtie2
Differential expression testing was conducted using DESeq2 library 1.24.0, scripts based on SARTools 1.7.0
Assembly: Clostridioides difficile 630 (NC_009089.1) complemented by the known ncRNA (PMID: 23675309)
Supplementary files format and content: Files in CSV that contains Gene_ID, log2FoldChange, pvalue

organism: Clostridioides difficile

growth_protocol: Strains were grown in anaerobic conditions (5% H2, 5% CO2, 90% N2) in MOB at 37°C with or without 120mM of Succinate

extract_protocol:
Cells were harvested at an OD of 0.6 by centrifugation for 2 min at 4°C. The cells were first broken by shaking in a Fastprep apparatus for 2 x 30 sec in the presence of one gram of 0.1-mm diameter glass Sigma beads, then treated with Trizol reagent, chloroform/ isoamylalcohol and precipitated with isopropanol. The pellet was resuspended in TE
RNA libraries were prepared for sequencing using standard Illumina protocols
Illumina stranded Total RNA prep Ligation kit with RiboZero Plus

treatment_protocol: Bacterial strains and plasmids used in this study are listed in Table S1 C. difficile strains were grown anaerobically in MOB medium

value: wild type


title: HD1

description:
non-infected leaves, non-diseased field, rep1
HD1


title: Screening_COII_pairID_45 [2B8]


title: Liver_ZT12_rep2


title: Liver_ZT13_rep1


title: Liver_ZT12_rep1


title: Liver_ZT11_rep2


title: 630CMOBSuccinate_3

description: 632 C. difficile strains in MOB medium with Succinate


title: mtDNAwide_CoII_T2A_Stable_without HHR_pairID_46 [5E4]


title: UN1

description:
resistant leaves, diseased field, , rep1
UN1


title: UD3

description:
BaMMV-infected leaves, diseased field, rep3
UD3

source_name: BaMMV-infected leaves

value: BaMMV-infected leaves


title: mtDNAwide_Nd3_T2A_Stable_without HHR_pairID_32 [5E2]


title: 630CMOBSuccinate_2

description: 631 C. difficile strains in MOB medium with Succinate


title: UD2

description:
BaMMV-infected leaves, diseased field, rep2
UD2


title: UD1

description:
BaMMV-infected leaves, diseased field, rep1
UD1


title: STB-Ks Rep1


title: 630CMOBSuccinate_1

description: 630 C. difficile strains in MOB medium with Succinate


title: Liver_ZT8_rep3


title: mtDNAwide_Cytb_T2A_Stable_without HHR_pairID_42 [5E3]


title: HZ3

description:
non-infected Leaves, non-diseased field, rep3
HZ3

source_name: non-infected Leaves

value: non-infected Leaves

value: Zaoshu 3


title: mtDNAwide_WT_T2A_Stable_without HHR_pairID_ [5E1]


title: 630CMOB_2

description: 630 C. difficile strains in MOB medium


title: HZ1

description:
non-infected Leaves, non-diseased field, rep1
HZ1

value: barley


title: Liver_ZT8_rep1


title: 630CMOB_4

description: 630 C. difficile strains in MOB medium


title: 630CMOB_1

description: 630 C. difficile strains in MOB medium


title: 630BMOBSuccinate_4


title: HZ2

description:
non-infected Leaves, non-diseased field, rep2
HZ2

value: leaves


title: UZ3

description:
BaYMV and BaMMV-infected leaves, diseased field, rep3
UZ3

source_name: BaYMV and BaMMV-infected leaves

value: BaYMV and BaMMV-infected leaves


title: FDXR sh434,biological rep2

city: wuhan

first: Gao

last: Ronghui

state: HuBei province

address: 115 DongHu Road

institute: 武汉大学医学研究院

description: Gene expression data from T50D cell line of Human breast ductal carcinoma.

hyb_protocol: Hyb protocol were followed by standard affymetrix protocol.

scan_protocol: Data Chip was scanned by using a Genearray scanner.

data_processing: Differentially regulated genes were identified by using the limma package(v3.50.3) with the adjusted p-value  197 < 0.05.

organism: Homo sapiens

label_protocol: cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: T47D cell were cultured in RPMI-1640 (Sigma-Aldrich) containing 10% fetal bovine serum with 1% penicillin–streptomycin.  Cell was maintained in an incubator at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted by Qiagen RNAeasy plus kit.

value: Human breast ductal carcinoma

tag: shRNA

value: FDXR sh434


title: Liver_ZT11_rep3


title: PARP1

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

data_processing:
Base-Calling was performed by CASAVA version 1.4
The high quality reads were mapped to the Human genome 19 of Ensembl by using Bowtie(version 0.12.8) with the default parameter.
Data were filtered using the following specification:A Perl program was used to filter of low quality sequences from raw sequencing data. The quality of each base was checked from the first base of each read. Once a low-quality base (quality<10) was  found,  it was removed together with following sequences. For paired-end reads, if one read was less than 30 bases after the trimming of low quality bases, the whole paired-end reads were  removed.
The expression peaks were detected by MACS (Model-based Analysis for ChIP-Seq) using the parameter
Assembly: hg19
Supplementary files format and content: Supplementary_files_format_and_content: bed files were generated using MACS2.

growth_protocol: MDA-MB-231 cells were cultured in DMEM medium supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated without CO2 at 37 ℃.

extract_protocol:
10 ng of ChIP DNA was end polished with T4 DNA polymerase and kinase. An 'A' base was added to the polished DNA fragments, followed by the Qiaquick column clean up. Solexa adaptors were ligated to the ChIP DNA fragments and enriched by 15 cycles of PCR amplification. 200-300 bp size fractions were selectively isolated from the 1% agarose gel and eluted by the Qiagen gel extraction kit. The extracted DNA was quantified by picogreen assay and subjected to HiSeq2000 sequencing according to the manufacturer‘s instructions.
DNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For a ChIP assay, approximately 1 x 10^6 cells were used.The chromatin DNA precipitated by antibodies against PRMT6 and PARP1. The DNA was obtained using Cleavage Under Targets and Tagmentation (CUT&Tag) kit.

tag: chip antibody

value: PARP1 (Cell Signaling Technology)


title: FDXR sh434,biological rep1

description: Gene expression data from T48D cell line of Human breast ductal carcinoma.


title: 630BMOBSuccinate_3

tag: strain


title: shControl,biological rep1

description: Gene expression data from T47D cell line of Human breast ductal carcinoma.

value: shControl


title: UZ1

description:
BaYMV and BaMMV-infected leaves, diseased field, rep1
UZ1

tag: treatment

value: diseased field


title: shControl,biological rep2

description: Gene expression data from T49D cell line of Human breast ductal carcinoma.


title: UZ2

description:
BaYMV and BaMMV-infected leaves, diseased field, rep2
UZ2


title: Liver_ZT8_rep2

tag: Sex

tag: age


title: 630BMOBSuccinate_2


title: PRMT6

value: PRMT6 (Cell Signaling Technology)


title: HN878 Rep3

organism: Mycobacterium tuberculosis

value: rough


title: Liver_ZT11_rep1

value: male

value: 13 week old

tag: time point

tag: replicate


title: Liver_ZT4_rep2


title: HN878 Rep2


title: 630BMOBSuccinate_1


title: Liver_ZT2_rep3


title: Liver_ZT4_rep1


title: I130-3

city: Valencia

first: Daniel

last: Perez-Cremades

state: Valencia

address: 15 Blasco Ibañez Avenue

department: Physiology Department

country: Spain

institute: University of Valencia

data_processing:
All samples were processed using an RNA-seq pipeline implemented by Genewiz (South Plainfield, NJ).
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
BAM files were generated as a result
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: GRCm38
Supplementary files format and content: cvs with row counts

source_name: HUVEC

extract_protocol:
Trizol (Invitrogen) was used for RNA isolation from white adipose tissue.
PolyA selection

treatment_protocol: Human umbilical cells endothelial cells (HUVECs;Lonza) were cultured in endothelial cell growth medium (EGM2;Lonza) and transfected using Lipofectamine 2000 (Invitrogen) with negative control mimic and hsa-miR-130b-3p mimic. Cells were harvested and RNA-Seq analysis was performed using Illumina HiSeq2500 V4 2x150 bp  (Genewiz, South Plainfield, NJ).

value: Transfected with miR-130 mimic


title: I130-2


title: 630BMOB_4

description: 630 C. difficile strains in MOB medium

value: wild type


title: Dpn-GFP, NanoDam, larval medulla NSCs, rep2

city: Hobart

first: Owen

last: Marshall

state: Tas

address: 17 Liverpool St

country: Australia

institute: Menzies Institute for Medical Research

data_processing:
All FASTQ files were processed with damidseq_pipeline v1.5.3, using default options and aligned to DmR6.
Peak calls were made using find_peaks v1.0.3, default options.
Assembly: DmR6
Supplementary files format and content: Score column in bedgraph files represents scaled, normalised log2 enrichment of Dam-fusion over control.
Supplementary files format and content: peaks.gff
Library strategy: DamID-seq

organism: Drosophila melanogaster

source_name: 3rd instar larval brains

extract_protocol:
Following sample collection, genomic DNA was extracted, cut with DpnI and cut fragments isolated. DamID adaptors were ligated to the isolated DNA, fragments were digested with DpnII, and amplified via PCR before next-generation sequencing library preparation.
2 µg DNA was sonicated in a Bioruptor Plus (Diagenode). DamID adaptors were removed by AlwI digestion, and 500 ng of the resulting fragments end-repaired with a mix of enzymes (T4 DNA ligase (NEB) + Klenow Fragment (NEB) + T4 polynucleotide kinase (NEB)), A-tailed with Klenow 3’ to 5’ exo- (NEB), ligated to Illumina TruSeq LT adaptors using Quick Ligase enzyme (NEB) and amplified via PCR with NEBNext Hi-fidelity enzyme (NEB).

