title: Lungs, Ism1-/-, P7, Rep2

city: Singapore

first: Mahalakshmi

last: Shanmugasundaram

state: Singapore

address: 16, Science Drive 4, Blk S3, Level 6

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

data_processing:
The raw sequencing data were filtered to remove low quality reads and reads containing adaptor sequence using fastp. Clean reads were mapped to the reference genome Mus musculus (GRCm38/mm10) using Spliced Transcripts Alignments to a Reference (STAR) software. The number of reads that map a cetain gene or transcript was measured using the FeatureCounts bioinformatics tool. To calculate the gene expression level, raw counts obtained were normalised to FPKM (Fragments per kilobase of transcript sequence per Millions base pairs sequence) that takes sequence depth and gene lenth into account.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include FPKM  and reads count value for each sample

source_name: Lungs

growth_protocol: Wildtype and Ism1-/- mice were housed in cages with autoclave bedding. Ventilation, temperature (24 degree celcius), humidity (40-70%) were controlled and an automated light cycle of 12-14 hours of light and 10-12 hours of darkness were maintained. Lungs of postnatal day 7 (P7) mice were utilized for this experiment.

extract_protocol:
P7 lungs were perfused with ice-cold PBS to remove the blood and lungs were homogenized into single cells suspension in Trizol reagent using the gentleMACS dissociator. RNA was extracted using the Trizol-cholorform separation method and after a series of washing steps RNA pellet was dissolved in RNase free water.
Directional mRNA library was prepared and sequencing was performed using Illumina NovaSeq 6000 platform at Novogene. In brief, totla RNA of high quality with RNA integrity number >8 was subjected to polyA enrichment and directional mRNA library construction. The prepared library was subjected to pair end sequencing of 150bp read length and a sequence depth of 40 million read pairs per sample.

treatment_protocol: Untreated P7 lungs of WT and Ism1-/- mice

value: Lungs

value: Whole lungs

value: Untreated, P7 lungs


title: ind3hpe_mesophyllum_5_swimming_larva_39

status: Public on Jun 11 2024

type: SRA

city: Brisbane

first: Tahsha

last: Say

state: QLD

address: The University of Queensland

department: School of Biological Sciences

country: Australia

institute: The University of Queensland

description: Transcriptomic data for a total of 144 individual swimming larvae and settled post-larvae of the sponge Amphimedon queenslandica that were exposed to one of three different settlement cues for 2 hours at 1.5, 3, 5 and 8 hours post emergence (hpe).

library_source: transcriptomic

data_processing:
Raw CEL-Seq reads were processed using a publicly available pipeline (https://github.com/yanailab/CEL-Seq-pipeline).
The demultiplexed reads were mapped to the Amphimedon queenslandica Aqu2.1 gene models (Fernandez-Valverde et al., 2015) and read counts were generated. The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/.
The identifiers in my processed data are searchable in the EnsemblMetazoa database (http://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index). The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/ and are cited in 'Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. Selene L. Fernandez-Valverde, Andrew D. Calcino and Bernard M. Degnan. BMC Genomics 2015, 16:387’.
Supplementary_files_format_and_content: Tab-delimited text file including raw count values for each sample.

molecule: total RNA

organism: Amphimedon queenslandica

source_name: single larva

extract_protocol:
RNA was isolated from individual Amphimedon queenslandica larvae and settled post-larvae using TRIzol as previously described (Jindrich et al., 2017).
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

tag: developmental state

tag: library

value: T

tag: time at induction (hours post emergence; hpe)

tag: age at sequencing (hours post emergence; hpe)

tag: treatment (settlement cue)

value: mesophyllum


title: MCF7 cells, +SerGly, rep 3

city: Chicago

first: Svetlana

last: Semina

address: 909 S Wolcott Avenue (MC 901), 2100 COMRB

department: physiology and Biophysics

country: USA

institute: University of Illinois at Chicago

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5). STAR used the method of Maximal Mappable Prefix(MMP) which can generate a precise mapping result for junction reads.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: NCBI/UCSC/Ensembl
Supplementary files format and content: NA

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: MCF7 cells were maintained in HPLM with 5% dFBS and pen/strep in a humidified incubator with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TRIzol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X) or by using sonication with Diagenode bioruptor Pico for breaking RNA strands. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: MCF7 cells were treated with and without serine and glycine for 48 hours.

tag: cell line

tag: cell type

value: breast cancer

tag: treatment

value: Plus Ser/Gly 48 hr


title: ind3hpe_mesophyllum_4_swimming_larva_38


title: ind3hpe_mesophyllum_9_swimming_larva_18

value: C


title: MCF7 cells, +SerGly, rep 2


title: ind3hpe_mesophyllum_3_swimming_larva_37


title: Lungs, Ism1-/-, P7, Rep1

organism: Mus musculus

tag: tissue

tag: age

tag: genotype


title: Lungs, Wildtype, P7, Rep3

value: WT


title: MCF7 cells, +SerGly, rep 1


title: SHSY5Y_lentiUSP44_Rep3

city: Stuttgart

first: Steven

middle: A

last: Johnsen

address: Auerbachstrasse 112

country: Germany

institute: Robert Bosch Center for Tumor Diseases

data_processing:
All steps were performed with default settings unless otherwise denoted
Sequence reads were trimmed with fastx_trimmer (fastx/0.0.14)
Trimmed sequence reads were mapped to hg38 using star/2.7.9a
Read count extraction was performed using htseq/0.9.1 reverse strand option
Assembly: hg38
Supplementary files format and content: tab-deliminted text files include htseq-count values for each sample

growth_protocol: Lentiviral transduction with empty vector or USP44 cDNA was used to cell lines. Cells were cultured in DMEM with 10% FBS.

extract_protocol:
Total RNA from SH-SY5Y cells was isolated using QIAzol reagent and processed with RNeasy Plus Mini Kit (Qiagen).
mRNA-seq libraries were prepared using the TruSeq RNA Library Prep Kit (Illumina).

value: Neuroblastoma

value: USP44 overexpression


title: ind3hpe_mesophyllum_11_swimming_larva_14


title: SHSY5Y_lentiUSP44_Rep2


title: Lungs, Wildtype, P7, Rep2


title: ind3hpe_mesophyllum_10_swimming_larva_19


title: SHSY5Y_lentiUSP44_Rep1


title: Lungs, Wildtype, P7, Rep1


title: HCT116 cells, Fn∆radD, rep2

city: Shanghai

first: Lu

last: Zhang

address: 145 Middle Shandong Road

country: China

institute: Renji Hospital, Shanghai Jiao Tong University School of Medicine

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 standard parameters.
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Data filtering steps Prior to assembly, the low quanlity reads (1, reads containing sequencing adaptors; 2, reads containing sequencing primer; 3, nucleotide with q quality score lower than 20) were removed.
Read alignment software, software HISAT, version 2.0, parameters -| fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9. Perform expression level for mRNAs by calculating FPKM.
Assembly: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary files format and content: Tab-delimited text file include gene ID for each sample.
Supplementary files format and content: Tab-delimited text file include counts for each sample.

source_name: Colon

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacture's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Colon

value: Human colorectal cancer cell


title: SHSY5Y_EV_Rep3

value: Empty vector


title: ind3hpe_fsw_9_swimming_larva_13

value: K

value: fsw


title: PN24, MBD2, ChIP03

city: Rochester

first: Xiaogang

last: Li

state: Minnesota

address: 200 1st Street, SW

institute: Mayo Clinic

library_source: genomic

data_processing:
Raw data was processed with packages "ShortRead", and aligned with "Rbowties". And BigWig files were exported with rtracklayer package.
Assembly: mm10
Supplementary files format and content: BigWig

molecule: genomic DNA

growth_protocol: DMEM/F12, 10% FBS, 1% P/S. Cells were cultured at 33 degree  incubator with 5% CO2.

extract_protocol:
Cells were fixed in a solution of 1% formaldehyde (final concentration) in 50 mM Hepes–KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA.
Library was prepared according to the instruction of NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (E6240).

tag: chip antibody

value: MBD2, abcam; ab38646

value: proximal tubule kidney cells

value: Pkd1 homozygous knockout


title: Brain_flx_2

city: Bethesda

first: Joana

last: Vidigal

state: MD

address: 37 Convent Dr, Room 6056

department: LBMB

institute: NIH/NCI

data_processing:
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (mm10) and the annotated transcripts using STAR. The average mapping rate of all samples is 96%
Assembly: mm10
Supplementary files format and content: count table

source_name: Brain

extract_protocol:
RNA from brains and livers from Vaultrc5+/+ and Vaultrc5-/- mice was isolated using TRIzol reagent (Invitrogen) following the manufacturers’ protocol. RNA was then treated with DNase I using Zymo RNA clean & concentrator kit
12 totalRNA-Seq samples were pooled and sequenced on NextSeq 2000 P2 using Illumina® Stranded Total RNA Prep, Ligation with Ribo-Zero Plus and single-end sequencing
Stranded Total RNA Prep

value: Brain

tag: Sex

value: male

value: wild-type


title: Brain_flx_1


title: Lungs, Ism1-/-, P7, Rep3

value: Lungs

value: Whole lungs

value: Untreated, P7 lungs


title: HCT116 cells, Fn∆radD, rep1

value: WT


title: SHSY5Y_EV_Rep2

value: Neuroblastoma


title: PN24, MBD2, ChIP02

value: MBD2, abcam; ab188474


title: ind3hpe_fsw_8_swimming_larva_12


title: human bone marrow-derived stromal cells, CL144, Day14, rep2

city: Seoul

first: Sol

last: Jeong

address: Gwanakgu, Gwanakro1

country: South Korea

institute: SNU

data_processing:
Illumina DRAGEN BCL Convert v 3.8.4
FastQC was employed to trim adapter sequences and filter out low-quality reads.
DESeq2 was conducted for differential expression analysis.
Assembly: Homo_sapiens.GRCh38.99
Supplementary files format and content: raw_counts.txt: A file containing the combined raw count data from all groups

source_name: bone marrow

extract_protocol:
Total RNA was obtained using Trizol reagent (invitorgen) and 1ug of total RNA was used for sequencing library contsruction.
RNA-seq libraries were generated using SRSLY Library Prep kit (Claretbio) following the manufacturer's protocols.

value: bone marrow

value: human bone marrow-derived stromal cells

value: mesenchymal stromal cells


title: ind3hpe_fsw_7_swimming_larva_11

value: K


title: PH2, MBD2, ChIP03

value: Pkd1 heterozygous


title: HCT116 cells, Fn WT, rep2

value: Colon

value: Human colorectal cancer cell


title: PH2, MBD2, ChIP02

value: proximal tubule kidney cells


title: human bone marrow-derived stromal cells, CL144, Day14, rep1


title: ind3hpe_fsw_5_swimming_larva_13

value: T

value: fsw


title: human bone marrow-derived stromal cells, Nutlin-3, Day14, rep2


title: PN24, DNMT1, ChIP03

value: DNMT1, abcam 19905

value: Pkd1 homozygous knockout


title: ind3hpe_fsw_4_swimming_larva_12


title: SHSY5Y_EV_Rep1

value: Empty vector


title: PN24, DNMT1, ChIP02

value: DNMT1 Antibody (60B1220.1) , Novus


title: HCT116 cells, PBS, rep2

value: WT


title: HCT116 cells, PBS, rep3


title: PH2, DNMT1, ChIP03


title: human bone marrow-derived stromal cells, Osteogenic media Control, Day14, rep2

value: control


title: human bone marrow-derived stromal cells, Nutlin-3, Day14, rep1


title: ind3hpe_fsw_10_swimming_larva_14


title: human bone marrow-derived stromal cells, Osteogenic media Control, Day14, rep1


title: HeLa_WT_COL1_5

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of HeLa WT COL1G610C trasfected , biological rep5

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq; Trimming and cleaning with bbduk; Alignment was performed with STAR 2.6.0a The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: HeLa WT cells COL1G610C transfected

growth_protocol: Cells were cultured in DMEM 10% FBS and 1% P/S at 37°C in 5% CO2.