value: 3rd instar larval brains

tag: gal4 driver

value: neuroblasts (neural stem cells, NSCs)


title: I130-1


title: Liver_ZT2_rep2


title: HN878 Rep1


title: 630BMOB_3

description: 630 C. difficile strains in MOB medium


title: Liver_ZT4_rep3


title: Liver_ZT2_rep1


title: Liver_ZT1_rep3


title: Dpn-GFP, NanoDam, larval medulla NSCs, rep1


title: 630BMOB_2

description: 630 C. difficile strains in MOB medium


title: H37Rv Rep3


title: INS-3

value: Transfected with non-specific mimic


title: INS-2


title: Liver_ZT1_rep2


title: H37Rv Rep1


title: w1118 genetic background control, NanoDam, larval medulla NSCs, rep1


title: INS-1


title: Liver_ZT0_rep2


title: 630BMOB_1

description: 630 C. difficile strains in MOB medium


title: w1118 genetic background control, NanoDam, larval medulla NSCs, rep2


title: Liver_ZT0_rep3


title: mutdesF5_rep3_H3K4me3

status: Public on May 23 2023

city: København

first: Steffen

last: Abay-Nørgaard

state: København

address: Ole Maaløes Vej 5

department: BRIC

country: Denmark

institute: Copenhagen University

data_processing:
Samples were sequenced by 41bp paired-end reads on the  Illumina NextSeq 500 platform
Paired-end reads were processed with trim_galore followed by mapping to the ce11 and mm10 genomes using bowtie1 v1.1.2. PCR duplicates were removed from uniquely mapping reads using samtools v1.10. The spike-in normalization factor was derived and further corrected using the ratio of mm10/ce11 total read counts in the corresponding inputs.  Peaks were called for each sample using macs2 v2.1.1.20160309 7 and further processed using bedtools v2.30.08. In each condition, peaks found in all three biological replicates were used for further analysis. Peaks found in all conditions were combined to generate a union of peaks -“Allpeaks”. Deeptools v3.2.1 was used to generated Spike-In normalized BigWigs under “All peaks” using a bin size of 10bp while excluding blacklisted regions (ce11.v2). BigWigs for inputs were generated using deeptols v3.2.1 with RPKM normalisation.
Assembly: ce11
Supplementary files format and content: BigWig, bed

source_name: all tissue

growth_protocol: On standard NGM media at 20C

extract_protocol: Libraries were constructed using the NEBNextUltra II DNA library kit following manufactures instructions, without size selection.

treatment_protocol: Outcrossing and following for generations

value: all tissue

value: mutdes from set-2(zr1208)

value: crossed


title: mutdesF5_rep1_H3K4me3


title: wt_rep1_H3K4me3

value: wt


title: mutdesF5_rep2_H3K4me3


title: wt_rep2_H3K4me4


title: mutdesF3_rep2_H3K4me3


title: mutdesF3_rep3_H3K4me3


title: mutdesF3_rep1_H3K4me3


title: wtdesF5_rep3_H3K4me3

value: wtdes from set-2(zr1208)


title: wtdesF5_rep2_H3K4me3


title: H37Rv Rep2


title: wtdesF3_rep3_H3K4me3


title: wtdesF3_rep2_H3K4me3


title: wtdesF5_rep1_H3K4me3


title: Liver_ZT0_rep1


title: Input_wt_rep2


title: Liver_ZT12_rep3


title: Input_mutdesF5_rep3


title: wtdesF3_rep1_H3K4me3


title: Input_wt_rep1


title: Input_mutdesF5_rep1


title: Input_mutdesF3_rep3


title: Input_wtdesF5_rep2


title: Input_mutdesF3_rep2


title: Input_mutdesF3_rep1


title: Input_wtdesF5_rep1


title: Input_wtdesF5_rep3


title: Input_wtdesF3_rep3


title: set-2 F1-25C bio rep 4

data_processing:
Usegalaxy.com 22.05.1 was used to analyze data
Reads were trimmed with standard parameters, Truseq3, CROP(73)
Reads were aligned with RNA star using standard parameters
Aligments were counted with htseq using ce10
To determine differentially expressed genes we used Deseq2
Assembly: ce10(WS220)

growth_protocol: On standard NGM media at 20C unless otherwise noted in treatment

extract_protocol:
Arcturus Picopure RNA isolation kit
TruSeq RNA Library Prep Kit v2

treatment_protocol: Different treatment as change in temperature and maternal age

value: L4 stage

value: 25 degrees one generation


title: set-2 F1-25C bio rep 2


title: Input_wtdesF3_rep1


title: 1DOA x 4DOA bio rep 4

value: young male crossed with old hermaphrodite


title: 1DOA x 4DOA bio rep 2


title: 1DOA x 4DOA bio rep 1


title: 1DOA x 4DOA bio rep 3


title: Input_mutdesF5_rep2


title: 1DOA x 1DOA bio rep 4

value: young male crossed with young hermaphrodite


title: 1DOA x 1DOA bio rep 2


title: set-2 F1-25C bio rep 3


title: 1DOA x 1DOA bio rep 3


title: set-2 F1-25C bio rep 1


title: Input_wtdesF3_rep2


title: F1back-20C bio rep 1

value: back to 20C one generation


title: set-2 1DOA bio rep 1


title: set-2 F1-4DOA bio rep 4

value: F1 from old mother


title: 1DOA x 1DOA bio rep 1


title: set-2 1DOA bio rep 2


title: F1-25C bio rep 1


title: set-2 F1-4DOA bio rep 1


title: F1-25C bio rep 2


title: set-2 1DOA bio rep 3


title: set-2 1DOA bio rep 4


title: F1back-20C bio rep 4


title: F1back-20C bio rep 3


title: F1back-20C bio rep 2


title: F1-25C bio rep 4


title: set-2 F1-4DOA bio rep 2


title: F1-4DOA bio rep 2


title: F1-25C bio rep 3


title: set-2 F1-4DOA bio rep 3


title: F1-4DOA bio rep 1


title: ctrl 1DOA progeny bio rep 4


title: ctrl 1DOA progeny bio rep 3


title: ctrl 1DOA progeny bio rep 1


title: ctrl 1DOA  progeny bio rep 2


title: mutdes F5 bio rep 3

value: mutdes set-2(zr1208)


title: mutdes F5 bio rep 2


title: mutdes F5 bio rep 1


title: F1-4DOA bio rep 4


title: F1-4DOA bio rep 3


title: mutdes F3 bio rep 2


title: wtdes F5 bio rep 4


title: wtctrl F5 bio rep 1


title: mutdes F3 bio rep 3


title: wtctrl F5 bio rep 3


title: wtdes F3 bio rep 3


title: wtctrl F3 bio rep 3


title: wtdes F3 bio rep 4


title: wtctrl F3 bio rep 4


title: mutdes F3 bio rep 1


title: wtdes F5 bio rep 1


title: HG2_mRNA_LncRNA

city: guiyang

first: liu

middle: zhang

last: nian

address: Qing Road, University Town, Huaxi District, Guiyang City, Guizhou Province

institute: Guizhou Medical University

description:
HG2
PE150

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm8
Supplementary files format and content: genes_fpkm_expression.txt: Tab-delimited text file includes FPKM and count values for each Sample.

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

treatment_protocol: ARPE-19 cells were treated with high glucose (high concentration of glucose) for 72 hours to replicate the HG-induced cell loss model and simulate the pathophysiological environment of diabetes in vitro.

value: retinal pigment epithelium

value: WT

value: high glucose, 72h


title: wtdes F5 bio rep 3


title: wtdes F5 bio rep 2


title: wtctrl F5 bio rep 2


title: wtdes F3 bio rep 2


title: HG3_mRNA_LncRNA

description:
HG3
PE150


title: Control3_mRNA_LncRNA

description:
Control3
PE150

treatment_protocol: Treat ARPE-19 with normal glucose concentration for 72 hours.

value: normal glucose, 72hr


title: HG1_mRNA_LncRNA

description:
HG1
PE150


title: wtdes F3 bio rep 1


title: wtctrl F3 bio rep 2


title: Control2_mRNA_LncRNA

description:
Control2
PE150


title: Control1_mRNA_LncRNA

description:
Control1
PE150


title: wtctrl F5 bio rep 4


title: wtctrl F3 bio rep 1


title: sic-MYC PHF8

city: Chongqing

first: Jun

last: Jiang

state: Chongqing

address: 10#, Changjiang Zhilu, Yuzhong District

department: Department of Urology

institute: Daping Hospital, Army Medical University

data_processing:
Raw reads were filtered to obtain high-quality clean reads by removing sequencing adapters, short reads (length <35 bp) and low-quality reads using trim-galore (v0.6.4)
Then FastQC (v0.11.9) and Multiqc (v1.8) is used to ensure high reads quality
The clean reads were mapped to the human genome (assembly human genome GRCh38) using the Burrow-Wheeler Aligner (BWA v0.7.17) software
Peak detection was performed using the MACS2 (v2.2.6) peak finding algorithm with 0.05 set as the q-value cutoff
Annotation of peak sites to gene features was performed using the homer annotatePeaks.pl (v4.10)
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: RPMI 1640, 10% fetal bovine serum, Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes and quenched with 125 mM glycine.
The DNA libraries were amplified for 15 cycles and sequenced using Illumina NovaSeq 6000 with paired-end 150 as the sequencing mode

treatment_protocol: c-MYC ChIP-seq in 786-O cells transfected with Ctrl-sgRNA (normal control, NC) and PHF8-sgRNA; PHF8 ChIP-seq in 786-O cells transfected with siRNA targeting c-MYC and scrambled siRNA as control.

value: clear cell renal cell carcinoma

tag: transfection

value: siRNA targeting c-MYC

value: PHF8 (Bethyl, A301-772A)


title: PHF8-sgRNA c-MYC

value: sgRNA targeting PHF8


title: PHF8-sgRNA Input


title: 630CMOB_3

description: 630 C. difficile strains in MOB medium

value: wild type


title: sic-MYC Input


title: NC c-MYC


title: siCtrl PHF8

value: scrambled siRNA


title: NC Input


title: siCtrl Input


title: Patient Piedmont Sample 89

city: Durham

first: Joel

last: Eisner

state: NC

address: 100 Capitola Dr. Suite 275

institute: GeneCentric Therapeutics, Inc

data_processing:
Expression values for the samples were derived from raw RNAseq fastq files. Reads were aligned with STAR-aligner (GrCH38 ver. 22) to human assembly using the STAR/Salmon pipeline.  Expression was quantified using the Salmon package and the GrCH38 human transcriptome reference.  Genes were filtered for a minimum expression count (at least 10 reads in at least 5 samples), and for a protein coding annotation by Ensembl (final set of genes = 16,901).
Assembly: GrCH38 human transcriptome reference

source_name: lung adenocarcinoma

extract_protocol:
H&E-stained FFPE sections underwent microscopic QC review by an anatomical pathologist to confirm histology diagnosis, evaluate percent tumor nuclei (≥ 5% required), percent necrosis and cellularity prior to macrodissection and dual DNA/RNA extraction using the truXTRAC FFPE total nucleic acid kit (Covaris).  RNA quantification was performed by Qubit measurement using ribogreen staining.  RNA was qualitatively assessed for integrity by Agilent TapeStation gel electrophoresis (optimal samples included 10 ng by ribogreen quantification and a TapeStation DV200 value ≥ 20%).
Library preparation was performed using AmpliSeq for Illumina Transcriptome Human Gene Expression Panel kit.  A no template control (NTC) and positive control sample (NA12878 FFPE RNA) were included in each run.  Libraries were individually captured, reviewed for appropriate size using a Bioanalyzer or TapeStation trace, and quantified (KAPA library quantification) prior to equal molar pooling. Sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2 flow cell to generate ~50M, 2 x 50 bp paired-end reads.

value: lung adenocarcinoma


title: Patient Piedmont Sample 87


title: Patient Piedmont Sample 81


title: Patient Piedmont Sample 82


title: Patient Piedmont Sample 79


title: Patient Piedmont Sample 80


title: Patient Piedmont Sample 91


title: Patient Piedmont Sample 92


title: Patient Piedmont Sample 84


title: Patient Piedmont Sample 95


title: Patient Piedmont Sample 86


title: Patient Piedmont Sample 94


title: Patient Piedmont Sample 90


title: Patient Piedmont Sample 88


title: Patient Piedmont Sample 85


title: Patient Piedmont Sample 93


title: Patient Piedmont Sample 77


title: NC PHF8


title: Patient Piedmont Sample 74


title: Patient Piedmont Sample 75


title: Patient Piedmont Sample 76


title: Patient Piedmont Sample 78


title: Patient Piedmont Sample 83


title: Patient Piedmont Sample 73


title: Patient Piedmont Sample 72


title: Patient Piedmont Sample 71


title: Liver_ZT1_rep1

data_processing:
data were processed using our in-house Galaxy instance with “GIANT” (Galaxy-based interactive tools for Analysis of Transcriptomic data).  It consists of modules allowing to perform quality control (QC), Robust Multi-Average method normalization, LIMMA differential analysis using apt-probeset-summarize tool (v.2.10.0). Normalization done on probeset level with NetAffx Annotation Release 36.
MoGene-2_0-st.pgf and MoGene-2_0-st.clf
MoGene-2_0-st-v1.na36.mm10.probeset.csv

value: male

value: 13 week old


title: Patient Piedmont Sample 61


title: Patient Piedmont Sample 63


title: Patient Piedmont Sample 64


title: Patient Piedmont Sample 60


title: Patient Piedmont Sample 67


title: Patient Piedmont Sample 66


title: Patient Piedmont Sample 65


title: Patient Piedmont Sample 52


title: Patient Piedmont Sample 55


title: Patient Piedmont Sample 62


title: Patient Piedmont Sample 57


title: Patient Piedmont Sample 54


title: Patient Piedmont Sample 51


title: Patient Piedmont Sample 53


title: Patient Piedmont Sample 56


title: Patient Piedmont Sample 43


title: Patient Piedmont Sample 46


title: Patient Piedmont Sample 70


title: Patient Piedmont Sample 48


title: Patient Piedmont Sample 68


title: Patient Piedmont Sample 47


title: Patient Piedmont Sample 44


title: Patient Piedmont Sample 49


title: Patient Piedmont Sample 50


title: Patient Piedmont Sample 42


title: Patient Piedmont Sample 41


title: Patient Piedmont Sample 58


title: Patient Piedmont Sample 59


title: Patient Piedmont Sample 69


title: Patient Piedmont Sample 45


title: Patient Piedmont Sample 34


title: Patient Piedmont Sample 37


title: Patient Piedmont Sample 38


title: Patient Piedmont Sample 36


title: Patient Piedmont Sample 35


title: Patient Piedmont Sample 31


title: Patient Piedmont Sample 40


title: Patient Piedmont Sample 39


title: Patient Piedmont Sample 33


title: Patient Piedmont Sample 32


title: Patient Piedmont Sample 28


title: Patient Piedmont Sample 27


title: Patient Piedmont Sample 25


title: Patient Piedmont Sample 24


title: Patient Piedmont Sample 23


title: Patient Piedmont Sample 22


title: Patient Piedmont Sample 21


title: Patient Piedmont Sample 18


title: Patient Piedmont Sample 20


title: Patient Piedmont Sample 17


title: Mouse anti-Flag (for flag-tagged Caper) [RIP6]

city: Colorado Springs

first: Michael

middle: Brandon

last: Titus

state: Colorado

address: 1420 Austin Bluffs Pkwy  Colorado Springs, CO  USA 80918

institute: University of Colorado Colorado Springs

data_processing:
Read quality trimming, adapter removal and sequence overrepresentation analysis with fastp (v0.20.1)
Quality check with fastqc (v0.11.8)
Read mapping to D. melanogaster reference genome (flybase dmel_r6.36) with STAR (v2.7.6a)
Extraction of coverage signal with igvtools (v2.4.18) and scaling to library size with own scripts
Count table creation with featureCounts (subread v2.0.1): featureCounts -T 8 -s 1 -p -Q 20 -t exon -g gene_id -F GTF -a ${params.dmel_star_gtf} -o feature_counts.tsv ${bams}
Assembly: flybase dmel_r6.36
Supplementary files format and content: feature_counts.tsv: featureCounts count-table
Supplementary files format and content: feature_counts.tsv.summary: featureCounts summary data

source_name: Adult Heads

growth_protocol: Adult Drosophila were incubated at 37C for 2 hours and then at 30C overnight for heat-shock induced expression  of FLAG-tagged Caper using the UAS-Gal4 System.

extract_protocol:
RNA was directly purified from beads using Trizol extraction and isopropanol/sodium acetate precipitation
Libraries were prepared using Tecan Universal Plus Total RNA-seq with Drosophila probes per manufacturer's protocol.

value: Adult Heads

value: Hsp70Gal4 x UASCaperFlag

value: Flag


title: Mouse anti-Flag (for flag-tagged Caper) [RIP5]


title: Patient Piedmont Sample 15


title: Patient Piedmont Sample 14


title: Patient Piedmont Sample 16


title: Patient Piedmont Sample 13


title: Patient Piedmont Sample 30


title: Patient Piedmont Sample 29


title: Patient Piedmont Sample 26


title: Rabbit anti-Caper1 [RIP3]

value: Caper


title: Patient Piedmont Sample 11


title: Rabbit anti-Caper1 [RIP1]


title: Patient Piedmont Sample 10


title: Rabbit anti-Caper1 [RIP2]


title: Patient Piedmont Sample 09


title: Patient Piedmont Sample 19


title: Patient Piedmont Sample 08


title: Input for RIP6 [RIN6]

value: N/A (Input)


title: Patient Piedmont Sample 06


title: Patient Piedmont Sample 05


title: Patient Piedmont Sample 07


title: Input for RIP3 [RIN3]


title: Input for RIP4 [RIN4]


title: Patient Piedmont Sample 04


title: Input for RIP5 [RIN5]


title: Input for RIP2 [RIN2]


title: Input for RIP1 [RIN1]


title: Patient Piedmont Sample 03


title: Patient Piedmont Sample 02


title: Patient Piedmont Sample 01


title: Patient Piedmont Sample 12


title: Mouse anti-Flag (for flag-tagged Caper) [RIP4]


title: 5xFAD_Card9KO rep3

city: Charlottesville

last: Shapiro

state: VA

address: 1340 Jefferson Park Ave

department: Neuroscience

institute: University of Virginia School of Medicine

data_processing:
The raw sequencing reads (FASTQ files) were aligned to the UCSC mm10 mouse genome build using the splice-aware read aligner HISAT2.
Samtools was used for quality control filtering/ PCR duplicate removal.
Reads were sorted into features with HTSeq, produing the processed .txt files.
Assembly: mm10
Supplementary files format and content: Microsoft Excel Open XML Spreadsheet include RPKM values for each Sample

source_name: RNA from microglia harvested from the mouse brain, female, 20 weeks

extract_protocol:
Mice were euthanized with CO2 and immediately transcardially perfused with 20 ml 1X PBS. Brains were collected and their meninges and choroid plexus removed then the MACS-sorting protocol was used to isolate microglia as described (Norris et al., 2018). Tissues were homogenized by gently mashing through a 70 um cell strainer.  After centrifugation the cell pellet was resuspended in MACS buffer (Miltenyi Biotec, 130-0910376) to proceed with column purification of microglia using CD11b microbeads (Miltenyi, 130-093-634). We then performed sorting utilizing LS columns and a QuadroMACS magnet (Miltenyi, 130-042-401 and 130-091-051) according to manufacturer’s instructions. Column-bound cells were analyzed for purity by flow cytometry and submitted for RNA-seq.
RNA libraries were prepared for sequencing by GENEWIZ

treatment_protocol: We performed bulk RNA sequencing on the MACs-sorted microglia harvested from WT control (5xFAD null),CARD9 deficient , 5xFAD, and CARD9 deficient 5xFAD brains at 20 weeks of age

value: microglia

value: brain

value: female

value: 20 weeks

value: Card9 -/- 5xFAD


title: 5xFAD rep4


title: 5xFAD_Card9KO rep4


title: 5xFAD rep1


title: 5xFAD_Card9KO rep1


title: 5xFAD rep3


title: 5xFAD rep2


title: P2_F04_S160, HCT116, Infected, plexWell

city: Bethesda

first: Welles

last: Robinson

state: Maryland

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description:
P2_F04_S160
plexWell

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was demultiplexed into individual sample fastq sets using bcl2fastq v2.20.0.
Raw FASTQ files were trimmed using fastp v0.20.1 with the arguments “--unqualified_percent_limit 40 --cut_tail --low_complexity_filter --trim_poly_x”. The trimmed FASTQ files were aligned to the reference human genome (GRCh38 gencode release 34) and any applicable spike-in sequences using STAR63 2.7.6a_patch_2020-11-16 with the arguments “--soloType SmartSeq --soloUMIdedup Exact --soloStrand Unstranded --outSAMunmapped Within”. For analysis, we used the previously described workflow “Lun 416B cell line (Smart-seq2)” from “Orchestrating Single-Cell Analysis with Bioconductor” to specifically handle ERCC spike-in sequences. Quality filtering was performed using the quickPerCellQC function from scuttle (version 1.8.0)
Assembly: GRCh38 gencode release 34
Supplementary files format and content: Tab-separated values files and matrix files and h5 matrix files

molecule: polyA RNA

extract_protocol:
Single cell suspensions were prepared and sorted on a BD FACS Aria IIU into 96 well PCR plates that were prepared with lysis buffer according to seqWell plexWell Rapid Single Cell method (user guide v20210402) and containing ERCC spike-in mix (Invitrogen # 4456740) at a dilution of 1:1E7. Following deposition of single cells into prepared plates, they were snap-frozen and stored at -80C until further processing.
Single cell cDNA and libraries were generated for each sorted sample according to seqWell plexWell Rapid Single Cell user guide. Multiplexed libraries containing indexed single cell RNA-Seq libraries were sequenced on the either the NextSeq 2000 or NovaSeq 6000 with a target read depth of 2 million reads per cell using the following read parameters: Read 1 61bp, Index 1 8bp, Index 2 8bp, Read 2 61bp.