extract_protocol:
Cells were harvested for RNA extraction using RNAeasy Mini Kit (Qiagen) accorging to manifacturer's instuctions. RNA extracted from MOCK cells was used as a control. RNA extracted was quantified and mixed at 50 ng/ul.
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: Cells were reverse-transfected with GFP-COL1G610C plasmid using Lipofectamine LTX and Plus reagent (Invitrogen) accorging to manifacturer's instuctions. After 24H of transfection, all GFP-positive cells were isolated by FACS analysis.

value: Uterus; Cervix derived cell line

value: HeLa


title: PH2, DNMT1, ChIP02


title: ind3hpe_fsw_2_swimming_larva_11


title: HCT116 cells, PBS, rep1


title: HCT116 cells, Fn WT, rep3


title: HeLa_WT_COL1_4

description: Transcriptome profile of HeLa WT COL1G610C trasfected , biological rep4


title: ind3hpe_fsw_1_swimming_larva_10


title: ind3hpe_fsw_6_swimming_larva_10


title: HCT116 cells, Fn WT, rep1


title: Ovary, 3 months old, estrus, mouse het_KO2

first: Chengcheng

last: Song

state: Shanghai

address: 220 Handan Rd.

institute: Fudan University

description: column names in raw_counts.txt: het_KO2

data_processing:
Raw reads were trimmed using fastp (v0.20.1) with parameters: --length_required 50.
Sequencing alignments were performed with HISAT2 (v2.1.0) with parameters: --rna-strandness rf --fr.
Read counts of each gene were obtained by HTSeq-count (v0.11.2) with parameters: -s reverse
Differential expression analysis was performed using DESeq2 (v1.38.3).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Ovary

growth_protocol: Growthed in the SPF-class animal house of Fudan University

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

value: Ovary

value: 3 months old

tag: estrus cycle

value: estrus


title: Red_Flesh_Mesocarp_RepC_R201

city: Beuacouzé

first: Jean-Marc

last: Celton

address: 42 ue Georges Morel

country: France

institute: IRHS

data_processing:
AnaDIff (10.5281/ZENODO.6477918)
Assembly: GDDH13 v1.1
Supplementary files format and content: .sf count files

organism: Malus domestica

source_name: Treatment 3

growth_protocol: This analysis included three semi-biological replicates of RF and WF mesocarps (fruits from different trees) from red-flesh cultivar, cv. 'R201' (plantation year : 2013). The transition stage between fully red fruits and heterogeneously pigmented fruits was targeted during fruit development (84 Days After Full Bloom - DAFB).\\

extract_protocol:
Total RNA was extracted from fruit mesocarp according to the method detailed by Celton et al., 2014
Library construction and Pair Ends 100bp reads sequencing were completed by BGI using Illumina technology, and the quality was checked using FastQC. The library construction method and sequencing process are carried out according to the following steps : 1) Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; (2) mRNA molecules were fragmented into small pieces; (3) The fragmented mRNA was synthesized into first strand cDNA using random primers; (4) The second strand cDNA was synthesized with dUTP instead of dTTP; (5) The synthesized cDNA was subjected to end-repair and 3'adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; (6) Digest the U-labeled second-strand template with Uracil-DNA-Glycosylase (UDG) and perform PCR amplification; (7) Library quality control; (8) Library circularization; (9) The library was amplified to make DNA nanoball (DNB); (10) Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Distinction between red-flesh and white-flesh mesocarps from same fruits

value: Red-Flesh Mesocarp

tag: cultivar


title: ind3hpe_amphiroa_9_swimming_larva_32

value: K

value: amphiroa


title: Ovary, 3 months old, estrus, mouse het_KO1

description: column names in raw_counts.txt: het_KO1


title: Red_Flesh_Mesocarp_RepB_R201

source_name: Treatment 2


title: Red_Flesh_Mesocarp_RepA_R201

source_name: Treatment 1


title: Ovary, 3 months old, estrus, mouse WT3

description: column names in raw_counts.txt: WT3

value: wild-type


title: HeLa_WT_COL1_2

description: Transcriptome profile of HeLa WT COL1G610C trasfected , biological rep2


title: ind3hpe_amphiroa_8_swimming_larva_31


title: HCT116 cells, Fn∆radD, rep3

value: Colon

value: Human colorectal cancer cell


title: Ovary, 3 months old, estrus, mouse het_KO3

description: column names in raw_counts.txt: het_KO3


title: Ovary, 3 months old, estrus, mouse WT1

description: column names in raw_counts.txt: WT1


title: ind3hpe_amphiroa_6_swimming_larva_30


title: HeLa_WT_COL1_1

description: Transcriptome profile of HeLa WT COL1G610C trasfected , biological rep1


title: White_Flesh_Mesocarp_RepC_R201

source_name: Control 3

value: White-Flesh Mesocarp


title: HeLa_WT_SCR_5

description: Transcriptome profile of HeLa WT , biological rep5

source_name: HeLa WT cells scramble


title: HeLa_WT_SCR_3

description: Transcriptome profile of HeLa WT , biological rep3


title: White_Flesh_Mesocarp_RepA_R201

source_name: Control 1


title: Ovary, 3 months old, estrus, mouse WT2

description: column names in raw_counts.txt: WT2


title: HeLa_WT_SCR_4

description: Transcriptome profile of HeLa WT , biological rep4


title: HeLa_WT_COL1_3

description: Transcriptome profile of HeLa WT COL1G610C trasfected , biological rep3


title: Nfkb2-/-0h Rep3

city: New Delhi

first: Soumen

last: Basak

state: Delhi

address: Aruna Asaf Ali Marg

department: Infection and immunity

country: India

institute: National Institute of Immunology

data_processing:
Adapters were trimmed from the paired-end reads in FASTQ files were mapped to mouse genome build GRCm38/mm10 using HISAT2 tool.
Counts of mapped reads were summarized to gene level.
Assembly: mm10
Supplementary files format and content: .mtx file for the read counts of all the samples

source_name: Bone marrow derived dendritic cells

growth_protocol: Bone marrow cells isolated from mouse femur/tibia were cultured in RPMI medium (supplemented with 10% FBS and Penicillin-Streptomycin antibiotic) with 20 ng/mL GM-CSF for five days, and subsequently with 20 ng/mL GM-CSF + 10 ng/mL IL-4 cocktail for four days to generate BMDCs. In this nine-day culture protocol, half the growth/differentiation media volume was replaced on day 3, day5 and day7 as previously reported.

extract_protocol: The total RNA was isolated using RNesasy RNA isolation kit (#74004) form Qaigen.

treatment_protocol: Basal; no stimulation was given to the BMDCs.

value: Bone marrow derived dendritic cells

value: GMCSF+ IL4 differentiation media


title: L3_6PL_L1CAM_NEGATIVE_3

city: Naples

first: Enza

last: Lonardo

address: Via Pietro Castellino 111

institute: Institute of Genetics and Biophysics "Adriano Buzzati Traverso", CNR

data_processing:
Illumina NextSeq 500
Raw data were aligned to HG38 - Release 37 (GRCh38.p13)
Read count extraction was performed using FeatureCounts. Normalization was performed using DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: tab-limited text file includes raw counts for each sample

source_name: pancreatic ductal adenocarcinoma

growth_protocol: The human L3.6PL cell lines were maintained in DMEM, 10% FBS, and 50 units/ml penicillin/streptomycin

extract_protocol:
Total RNAs were extracted with Eurogold TRIFAST kit (Euroclone) according to the manufacturer’s instructions. One microgram of total RNA was used for the construction of the sequencing libraries
Libraries for RNA-seq were prepared using standard using Illumina platform.

value: pancreatic ductal adenocarcinoma

tag: disease

value: Pancreatic adenosquamous carcinoma

tag: cell population


title: ind3hpe_amphiroa_4_swimming_larva_25

tag: developmental state

value: T


title: HeLa_WT_SCR_2

description: Transcriptome profile of HeLa WT , biological rep2

value: Uterus; Cervix derived cell line


title: Nfkb2-/-0h Rep2


title: Nfkb2-/-0h Rep1


title: L3_6PL_L1CAM_NEGATIVE_2


title: ind3hpe_amphiroa_13_swimming_larva_17

tag: library

value: C


title: HeLa_WT_SCR_1

description: Transcriptome profile of HeLa WT , biological rep1

value: HeLa


title: ind3hpe_amphiroa_12_swimming_larva_16

tag: time at induction (hours post emergence; hpe)


title: WT0h Rep3

value: WT


title: ind3hpe_amphiroa_5_swimming_larva_26

tag: age at sequencing (hours post emergence; hpe)


title: S2-RNA-seq-HEK293T

city: Shenzhen

first: Changbin

last: Sun

address: Dapeng

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
Trimmed sequence reads were mapped to GRCh38 using HISTAT2 (version 2.2.1) with default parameters.
Assembly: GRCh38
Supplementary files format and content: Raw counts for the feature of genes were extracted by featureCounts (version 2.0.3).

extract_protocol:
Total RNA was extracted according to the manual of TRIzol™ (ThermoFisher Scintific#:15596026) from the manufacturer. DNase I (ThermoFisher Scintific#: EN0521) treatment was performed at 37°C to remove potential gDNA contamination.
cDNA hybrids were synthesized by ProtoScript® II Reverse Transcriptase with d(T)23VN primer according to the manufacturer’s manual. Then, cDNA hybrids were incubated with MBN at 30°C for 30 min to remove remaining primers and RNA. For library construction, synthesized cDNA hybrids were sonicated to 250 bp using ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4 – 20°C). For RNA-seq library preparation, denaturation was performed by heating at 95°C for 2 minutes followed by immediately cooling on ice for 2 minutes. Then, Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences) was used for library preparation according to the manufacturer’s manual.

value: Untreated


title: ind3hpe_amphiroa_1_swimming_larva_24

tag: treatment (settlement cue)


title: White_Flesh_Mesocarp_RepB_R201

source_name: Control 2


title: L3_6PL_L1CAM_POSITIVE_3

tag: cell line


title: ind3hpe_amphiroa_14_swimming_larva_13


title: ind1.5hpe_mesophyllum_9_swimming_larva_44

value: mesophyllum


title: WT0h Rep2

tag: cell type


title: S1-RNA-seq-HEK293T

tag: treatment


title: ind1.5hpe_mesophyllum_8_swimming_larva_43

value: K


title: WT0h Rep1


title: L3_6PL_L1CAM_POSITIVE_2

tag: tissue


title: L3_6PL_L1CAM_POSITIVE_1


title: S3-ssDRIP-seq-HEK293T-DMSO

data_processing:
library strategy: ssDRIP-seq
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
After trimming, clean reads were aligned to the genomes (BW25113 genome for E. coli, GRCh38 genome for humans, mm10 genome for mice) with Bowtie 2 (version 2.2.5) using local alignment mode.
Assembly: BW25113 genome for E. coli, GRCh38 genome for humans, mm10 genome for mice.
Supplementary files format and content: bigWig

extract_protocol:
Cells were lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method.
Genomic DNA was directly sonicated to 250 bp using ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4–20°C) before DRIP. After DRIP with antibody S9.6, Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences) was used for library preparation following the manufacturer’s manual.

value: DMSO


title: S4-ssDRIP-seq-HEK293T-DMSO


title: Striatal Microglia, Abstinence, rep7

city: Miami

first: Alexander

middle: Ve

last: Margetts

state: FL

address: 1600 NW 10th Ave, Rosenstiel Med Sci 7014A

department: Psychiatry and Behavioral Sciences

institute: University of Miami

data_processing:
Sequenced reads were concatenated into files by lane
Concatenated reads were then trimmed using Trimgalore (v.0.6.7) and cutadapt (v.1.18) for low-quality reads, Illumina sequence adaptors were removed, the leading and tailing low-quality base-pairs were trimmed following default parameters
Pair-end reads were mapped to the mm10 genome using STAR (v.2.7.10a) with the following parameters: –outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outFilterType BySJout –outSAMattributes NH HI AS NM MD XS –outFilterMultimapNmax 20 –outFilterMismatchNoverLmax 0.3 --quantMode TranscriptomeSAM GeneCounts
Resulting bam files were then passed to StringTie (v.2.1.5) to assemble sequenced alignments into estimated transcript and gene count abundance given the NCBI RefSeq GRCm38 (mm10) transcriptome assembly.
Gene count matrices from StringTie were then passed to the R/Bioconductor DESeq2 package (v.1.38.3) for normalization and differential gene expression analyses
Assembly: mm10
Supplementary files format and content: comma separated values file includes gene count matrix output from StringTie with no normalization
Supplementary files format and content: tab-delimited text file contains normalized counts conducted by DESeq2 for differential gene expression analysis

source_name: Neuronal

extract_protocol:
Isolated microglia were centrifuged for 5 min at 600xg and resuspended in RLT plus buffer (Qiagen) for extraction and purification of total RNA.
RNA input was normalized and NGS libraries were prepared using NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer’s instructions.