value: Infected


title: P2_F12_S168, HCT116, Infected, plexWell

description:
P2_F12_S168
plexWell


title: P2_F09_S165, HCT116, Infected, plexWell

description:
P2_F09_S165
plexWell


title: P2_G04_S172, HCT116, Infected, plexWell

description:
P2_G04_S172
plexWell


title: P2_G07_S175, HCT116, Infected, plexWell

description:
P2_G07_S175
plexWell


title: P2_G03_S171, HCT116, Infected, plexWell

description:
P2_G03_S171
plexWell


title: P2_G11_S179, HCT116, Infected, plexWell

description:
P2_G11_S179
plexWell


title: P2_F06_S162, HCT116, Infected, plexWell

description:
P2_F06_S162
plexWell


title: P2_F01_S157, Empty Well, Empty Well, plexWell

description:
P2_F01_S157
plexWell

source_name: Empty Well

value: Empty Well


title: P2_F02_S158, HCT116, Infected, plexWell

description:
P2_F02_S158
plexWell


title: Control rep3

value: WT (Control)


title: Card9KO rep1

value: Card9 -/-


title: Card9KO rep3


title: P2_E11_S155, HCT116, Infected, plexWell

description:
P2_E11_S155
plexWell


title: Card9KO rep2


title: P2_E12_S156, HCT116, Infected, plexWell

description:
P2_E12_S156
plexWell


title: Card9KO rep4


title: Control rep4


title: 5xFAD_Card9KO rep2


title: Control rep2


title: P2_E10_S154, HCT116, Infected, plexWell

description:
P2_E10_S154
plexWell


title: Control rep1


title: P2_E09_S153, HCT116, Infected, plexWell

description:
P2_E09_S153
plexWell


title: P2_E06_S150, HCT116, Infected, plexWell

description:
P2_E06_S150
plexWell


title: P2_E01_S145, Empty Well, Empty Well, plexWell

description:
P2_E01_S145
plexWell


title: P2_C01_S121, Empty Well, Empty Well, plexWell

description:
P2_C01_S121
plexWell


title: P2_D01_S133, Empty Well, Empty Well, plexWell

description:
P2_D01_S133
plexWell


title: P1_G11_S83, HCT116, Infected, plexWell

description:
P1_G11_S83
plexWell


title: P2_B01_S109, Empty Well, Empty Well, plexWell

description:
P2_B01_S109
plexWell


title: P1_H02_S86, HCT116, Infected, plexWell

description:
P1_H02_S86
plexWell


title: P1_H05_S89, HCT116, Infected, plexWell

description:
P1_H05_S89
plexWell


title: P2_D08_S140, HCT116, Infected, plexWell

description:
P2_D08_S140
plexWell


title: P2_A01_S97, Empty Well, Empty Well, plexWell

description:
P2_A01_S97
plexWell


title: P2_E05_S149, HCT116, Infected, plexWell

description:
P2_E05_S149
plexWell


title: P2_C05_S125, Jurkat, Infected, plexWell

description:
P2_C05_S125
plexWell

source_name: Jurkat

value: Jurkat


title: P1_G04_S76, HCT116, Infected, plexWell

description:
P1_G04_S76
plexWell


title: P1_G03_S75, HCT116, Infected, plexWell

description:
P1_G03_S75
plexWell


title: P2_D06_S138, HCT116, Infected, plexWell

description:
P2_D06_S138
plexWell


title: P1_H10_S94, HCT116, Infected, plexWell

description:
P1_H10_S94
plexWell


title: Retina5_uninj

city: Farmington

first: Ephraim

last: Trakhtenberg

state: Connecticut

address: 263 Farmington Ave

institute: UConn Health

data_processing:
Illumina base-call files (*.bcl) were converted to FASTQs using CellRanger v1.3, which uses bcl2fastq v2.17.1.14. FASTQ files were then aligned to mm10 mouse reference genome and transcriptome using the CellRanger v1.3 software pipeline with default parameters which demultiplexes the samples and generates a gene versus cell expression matrix based on the barcodes and assigned unique molecular identifiers (UMIs) that enable determining the individual cells from which each RNA molecule originated.
Cell ranger routput was loaded into Rstudio using the single cell RNAseq R package Seurat (v. 4.0.3). A seurat object was created for each batch of retina and optic nerve cells. Cells with > 200 and < 6500 genes were retained for downstream analysis. Batches were merged, normalized and scaled in Seurat.
Batch correction/integration was performed on the merged seurat object using the R package harmony. RunUMAP with "dims=1:4" and all other parameters as default was run. A cell counts matrix for the merged dataset was then generating by extracting counts matrix from the merged Seurat object and batch id, condition (uninjured or injured), and Rbpms expression (positive or negative) metadata was appended to the first two rows of the matrix which was saved as csv file.
Assembly: mm10
Supplementary files format and content: One CSV files: Containing all retinal and optic nerve macrophage/microglia batches

source_name: Retina

extract_protocol: The amplified cDNA from each channel of the Chromium System was used to construct an Illumina sequencing library and sequenced on HiSeq 4000 with 150 cycle sequencing.

value: Retina

value: (P56); 129S1/SvlmJ strain

value: retinal microglia/macrophage

value: Wildtype


title: optic_nerve2_uninj

source_name: Optic Nerve

value: Optic Nerve

value: optic nerve microglia/macrophage


title: Retina4_inj

value: 2 weeks after crush


title: Retina6_uninj


title: optic_nerve3_inj


title: P1_G07_S79, HCT116, Infected, plexWell

description:
P1_G07_S79
plexWell


title: time_4, dom, treatment_3, rep_c

city: Marseille

first: Thomas

last: Vannier

address: Campus de Luminy, 163 Av. de Luminy

institute: Aix-Marseille University

data_processing:
The quality of the raw reads was assessed using the FastQC v0.11.9 toolkit
NexteraPE Adapters and low-quality reads were trimmed using Trimmomatic v0.39
The non rRNA reads were aligned with HiSat2  v2.2.1 using default options.
Gene counts were quantified using feature Counts from the Subread v2.0.1 package.
Gene counts were normalized and used for differential expression testing using DESeq2 v1.28.0
Assembly: Crocosphaera watsonii WH8501 genes (downloaded from JGI Genome Portal, GenBank GI #67858163).
Supplementary files format and content: raw_counts.tsv: Tab-delimited text files include gene count for each samples
Supplementary files format and content: normalized_abundance.tsv: tab-delimited text files include normalized counts for each samples

organism: Crocosphaera watsonii WH 8501

source_name: Diazotroph

growth_protocol: Batch cultures of Crocosphaera watsonii WH8501 (Waterbury and Rippka, 1989) (hereafter Crocosphaera) were grown in 0.2 µm-filtered seawater based nitrogen-free YBC-II medium (Chen et al., 1996) at 26 ºC with 12 h light :12 h dark cycle and a daytime photon flux of ~250 µmol photons m-2 s-1. The cultures were gradually adapted to lower phosphate concentrations than the usual phosphate YBC-II medium composition for eight weeks (~25 µM P). Two weeks prior to the experiment, the cultures were acclimated to three temperature and pH target levels, i.e. 26 °C and pH 8.1, 28 °C and pH 8.0 and, 30°C and pH 7.9, corresponding to RCP 2.6, 4.5 and 6.0 (IPCC, 2014).

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen Sciences, MD, USA) with β-mercaptoethanol (M6250, Sigma Aldrich, Hamburg, Germany) added to the lysis buffer RLT to enhance intracellular RNAse denaturation (Moisander et al., 2008). Prior to extraction, filters were ground and submitted to five to ten flash freezing steps with liquid nitrogen to maximise the extraction yield. An extra DNAase treatment was performed using the TURBO DNA-freeTM Kit (Ambion, Thermo Fisher Scientific), followed by a Zymo-5 column clean up kit (Zymo Research, USA).
RNA libraries for RNA-seq were prepared using total stranded RNA following NovaSeq6000  manufacturer's protocols.

treatment_protocol: Acclimated Crocosphaera cultures were transferred to 40 L transparent methacrylate tanks and mixed with YBC-II medium to achieve a starting concentration of ~1.5 x 10^4 cells ml-1. Two tanks were used as low treatment (26 ºC, pH 8.1, low), three tanks were set to intermediate conditions (28ºC, pH 8.0, intermediate), and another three tanks were set to extreme conditions (30ºC, pH 7.9, extreme). From each treatment, three bottles (~320 ml) were amended with 80 µL of 0.08M 13C-DOM mix (final concentration 20 µM C) and the other three were kept as unamended control. The six flasks were incubated in separate incubators with the same temperature and light conditions as in the original experiment.

tag: condition

value: dom

value: c

tag: temperature (celsius)

tag: ph

value: Diazotroph


title: time_4, dom, treatment_3, rep_b

value: b

tag: time


title: P2_D05_S137, HCT116, Infected, plexWell

description:
P2_D05_S137
plexWell

tag: cell line


title: optic_nerve4_uninj

tag: tissue

tag: cell type


title: P2_D04_S136, HCT116, Infected, plexWell

description:
P2_D04_S136
plexWell


title: P1_G02_S74, HCT116, Infected, plexWell

description:
P1_G02_S74
plexWell


title: optic_nerve1_inj

tag: genotype


title: P1_G06_S78, HCT116, Infected, plexWell

description:
P1_G06_S78
plexWell


title: Retina3_inj


title: time_4, dom, treatment_3, rep_a

value: a


title: P1_F02_S62, Jurkat, Infected, plexWell

description:
P1_F02_S62
plexWell

value: Infected


title: Retina2_inj


title: P1_E11_S59, Jurkat, Infected, plexWell

description:
P1_E11_S59
plexWell


title: time_4, dom, treatment_2, rep_c


title: P1_E10_S58, Jurkat, Infected, plexWell

description:
P1_E10_S58
plexWell


title: Retina1_inj


title: P1_E01_S49, Empty Well, Empty Well, plexWell

description:
P1_E01_S49
plexWell

value: Empty Well


title: P1_F09_S69, Jurkat, Infected, plexWell

description:
P1_F09_S69
plexWell


title: P1_D10_S46, HCT116, Heat Killed, plexWell

description:
P1_D10_S46
plexWell

value: Heat Killed


title: P1_D11_S47, HCT116, Heat Killed, plexWell

description:
P1_D11_S47
plexWell


title: P1_E09_S57, Jurkat, Infected, plexWell

description:
P1_E09_S57
plexWell


title: Epith.PBS.3

city: London

first: Andreas

last: Wack

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
The RSEM package (version 1.3.0) (Li and Dewey, 2011) was used in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) for the mapping and subsequent gene-level counting of the sequenced reads with respect to Ensembl mouse GRCm38 release 89  transcriptome
Normalisation of raw count data and differential expression analysis was performed with the DESeq2 package (version 1.16.1)  within the R programming environment (version 3.6.0)
Assembly: Ensembl GRCm38
Supplementary files format and content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: lung epithelial cells (EpCam+ CD31- CD45-) prepared freshly from mouse lung

growth_protocol: not applicable as freshly isolated from mouse lung

extract_protocol:
RNA was extracted from cell lysates using a Qiagen micro kit
RNA (200 ng) was used to prepare cDNA libraries using the TruSeq Stranded mRNA HT Library Preparation Kit (Illumina). Libraries were normalized, pooled and then clustered using the HiSeq® 3000/4000 PE Cluster Kit (Illumina). The libraries were imaged and sequenced on an Illumina HiSeq 4000 sequencer using the HiSeq® 3000/4000 SBS kit (Illumina) at a minimum of 25 million paired-end reads (75 bp/100 bp) per sample.

value: Epithelial

value: PBS

tag: gender

value: Female


title: time_4, dom, treatment_2, rep_a


title: Epith.PBS.2

treatment_protocol: not applicable as freshly isolated from mouse lung


title: time_4, dom, treatment_2, rep_b


title: time_4, dom, treatment_1, rep_c


title: Epith.PBS.1


title: P1_D03_S39, HCT116, Heat Killed, plexWell

description:
P1_D03_S39
plexWell


title: P1_D02_S38, HCT116, Heat Killed, plexWell

description:
P1_D02_S38
plexWell


title: Epith.MM54.3


title: P1_D05_S41, HCT116, Heat Killed, plexWell

description:
P1_D05_S41
plexWell


title: time_4, dom, treatment_1, rep_a


title: time_4, dom, treatment_1, rep_b


title: P1_D01_S37, Empty Well, Empty Well, plexWell

description:
P1_D01_S37
plexWell


title: P1_D08_S44, HCT116, Heat Killed, plexWell

description:
P1_D08_S44
plexWell


title: Epith.MM54.2


title: P1_C01_S25, Empty Well, Empty Well, plexWell

description:
P1_C01_S25
plexWell


title: time_4, ctl, treatment_3, rep_c

value: ctl


title: P1_F01_S61, Empty Well, Empty Well, plexWell

description:
P1_F01_S61
plexWell


title: P1_B11_S23, HCT116, Uninfected, plexWell

description:
P1_B11_S23
plexWell

value: Uninfected


title: P1_B10_S22, HCT116, Uninfected, plexWell

description:
P1_B10_S22
plexWell


title: P1_B09_S21, HCT116, Uninfected, plexWell

description:
P1_B09_S21
plexWell


title: P1_B12_S24, HCT116, Uninfected, plexWell

description:
P1_B12_S24
plexWell


title: Epith.MM54.1


title: time_4, ctl, treatment_3, rep_a


title: time_4, ctl, treatment_3, rep_b


title: Endo.PBS.3

source_name: lung endothelial cells (CD31+ EpCam- CD45-) prepared freshly from mouse lung

value: Endothelial


title: Endo.PBS.4


title: P1_B05_S17, HCT116, Uninfected, plexWell

description:
P1_B05_S17
plexWell


title: P1_B04_S16, HCT116, Uninfected, plexWell

description:
P1_B04_S16
plexWell


title: P1_B02_S14, HCT116, Uninfected, plexWell

description:
P1_B02_S14
plexWell


title: time_4, ctl, treatment_2, rep_c


title: P1_A01_S1, Empty Well, Empty Well, plexWell

description:
P1_A01_S1
plexWell


title: P1_B01_S13, Empty Well, Empty Well, plexWell

description:
P1_B01_S13
plexWell


title: Endo.MM54.2


title: P2_G12_S180, HCT116, Infected, plexWell

description:
P2_G12_S180
plexWell


title: P2_G08_S176, HCT116, Infected, plexWell

description:
P2_G08_S176
plexWell


title: P2_G06_S174, HCT116, Infected, plexWell

description:
P2_G06_S174
plexWell


title: P2_G09_S177, HCT116, Infected, plexWell

description:
P2_G09_S177
plexWell


title: P2_G10_S178, HCT116, Infected, plexWell

description:
P2_G10_S178
plexWell


title: time_4, ctl, treatment_1, rep_c


title: time_4, ctl, treatment_2, rep_a


title: Endo.PBS.2


title: time_4, ctl, treatment_2, rep_b


title: Endo.PBS.1


title: time_4, ctl, treatment_1, rep_b


title: time_4, ctl, treatment_1, rep_a


title: P2_G02_S170, HCT116, Infected, plexWell

description:
P2_G02_S170
plexWell


title: Influenza.KO.Epithelial.3

value: Ahr flox Cdh5-Cre+ (KO)

tag: infection

value: Influenza


title: Influenza.KO.Epithelial.2


title: P2_F10_S166, HCT116, Infected, plexWell

description:
P2_F10_S166
plexWell

tag: treatment


title: time_2, dom, treatment_3, rep_c


title: P2_F08_S164, HCT116, Infected, plexWell

description:
P2_F08_S164
plexWell


title: Endo.MM54.1


title: Influenza.KO.Epithelial.1


title: time_2, dom, treatment_3, rep_b


title: P2_F07_S163, HCT116, Infected, plexWell

description:
P2_F07_S163
plexWell


title: Influenza.WT.Epithelial.3

value: Ahr flox Cdh5-Cre- (WT)


title: Influenza.WT.Epithelial.2


title: time_2, dom, treatment_3, rep_a

value: dom


title: P2_F05_S161, HCT116, Infected, plexWell

description:
P2_F05_S161
plexWell


title: P2_E08_S152, HCT116, Infected, plexWell

description:
P2_E08_S152
plexWell


title: P2_F03_S159, HCT116, Infected, plexWell

description:
P2_F03_S159
plexWell


title: time_2, dom, treatment_2, rep_c

value: c


title: Influenza.WT.Epithelial.1


title: P2_E04_S148, HCT116, Infected, plexWell

description:
P2_E04_S148
plexWell


title: time_2, dom, treatment_2, rep_b

value: Diazotroph


title: P2_E07_S151, HCT116, Infected, plexWell

description:
P2_E07_S151
plexWell


title: P2_E02_S146, HCT116, Infected, plexWell

description:
P2_E02_S146
plexWell


title: P2_E03_S147, HCT116, Infected, plexWell

description:
P2_E03_S147
plexWell


title: time_2, dom, treatment_2, rep_a


title: P2_G05_S173, HCT116, Infected, plexWell

description:
P2_G05_S173
plexWell


title: P2_D12_S144, HCT116, Infected, plexWell

description:
P2_D12_S144
plexWell


title: P2_G01_S169, HCT116, Infected, plexWell

description:
P2_G01_S169
plexWell


title: P2_F11_S167, HCT116, Infected, plexWell

description:
P2_F11_S167
plexWell


title: time_2, dom, treatment_1, rep_c


title: P2_D11_S143, HCT116, Infected, plexWell

description:
P2_D11_S143
plexWell


title: P2_D10_S142, HCT116, Infected, plexWell

description:
P2_D10_S142
plexWell


title: P2_D09_S141, HCT116, Infected, plexWell

description:
P2_D09_S141
plexWell


title: time_2, dom, treatment_1, rep_b

value: b


title: P2_D07_S139, HCT116, Infected, plexWell

description:
P2_D07_S139
plexWell


title: time_2, dom, treatment_1, rep_a

value: a


title: P2_D03_S135, HCT116, Infected, plexWell

description:
P2_D03_S135
plexWell

value: Infected


title: P2_D02_S134, HCT116, Infected, plexWell

description:
P2_D02_S134
plexWell


title: Naive.KO.Epithelial.1

value: Naive


title: Naive.WT.Epithelial.3


title: P2_C12_S132, Jurkat, Infected, plexWell

description:
P2_C12_S132
plexWell

value: Jurkat


title: Naive.KO.Epithelial.4

value: Epithelial


title: Naive.WT.Epithelial.2


title: P2_C11_S131, Jurkat, Infected, plexWell

description:
P2_C11_S131
plexWell


title: P2_C09_S129, Jurkat, Infected, plexWell

description:
P2_C09_S129
plexWell


title: P2_C10_S130, Jurkat, Infected, plexWell

description:
P2_C10_S130
plexWell


title: Naive.WT.Epithelial.1


title: P2_C08_S128, Jurkat, Infected, plexWell

description:
P2_C08_S128
plexWell


title: P2_C07_S127, Jurkat, Infected, plexWell

description:
P2_C07_S127
plexWell


title: Influenza.KO.Endothelial.3


title: time_2, ctl, treatment_3, rep_b


title: P2_C06_S126, Jurkat, Infected, plexWell

description:
P2_C06_S126
plexWell


title: time_2, ctl, treatment_3, rep_a


title: Naive.KO.Epithelial.3


title: P2_C04_S124, Jurkat, Infected, plexWell

description:
P2_C04_S124
plexWell


title: Influenza.KO.Endothelial.2


title: time_2, ctl, treatment_2, rep_c


title: Naive.KO.Epithelial.2


title: P2_C03_S123, Jurkat, Infected, plexWell

description:
P2_C03_S123
plexWell


title: P2_C02_S122, Jurkat, Infected, plexWell

description:
P2_C02_S122
plexWell


title: P2_B12_S120, Jurkat, Infected, plexWell

description:
P2_B12_S120
plexWell


title: Influenza.KO.Endothelial.1


title: time_2, ctl, treatment_3, rep_c


title: P2_B11_S119, Jurkat, Infected, plexWell

description:
P2_B11_S119
plexWell


title: time_2, ctl, treatment_2, rep_a


title: Influenza.WT.Endothelial.3


title: P2_B10_S118, Jurkat, Infected, plexWell

description:
P2_B10_S118
plexWell


title: time_2, ctl, treatment_1, rep_c


title: Influenza.WT.Endothelial.2


title: P2_B08_S116, Jurkat, Infected, plexWell

description:
P2_B08_S116
plexWell


title: P2_B09_S117, Jurkat, Infected, plexWell

description:
P2_B09_S117
plexWell


title: time_2, ctl, treatment_1, rep_b


title: P2_B07_S115, Jurkat, Infected, plexWell

description:
P2_B07_S115
plexWell


title: Influenza.WT.Endothelial.1


title: P2_B05_S113, Jurkat, Infected, plexWell

description:
P2_B05_S113
plexWell


title: P2_B06_S114, Jurkat, Infected, plexWell

description:
P2_B06_S114
plexWell


title: time_2, ctl, treatment_2, rep_b


title: P2_B03_S111, Jurkat, Infected, plexWell

description:
P2_B03_S111
plexWell


title: P2_A11_S107, Jurkat, Infected, plexWell

description:
P2_A11_S107
plexWell


title: P2_B04_S112, Jurkat, Infected, plexWell

description:
P2_B04_S112
plexWell


title: Naive.KO.Endothelial.2


title: P2_B02_S110, Jurkat, Infected, plexWell

description:
P2_B02_S110
plexWell


title: Naive.KO.Endothelial.3


title: P2_A10_S106, Jurkat, Infected, plexWell

description:
P2_A10_S106
plexWell


title: P2_A09_S105, Jurkat, Infected, plexWell

description:
P2_A09_S105
plexWell


title: Naive.KO.Endothelial.1


title: P2_A08_S104, Jurkat, Infected, plexWell

description:
P2_A08_S104
plexWell


title: Naive.WT.Endothelial.3


title: P2_A07_S103, Jurkat, Infected, plexWell

description:
P2_A07_S103
plexWell


title: P2_A06_S102, Jurkat, Infected, plexWell

description:
P2_A06_S102
plexWell


title: P2_A12_S108, Jurkat, Infected, plexWell

description:
P2_A12_S108
plexWell


title: Naive.KO.Endothelial.4


title: DNase l-treated- ligature mouse 5 [DL_5]