treatment_protocol:
Male C57BL/6J mice (9 weeks old ~25-30 g; Jackson Laboratories, Bar Harbor, ME; SN: 000664) were housed in the animal facilities at the University of Miami Miller School of Medicine. Mice were maintained on a 12:12 h light/dark cycle (0600 hours lights on; 1800 hours lights off) and were housed 3 to 5 per cage. Animals were provided with food and water ad libitum. Mice representing each experimental group were evenly distributed among testing sessions. All animals were maintained according to the National Institutes of Health guidelines in Association for Assessment and Accreditation of Laboratory Animal Care accredited facilities. All experimental protocols were approved by the Institutional Animal Care and Use Committee at the University of Miami Miller School of Medicine. Whenever possible, the experimenter was blind to the experimental and/or treatment group. For self-administration experiments in mice, methamphetamine hydrochloride (NIDA Drug Supply Program, Research Triangle Park, NC, USA) was dissolved in 0.9% sterile saline. Mice were permitted to self-administer methamphetamine or saline intravenous infusions during daily 2-hr sessions. Infusions were delivered through Tygon catheter tubing (Braintree Scientific, MA, USA) into the intravenous catheter by a variable speed syringe pump (Med Associates Inc, Fairfax, VT, USA). Self-administration sessions were carried out in operant chambers containing 2 retractable levers (1 active, 1 inactive) and a yellow cue light located above the active lever which illuminated during the intravenous infusion as well as during the post-infusion time out (TO). During Acquisition, mice started on a fixed ratio 1 (FR1) schedule of reinforcement for infusions 1 to 5, then FR2 for infusions 6 to 10, and FR3 for the remainder of the session. Completion of the response criteria on the active lever resulted in the delivery of an intravenous infusion (14 µL over 2 sec) of methamphetamine (0.05 mg/kg/infusion) or 0.9% saline. Responses on the inactive lever were recorded but had no scheduled consequences. After 5 consecutive days of Acquisition, mice were allowed to self-administer methamphetamine or saline during 10 consecutive daily 2-hr Maintenance sessions. Animals that did not demonstrate stable responding (less than 7 infusions per 2-hr session) or showed signs of compromised catheter patency were excluded from analysis. After 15 days of methamphetamine self-administration (Acquisition and Maintenance), mice underwent 21 days of forced home cage abstinence. Context-induced reinstatement session was then conducted on Day 21, where completion of response criteria resulted in the presentation of the light stimulus previously paired with methamphetamine or saline infusion delivery; however, no reward was delivered. Active lever presses were recorded and interpreted as a measure of drug-seeking.
Mice were anesthetized with isoflurane and perfused through the ascending aorta with 0.1 M phosphate buffer saline (PBS pH 7.4, Gibco, Waltham, MA, USA) plus heparin (7,500 USP units). Tissues were dissected and transported in Hibernate A Medium (Gibco) before dissociation. Briefly, tissue was enzymatically and mechanically dissociated, and debris removed using the Adult Brain Dissociation Kit (Miltenyi Biotec, Bergisch Gladbach, Germany). The resulting single cell suspension was incubated with anti-mouse CD11b (i.e., microglia-specific) magnetic MicroBeads (Miltenyi Biotec, #130–093–634) and microglia were positively selected for via column purification (Miltentyi Biotec, #130-042-201).

value: Neuronal

tag: region

value: Striatum

value: Microglia

value: Male

value: Methamphetamine intravenous self administration

tag: group

value: Abstinence


title: Striatal Microglia, Abstinence, rep6


title: ventricles, lincRNA-p21 knockout mice, TAC surgery, replicate 3

city: Boston

first: Yi

last: Wang

state: MA

address: 320 Longwood Avenue

institute: Boston Children's Hospital

data_processing:
The RNA-seq reads were aligned to mouse genome GRCm38.p6 with the aligner STAR. The Gencode nucleotide sequence (gencode.vM22; regions: ALL) was chosen as the annotation reference. The output file was indexed with Samtools for the read counting. Read counts were calculated with FeatureCounts. The read counts of each gene were normalized to the total mapped read counts in each library.
Assembly: mouse genome GRCm38.p6
Supplementary files format and content: comma-separated values (CSV) text file with normalized read counts for each sample

source_name: left ventricle apex

extract_protocol:
5ug total RNA was extracted from left ventricle apex of lincRNA-p21 global knockout mice and littermates, 8 weeks after sham or TAC surgery, using TRIzol Reagent (Thermo Fisher Scientific, #15596026).
The enriched ployA RNA was used to prepare 12 barcoded Illumina libraries with TruSeq Stranded mRNA Library Prep Kit, following the manufacturer’s instructions (Illumina).

value: left ventricle apex

tag: genotype

value: lincRNA-p21 knockout

value: TAC surgery


title: S94-mDRIP-seq-HEK293T

data_processing:
library strategy: mDRIP-seq
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
Raw reads with low quality and adaptor contamination were trimmed, and short reads less than 50 pb were filtered by Trim Galore (version 0.6.7)
After trimming, clean reads were aligned to the genomes (BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice, TAIR10 genome for Arabidopsis, MSU version 7.0 for rice) with Bowtie 2 (version 2.2.5) using local alignment mode.
Assembly: BW25113 genome for E. coli, sacCer3 genome for yeast, GRCh38 genome for humans, mm10 genome for mice, TAIR10 genome for Arabidopsis, MSU version 7.0 for rice
Supplementary files format and content: bigWig

extract_protocol:
For mammal and E. coli genomic DNA extraction, cells were lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For Arabidopsis and rice gDNA extraction, seedlings were grounded in liquid nitrogen and then lysed by 0.5% SDS and digested with 0.1 mg/mL proteinase K (TransGen Biotech#: GE201-01) at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For yeast gDNA extraction, cells were resuspended in TE buffer with 0.5% NP40 and equal volume glass beads (Sigma#: G8772), and beat 6 times in 30 sec at 60 Hz with 1 min pausing at 4°C to destroy cell walls. Then cells were collected, lysed by 0.5% SDS and digested with 0.1mg/mL proteinase K at 37°C in a shake with 220 rpm for 4-6 hours followed by phenol-chloroform nucleic acid extraction method. For cDNA hybrids synthesis, total RNA was extracted according to the manual of TRIzol™ (ThermoFisher Scintific#:15596026) from the manufacturer. DNase I (ThermoFisher Scintific#: EN0521) treatment was performed at 37°C to remove potential gDNA contamination. cDNA hybrids were synthesized by ProtoScript® II Reverse Transcriptase with d(T)23VN primer according to the manufacturer’s manual. Then, cDNA hybrids were incubated with MBN at 30°C for 30 min to remove remaining primers and RNA while only production with DNA:RNA hybrid form can be retained.
Nucleic acid was digested with MBN at 30°C for 1 hour and purified using the phenol-chloroform nucleic acid extraction method followed by resuspending the pellet in 130 μl TE buffer. Sonication with Covaris™ ME220 (Covaris, 70 W, 20% Duty factor, 1000 cycles per burst, 130 s, at 4–20°C) was performed to fragment nucleic acid with peak size around 250 bp and quantified by Qubit™ dsDNA HS Assay Kit (ThermoFisher Scintific#:Q32851). For multiple samples that would be used as a pool for DRIP, sonicated DNA was diluted to the needed concentration and barcoded in DNA:RNA hybrids tailing and ligation reaction for each sample as above mentioned at 37°C for 1 hour with barcode adaptors (Table S2) followed by adding 2 μL 0.5 M EDTA to stop the reaction. Then, these barcoded samples were pooled together and purified using the phenol-chloroform nucleic acid extraction method. The purified nucleic acid pellet was resuspended in TE buffer followed by DRIP and library construction for sequencing as described in ssDRIP-seq.


title: Striatal Microglia, Abstinence, rep5

tag: Sex


title: ventricles, lincRNA-p21 knockout mice, TAC surgery, replicate 2


title: L3_6PL_L1CAM_NEGATIVE_1

value: pancreatic ductal adenocarcinoma

value: Pancreatic adenosquamous carcinoma


title: ind1.5hpe_mesophyllum_4_swimming_larva_36

data_processing:
Raw CEL-Seq reads were processed using a publicly available pipeline (https://github.com/yanailab/CEL-Seq-pipeline).
The demultiplexed reads were mapped to the Amphimedon queenslandica Aqu2.1 gene models (Fernandez-Valverde et al., 2015) and read counts were generated. The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/.
The identifiers in my processed data are searchable in the EnsemblMetazoa database (http://metazoa.ensembl.org/Amphimedon_queenslandica/Info/Index). The Aqu2.1 gene models are also available at  http://amphimedon-degnan.qfab.org/ and are cited in 'Deep developmental transcriptome sequencing uncovers numerous new genes and enhances gene annotation in the sponge Amphimedon queenslandica. Selene L. Fernandez-Valverde, Andrew D. Calcino and Bernard M. Degnan. BMC Genomics 2015, 16:387’.
Supplementary_files_format_and_content: Tab-delimited text file including raw count values for each sample.

source_name: single larva

extract_protocol:
RNA was isolated from individual Amphimedon queenslandica larvae and settled post-larvae using TRIzol as previously described (Jindrich et al., 2017).
The CEL-Seq2 protocol (Hashimshony, et al. 2016) was used to amplify and sequence. CEL-seq multiplexing barocdes were used.