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

description:
RawCountFile.txt
RawCountFile_filtered.txt
CPM_TMM_counts.txt

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to the GRCm38.M23 version of the Mus musculus genome using STAR v2.7.3a in single-pass mode with the following parameters: --outFilterMultimapNmax 20 –outFilterType BySJout --alignSJoverhangMin 3 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.01 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.7.3a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM23 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Assembly: GRCm38 vM23
Supplementary files format and content: Raw counts expression matrix.
Supplementary files format and content: Filtered counts expression matrix. Genes with less than 5 counts in at least one sample were removed.
Supplementary files format and content: TMM-normalized Counts Per Million expression matrix.

source_name: gingiva tissues

extract_protocol:
Total RNA was isolated from mouse gingival tissues using Trizol reagent (15596018, Life Technologies), Lysing Matrix D (6913500, MP Biomedicals) tubes and quantified by NanoDrop spectrometer at 260 and 280 nm.
Library preparation was performed according to the manufacturer’s instructions for the Illumina TruSeq stranded library kit. The libraries were then pooled and sequenced on a NextSeq 2000 sequencer (Illumina).

treatment_protocol: Mice were injected i.p. with either DNase-Ⅰ or vehicle with or without LIP placement.

value: gingiva tissues

value: WT

value: DNase l


title: DNase l-treated- ligature mouse 1 [DL_1]


title: DNase l-treated- ligature mouse 2 [DL_2]


title: DNase l-treated- ligature mouse 3 [DL_3]


title: DNase l-treated- ligature mouse 4 [DL_4]


title: time_2, ctl, treatment_1, rep_a

value: ctl


title: Naive.WT.Endothelial.2

value: Endothelial

value: Female


title: P2_A05_S101, Jurkat, Infected, plexWell

description:
P2_A05_S101
plexWell


title: DNase l-treated- control mouse 5 [DU_5]


title: P2_A03_S99, Jurkat, Infected, plexWell

description:
P2_A03_S99
plexWell


title: Naive.WT.Endothelial.1


title: P2_A04_S100, Jurkat, Infected, plexWell

description:
P2_A04_S100
plexWell


title: DNase l-treated- control mouse 4 [DU_4]


title: P2_A02_S98, Jurkat, Infected, plexWell

description:
P2_A02_S98
plexWell


title: P1_H12_S96, HCT116, Infected, plexWell

description:
P1_H12_S96
plexWell


title: DNase l-treated- control mouse 3 [DU_3]


title: 65Dn mir200 POA 4

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of Mus musculus genome using STAR v.2.5.3a
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 100 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: total RNA extracted from brain tissue (hippocampus and preoptic area)

extract_protocol:
Total RNA was isolated from mice ovaries using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer instructions
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: Adult Ts65Dn mice received a unilateral injection with scAAV9-EF1a-mmu-miR-200b-eGFP (AAV-miR200b, 2.1×10^13 gc/ml) or scAAV9-EF1a-ctrl-miR-eGFP (AAV-GFP, 2.2×10^13 gc/ml) (Vector Biolabs) into the rPOA

value: Ts65Dn with a viral-overexpression of miR-200b

value: preoptic area


title: DNase l-treated- control mouse 2 [DU_2]


title: 65Dn mir200 POA 3


title: P1_H09_S93, HCT116, Infected, plexWell

description:
P1_H09_S93
plexWell


title: P1_H08_S92, HCT116, Infected, plexWell

description:
P1_H08_S92
plexWell


title: P1_H07_S91, HCT116, Infected, plexWell

description:
P1_H07_S91
plexWell


title: P1_H06_S90, HCT116, Infected, plexWell

description:
P1_H06_S90
plexWell


title: 65Dn mir200 POA 1


title: Vehicle-treated- ligature mouse 5 [VL_5]

value: Vehicle


title: P1_H01_S85, HCT116, Infected, plexWell

description:
P1_H01_S85
plexWell


title: Vehicle-treated- ligature mouse 4 [VL_4]


title: P1_H03_S87, HCT116, Infected, plexWell

description:
P1_H03_S87
plexWell


title: P1_G10_S82, HCT116, Infected, plexWell

description:
P1_G10_S82
plexWell


title: P1_G09_S81, HCT116, Infected, plexWell

description:
P1_G09_S81
plexWell


title: 65Dn POA 3


title: 65Dn POA 4


title: P1_G12_S84, HCT116, Infected, plexWell

description:
P1_G12_S84
plexWell


title: P1_G08_S80, HCT116, Infected, plexWell

description:
P1_G08_S80
plexWell


title: 65Dn POA 2


title: 65Dn POA 1


title: P1_G01_S73, HCT116, Infected, plexWell

description:
P1_G01_S73
plexWell


title: P1_H11_S95, HCT116, Infected, plexWell

description:
P1_H11_S95
plexWell


title: Vehicle-treated- ligature mouse 2 [VL_2]


title: P1_F12_S72, Jurkat, Infected, plexWell

description:
P1_F12_S72
plexWell


title: Vehicle-treated- ligature mouse 1 [VL_1]


title: WT POA 4

value: wild type


title: P1_F11_S71, Jurkat, Infected, plexWell

description:
P1_F11_S71
plexWell


title: P1_F10_S70, Jurkat, Infected, plexWell

description:
P1_F10_S70
plexWell


title: 65Dn mir200 POA 2


title: Vehicle-treated- control mouse 5 [VU_5]


title: DNase l-treated- control mouse 1 [DU_1]


title: P1_H04_S88, HCT116, Infected, plexWell

description:
P1_H04_S88
plexWell


title: P1_F08_S68, Jurkat, Infected, plexWell

description:
P1_F08_S68
plexWell


title: Vehicle-treated- control mouse 4 [VU_4]


title: WT POA 3


title: Vehicle-treated- ligature mouse 3 [VL_3]


title: WT POA 2


title: P1_F06_S66, Jurkat, Infected, plexWell

description:
P1_F06_S66
plexWell


title: P1_F05_S65, Jurkat, Infected, plexWell

description:
P1_F05_S65
plexWell


title: Vehicle-treated- control mouse 3 [VU_3]


title: P1_G05_S77, HCT116, Infected, plexWell

description:
P1_G05_S77
plexWell


title: WT POA 1


title: P1_F03_S63, Jurkat, Infected, plexWell

description:
P1_F03_S63
plexWell


title: P1_E12_S60, Jurkat, Infected, plexWell

description:
P1_E12_S60
plexWell


title: 65Dn mir200 Hipp 3

value: hippocampus


title: P1_F04_S64, Jurkat, Infected, plexWell

description:
P1_F04_S64
plexWell


title: 65Dn mir200 Hipp 4


title: P1_E08_S56, Jurkat, Infected, plexWell

description:
P1_E08_S56
plexWell


title: LSK_OP4_NM_9d_1 gRNA

city: Cambridge

first: Brian

last: Huntly

address: Hills Road

department: Department of Haematology

institute: University of Cambridge

description:
Perturb-seq of mouse cells ex vivo
LSK_OP4_NM_9d_1.h5
CellAnnotation_exvivo.tsv

data_processing:
Raw sequencing data were demultiplexed using the function mkfastq in Cell Ranger (version 6.1.1).
Sequencing data were aligned to the reference genome with Cell Ranger count
Assembly: GRCm38/mm10 reference genome assembly (GENCODE vM23/Ensembl 98) with BFP and GFP sequences
Supplementary files format and content: h5 matrices: read count matrix with cells / barcodes (columns) and genes (rows); one for each sample
Supplementary files format and content: CellAnnotation: mapping of cell types and other information to barcodes across samples; one for each source (leukemia, in vivo, ex vivo)

growth_protocol: Primary LSKs were isolated from 12-14 weeks-old ROSA26xCas9 mice and grown ex vivo for 36 hours under Stem Cell conditions (DMEM/F12, ITSX 1X, 1 mg/mL PVA 87%, 10 mM Hepes, 100 ng/uL Tpo, 10 ng/uL SCF). Then, 50,000 viable cells were transplanted to irradiated (902 cGy, 1 minute) 12 weeks-old adult B6.SJL-Ptprca Pepcb/BoyJ (CD45.1) mice via tail injection.

extract_protocol:
After two weeks, the transplanted mice were euthanised and bone marrow cells were harvested and stained with BV510 anti Lineage (CD3, CD19, Ter119, CD11b, Gr1) and APC anti c-Kit antibodies. For single-cell RNAseq we FACS-sorted Lineage- and Lineage+/cKit+ fractions and processed each of them in a 10X single-cell RNA-seq partition aimed at a final coverage of 500 single-cells per sgRNA.
Single-cell libraries were generated using the Chromium Next GEM Single-Cell 3’ Reagent Kits v3.1 (Dual Index) using the 10x Genomics manufacturer recommended protocol and targeting 16,000 cells per library.The resulting libraries were quantified using Qbit and qPCR and analysed on a Tape Station. Libraries were sequenced in a NextSeq 1000 or a Novaseq 6000 to a final coverage of 50,000 reads/cell for 3’ Gene Expression libraries and 5,000 reads/cell for CRISPR Feature Barcode libraries.

treatment_protocol: Cas9-LSK cells were transduced with lentiviral vectors expressing sgRNAs against specific CFs.

tag: sort markers

value: nomarker

tag: secondary readout

value: CRISPR screen (Perturb-seq)


title: P1_E06_S54, Jurkat, Infected, plexWell

description:
P1_E06_S54
plexWell

value: Infected


title: P1_E07_S55, Jurkat, Infected, plexWell

description:
P1_E07_S55
plexWell


title: P1_E05_S53, Jurkat, Infected, plexWell

description:
P1_E05_S53
plexWell


title: LSK_OP4_NM_9d_1 mRNA

tag: time point


title: P1_E04_S52, Jurkat, Infected, plexWell

description:
P1_E04_S52
plexWell


title: Vehicle-treated- control mouse 2 [VU_2]


title: Vehicle-treated- control mouse 1 [VU_1]


title: P1_E03_S51, Jurkat, Infected, plexWell

description:
P1_E03_S51
plexWell


title: P1_E02_S50, Jurkat, Infected, plexWell

description:
P1_E02_S50
plexWell


title: LSK_OP4_NM_7d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP4_NM_7d_1.h5
CellAnnotation_exvivo.tsv


title: 65Dn mir200 Hipp 1


title: 65Dn mir200 Hipp 2


title: P1_D12_S48, HCT116, Heat Killed, plexWell

description:
P1_D12_S48
plexWell

value: Heat Killed


title: P1_F07_S67, Jurkat, Infected, plexWell

description:
P1_F07_S67
plexWell

value: Jurkat


title: P1_D09_S45, HCT116, Heat Killed, plexWell

description:
P1_D09_S45
plexWell


title: P1_D07_S43, HCT116, Heat Killed, plexWell

description:
P1_D07_S43
plexWell


title: P1_D06_S42, HCT116, Heat Killed, plexWell

description:
P1_D06_S42
plexWell


title: 65Dn Hipp 3


title: LSK_OP3_NM_9d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP3_NM_9d_1.h5
CellAnnotation_exvivo.tsv


title: 65Dn Hipp 1


title: P1_D04_S40, HCT116, Heat Killed, plexWell

description:
P1_D04_S40
plexWell


title: P1_C12_S36, Jurkat, Heat Killed, plexWell

description:
P1_C12_S36
plexWell


title: LSK_OP3_NM_9d_1 mRNA


title: P1_C11_S35, Jurkat, Heat Killed, plexWell

description:
P1_C11_S35
plexWell


title: LSK_OP3_NM_7d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP3_NM_7d_1.h5
CellAnnotation_exvivo.tsv


title: P1_C09_S33, Jurkat, Heat Killed, plexWell

description:
P1_C09_S33
plexWell


title: P1_C10_S34, Jurkat, Heat Killed, plexWell

description:
P1_C10_S34
plexWell


title: LSK_OP3_NM_7d_1 mRNA


title: 65Dn Hipp 4


title: P1_C07_S31, Jurkat, Heat Killed, plexWell

description:
P1_C07_S31
plexWell


title: WT Hipp 1


title: P1_C08_S32, Jurkat, Heat Killed, plexWell

description:
P1_C08_S32
plexWell


title: LSK_OP4_NM_7d_1 mRNA


title: LSK_OP2_NM_9d_1 mRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP2_NM_9d_1.h5
CellAnnotation_exvivo.tsv


title: LSK_OP2_NM_9d_1 gRNA


title: P1_C04_S28, Jurkat, Heat Killed, plexWell

description:
P1_C04_S28
plexWell


title: P1_C05_S29, Jurkat, Heat Killed, plexWell

description:
P1_C05_S29
plexWell


title: P1_C03_S27, Jurkat, Heat Killed, plexWell

description:
P1_C03_S27
plexWell


title: P1_C02_S26, Jurkat, Heat Killed, plexWell

description:
P1_C02_S26
plexWell


title: LSK_OP2_NM_7d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP2_NM_7d_1.h5
CellAnnotation_exvivo.tsv


title: mammary tumor 311

city: Davis

first: Michele

last: La Merrill

state: CA

address: 4138 Meyer Hall

department: Department of Environmental Toxicology

institute: University of California, Davis

data_processing:
Illumina bcl2fastq version 2.20.0.422 was used for base-calling
Data was filtered using HTStream version 1.0.0
Data was aligned using STAR 2.6.1d
Unique molecular identifiers (UMI) processing was done using umitools version 0.5.5
Read counts were conducted using HTSeq version 0.10.0
Genome_build: GRCm38
Supplementary_files_format_and_content: normalized counts per gene per mouse
Supplementary_files_format_and_content: normalized intron counts per gene per mouse

source_name: mammary tumor

extract_protocol:
Mice were euthanized and tumors were excised and cut in half, with one half flash frozen in liquid nitrogen. Flash-frozen tumors were later pulverized and total RNA was extracted using the Qiagen AllPrep kit (80004).
RNA quality, quantity, and purity (260/280 absorbance ratios) were assessed using a Fragment Analyzer, a Qubit fluorometer, and a Nanoquant plate using an Infinite 200 PRO absorbance reader, respectively. Total RNA was diluted with nuclease free water to a normalized concentration (33.33 ng/uL) and sequenced.

value: mammary tumor

tag: strain

value: Propylparaben


title: LSK_OP2_NM_7d_1 mRNA


title: P1_B08_S20, HCT116, Uninfected, plexWell

description:
P1_B08_S20
plexWell

value: Uninfected


title: P1_B07_S19, HCT116, Uninfected, plexWell

description:
P1_B07_S19
plexWell


title: P1_B06_S18, HCT116, Uninfected, plexWell

description:
P1_B06_S18
plexWell


title: WT Hipp 3


title: mammary tumor 287


title: LSK_OP1_NM_9d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP1_NM_9d_1.h5
CellAnnotation_exvivo.tsv


title: P1_C06_S30, Jurkat, Heat Killed, plexWell

description:
P1_C06_S30
plexWell


title: P1_A11_S11, Jurkat, Uninfected, plexWell

description:
P1_A11_S11
plexWell


title: WT Hipp 2


title: P1_A12_S12, Jurkat, Uninfected, plexWell

description:
P1_A12_S12
plexWell


title: mammary tumor 278


title: WT Hipp 4


title: P1_B03_S15, HCT116, Uninfected, plexWell

description:
P1_B03_S15
plexWell


title: mammary tumor 279

value: Methylparaben


title: P1_A10_S10, Jurkat, Uninfected, plexWell

description:
P1_A10_S10
plexWell


title: LSK_OP1_NM_7d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP1_NM_7d_1.h5
CellAnnotation_exvivo.tsv


title: LSK_OP1_NM_7d_1 mRNA


title: P1_A07_S7, Jurkat, Uninfected, plexWell

description:
P1_A07_S7
plexWell


title: mammary tumor 276


title: P1_A06_S6, Jurkat, Uninfected, plexWell

description:
P1_A06_S6
plexWell


title: P1_A08_S8, Jurkat, Uninfected, plexWell

description:
P1_A08_S8
plexWell


title: P1_A09_S9, Jurkat, Uninfected, plexWell

description:
P1_A09_S9
plexWell


title: LSK_OP1_NM_9d_1 mRNA


title: LSK_OP0_NM_7d_1 gRNA

description:
Perturb-seq of mouse cells ex vivo
LSK_OP0_NM_7d_1.h5
CellAnnotation_exvivo.tsv


title: mammary tumor 296


title: mammary tumor 265


title: mammary tumor 264


title: P1_A03_S3, Jurkat, Uninfected, plexWell

description:
P1_A03_S3
plexWell


title: P1_A04_S4, Jurkat, Uninfected, plexWell

description:
P1_A04_S4
plexWell


title: P1_A05_S5, Jurkat, Uninfected, plexWell

description:
P1_A05_S5
plexWell


title: mammary tumor 261


title: P1_A02_S2, Jurkat, Uninfected, plexWell

description:
P1_A02_S2
plexWell


title: LSK_OP0_NM_7d_1 mRNA


title: inVivo_OP4_lin-_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP4_lin-_14d_1.h5
CellAnnotation_invivo.tsv

value: lin-


title: P1-SCAF2965_5_Live, HCT116, THP1 and Jurkat T, Infected, 10x genomics 5' v2

description:
P1-SCAF2965_5_Live
10x genomics 5' v2

data_processing:
Reads from multiplexed sequencing runs were demultiplexed using cellranger mkfastq v7.0.0 (10x Genomics).
Raw FASTQ files were aligned to the reference human genome (GRCh38 gencode release 34) using CellRanger v5.0.1. The annotated polyA and template sequence oligonucleotide (TSO) sequences were trimmed, the unmapped reads were converted to the FASTQ file format trimmed and filtered using FASTP v0.20.1 with the arguments “--unqualified_percent_limit 40 --cut_tail --low_complexity_filter --trim_poly_x” before being converted to BAM files. For quality filtering, we removed genes found in fewer than 3 cells and remove cells with fewer than 3,000 gene features or greater than 15% of reads mapping to mitochondrial genes.
Assembly: GRCh38 gencode release 34
Supplementary files format and content: Tab-separated values files and matrix files and h5 matrix files

source_name: HCT116, THP1 and Jurkat T

extract_protocol:
Single cell suspensions were prepared, and concentration and viability measured on an automated dual-fluorescence cell counter with acridine orange and propidium iodide stain (Luna Fx7, Logos Biosystems).
Single cell partitioning and RNA-Seq library preparation was performed using 10X Genomics Chromium NextGEM 5’ v2 chemistry (user guide CG000331) according to vendor recommendations. Sample viability was above 80% for all conditions. 6,000-8,000 cells were targeted to be captured for each sample. Libraries were sequenced on the NovaSeq 6000 with a target depth of 50,000 reads per cell using read parameters recommended by 10x Genomics user guides.

value: HCT116, THP1 and Jurkat T


title: P1-SCAF2962_2_HK, HCT116, THP1 and Jurkat T, Heat Killed, 10x genomics 3' v3

description:
P1-SCAF2962_2_HK
10x genomics 3' v3

extract_protocol:
Single cell suspensions were prepared, and concentration and viability measured on an automated dual-fluorescence cell counter with acridine orange and propidium iodide stain (Luna Fx7, Logos Biosystems).
Single cell partitioning and RNA-Seq library preparation was performed using 10X genomics 3’ v3.1 chemistry (user guide CG000204) according to vendor recommendations. Sample viability was above 80% for all conditions. 6,000-8,000 cells were targeted to be captured for each sample. Libraries were sequenced on the NovaSeq 6000 with a target depth of 50,000 reads per cell using read parameters recommended by 10x Genomics user guides.


title: P1-SCAF2963_3_Live, HCT116, THP1 and Jurkat T, Infected, 10x genomics 3' v3

description:
P1-SCAF2963_3_Live
10x genomics 3' v3


title: mammary tumor 233


title: P1-SCAF2961_1_Uninfected, HCT116, THP1 and Jurkat T, Uninfected, 10x genomics 3' v3

description:
P1-SCAF2961_1_Uninfected
10x genomics 3' v3


title: inVivo_OP4_ckit_14d_1 mRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP4_ckit_14d_1.h5
CellAnnotation_invivo.tsv

value: lin+ckit+


title: inVivo_OP4_ckit_14d_1 gRNA


title: D25 NLW50 Ctrl

city: Ann Arbor

first: Jennifer

last: Harder

state: MI

address: 1301 Catherine St.