value: T


title: ventricles, lincRNA-p21 knockout mice, TAC surgery, replicate 1


title: Striatal Microglia, Abstinence, rep4


title: ind1.5hpe_mesophyllum_3_swimming_larva_35


title: ventricles, lincRNA-p21 control mice, TAC surgery, replicate 3

value: lincRNA-p21 heterozygous


title: ind1.5hpe_mesophyllum_2_swimming_larva_34


title: S90-mDRIP-seq-Input-HEK293T-cDNA

value: WT

value: Untreated


title: S78-mDRIP-seq-Input-HEK293T


title: ventricles, lincRNA-p21 control mice, TAC surgery, replicate 2


title: ind1.5hpe_mesophyllum_7_swimming_larva_42

value: K

value: mesophyllum


title: ind1.5hpe_mesophyllum_11_swimming_larva_08

value: C


title: S77-mDRIP-seq-Input-HEK293T


title: ind1.5hpe_mesophyllum_6_swimming_larva_41


title: Striatal Microglia, Abstinence, rep2

value: Neuronal

value: Striatum


title: S90-mDRIP-seq-HEK293T-cDNA


title: S93-mDRIP-seq-HEK293T


title: Striatal Microglia, Abstinence, rep1

value: Microglia

value: Male


title: ventricles, lincRNA-p21 control mice, TAC surgery, replicate 1


title: ventricles, lincRNA-p21 knockout mice, sham surgery, replicate 3

value: sham surgery


title: ind1.5hpe_fsw_9_swimming_larva_08

value: fsw


title: Striatal Microglia, Maintenance, rep8

value: Methamphetamine intravenous self administration

value: Maintenance


title: Striatal Microglia, Maintenance, rep7


title: ventricles, lincRNA-p21 knockout mice, sham surgery, replicate 2

value: left ventricle apex

value: lincRNA-p21 knockout


title: ventricles, lincRNA-p21 knockout mice, sham surgery, replicate 1


title: Striatal Microglia, Maintenance, rep6


title: S77-mDRIP-seq-HEK293T


title: S76-mDRIP-seq-WRL68


title: S78-mDRIP-seq-HEK293T


title: Striatal Microglia, Abstinence, rep3

value: Abstinence


title: ind1.5hpe_fsw_7_swimming_larva_06


title: ind1.5hpe_fsw_8_swimming_larva_07


title: Striatal Microglia, Maintenance, rep5


title: ind1.5hpe_fsw_5_swimming_larva_09

value: T


title: S75-mDRIP-seq-WRL68

value: WT


title: ind1.5hpe_mesophyllum_10_swimming_larva_45


title: ventricles, lincRNA-p21 control mice, sham surgery, replicate 2

value: lincRNA-p21 heterozygous


title: Striatal Microglia, Maintenance, rep4


title: ind1.5hpe_fsw_4_swimming_larva_08


title: ventricles, lincRNA-p21 control mice, sham surgery, replicate 1


title: Striatal Microglia, Maintenance, rep3


title: ind1.5hpe_fsw_3_swimming_larva_07


title: ind1.5hpe_fsw_2_swimming_larva_06


title: S72-mDRIP-seq-Calu-1

value: Untreated


title: S71-mDRIP-seq-Calu-1


title: Striatal Microglia, Maintenance, rep2


title: PH2, MBD2, ChIP01

tag: chip antibody

value: MBD2， abcam; ab38646

value: proximal tubule kidney cells

value: Pkd1 heterozygous


title: PN24, DNMT1, ChIP01

value: DNMT1 Antibody (60B1220.1) , Novus

value: Pkd1 homozygous knockout


title: ventricles, lincRNA-p21 control mice, sham surgery, replicate 3


title: Striatal Microglia, Saline, rep7

value: Neuronal

value: Striatum

value: Microglia

value: Male

value: Saline


title: Striatal Microglia, Saline, rep6

value: Methamphetamine intravenous self administration


title: Striatal Microglia, Maintenance, rep1

value: Maintenance


title: ind1.5hpe_fsw_10_swimming_larva_09

value: K

value: fsw


title: Striatal Microglia, Saline, rep8


title: Saline control  78

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina Casava2.20 software used for basecalling.
Reads were aligned to UCSC mouse genome (mm10) using Tophat2 (2.1.1)
Gene-based read counts were performed using Rsubread from FeatureCounts
Assembly: UCSC mouse genome (mm10)
Supplementary files format and content: csv file includes Gene counts for each sample

source_name: Liver

extract_protocol:
Livers were removed, flash frozen on dry ice, stored at -80'C . RNA was extracted using Trizol reagent.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit with NEBNext Poly(A) mRNA Magnetic Isolation Module.

value: Liver

tag: strain

tag: age

value: 22 weeks

value: Saline control


title: S70-mDRIP-seq-Eca109

value: WT

value: Untreated


title: ind1.5hpe_fsw_1_swimming_larva_05

value: T


title: S69-mDRIP-seq-Eca109


title: PH2, DNMT1, ChIP01

value: DNMT1 Antibody (60B1220.1) , Novus

value: proximal tubule kidney cells

value: Pkd1 heterozygous


title: Striatal Microglia, Saline, rep5

value: Neuronal

value: Striatum


title: ind1.5hpe_amphiroa_9_swimming_larva_28

value: amphiroa


title: ind1.5hpe_amphiroa_7_swimming_larva_26


title: S67-mDRIP-seq-Iose80


title: PN24, MBD2, ChIP01

value: MBD2， abcam; ab38646

value: Pkd1 homozygous knockout


title: Striatal Microglia, Saline, rep4

value: Microglia

value: Male

value: Methamphetamine intravenous self administration

value: Saline


title: ind1.5hpe_amphiroa_6_swimming_larva_25

value: K


title: S64-mDRIP-seq-A2780


title: ind1.5hpe_amphiroa_5_swimming_larva_23


title: ind1.5hpe_amphiroa_8_swimming_larva_27


title: S66-mDRIP-seq-BEL7042


title: S63-mDRIP-seq-A2780


title: Saline control  73

value: Liver

value: 22 weeks

value: Saline control


title: Striatal Microglia, Saline, rep2


title: S68-mDRIP-seq-Iose80

value: WT

value: Untreated


title: S65-mDRIP-seq-BEL7042


title: Saline control  50


title: ind1.5hpe_amphiroa_4_swimming_larva_22

value: T


title: Calorie restricted 52

value: Calorie restricted


title: Striatal Microglia, Saline, rep1

value: Neuronal


title: Striatal Microglia, Saline, rep3

value: Striatum


title: Saline control 35


title: Calorie restricted 79


title: ind1.5hpe_amphiroa_1_swimming_larva_21

value: amphiroa


title: ind1.5hpe_amphiroa_11_swimming_larva_06

value: C


title: S61-mDRIP-seq-HCT116


title: Calorie restricted 8


title: Dicretin 65

value: Dicretin


title: Mixed Multiplexed_Hashtag_Lib2

city: Cambridge

first: Adelyne

middle: SL

last: Chan

address: Li Ka Shing Way

department: Cancer Research UK

institute: University of Cambridge

description: 10x Genomics

library_source: transcriptomic single cell

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: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Hepatocytes, HTO-derived cDNA

extract_protocol:
Livers were harvested and digested using the Miltenyi Biotec Mouse Liver Dissociation kit and individually-labelled with hashtag-oligos according to manufacturer's protocol (Biolegend, TotalSeqTM-B, v3.1 single index). 8000 mVenus-expressing cells from each sample was flow-sorted, and multiplexed for single-cell RNAseq.
Libraries were prepared according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics), the multiplexed cell suspension was loaded onto 2 lanes n the 10x Chromium Genomics platform for single cell encapsulation and library preparation according to the manufacturer’s instructions (10x Genomics Chromium Single Cell 3' GEM v3 workflow). Standard 10x Genomics parameters were used for sequencing: read1: 28bp, index1: 8bp, index2: 0bp, read2: 91bp. The libraries were sequenced on 1 lane of an S1 flowcell on an Illumina NovaSeq 6000.

value: Hepatocytes

value: HDTV


title: Hepatocytes, HTO-derived cDNA

description: 10x Genomics

extract_protocol:
Livers were harvested and digested using the Miltenyi Biotec Mouse Liver Dissociation kit and individually-labelled with hashtag-oligos according to manufacturer's protocol (Biolegend, TotalSeqTM-A). mVenus-expressing cells from each sample was flow-sorted, and multiplexed for single-cell RNAseq.
Libraries were prepared according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics), the multiplexed cell suspension was loaded onto 2 lanes n the 10x Chromium Genomics platform for single cell encapsulation and library preparation according to the manufacturer’s instructions (10x Genomics Chromium Single Cell 3' GEM v3 workflow). Standard 10x Genomics parameters were used for sequencing: read1: 28bp, index1: 8bp, index2: 0bp, read2: 91bp. The libraries were sequenced on 1 lane of an S1 flowcell on an Illumina NovaSeq 6000.


title: ind1.5hpe_amphiroa_10_swimming_larva_29

first: Tahsha

last: Say

address: The University of Queensland

institute: The University of Queensland


title: S60-mDRIP-seq-HEK293T


title: Dicretin 64


title: Hepatocytes, mRNA-derived cDNA

description: 10x Genomics


title: Dicretin 23


title: 0.5hpe_7_swimming_larva_02


title: Semaglutide 51

value: Semaglutide


title: Dicretin 14


title: S59-mDRIP-seq-HEK293T


title: S55-mDRIP-seq-WRL68


title: Mixed Multiplexed_Gene Expression_Lib1

description: 10x Genomics

source_name: Hepatocytes, mRNA-derived cDNA


title: 0.5hpe_6_swimming_larva_01


title: 0.5hpe_5_swimming_larva_04


title: Mixed Multiplexed_Hashtag_Lib1

description: 10x Genomics


title: S62-mDRIP-seq-HCT116


title: 0.5hpe_9_swimming_larva_04


title: S58-mDRIP-seq-Hela

source_name: Hela

value: Hela


title: Mixed Multiplexed_Gene Expression_Lib2

description: 10x Genomics


title: S57-mDRIP-seq-Hela


title: 0.5hpe_8_swimming_larva_03

value: K


title: S56-mDRIP-seq-WRL68


title: Semaglutide 31

value: Liver


title: 0.5hpe_4_swimming_larva_03


title: S6-ssDRIP-seq-3T3-DMSO

value: DMSO


title: Calorie restricted 7

value: 22 weeks


title: S54-mDRIP-seq-3T3

value: WT


title: S53-mDRIP-seq-3T3

value: Untreated


title: S5-ssDRIP-seq-3T3-DMSO


title: 0.5hpe_10_swimming_larva_05


title: Semaglutide 15


title: S96-mDRIP-seq-3T3


title: S51-mDRIP-seq-Calu-1


title: Semaglutide 11


title: 0.5hpe_2_swimming_larva_02

value: T


title: S95-mDRIP-seq-3T3


title: S52-mDRIP-seq-Calu-1


title: 0.5hpe_1_swimming_larva_01


title: S80-mDRIP-seq-Input-3T3


title: mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 2

source_name: cardiomyocytes

extract_protocol:
2ug total RNA was extracted from neonatal mouse cardiomyocytes (CMs) treated with the hypertrophic agonist phenylephrine (PE) combined with GapmeR negative control and lincRNA-p21, using TRIzol Reagent (Thermo Fisher Scientific, #15596026).
For cardiomyocyte samples, cDNA library preparation and NGS sequencing were performed in BGI Corporation Inc. Finally, a total of approximately 300 million pair-ended reads (100 bp) were sequenced for the 12 cardiomyocyte cDNA libraries.

value: cardiomyocytes

value: GapmeR lincRNA-p21

value: PE


title: MEFs_Ferroptotic_1

city: Sendai

first: Hironari

last: Nishizawa

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
Quality of the reads was evaluated with FastQC (v0.11.9).
Sequence reads were trimmed for low quality sequence using Trimmomatic (v0.39).
Trimmed sequence reads were mapped to GRCm38/mm10 using STAR (2.7.10a).
Read count extraction was performed using HTSeq (v0.9.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Bach1-/- pMEFs

growth_protocol: Control or Bach1-re-expressed (ferroptotic) immortalized MEFs (iMEFs) were cultured in DMEM including 10% fetal bovine serum (FBS), 1% penicillin-streptomycin, 1% nonessential amino acids for 48 h. The supernatant medium was used for the following culture of Hepa1 or Bach1-/- primary MEFs (pMEFs).

extract_protocol:
RNA was harvested using Rneasy plus mini kit (Qiagen).
Libraries for RNA-seq were prepared from 100 ng of total RNA using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) with the protocol described in the manufacturer’s manual.

treatment_protocol:
Hepa1 cells and Bach1-/- pMEFs were cultured in the medium derived from control or ferroptotic iMEFs for totally 4 days. 2-ME (0.1mM) and vitamin.E (0.4 mg/mL) were added to the medium.
The culture medium was replaced daily with a new one derived from control or ferroptotic iMEFs.

value: Bach1-/- pMEFs

value: Mouse embryonic fibroblasts

value: Bach1 knockout

value: Cultured in ferroptotic-cells-derived medium


title: MEFs_Ferroptotic_2


title: MEFs_Control_3

value: Cultured in control-cells-derived medium


title: S79-mDRIP-seq-3T3


title: S50-mDRIP-seq-Eca109


title: S80-mDRIP-seq-3T3


title: MEFs_Ferroptotic_3


title: mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 3


title: S49-mDRIP-seq-Eca109


title: S48-mDRIP-seq-Iose80


title: S74-mDRIP-seq-3T3


title: mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 3

value: GapmeR negative control


title: MEFs_Control_2


title: mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 2


title: mouse cardiomyocytes, PE treatment, GapmeR lincRNA-p21, replicate 1


title: S46-mDRIP-seq-BEL7042


title: S47-mDRIP-seq-Iose80


title: mouse cardiomyocytes, PE treatment, GapmeR negative control, replicate 1


title: Hepa1_Ferroptotic_2

value: Hepatoma cells

value: Wild type


title: S73-mDRIP-seq-3T3


title: MEFs_Control_1


title: Hepa1_Ferroptotic_3


title: S45-mDRIP-seq-BEL7042


title: S79-mDRIP-seq-Input-3T3


title: mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 3

value: PBS


title: S44-mDRIP-seq-A2780


title: mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 2


title: S34-mDRIP-seq-3T3


title: S33-mDRIP-seq-3T3


title: mouse cardiomyocytes, PBS treatment, GapmeR lincRNA-p21, replicate 1


title: S42-mDRIP-seq-HCT116


title: S43-mDRIP-seq-A2780


title: S15-mDRIP-seq-Input-3T3-DRB

value: DRB


title: mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 3


title: S41-mDRIP-seq-HCT116


title: Hepa1_Control_2


title: S14-mDRIP-seq-Input-3T3-DMSO

value: DMSO


title: S14-mDRIP-seq-3T3-DMSO

value: WT


title: S40-mDRIP-seq-HEK293T

value: Untreated


title: Hepa1_Control_1


title: S15-mDRIP-seq-3T3-DRB


title: mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 2


title: S39-mDRIP-seq-HEK293T


title: S. enterica ∆rpoS, 15°C, replicate E

city: Claremont

first: Daniel

last: Stoebel

state: CA

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Sequencing reads from each sample in a pool were demultiplexed based on their associated barcode sequence using custom scripts. Up to 1 mismatch in the barcode was allowed provided it did not make assignment of the read to a different barcode possible. Barcode sequences were removed from the first read as were terminal G’s from the second read that may have been added by SMARTScribe during template switching.
Reads were aligned to the reference genomes using BWA v0.7.17 . Reads were counted with htseq-count v2.0.1
Assembly: 6 species are present here, so there are six reference sequences: GCF_000005845.2,GCF_000022165.1,GCF_000027085.1,GCF_000281535.2,GCF_000025565.1,GCF_000513215.1
Supplementary files format and content: Processed files are text files of (unnormalized) counts for each sample.

organism: Salmonella enterica

growth_protocol: Bacteria were grown in LB at 37°C

extract_protocol:
1.5 mL of bacterial culture was pelleted and resuspended in 500 μL of Trizol pre-heated to 65°C and then stored at -80°C until use. Samples were purified on a column using the Zymo Direct-Zol RNA Miniprep kit. They were then treated twice with DNase I using Turbo DNA-free (Invitrogen) for 30 minutes each at 37˚C to ensure that all DNA was degraded. The samples were further purified on a column using the Zymo RNA Clean and Concentrator Kit and again stored at -80˚C until sequencing.
Illumina cDNA libraries were generated using a modified version of the RNAtag-seq protocol. Briefly, 500 ng to 1 μg of total RNA was fragmented by heating to 94°C in NEB Alkaline Phosphatase Buffer, depleted of any residual genomic DNA, dephosphorylated, and ligated to DNA adapters carrying 5’-AN8-3’ barcodes of known sequence with a 5’ phosphate and a 3’ blocking group. Barcoded RNAs were pooled and depleted of rRNA using the RiboZero rRNA depletion kit (Epicentre). Pools of barcoded RNAs were converted to Illumina cDNA libraries in 2 main steps: (i) reverse transcription of the RNA using a primer designed to the constant region of the barcoded adaptor with addition of an adapter to the 3’ end of the cDNA by template switching using SMARTScribe (Clontech) as described (23); (ii) PCR amplification using primers whose 5’ ends target the constant regions of the 3’ or 5’ adaptors and whose 3’ ends contain the full Illumina P5 or P7 sequences. cDNA libraries were sequenced on the Illumina [NextSeq 500] platform at the Broad Institute to generate paired end reads.

treatment_protocol: At time 0, samples were taken and cultures shifted to 15°C. Cells grew at 15°C for 3 hours, and then sampleres were taken again

value: {delta}rpoS

tag: biological replicate

value: E


title: S10-mDRIP-seq-Input-3T3-DRB


title: mouse cardiomyocytes, PBS treatment, GapmeR negative control, replicate 1

value: cardiomyocytes


title: S38-mDRIP-seq-Hela

value: Hela


title: S9-mDRIP-seq-Input-3T3-DMSO


title: Hepa1_Ferroptotic_1


title: S. marcescens wild-type, 15°C, replicate E

organism: Serratia marcescens

value: wild-type


title: Hepa1_Control_3


title: S37-mDRIP-seq-Hela


title: S. enterica ∆rpoS, 37°C, replicate E


title: S10-mDRIP-seq-3T3-DRB


title: S. enterica wild-type, 37°C, replicate E


title: S. marcescens wild-type, 37°C, replicate E


title: S36-mDRIP-seq-WRL68


title: S35-mDRIP-seq-WRL68


title: S9-mDRIP-seq-3T3-DMSO


title: S. enterica ∆rpoS, 15°C, replicate D

value: D


title: Hi-C of Bos taurus DNA Zoo Sample6626, Freeze-dried liver, +1y @RT

city: Houston

first: Olga

last: Dudchenko

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Hi-C-guided genome assembly (3D-DNA, JBAT)
Reference-guided 3D genome assembly (Anonamos, 3D-DNA, JBAT)
Construction of the chromosome-length Hi-C contact map (BWA, Juicer, 3D-DNA)
liftover (KentUtils, 3D-DNA)
Gene annotation (TOGA)
Compartment annotation (CRUSH)
Loop calling and aggregate analysis (HiCCUPS, Juicer Tools, SIP, SIP META)
Aggregate chromosome analysis (3D-DNA)
Modeling of 3D structures of woolly mammoth chromosomes (OpenMiChroM)
DNA degradation simulations (NuChroM, custom script)
Assembly: The following existing genome builds were used in parts of the study: Loxafr3.0 (GCA_000001905.1), ASM1433276v1 (GCA_014332765.1), EquCab2.0 (GCF_000002305.2), ASM303372v1 (GCA_003033725.1), bosTau9 (GCF_002263795.3), ASM651725v1 (GCF_006517255.1), ASM3043605v1 (GCF_030436055.1), ASM331443v2 (GCF_003314435.2), hg38, hg19.
Supplementary files format and content: fasta.gz: chromosome-length nucleotide sequences generated usign Hi-C-guided genome assembly
Supplementary files format and content: hic: contact maps generated by aligning Hi-C data to reference sequences. In addition to "standard" hic maps build against chromosome-length references included are "assembly" maps generated by 3D-DNA for before and after genome assembly and an aggregate chromosome analysis (ACA) map.
Supplementary files format and content: bedpe: chromatin loops
Supplementary files format and content: bedgraph: A/B compartment annotations
Supplementary files format and content: sw: HDF5-based file for storing 3D structure ensembles
Supplementary files format and content: assembly: text file describing the relationship between the draft assembly and the chromosome-length upgrade
Supplementary files format and content: bed: gene annotations

organism: Bos taurus

source_name: liver

extract_protocol:
The protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024. Briefly, PaleoHi-C is a a modified in situ Hi-C protocol, tailored towards working with highly degraded samples. The principal modifications were: (i) immediate preservation in the field using ethanol to reduce microbial activity; and (ii) sequestration of chromatin bodies on beads; (iii) removal of shearing and size selection given the lack of high molecular weight DNA; and (iv) library amplification using a paleo-compatible workflow
Library contruction protocol is described in detail in Sandoval-Velasco, Dudchenko, Rodríguez, Pérez Estrada et al., 2024.
Modified Hi-C.

value: liver

value: tissue

value: Freeze-dried liver, +1y @RT


title: S. marcescens wild-type, 37°C, replicate D


title: S. marcescens wild-type, 15°C, replicate B

value: B


title: Hi-C of Bos taurus DNA Zoo Sample6913, Bovine liver, after 22h in dehydrator +1mo @RT


title: S92-ssDRIP-seq-K12

organism: Escherichia coli


title: S. marcescens wild-type, 15°C, replicate D


title: S. enterica wild-type, 15°C, replicate E


title: S31-mDRIP-seq-Calu-1


title: S. enterica ∆rpoS, 37°C, replicate D


title: S. marcescens wild-type, 37°C, replicate B


title: S91-ssDRIP-seq-K12


title: S32-mDRIP-seq-Calu-1


title: S29-mDRIP-seq-Eca109


title: S. marcescens wild-type, 15°C, replicate A

value: A


title: S. enterica wild-type, 37°C, replicate D


title: S. enterica ∆rpoS, 15°C, replicate B


title: S82-mDRIP-seq-Input-K12


title: S28-mDRIP-seq-Iose80


title: S. enterica wild-type, 15°C, replicate B


title: S27-mDRIP-seq-Iose80


title: S26-mDRIP-seq-BEL7042


title: wrky10, 0%Nitrate, rep 2

city: Singapore

first: Shalini

last: Ravi

address: 1 Research link

institute: Temasek lifesciences laboratory

data_processing:
The raw sequence reads was mapped using STAR (v.2.7) with the reference genome
The raw readcounts were normalised using DeSeq2 package from R
The differentially expressed genes were used for downstream analysis
Assembly: M.Polymorpha v5.1, Lactuca_sativa_v11

organism: Marchantia polymorpha

source_name: Whole plant

growth_protocol:
M. polymorpha gemma was spread on Full strength liquid Yamagami media with 1% agar and grown at 22oC under continuous light (50–60 µmol m−2 s−1)
The lettuce seeds were sterilised and growed on 1/2 MS media and grown at 22oC under continuous light (50–60 µmol m−2 s−1)

extract_protocol:
The 5 day old gemmalings and 7 day seedlings were collected and total RNA was extracted using Rneasy Plant Mini Kit
Directional mRNA library preparation (poly A enrichment)

treatment_protocol:
7-day old gemmalings were transferred Full strength, 0% phosphate and 0% nitrate yamagami liquid media and treated for 5 days
4-day old seedlings were transferred Full strength, 0% phosphate and 0% nitrate yamagami liquid media and treated for 7 days

value: Whole plant

value: 0% Nitrate


title: S81-mDRIP-seq-Input-K12


title: S30-mDRIP-seq-Eca109


title: wrky10, 0%Nitrate, rep 1


title: S. enterica wild-type, 15°C, replicate D


title: S. marcescens wild-type, 37°C, replicate A


title: S81-mDRIP-seq-K12


title: K. pneumoniae wild-type, 15°C, replicate E

organism: Klebsiella pneumoniae


title: S. enterica wild-type, 37°C, replicate B


title: wrky10, 0% phosphate, rep 3

value: 0% Phosphate


title: S24-mDRIP-seq-A2780


title: K. pneumoniae wild-type, 37°C, replicate E


title: wrky10, 0% phosphate, rep 2


title: S. enterica wild-type, 15°C, replicate A


title: S. enterica ∆rpoS, 37°C, replicate A


title: K. pneumoniae wild-type, 15°C, replicate D


title: S23-mDRIP-seq-A2780


title: wrky10, 0% phosphate, rep 1


title: wrky10, 0%Nitrate, rep 3


title: S82-mDRIP-seq-K12


title: S. enterica ∆rpoS, 37°C, replicate B


title: S. enterica wild-type, 37°C, replicate A


title: S22-mDRIP-seq-HCT116


title: wrky10, Full yamagami, rep 3

value: Full strength


title: S21-mDRIP-seq-HCT116

value: WT


title: K. pneumoniae wild-type, 37°C, replicate D


title: S25-mDRIP-seq-BEL7042

value: Untreated


title: iMECs cells,BFRTV8d,Day8 [GEF5i8d_3]

city: Guangxi

first: ben

last: huang

address: NO.100. DAXUE EAST RD, Nanning

institute: School of Animal Science and Technology, Guangxi University

data_processing:
Illumina seqencing reads were cleaned for quality control and tested the results using FastQC(version0.10.1).
Ribosome RNA were removed again from clean reads
High-quality reads were mapped to the refer genome to obtain BAM files
the read count for each gene in each sample was counted by HTSeq, and the fragments per kilobase of million mapped reads (FPKM) was then calculated
Differential expression analysis was performed using DESeq2 (v1.16.0) with read count
Assembly: CaprahircusARS1
Supplementary files format and content: counts

organism: Capra hircus

source_name: iMECs

growth_protocol: GEFs were seeded at a density of 5×105 cells per 60 mm dish and cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with fibroblast culture medium; GMECs  were cultured in the incubator at 37.5°C in a humidified atmosphere of 5% CO2 with GMEC culture medium.

extract_protocol:
Total RNA was extracted from the treated iMECs with BERTV from day 0 and day 8 using TRIzol Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara).
RNA-seq transcriptome library was prepared following TruSeqTM RNA sample preparation Kit from Illumina using 1μg of total RNA.