department: Internal Medicine, Division of Nephrology

institute: University of Michigan Medical School

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: hg19 (NLW50 only), hg38 (all other samples)

source_name: hESC

extract_protocol:
Cells were dissociated from kidney organoids using cold active protease into single cells and 10x Genomics sequencing was performed in the Advanced Genomics Core at the University of Michigan.
Library was performed according to the manufacter’s instructions  (single cell 3’ v2 protocol, 10x Genomics for the NLW50 sample, single cell 3' v3 protocol, 10X Genomics for all other samples). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hESC

value: Kidney organoid


title: D24 TNF 24h


title: D24 Ctrl 24h


title: mammary tumor 232


title: mammary tumor 228


title: inVivo_OP3_lin-_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP3_lin-_14d_1.h5
CellAnnotation_invivo.tsv


title: Sample_4372-MF-3, VC 48h

data_processing:
Total RNA from whole wells underwent library preparation usingNEBNext Ultra II kitand sequencing using paired end read length of 150 bases on a NovaSeq6000.
RNAseq was performed by the University of Michigan Advanced Genomics Core (https://brcf.medicine.umich.edu/cores/advanced-genomics/).
Fastq files were mapped to ENSEMBL 38.104 using STAR 2.7.8a (PMID: 23104886)
Read counts were extracted from the fastq files using HTSeq (version0.11) (PMID: 25260700), voom-transformed (PMID: 24485249) and log-2 transformed.
Assembly: ENSEMBL GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: Kidney organoid

extract_protocol: Kidney organoids were generated from human embryonic stem cells (UM77-2, NIH registry #0278) according to published protocol (Harder et al., JCI Insight 2019). Isolated spheroids were from samples 3853-JES were collected at day 21, day 25 and day 29 with daily refeeding starting on day 17.  Isolated spheroids from samples 4372-MF were treated at D23 with TNFα 5ng/ml for 24h and 48h, with replenishment of treatment at D24 for the 48h wells, and then all of the 4372-MF spheroids were collected at day 25. All samples were lysed and RNA extracted for sequencing. Library prep and next-generation sequencing of total RNA on a NovaSeq6000 (150 bp, paired end) were carried out in the Advanced Genomics Core at the University of Michigan.

value: VC 48h


title: Sample_4372-MF-2, TNF 24h

value: TNF 24h


title: Sample_4372-MF-4, TNF 48h

value: TNF 48h


title: Sample_4372-MF-1, VC 24h

value: VC 24h


title: Sample_3853-JES-6, D29 Org2

value: Day 29


title: inVivo_OP3_lin-_14d_1 mRNA

value: CRISPR screen (Perturb-seq)


title: Sample_3853-JES-5, D29 Org1


title: inVivo_OP3_ckit_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP3_ckit_14d_1.h5
CellAnnotation_invivo.tsv


title: mammary tumor 205


title: mammary tumor 203


title: inVivo_OP3_ckit_14d_1 mRNA


title: Sample_3853-JES-3, D25 Org1

value: Day 25


title: mammary tumor 202

value: Vehicle


title: mammary tumor 239

value: mammary tumor


title: Sample_3853-JES-2, D21 Org2

value: Day 21


title: inVivo_OP4_lin-_14d_1 mRNA


title: inVivo_OP2_lin-_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP2_lin-_14d_1.h5
CellAnnotation_invivo.tsv


title: mammary tumor 199

value: Propylparaben


title: Sample_3853-JES-1, D21 Org1


title: mammary tumor 209


title: EAOC4

city: Changchun

first: Lijing

last: Zhao

state: jilin

address: Office Building, School of Nursing, Jilin University, No. 965 Xinjiang Street

department: gynaecology and obstetrics

institute: The second hospital of jilin university

data_processing:
sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp 0.20.1
Trimmed sequence reads were mapped to GRCm38 using hisat2 2.2.1
read count extraction and normalization were performed using stringtie 2.1.5（-e -b）and R Package "ballgown"

source_name: Endometriosis-associated ovarian cancer over time (EAOC)

extract_protocol:
RNA extraction adopts traditional trizol method
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.


title: EAOC3

value: Endometriosis-associated ovarian cancer over time (EAOC)


title: inVivo_OP2_lin-_14d_1 mRNA

value: lin-


title: inVivo_OP2_ckit_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP2_ckit_14d_1.h5
CellAnnotation_invivo.tsv


title: EAOC2


title: EAOC1


title: Sample_3853-JES-4, D25 Org2


title: mammary tumor 181

value: Methylparaben


title: inVivo_OP1_lin-_28d_2 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_lin-_28d_2.h5
CellAnnotation_invivo.tsv


title: EM2

source_name: Endometrialcyst of ovary (EMC)

value: Endometrialcyst of ovary (EMC)


title: EM3


title: EM


title: inVivo_OP2_ckit_14d_1 mRNA

value: lin+ckit+


title: mammary tumor 173


title: H1975 cells, untreated

city: Taoyuan

first: Jang-Hau

last: Lian

address: No. 5, Fuxing Street

country: Taiwan

institute: Chang Gung Memorial Hospital

data_processing:
TRIMMOMATIC v0.36 was used to remove adaptors and trim low quality bases (LEADING:20 TRAILING:13 SLIDINGWINDOW:5:20 MINLEN:30).
Trimmed reads were aligned to the reference genome sequence (GRCh38) using HISAT2 v2.1.0 to produce SAM file and then converted to sorted BAM files using SAMTOOLS v1.2.
Read count extraction and normalization were performed using StringTie v2.1.2.
Differential expression analysis was performed using DESeq (for non-replicate samples) R package v1.39.0 to test for differential expression for each group of samples, then functional enrichment assay was performed using clusterProfiler v3.6.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
RNA was harvested using Trizol method (Invitogen). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Agilent SureSelect Strand-Specific RNA Library Prep Kit following manufacturer's protocols.

value: lung cancer cells

value: Non-Small Cell Lung Cancer

value: EGFR T790M

value: PM2.5 untreated


title: EAOC


title: mammary tumor 178


title: H1975 cells, PM2.5-treated

value: PM2.5 treated


title: mammary tumor 193


title: Sample_2234-JES-3, Day29

data_processing:
Total RNA from whole wells underwent library preparation using NEBNext Ultra II kit and sequencing using paired end read length of 150 bases on a NovaSeq4000.
RNAseq was performed by the University of Michigan Advanced Genomics Core (https://brcf.medicine.umich.edu/cores/advanced-genomics/).
Fastq files were mapped to ENSEMBL 38.104 using STAR 2.7.8a (PMID: 23104886)
Assembly: Read counts were extracted from the fastq files using HTSeq (version0.11) (PMID: 25260700), voom-transformed (PMID: 24485249) and log-2 transformed.
Supplementary files format and content: ENSEMBL GRCh38.104
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

extract_protocol: Kidney organoids were generated from human embryonic stem cells (UM77-2, NIH registry #0278) according to published protocol (Harder et al., JCI Insight 2019).  Isolated spheroids were collected at day 21, day 25 and day 29, then lysed and RNA extracted.  Library prep and next-generation sequencing of total RNA on a NovaSeq4000 (150 bp, paired end) were carried out in the Advanced Genomics Core at the University of Michigan.

value: Kidney organoid

value: UM77-2 hESC

value: Day 29


title: mammary tumor 169

value: Vehicle


title: EM1


title: Sample_2234-JES-2, Day25

value: Day 25


title: inVivo_OP1_lin-_28d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_lin-_28d_1.h5
CellAnnotation_invivo.tsv

value: CRISPR screen (Perturb-seq)


title: inVivo_OP1_lin-_28d_1 mRNA


title: mammary tumor 198

value: mammary tumor


title: inVivo_OP1_lin-_28d_2 mRNA


title: mammary tumor 167

value: Propylparaben


title: HCT116 cells, shTRIM21, biol rep 3

city: Suzhou

first: Xiaoqin

last: Yang

state: Jiangsu

address: No. 199, Ren'ai Road

institute: Suzhou Medical College of Soochow University

data_processing:
All libraries were sequenced on the Illumina NovaSeq 6000 instrument, and 150 bp paired-end reads were generated.
Sequencing reads were aligned back to the human genome (hg38) by TopHat 2 (V 2.1.1).
Read count extraction was performed using GFOLD software (V1.1.4).
The expression matrix of all samples was subjected to the Bayesian workflow for differential gene modeling based on the “edgeR” (V3.38.1) and “limma” (V3.52.2) R packages.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads count for each Sample

growth_protocol: HCT116 cell lines stably expressing TRIM21-specific shRNA (shRNA/TRIM21) or scrambled shRNA control (shRNA/Control) were constructed using a lentiviral shRNA technique. The cells were infected with the lentivirus, and 36 h later, cells were selected using 5 μg/ml puromycin for 2–3 weeks.

extract_protocol:
Total RNA was isolated from the colorectal cancer cells using Trizol reagent (Invitrogen; ThermoFisher) according to the manufacturer’s instructions. Then, the ribosomal RNA was depleted from the Trizol-harvested total RNA with the GenSeq rRNA Removal Kit (GenSeq, Inc.) by adhering to its operation guideline.
Next, RNA-seq libraries (with each treatment in triplicate) were constructed with the GenSeq Low Input RNA Library Prep Kit (GenSeq, Inc.) following the manual specifications.

value: a poorly differentiated colon carcinoma cell line

value: TRIM21 knockdown

value: TRIM21-specific shRNA (shRNA/TRIM21) using a lentiviral shRNA technique

value: Day 21


title: HCT116 cells, shTRIM21, biol rep 2


title: inVivo_OP1_lin-_14d_2 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_lin-_14d_2.h5
CellAnnotation_invivo.tsv

value: lin-


title: mammary tumor 166

value: Methylparaben


title: HCT116 cells, shTRIM21, biol rep 1


title: inVivo_OP1_lin-_14d_2 mRNA


title: HCT116 cells, shControl, biol rep 3

value: WT

value: scrambled shRNA control (shRNA/Control) using a lentiviral shRNA technique


title: HCT116 cells, shControl, biol rep 1


title: mammary tumor 155


title: HCT116 cells, shControl, biol rep 2


title: mammary tumor 158


title: inVivo_OP1_lin-_14d_1 gRNA

description:
Perturb-seq of mouse cells in vivo
inVivo_OP1_lin-_14d_1.h5
CellAnnotation_invivo.tsv


title: mammary tumor 139


title: mammary tumor 135