treatment_protocol: iMECs from fibroblasts with N2B27 and small molecule compounds cocktail induction medium “VTFBR” (500μg/mL VPA, 10 μM Tranylcypromine, 10 μM Forskolin, 1 μM TTNPB, 10 μM RepSox),the induction culture was continued for 8 days.

value: iMECs

value: induced Mammary Epithelial Cells

value: reprogramming


title: K. pneumoniae wild-type, 15°C, replicate B


title: S20-mDRIP-seq-HEK293T


title: iMECs cells,BFRTV8d,Day8 [GEF5i8d_2]


title: wrky10, Full yamagami, rep 1


title: K. pneumoniae wild-type, 15°C, replicate A


title: K. pneumoniae wild-type, 37°C, replicate B


title: S19-mDRIP-seq-HEK293T


title: iMECs cells,BFRTV8d,Day8 [GEF5i8d_1]


title: Tak1, 0%Nitrate, rep 3

value: Wildtype


title: S. enterica ∆rpoS, 15°C, replicate A

value: {delta}rpoS


title: K. pneumoniae wild-type, 37°C, replicate A

value: wild-type


title: Tak1, 0%Nitrate, rep 2


title: GEF cells, BERTV,Day0 [GEF_2]

source_name: GEF

value: GEF

value: Fibroblast cells


title: E. coli ∆rpoS, 15°C, replicate E

value: E


title: GEF cells, BERTV,Day0 [GEF_3]


title: S17-mDRIP-seq-Hela

value: Hela


title: S18-mDRIP-seq-Hela


title: S16-mDRIP-seq-Input-HEK293T-RNaseH

value: RNase H


title: GEF cells, BERTV,Day0 [GEF_1]


title: S13-mDRIP-seq-Input-HEK293T-DRB

value: DRB


title: E. coli wild-type, 15°C, replicate E


title: D56-00iCTR-NT_S15

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

data_processing:
Partek Flow (build 10.0.21.1116).
Trim bases based on quality score, min Phred score 20.
STAR- 2.7.8a aligned to hg38.
Quantify to annotation model (Partek E/M). Gene level qualntifiaction, RPKM normalization.
Assembly: hg38
Supplementary files format and content: Normalized (DESeq2 Median ratio normalization) gene expression data,

source_name: human induced-pluripotent stem cell (iPSC) derived P-ANS sympathetic neurons

growth_protocol: iPSCs were cultured to a confluence of ~1.5 million cells/well, and harvested using versene solution (Gibco, 15040033). Cells were then resuspended  at a density of 400,000 cells/ml in T25 flasks coated with Poly-Hema (2-hydroxyethyl methacrylate) in neuromesodermal progenitor cell induction medium (NMP) containing Essential 6 media (Gibco, A1516401), 1.5 mM CHIR 99021 (Tocris, UK), 10 μM SB (Tocris biotech, 431542), penicillin-streptomycin-amphotericin  B solution (PSA, Biological Industries, 03-033-1B) and 10 μM ROCK inhibitor (ROCKi Enzo, ALX270333).

extract_protocol:
RNA was extracted using RNeasy Mini Kit (QIAGEN).After RNA extraction, samples were treated with TURBO DNA-free™ DNase Kit (ambion), with 20 minutes DNase digestion according to manufacturer’s instructions.
Libraries were prepared starting from 10-100 ng of total RNA, using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina with the NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) module (NEB). Protocol was performed according to manufacturer’s instructions
RNA-seq, a NextSeq™ 500 platform (Illumina) with the NextSeq 500/550 High Output Kit v2.5 (75 Cycles) kit (Illumina)

treatment_protocol: Following differentiation, spheres were dissociated with Accutase and plated onto poly-ornithine/laminin-coated (Sigma-Aldrich) coverslips or laminin-coated culture or MEA plates. Half neuronal maturation medium (NMM) was replaced every 2-3 days. Rotenone was then added to NMM. For inducing acute rotenone exposure, 25 nM rotenone was added for a period of 48 hr. To induce chronic rotenone exposure, 1 nM rotenone was added for a period of 14 days, during which half medium was replaced every 2-3 days.

value: not treated (NT)


title: wrky10, Full yamagami, rep 2

value: Whole plant


title: E. coli ∆rpoS, 37°C, replicate E


title: Tak1, 0% phosphate,rep 3

value: 0% Phosphate


title: D56-00iCTR-1nM_S14

value: human induced-pluripotent stem cell (iPSC) derived P-ANS sympathetic neurons

value: 1nM; 14 days


title: S12-mDRIP-seq-Input-HEK293T-DMSO

value: WT

value: DMSO


title: E. coli wild-type, 37°C, replicate E


title: S16-mDRIP-seq-HEK293T-RNaseH


title: D42-00iCTR-NT_S13


title: E. coli ∆rpoS, 15°C, replicate D

value: D


title: S13-mDRIP-seq-HEK293T-DRB


title: D42-WP3-CTR-25nM_S12

value: 25nM; 48 hrs


title: Tak1, Full yamagami,rep 3

value: Wildtype

value: Full strength


title: S12-mDRIP-seq-HEK293T-DMSO


title: E. coli wild-type, 15°C, replicate D

value: wild-type


title: Tak1, 0%Nitrate, rep 1

value: 0% Nitrate


title: E. coli ∆rpoS, 37°C, replicate D

value: {delta}rpoS


title: D50-WP3-CTR-NT_S11


title: S11-mDRIP-seq-Input-HEK293T-RNaseH


title: Tak1, Full yamagami,rep 1


title: E. coli wild-type, 37°C, replicate D


title: Lactuca sativa, 0%Nitrate, rep 3

organism: Lactuca sativa

source_name: Shoot

value: Shoot

value: Red fire


title: D50-WP3-CTR-1nM_S10


title: Tak1, 0% phosphate,rep 2


title: S8-mDRIP-seq-Input-HEK293T-DRB

value: DRB


title: Lactuca sativa, 0%Nitrate, rep 2


title: D38-WP3-CTR-NT_S9

value: not treated (NT)


title: Tak1, 0% phosphate,rep 1

value: Whole plant


title: E. coli wild-type, 15°C, replicate B

value: B


title: E. coli ∆rpoS, 15°C, replicate B


title: D38-WP3-CTR-25nM_S8

value: human induced-pluripotent stem cell (iPSC) derived P-ANS sympathetic neurons


title: D38-002-CTR-NT_S7


title: E. coli ∆rpoS, 37°C, replicate B


title: Lactuca sativa, 0%Nitrate, rep 1


title: Tak1, Full yamagami,rep 2


title: Lactuca sativa, 0% phosphate,rep 3

value: 0% Phosphate


title: D38-002-CTR-25nM_S6


title: S8-mDRIP-seq-HEK293T-DRB

value: WT


title: S11-mDRIP-seq-HEK293T-RNaseH

value: RNase H


title: Lactuca sativa, 0% phosphate,rep 2


title: D38-002-iCTR-1nM_S5

value: 1nM; 14 days


title: E. coli ∆rpoS, 15°C, replicate A

value: A


title: E. coli wild-type, 37°C, replicate B


title: Lactuca sativa, 0% phosphate,rep 1


title: D56-WP3-CTR-NT_S4


title: S2-mDRIP-seq-HEK293T-cDNA

value: Untreated


title: S1-mDRIP-seq-HEK293T-cDNA


title: E. coli ∆rpoS, 37°C, replicate A


title: E. coli wild-type, 15°C, replicate A


title: D56-WP3-CTR-1nM_S3


title: Lactuca sativa, Full yamagami,rep 2

value: Full strength


title: S7-mDRIP-seq-Input-HEK293T-DMSO

value: DMSO


title: D42-WP3-CTR-NT_S2


title: E. coli wild-type, 37°C, replicate A

value: wild-type


title: D42-WP3-CTR-25nM_S1

value: 25nM; 48 hrs


title: S1-mDRIP-seq-Input-HEK293T-cDNA


title: Lactuca sativa, Full yamagami,rep 1

value: Shoot


title: S7-mDRIP-seq-HEK293T-DMSO


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO, rep3 [PD11]

status: Public on Jun 10 2024

city: Łódź

first: Jędrzej

last: Chrzanowski

state: łódzkie

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

country: Poland

institute: Medical University of Lodz

data_processing:
Raw data with adapter sequences or low-quality sequences were filtered using SOAPnuke software with filter parameters “-n 0.03 -l 20 -q 0.4 -A 0.28”.
For PGAT cohort 1, BAT and MEFS: After base calling FASTQ files were preprocessed with fastp version 0.20.1 and next aligned to the mouse reference genome (GRCm39) with HISAT version 2.1.0. The standard alignment protocol was followed, with mus musculus Ensembl version 104 GTF annotation file. Read counts were analyzed using featureCounts version 2.0.1.
For PGAT cohort 2, hypothalamus and liver: After base calling, FASTQ were used to obtain RNAseq abundances using kallisto 0.46.0 with mus musculus GENCODE version M22 GTF annotation file.
The counts were normalized to the trimmed mean of M values (TMM) as implemented in the edgeR 3.12 package.
Assembly: mm39
Supplementary files format and content: *.tabular are tab-delimited text files include raw count values for each sample
Supplementary files format and content: *_abundance.tsv are tab-delimited text files include ensembl mouse trascript ID, length, effective length, estimated count and TPM values for each sample
Supplementary files format and content: *_data.txt are tab-delimited text files includeing TMM values for each sample

source_name: mouse embryonic fibroblasts cells

growth_protocol: All animal procedures were conducted in compliance with protocols approved by IACUC and were in accordance with NIH guidelines. Mice were housed at 22–24°C using a 12h light/12h dark cycle. Only male mice were used in the metabolic studies to avoid the effect of different stages of estrous cycle on glucose homeostasis. All mouse strains were on a C57B6 background, and littermate controls were used at all times. Animals were fed NCD, had ad libitum access to water at all times, and food was only withdrawn if required for an experiment.

extract_protocol:
RNA was isolated with Qiagen RNeasy lipid tissue kit for adipose tissue samples according to the manufacturers protocol, all other samples were isolated with Qiagen RNeasy kit.
For each sample, approximately 200ng of total RNA was enriched for poly-A RNA, fragmented into 200 to 300 bases, and converted to double-stranded cDNA libraries. Samples were then sequenced following the manufacturer’s instructions to generate paired-end reads of 100-bases.

treatment_protocol: TIRRfl/wt mice were generated by conditional gene targeting, flanking by loxP sites, of the first two exons of the TIRR gene in collaboration with Cyagen.  To obtain TIRRKO mice, TIRRfl/wt mice were crossed to EIIaCre (Jax stock #003724) and after the generation of mice with germline deletion of the TIRR gene, the EIIaCre transgene was crossed out to avoid potential toxic effects of Cre expression in the whole body. To generate B cell-specific TIRR deficient mice, TIRRfl/fl mice were bred to mice expressing Cre recombinase under the control of the CD19 promoter (CD19-Cre, Jax stock #006785). To generate adipocyte-specific TIRR deficient mice, TIRRfl/fl mice were bred to C57BL/6J mice expressing Cre recombinase under the control of the adiponectin promoter (Adp-Cre, Jax stock #028020). To generate CNS-specific TIRR deficient mice, TIRRfl/fl mice were bred to C57BL/6J mice expressing Cre recombinase under the control of the calcium/calmodulin-dependent protein kinase II alpha promoter which is expressed in the forebrain and the CA1 pyramidal cell layer of the hippocampus (Camk2a-Cre, Jax stock #005359). To generate p53KO;TIRRKO mice, TIRRKO mice were crossed to p53KO obtained from Jax (stock #002101). Breedings with p53KO mice yielded significantly less litters, therefore p53HET;TIRRWT and p53HET;TIRRHET mice were pooled and are referred to as p53HET;TIRRCONTROL. Similarly, p53KO;TIRRWT and p53KO;TIRRHET mice were pooled and are referred to as p53KO;TIRRCONTROL. Tumor bearing mouse were euthanized when the tumors reached a size of 2.0 cm in any dimension or if the tumors interfered with eating, drinking or ambulation, regardless of the size, or when they resulted in poor body condition, according to the guidelines of the DFCI animal research facility. 15% body weight loss was also endpoint for tumor-bearing mice. MEFs were isolated at embryonic day 13.5, immortalized by subsequent passaging and cultured in DMEM, 10% FBS.

value: mouse embryonic fibroblasts cells

value: C57Bl6 background

value: TIRR KO


title: C57Bl6 background, mouse embryonic fibroblasts cells, TP53 KO, rep3 [PD10]

value: P53 KO


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO TP53 KO, rep3 [PD12]

value: P53 KO TIRR KO


title: Lactuca sativa, Full yamagami,rep 3

value: Red fire


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR fl/fl, rep3 [PD9]

value: TIRR FL/FL


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO TP53 KO, rep2 [PD8]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TP53 KO, rep2 [PD6]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR fl/fl, rep2 [PD5]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO TP53 KO, rep1 [PD4]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO, rep1 [PD3]


title: S2-mDRIP-seq-Input-HEK293T-cDNA

value: WT


title: C57Bl6 background, mouse embryonic fibroblasts cells, TP53 KO, rep1 [PD2]


title: C57Bl6 background, liver tissue, TIRR KO, rep2 [29LDD26]

source_name: liver tissue

value: liver tissue

value: normal chow diet


title: C57Bl6 background, liver tissue, TIRR WT, rep2 [26LN113]

value: TIRR WT


title: C57Bl6 background, liver tissue, TIRR WT, rep1 [25LN112]


title: C57Bl6 background, perigonadal adipose tissue, TIRR WT, rep3 [15WN115]

source_name: perigonadal adipose tissue

value: perigonadal adipose tissue

tag: cohort

value: 2nd PGAT cohort


title: C57Bl6 background, perigonadal adipose tissue, TIRR KO, rep1 [16WDD22]


title: C57Bl6 background, perigonadal adipose tissue, TIRR WT, rep2 [14WN113]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR KO, rep2 [PD7]


title: C57Bl6 background, perigonadal adipose tissue, TIRR WT, rep1 [13WN112]


title: C57Bl6 background, perigonadal adipose tissue, TIRR KO, rep2 [17WDD26]


title: C57Bl6 background, perigonadal adipose tissue, TIRR KO, rep3 [18WDD35]


title: C57Bl6 background, hypothalamus tissue, TIRR KO, rep3 [6htmdd35]

source_name: hypothalamus tissue

value: hypothalamus tissue


title: C57Bl6 background, hypothalamus tissue, TIRR KO, rep2 [5htmd26]


title: C57Bl6 background, hypothalamus tissue, TIRR WT, rep3 [3htmn115]


title: C57Bl6 background, hypothalamus tissue, TIRR KO, rep1 [4htmdd22]


title: C57Bl6 background, mouse embryonic fibroblasts cells, TIRR fl/fl, rep1 [PD1]


title: C57Bl6 background, liver tissue, TIRR KO, rep3 [30LDD35]


title: C57Bl6 background, hypothalamus tissue, TIRR WT, rep1 [1htmn112]


title: sample60_C57Bl6 background, brown adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 5rep

source_name: brown adipose tissue

value: brown adipose tissue

value: AdipoQCreTG/WT TIRR FL/FL


title: DS34L_p

type: RNA

city: Fukuoka

first: Yasunari

last: Sakai

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pediatrics

institute: Kyushu University

description: Gene expression after LPS treatment

hyb_protocol: cRNA was hybridized to Affymetrix  Clariom D Assay human array, washed and stained according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Affymetrix scanner.

data_processing: The raw data were normalized with SST-RMA algorithm (gene level) using Affymetrix Expression Console 1.4.1 software.

label: biotin

source_name: DS, MoDCs, LPS

label_protocol: The cRNA was amplified, labeled using GeneChip WT PLUS Reagent Kit according to the manufacturer's instructions.

growth_protocol: Standard methods for differentiation of peripheral monocytes into dendritic cells

extract_protocol: Total RNA was isolated from cells using using RNeasy Kits (QIAGEN) according to the manufacturer's instructions.

treatment_protocol: 10 ng/ml LPS for 48 hr

tag: condition

value: Down syndrome

value: monocyte-derived dendritic cells

tag: gender

value: Male

value: LPS


title: sample59_C57Bl6 background, brown adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 4rep

value: C57Bl6 background


title: C57Bl6 background, liver tissue, TIRR KO, rep1 [28LDD22]

value: TIRR KO


title: sample57_C57Bl6 background, brown adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 2rep


title: C57Bl6 background, liver tissue, TIRR WT, rep3 [27LN115]


title: C57Bl6 background, hypothalamus tissue, TIRR WT, rep2 [2htmn113]


title: sample56_C57Bl6 background, brown adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 1rep


title: sample55_C57Bl6 background, brown adipose tissue, TIRR FL/FL, 5rep


title: Con39L_p

description: Gene expression after LPS treatment

source_name: control, MoDCs, LPS

value: control


title: DS27L_p

description: Gene expression after LPS treatment


title: sample54_C57Bl6 background, brown adipose tissue, TIRR FL/FL, 4rep

value: TIRR FL/FL


title: sample53_C57Bl6 background, brown adipose tissue, TIRR FL/FL, 3rep


title: sample51_C57Bl6 background, brown adipose tissue, TIRR FL/FL, 1rep


title: sample48_C57Bl6 background, perigonadal adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 2rep

value: 1st PGAT cohort


title: sample49_C57Bl6 background, perigonadal adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 3rep


title: sample52_C57Bl6 background, brown adipose tissue, TIRR FL/FL, 2rep


title: sample43_C57Bl6 background, perigonadal adipose tissue, TIRR FL/FL, 3rep


title: sample41_C57Bl6 background, perigonadal adipose tissue, TIRR FL/FL, 1rep


title: sample46_C57Bl6 background, perigonadal adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 1rep


title: sample39_C57Bl6 background, brown adipose tissue, P53KO TIRRKO, 4rep

value: P53KO TIRRKO


title: sample44_C57Bl6 background, perigonadal adipose tissue, TIRR FL/FL, 4rep

value: normal chow diet


title: sample40_C57Bl6 background, brown adipose tissue, P53KO TIRRKO, 5rep


title: sample58_C57Bl6 background, brown adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 3rep


title: sample45_C57Bl6 background, perigonadal adipose tissue, TIRR FL/FL, 5rep


title: sample42_C57Bl6 background, perigonadal adipose tissue, TIRR FL/FL, 2rep


title: sample37_C57Bl6 background, brown adipose tissue, P53KO TIRRKO, 2rep


title: sample36_C57Bl6 background, brown adipose tissue, P53KO TIRRKO, 1rep


title: sample34_C57Bl6 background, brown adipose tissue, P53KO TIRRWT, 3rep

value: P53KO TIRRCONTROL


title: Con25L_p

description: Gene expression after LPS treatment


title: sample32_C57Bl6 background, brown adipose tissue, P53KO TIRRWT, 1rep


title: sample35_C57Bl6 background, brown adipose tissue, P53KO TIRRWT, 4rep


title: sample38_C57Bl6 background, brown adipose tissue, P53KO TIRRKO, 3rep


title: sample30_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRKO, 5rep

value: perigonadal adipose tissue


title: sample29_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRKO, 4rep


title: sample50_C57Bl6 background, perigonadal adipose tissue, AdipoQCreTG/WT TIRR FL/FL, 4rep


title: sample33_C57Bl6 background, brown adipose tissue, P53KO TIRRWT, 2rep


title: sample28_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRKO, 3rep


title: sample27_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRKO, 2rep


title: sample24_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRWT, 4rep


title: sample23_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRWT, 3rep


title: sample22_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRWT, 2rep


title: sample25_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRWT, 5rep


title: sample19_C57Bl6 background, brown adipose tissue, TIRR KO, 3rep

value: P53WT TIRRKO


title: sample20_C57Bl6 background, brown adipose tissue, TIRR KO, 4rep


title: sample26_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRKO, 1rep


title: sample13_C57Bl6 background, brown adipose tissue, TIRR WT, 3rep

value: P53WT TIRRWT


title: sample9_C57Bl6 background, perigonadal adipose tissue, TIRR KO, 3rep


title: sample21_C57Bl6 background, perigonadal adipose tissue, P53KO TIRRWT, 1rep


title: sample17_C57Bl6 background, brown adipose tissue, TIRR KO, 2rep

value: brown adipose tissue


title: sample12_C57Bl6 background, brown adipose tissue, TIRR WT, 2rep


title: sample16_C57Bl6 background, brown adipose tissue, TIRR KO, 1rep


title: sample10_C57Bl6 background, perigonadal adipose tissue, TIRR KO, 4rep


title: sample11_C57Bl6 background, brown adipose tissue, TIRR WT, 1rep


title: sample7_C57Bl6 background, perigonadal adipose tissue, TIRR KO, 2rep


title: sample6_C57Bl6 background, perigonadal adipose tissue, TIRR KO, 1rep


title: sample3_C57Bl6 background, perigonadal adipose tissue, TIRR WT, 3rep


title: sample2_C57Bl6 background, perigonadal adipose tissue, TIRR WT, 2rep


title: Q146A-B

first: Anthony

last: Flores

address: 6431 Fannin St., MSB 3.130

institute: UTHSC/McGovern Medical School

data_processing:
Base calls onboard Illumina HiSeq
Raw data files processed using CLC Genomics Workbench v23
Reads mapped to reference genome MGAS10870 (CP067090.1)
Peaks called using Transcription Factor ChIP-seq module (CLC Genomics Workbench v23)
Assembly: MGAS10870 (CP067090.1)
Supplementary files format and content: Spreadsheet, peak score

organism: Streptococcus pyogenes

source_name: hyperphosphorylated mutant

growth_protocol: GAS cells were grown in rich medium (Todd-Hewitt, 0.2% yeast extract) to an OD of 0.5 (mid-exponential phase)

extract_protocol:
Proteins crosslinked to DNA with 1% formaldehyde, cells harvested by centrifugation, extraction using sonication as described in methods
Libraries constructed by Genewiz (Azenta Life Sciences)

treatment_protocol: No treatment

value: hyperphosphorylated mutant

tag: replicate

value: B

tag: growth condition

value: in vitro

value: custom, rabbit anti-LiaR


title: Q146A-C

value: C


title: Q146A-input


title: dLiaR-B

source_name: LiaR knockout

value: LiaR knockout


title: Q146A-A

value: A


title: RNA-Seq of mus musculus:Embryo 4

city: Changchun

first: Zhengyang

last: Jin

state: Jilin

address: No. 1163 Xinmin Street

institute: Jilin University

description:
Well-ST-seq_30_1
Well-ST-seq_30 resolution

data_processing:
*library strategy: Well-ST-seq
The filtered data was mapped to the mouse genome (mm10 mouse) using SpaceRanger V1.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Embryo

extract_protocol:
Tissue was permeabilized with tissue permeabilizing enzyme for 12 minutes
RNA libraries for RNA-seq were prepared using Kapa HIFI HotStart ReadyMix PCR Kit following manufacturer's protocols.

value: Embryo

value: Female


title: RNA-Seq of mus musculus:Adult female spleen

description:
Well-ST-seq_10_5
Well-ST-seq_10 resolution

source_name: Spleen

value: Spleen

value: 12 weeks


title: RNA-Seq of mus musculus:Embryo 7

description:
Well-ST-seq_30_4
Well-ST-seq_30 resolution


title: RNA-Seq of mus musculus:Embryo 9

description:
Well-ST-seq_30_6
Well-ST-seq_30 resolution


title: RNA-Seq of mus musculus:Embryo 8

description:
Well-ST-seq_30_5
Well-ST-seq_30 resolution


title: RNA-Seq of mus musculus:Embryo 5

description:
Well-ST-seq_30_2
Well-ST-seq_30 resolution


title: RNA-Seq of mus musculus:Embryo 2

description:
Well-ST-seq_10_3
Well-ST-seq_10 resolution


title: 331CTX

city: Hong Kong

first: Jianlin

last: Li

address: L 7-08, Department of Obstetrics and Gynecology  Laboratory block, 21th Sassoon Road, Hong Kong

country: Hong Kong

institute: The University of Hong Kong

description:
Raw_1.csv
Normalized_1.csv

data_processing:
Low-quality reads were removed by fastp with default parameters
Remaining clean reads were align to the Homo sapiens (human) genome assembly GRCh38 (hg38)/Mus musculus (house mouse) genome assembly GRCm39 (mm39) according to the corresponding species by Hisat2 with default parameters
Raw gene counts were generated by featurecount and then normalized by DEseq2
Assembly: hg38 or mm39
Supplementary files format and content: Matrix table with raw gene counts
Supplementary files format and content: Matrix table with normalized gene counts

source_name: cortex

growth_protocol: For sample 1-12, mice were breed in cages before collection of tissue. For Sample 13 - 14, the monocyte-derived microglia were maintain in RPMI1640 medium, supplemented with 1 % P/S, 0.1 μg/ml IL-34 and 0.01 μg/ml GM-CSF

extract_protocol:
Total RNA from cultured MDMi and mouse cortex samples was extracted using TRIzol Reagent (Invitrogen, 15596026) according to the instruction.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: For sample 1-6, they were treated with SM03 (anti-human CD22 antibody) or IgG1 isotype 21 days before sacrifce. Antibodies were intravenously adminstrated once a week. For sample 7-12, mice were intracerebroventricularly injected with PBS or 9 μg mouse soluble CD22. Mouse cortice were collected 3 days after administration. For sample 13-20, cells were treated with 10 μg/mL sCD22 for 24 hours. Cells were then collected for RNA.

value: cortex


title: 336CTX

description:
Raw_1.csv
Normalized_1.csv


title: RNA-Seq of mus musculus:Embryo 1

description:
Well-ST-seq_10_2
Well-ST-seq_10 resolution


title: Nlrp3 knockout, replicate 1, scRNAseq

city: Shanghai

first: Haihan

last: Gao

address: Xuhui District

department: Department of Orthopaedic Surgery

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
The demultiplexing,barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix flils

source_name: rotator cuff

extract_protocol:
Enthesis at 7 dpi from wild type and Nlrp3 -/- mice were carefully harvested under surgical microscope and pooled together.
The cell survival rate is typically above 80% for quality control and enumeration of single cell suspension. After the cells have passed the quality control, they are rinsed and resuspended to prepare a suitable cell concentration of 700-1200 cells/ul for 10x Genomics ChromiumTM. GEMs (Gel Bead in Emulsion) were constructed for single cell separation and collected for reverse transcription in a PCR machine for labeling. The amplified cDNA was purified by magnetic beads, and then subjected to cDNA amplification. The Gene Expression Library was constructed with the quality-qualified cDNA. The final library pool was sequenced on the Illumina Nova 6000 instrument using 150-base-pair paired-end reads.

value: rotator cuff

value: enthesis

value: Nlrp3 knockout

value: injury and repair


title: 334CTX

description:
Raw_1.csv
Normalized_1.csv


title: 330CTX

description:
Raw_1.csv
Normalized_1.csv


title: Nlrp3 knockout, replicate 3, scRNAseq

value: Nlrp5 knockout


title: 335CTX

description:
Raw_1.csv
Normalized_1.csv


title: Nlrp3 knockout, replicate 2, scRNAseq

value: Nlrp4 knockout


title: wild type, replicate 3, scRNAseq

value: wild type


title: dLiaR-input


title: TOXOTRM6 Latency d46pi RNA

city: Toulouse Cedex 3

first: Nicolas

last: Blanchard

address: CHU Purpan BP3028

department: Inserm UMR1291

institute: Toulouse Institute for Infectious and Inflammatory Diseases (Infinity)

description: GEX library

data_processing:
Cell Ranger software (10X Genomics, version 3.1.0 for scRNA-seq and version 6.1.2 for CITE-seq) was used to perform alignments against Mus musculus genome (GRCm38.98 for scRNA-seq and GRCm39.105 for CITE-seq), generating gene expression matrices that were further analyzed with Seurat v4.3.0 (9) on R v4.2.2 (R Core Team.  R Foundation for Statistical Computing, 2022).
Assembly: Mus musculus (GRCm38.98 for scRNA-seq and GRCm39.105 for CITE-seq)
Supplementary files format and content: .rds file

source_name: brain

extract_protocol:
Whole brains (including the pia mater, but excluding the dura mater and arachnoid tissue which remain attached to the skull) were collected in complete RPMI supplemented with 10% vol/vol FCS, homogenized using a glass Potter and digested for 45 min at room temperature in HBSS with collagenase D (1 mg/mL) and deoxyribonuclease (DNase) I (20 ug/mL). After digestion, cells were suspended in 30% Percoll (GE Healthcare) and centrifuged at 1590g for 30 min without brake.  Myelin and debris were removed, brain leukocytes were recovered from the interface. Before scRNA-seq, CD103-negative and CD103-positive subpopulations of Kb-OVA dextramer+ CD8+ T cells were separated by Facs-sorting.  For CITE-seq, brain cell suspensions were incubated for 45 min at RT with the following barcoded dextramers diluted in complete RPMI: Kb-SIINFEKL (Immudex cat # JD2163-PfBC, barcode fBC0074: CGGTCTTAGTCGCGC, dilution 1:50), Ld-HPGSVNEFDF (Immudex cat # JG5820-PfBC0301, barcode fBC0301: CGGCCTCGCGACGAC, dilution 1:50), control Kb-SIYRYYGL (Immudex cat # JD2164-PfBC, barcode fBC0068: TTGCGCGGCGTCGTA, dilution 1:50), and then surface labelled for 30 min at 4°C with TotalSeq-C0182 anti-mouse CD3 (clone 17A2, dilution 1:50, Biolegend, cat # 100263) and TotalSeq-C0002 anti-mouse CD8 (clone 53-6.7, dilution 1:50, Biolegend, cat # 100785) diluted in ‘Facs buffer’ (PBS, 2mM EDTA, 0.5% FCS).
For scRNA-seq, single-cell libraries were generated after Facs-sorting using the Chromium Controller Instrument and Chromium Single Cell 3’ Library & Gel Bead Kit v3 (10X Genomics). For CITE-seq, single-cell libraries were generated with Chromium Next GEM Single Cell 5' Kit v2 and 5' Feature Barcode Kit (10X Genomics).

value: brain

value: total CD8+ T cells


title: sample1_C57Bl6 background, perigonadal adipose tissue, TIRR WT, 1rep

value: perigonadal adipose tissue

value: C57Bl6 background

value: P53WT TIRRWT

value: normal chow diet

value: 1st PGAT cohort


title: TOXOTRM6 Latency d46pi CSP

description: CSP library

library_source: other

molecule: other


title: RNA-Seq of mus musculus:Embryo 6

description:
Well-ST-seq_30_3
Well-ST-seq_30 resolution

value: Embryo

value: Female


title: wild type, replicate 1, scRNAseq


title: TOXOTRM4 Latency 160dpi CD103-pos

value: OVA-specific CD8+ T cells


title: TOXOTRM2 Encephalitis 52 dpi CD103-pos


title: Integrated sgRNAs in liver-derived ANKL1 cells 14 days after establishment of ANKL-PDX #2

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

description: sgRNAs integrated in genomic DNA

data_processing:
*library strategy: DNA-seq of sgRNAs; CRISPR screening
Sequenced Reads were mapped using Rsubread version 2.12.3 and GenomicAlignments version 1.34.1.
Positively- and Negatively-selected sgRNAs were statistically analyzed using "test" command of MAGeCK version 0.5.9.5.
Gene-set enrichment analysis was performed using "pathway" command of MAGeCK with MSigDB-HALLMARK dataset.
Assembly: sgRNA library file (FeLib.fa)
Supplementary files format and content: CSV-formatted file including Reads Per Million (RPM) values for each sample

source_name: ANKL1 (primary ANKL cells derived from PDX)

growth_protocol: sgRNA library-integrated ANKL1 cells were intravenously inoculated into a NOG mouse, and cultivated in vivo for 14 days.

extract_protocol:
Liver was obtained from ANKL1-PDX mouse, followed by degradaded with 1 mg/mL of collagenase and 20 U/mL of DNase I. After density gradient centrifugation with 35% Percoll to remove hepatocytes, ANKL1 cells were harvested using autoMACS after stained with a biotin conjugated anti human CD45 antibody and anti-biotin microbeads.
Genomic DNA was extracted using DNeasy blood and tissue kit. After amplification of integrated sgRNAs using TaKaRa Gflex DNA polymerase, illumina i7 index primers were added.


title: 338CTX

description:
Raw_1.csv
Normalized_1.csv

value: cortex


title: wild type, replicate 2, scRNAseq

value: rotator cuff

value: enthesis


title: Integrated sgRNAs in ANKL1 cells before establishment of ANKL-PDX #3

description: sgRNAs integrated in genomic DNA

value: ANKL1 (primary ANKL cells derived from PDX)


title: TOXOTRM2 Latency 52dpi CD103-pos


title: TOXOTRM4 Latency 160dpi CD103-neg


title: Integrated sgRNAs in liver-derived ANKL1 cells 14 days after establishment of ANKL-PDX #3

description: sgRNAs integrated in genomic DNA


title: Integrated sgRNAs in liver-derived ANKL1 cells 14 days after establishment of ANKL-PDX #1

description: sgRNAs integrated in genomic DNA


title: TOXOTRM2 Encephalitis 52 dpi CD103-neg


title: Integrated sgRNAs in ANKL1 cells before establishment of ANKL-PDX #1

description: sgRNAs integrated in genomic DNA


title: Integrated sgRNAs in ANKL1 cells before establishment of ANKL-PDX #2

description: sgRNAs integrated in genomic DNA


title: MGAS10870-C

data_processing:
Base calls onboard Illumina HiSeq
Raw data files processed using CLC Genomics Workbench v23
Reads mapped to reference genome MGAS10870 (CP067090.1)
RPKM/TPM calculated using CLC Genomics Workbench v23
Assembly: MGAS10870 (CP067090.1)
Supplementary files format and content: Spreadsheet, normalized read counts

source_name: wild-type

extract_protocol:
Cells collected in RNA protect and total RNA extracted using Qiagen RNeasy protocol adapted for GAS as described in Methods
Libraries constructed using Illumina ScriptSeq Complete v3

value: wild-type

value: C

value: in vitro


title: Par1_ECko_APAP_Bead_3

city: Oklahoma City

first: Rahul

last: Rajala

state: Oklahoma

address: 825 NE 13th Street

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment of raw sequences using HISAT2 and independently by SALMON
Differential gene expression performed by DESEQ2 and edgeR
Assembly: HISAT2 (Mus_musculus.GRCm39.dna.primary_assembly) /SALMON (Mus_musculus.GRCm39.107.transcripts.fa.salmon)
Supplementary files format and content: Collated HISAT2 data given as (CountsFile.csv), Collated SALMON data given as (TPMValues.csv)

source_name: Liver EC

extract_protocol:
RNA (before/after TRAP) was isolated using the Qiagen RNeasy kit. SMARTer Ultra Low Input kit (Clontech) was used for RNA conversion (5 ng for tissue lysate, 10 ng for EC-TRAP samples).
cDNA samples were sheared using the Covaris E220 Focused Ultra-sonicator which was followed by Quant-iT PicoGreen quantification (Thermo Fisher Scientific, catalog number P11496). A total of 5 ng cDNA per sample was used for library preparation based on the KAPA Hyper Prep method (KAPA Biosystems, catalog number KK8504). Following NEXTflex adapter ligation (BIOO Scientific, catalog number 514104), libraries were size-selected based on a double bead purification prior to amplification.

treatment_protocol: Tissues were flash-frozen in liquid nitrogen following a cycloheximide perfusion and mechanically dissociated

value: Liver EC

value: APAP


title: Par1_EChet_Saline_Bead_3

value: Saline


title: MGAS10870-B

value: B


title: MGAS10870-A

value: A


title: Par1_EChet_APAP_Bead_2


title: Par1_EChet_APAP_Bead_3


title: LiaS-Q146A-C

source_name: mutant

value: mutant


title: TOXOTRM2 Latency 52dpi CD103-neg

value: brain


title: Par1_ECko_APAP_Bead_2


title: LiaS-Q146A-B